APPLIED CHEMISTRY AND

CHEMICAL ENGINEERING
Volume 4
Experimental Techniques and
Methodical Developments
APPLIED CHEMISTRY AND
CHEMICAL ENGINEERING
Volume 4
Experimental Techniques and
Methodical Developments

Edited by
A. K. Haghi, PhD
Lionello Pogliani, PhD
Eduardo A. Castro, PhD
Devrim Balköse, PhD
Omari V. Mukbaniani, PhD
Chin Hua Chia, PhD
Apple Academic Press Inc. Apple Academic Press Inc.
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Applied chemistry and chemical engineering / edited by A.K. Haghi, PhD, Devrim Balköse, PhD, Omari V.
Mukbaniani, DSc, Andrew G. Mercader, PhD.
Includes bibliographical references and indexes.
Contents: Volume 1. Mathematical and analytical techniques --Volume 2. Principles, methodology, and evalu-
ation methods --Volume 3. Interdisciplinary approaches to theory and modeling with applications --Volume
4. Experimental techniques and methodical developments --Volume 5. Research methodologies in modern
chemistry and applied science.
Issued in print and electronic formats.
ISBN 978-1-77188-515-7 (v. 1 : hardcover).--ISBN 978-1-77188-558-4 (v. 2 : hardcover).--ISBN 978-1-
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1. Chemistry, Technical. 2. Chemical engineering. I. Haghi, A. K., editor
TP145.A67 2017 660 C2017-906062-7 C2017-906063-5

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Names: Haghi, A. K., editor.

Title: Applied chemistry and chemical engineering / editors, A.K. Haghi, PhD [and 3 others].
Description: Toronto ; New Jersey : Apple Academic Press, 2018- | Includes bibliographical references and index.
Identifiers: LCCN 2017041946 (print) | LCCN 2017042598 (ebook) | ISBN 9781315365626 (ebook) | ISBN
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ABOUT THE EDITORS

A. K. Haghi, PhD
A. K. Haghi, PhD, holds a BSc in Urban and Environmental Engineering
from the University of North Carolina (USA), an MSc in Mechanical Engi-
neering from North Carolina A&T State University (USA), a DEA in applied
mechanics, acoustics and materials from the Université de Technologie de
Compiègne (France), and a PhD in engineering sciences from the Univer-
sité de Franche-Comté (France). He is the author and editor of 165 books,
as well as of 1000 published papers in various journals and conference
proceedings. Dr. Haghi has received several grants, consulted for a number
of major corporations, and is a frequent speaker to national and interna-
tional audiences. Since 1983, he served as professor at several universities.
He is currently Editor-in-Chief of the International Journal of Chemoinfor-
matics and Chemical Engineering and the Polymers Research Journal and
on the editorial boards of many international journals. He is also a member
of the Canadian Research and Development Center of Sciences and Cultures
(CRDCSC), Montreal, Quebec, Canada.

Lionello Pogliani, PhD

Lionello Pogliani, PhD, was Professor of Physical Chemistry at the Univer-
sity of Calabria, Italy. He studied Chemistry at Firenze University, Italy, and
received his postdoctoral training at the Department of Molecular Biology
of the C. E. A. (Centre d’Etudes Atomiques) of Saclay, France, the Physical
Chemistry Institute of the Technical and Free University of Berlin, and the
Pharmaceutical Department of the University of California, San Francisco,
CA. Dr. Pogliani has coauthored an experimental work that was awarded
the GM Neural Trauma Research Award. He spent his sabbatical years at the
Centro de Química-Física Molecular of the Technical University of Lisbon,
Portugal, and at the Department of Physical Chemistry of the Faculty of
Pharmacy of the University of Valencia-Burjassot, Spain. He has contrib-
uted nearly 200 papers in the experimental, theoretical, and didactical fields
of physical chemistry, including chapters in specialized books. He has also
presented at more than 40 symposiums. He also published a book on the
numbers 0, 1, 2, and 3. He is a member of the International Academy of
vi About the Editors

Mathematical Chemistry. He retired in 2011 and is part-time teammate at

the University of Valencia-Burjassot, Spain.

Eduardo A. Castro, PhD

Eduardo A. Castro, PhD, is full professor in theoretical chemistry at the
Universidad Nacional de La Plata and a career investigator with the Consejo
Nacional de Investigaciones Cientificas y Tecnicas, both based in Buenos
Aires, Argentina. He is the author of nearly 1000 academic papers in theo-
retical chemistry and other topics, and he has published several books. He
serves on the editorial advisory boards of several chemistry journals and is
often an invited speaker at international conferences in South America and
elsewhere.

Devrim Balköse, PhD

Devrim Balköse, PhD, is currently a faculty member in the Chemical Engi-
neering Department at the Izmir Institute of Technology, Izmir, Turkey. She
graduated from the Middle East Technical University in Ankara, Turkey,
with a degree in Chemical Engineering. She received her MS and PhD
degrees from Ege University, Izmir, Turkey, in 1974 and 1977, respectively.
She became Associate Professor in Macromolecular Chemistry in 1983
and Professor in process and reactor engineering in 1990. She worked as
Research Assistant, Assistant Professor, Associate Professor, and Professor
between 1970 and 2000 at Ege University. She was the Head of the Chemical
Engineering Department at the Izmir Institute of Technology, Izmir, Turkey,
between 2000 and 2009. Her research interests are in polymer reaction engi-
neering, polymer foams and films, adsorbent development, and moisture
sorption. Her research projects are on nanosized zinc borate production,
ZnO polymer composites, zinc borate lubricants, antistatic additives, and
metal soaps.

Omari V. Mukbaniani, DSc

Omari Vasilii Mukbaniani, DSc, is Professor and Head of the Macromolecular
Chemistry Department of Iv. Javakhishvili Tbilisi State University, Tbilisi,
Georgia. He is also the Director of the Institute of Macromolecular Chem-
istry and Polymeric Materials. He is a member of the Academy of Natural
Sciences of the Georgian Republic. For several years he was a member of the
advisory board of the Journal Proceedings of Iv. Javakhishvili Tbilisi State
About the Editors vii

University (Chemical Series) and contributing editor of the journal Polymer

News and the Polymers Research Journal. He is a member of editorial board
of the Journal of Chemistry and Chemical Technology. His research interests
include polymer chemistry, polymeric materials, and chemistry of organosil-
icon compounds. He is an author more than 420 publications, 13 books, four
monographs, and 10 inventions. He created in the 2007s the “International
Caucasian Symposium on Polymers & Advanced Materials,” ICSP, which
takes place every other two years in Georgia.

Chin Hua Chia, PhD

Chin Hua Chia, PhD, is an Associate Professor at the School of Applied
Physics, Faculty of Science and Technology at Universiti Kebangsaan
Malaysia (National University of Malaysia), Malaysia. A recipient of the
Young Scientist Award from the National University of Malaysia and the
Malaysian Solid State Science and Technology (MASS) in 2012 and 2014,
respectively, he is a member of several professional organizations and has
published several book chapters and more than 100 articles in professional
journals as well as has presented at many professional meetings. His core
research interests include polymer, nanocomposites, chemistry of lignocel-
lulosic materials, and magnetic nanomaterials.
Applied Chemistry and Chemical Engineering, 5 Volumes

Applied Chemistry and Chemical Engineering,

Volume 1: Mathematical and Analytical Techniques
Editors: A. K. Haghi, PhD, Devrim Balköse, PhD, Omari V. Mukbaniani, DSc, and
Andrew G. Mercader, PhD

Applied Chemistry and Chemical Engineering,

Volume 2: Principles, Methodology, and Evaluation Methods
Editors: A. K. Haghi, PhD, Lionello Pogliani, PhD, Devrim Balköse, PhD,
Omari V. Mukbaniani, DSc, and Andrew G. Mercader, PhD

Applied Chemistry and Chemical Engineering,

Volume 3: Interdisciplinary Approaches to Theory and Modeling with
Applications
Editors: A. K. Haghi, PhD, Lionello Pogliani, PhD, Francisco Torrens, PhD,
Devrim Balköse, PhD, Omari V. Mukbaniani, DSc, and Andrew G. Mercader, PhD

Applied Chemistry and Chemical Engineering,

Volume 4: Experimental Techniques and Methodical Developments
Editors: A. K. Haghi, PhD, Lionello Pogliani, PhD, Eduardo A. Castro, PhD,
Devrim Balköse, PhD, Omari V. Mukbaniani, PhD, and Chin Hua Chia, PhD

Applied Chemistry and Chemical Engineering,

Volume 5: Research Methodologies in Modern Chemistry and Applied Science
Editors: A. K. Haghi, PhD, Ana Cristina Faria Ribeiro, PhD,
Lionello Pogliani, PhD, Devrim Balköse, PhD, Francisco Torrens, PhD,
and Omari V. Mukbaniani, PhD
CONTENTS

List of Contributors......................................................................................xiii
List of Abbreviations................................................................................... xvii
Preface......................................................................................................... xxi

Part I: Polymer Chemistry and Technology.............................................1

1. Synthesis of Unsaturated Biodegradable Poly (Ester Amide)s
and Study of Their Thermal and Mechanical Properties.............................3
E. Chkhaidze and D. Kharadze

2. Experimental Design and Properties of PVC Foams: Azodicarbon

Amide and Zinc Oxide...................................................................................17
Filiz Ö. Ömürlü and Devrim Balkose

3. Thermal and Tribochemical Processes in Polyphenylene

Oxide in the Process of Friction....................................................................45
M. B. Gurgenishvili, G. Sh. Papava, R. G. Liparteliani, Sh. R. Papava,
Z. N. Chubinishvili, N. Z. Khotenashvili, and Z. Sh. Tabukashvili

4. Compatibility and Thermal Properties of Poly (Ethylene Oxide)

and Natural Rubber-Graft-Poly (Methyl Methacrylate) Blends...............55
N. F. A. Zainal, C. H. Chan, and A. M. M. Ali

5. Thermal Properties and Intermolecular Interaction of

Binary Polymer Blends of Poly (Ethylene Oxide) and
Poly (N-Butyl Methacrylate).........................................................................77
H. Ramli, C. H. Chan, and A. M. M. Ali

6. Cross-Linking of Epoxy–Isocyanate Mixtures in the

Presence of Hydroxyl-Acrylic Oligomer......................................................93
Ostap Ivashkiv, Bogdana Bashta, Olena Shyshchak, Jozef Haponiuk,
and Michael Bratychak

Part II: Computational Approaches......................................................107

7. The Superposing Significant Interaction Rules (SSIR) Method..............109
Emili Besalú, Lionello Pogliani, and J. Vicente Julian-Ortiz
x Contents

8. The Vision of Application of Multiobjective Optimization and

Genetic Algorithm in Modeling and Simulation of the Riser
Reactor of a Fluidized Catalytic Cracking Unit: A Critical Review.......135
Sukanchan Palit

9. A Theoretical Study of Bimetallic CuAun (n = 1–7) Nanoalloy

Clusters Invoking Conceptual DFT-Based Descriptors...........................165
Prabhat Ranjan, Tanmoy Chakraborty, and Ajay Kumar

Part III: Clinical Chemistry and Bioinformatics.................................179

10. Biochemistry Apps as Enabler of Compound and DNA
Computational: Next-Generation Computing Technology......................181
Heru Susanto

11. Adsorbents for DNA Separations...............................................................203

Senem Yetgin and Devrim Balkose

12. Adsorption of DNA on Silica, Alumina, and Hydroxylapatite.................233

Senem Yetgin and Devrim Balkose

13. Thermal Behavior of Sodium Salt of Calf Thymus DNA.........................263

Aysun Topaloğlu, Güler Narin, and Devrim Balköse

Part IV: Special Topics...........................................................................305

14. Environmental Engineering, Membrane Technology and
Novel Separation Processes: A Broad Scientific Perspective
and a Critical Overview...............................................................................307
Sukanchan Palit

15. A Comparative Study on Electrocentrifuge Spinning and

Electrospinning Process as Two Different Nanofiber Creation
Techniques....................................................................................................325
S. Rafiei

16. Results of Testing of Heliodrying Apparatus with

Polycarbonate Covering..............................................................................343
K. T. Archvadze, T. I. Megrelidze, L. V. Tabatadze, and I. R. Chachava

17. Dependence of Morphology on Optical and Electrical

Properties of Metal Oxide Nanostructures................................................353
Paulose Thomas and Ajith James Jose
Contents xi

18. Mechanism of Ni(Fe) ARD Action in Methionine Salvage

Pathway, in Biosynthesis of Ethylene, and Role of Tyr-Fragment
as Regulatory Factor....................................................................................367
Ludmila I. Matienko, Larisa A. Mosolova, Vladimir I. Binyukov,
Elena M. Mil, and Gennady E. Zaikov

Index......................................................................................................................389
LIST OF CONTRIBUTORS

A. M. M. Ali
Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor,
Malaysia
K. T. Archvadze
Food Industry Department, Georgian Technical University, 77 Kostava 0175, Tbilisi, Georgia
Department of Technology, Sukhumi State University, Ana Politkobskaia 9, 0186, Tbilisi, Georgia

Devrim Balköse
Department of Chemical Engineering, İzmir Institute of Technology, Gulbahçe Urla, Izmir, Turkey.
E-mail: [email protected]

Bogdana Bashta
Lviv Polytechnic National University, 12, St. Bandera Str., Lviv 79013, Ukraine

Emili Besalú
Departament de Química, Institut de Química Computacional i Catàlisi (IQCC), Universitat de Girona,
17003 Girona, Catalonia, Spain

Vladimir I. Binyukov
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygin Str., Moscow
119334, Russia

Michael Bratychak
Lviv Polytechnic National University, 12, St. Bandera Str., Lviv 79013, Ukraine. E-mail: mbratych@
polynet.lviv.ua

I. R. Chachava
Food Industry Department, Georgian Technical University, 77 Kostava 0175, Tbilisi, Georgia
Department of Technology, Sukhumi State University, Ana Politkobskaia 9, 0186, Tbilisi, Georgia

Tanmoy Chakraborty
Department of Chemistry, Manipal University Jaipur, Dehmi-Kalan, Jaipur 303007, India.
E-mail: [email protected]; [email protected]

C. H. Chan
Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Selangor,
Malaysia. E-mail: [email protected]

E. Chkhaidze
Faculty of Chemical Technology and Metallurgy, Georgian Technical University, Tbilisi, Georgia.
E-mail: [email protected]

Z. N. Chubinishvili
TSU Petre Melikishvili Institute of Physical and Organic Chemistry, 31 A. Politkovskaia Str., 0186
Tbilisi, Georgia

M. B. Gurgenishvili
TSU Petre Melikishvili Institute of Physical and Organic Chemistry, 31 A. Politkovskaia Str., 0186
Tbilisi, Georgia. E-mail: [email protected]
xiv List of Contributors

Jozef Haponiuk
Gdansk University of Technology, 11/12 G. Narutowicza Str., 80233 Gdansk, Poland

Ostap Ivashkiv
Lviv Polytechnic National University, 12, St. Bandera str., Lviv 79013, Ukraine

Ajith James Jose

Research Department of Chemistry, St. Berchmans College, Changanassery, Kerala, India

J. Vicente Julian-Ortiz
Departamento de Química Física, Unidad de Investigación de Diseño de Fármacos y Conectividad
Molecular, Facultad de Farmacia, Universitat de València, Burjassot (València), Spain, and MOLware
SL, Valencia, Spain. E-mail: [email protected]

D. Kharadze
Ivane Beritashvili Center of Experimental Biomedicine

N. Z. Khotenashvili
TSU Petre Melikishvili Institute of Physical and Organic Chemistry, 31 A. Politkovskaia Str., 0186
Tbilisi, Georgia

Ajay Kumar
Department of Mechatronics Engineering, Manipal University Jaipur, Dehmi-Kalan, Jaipur 303007,
India
R. G. Liparteliani
TSU Petre Melikishvili Institute of Physical and Organic Chemistry, 31 A. Politkovskaia Str., 0186
Tbilisi, Georgia
Ludmila I. Matienko
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygin Str., Moscow
119334, Russia. E-mail: [email protected]

T. I. Megrelidze
Food Industry Department, Georgian Technical University, 77 Kostava 0175, Tbilisi, Georgia
Department of Technology, Sukhumi State University, Ana Politkobskaia 9, 0186, Tbilisi, Georgia
Elena M. Mil
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygin Str., Moscow
119334, Russia

Larisa A. Mosolova
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygin Str., Moscow
119334, Russia

Güler Narin
Department of Chemical Engineering, Uşak University, Uşak, Turkey. E-mail: [email protected]

Filiz Özmıhçı Ömürlü

Department of Chemical Engineering, İzmir Institute of Technology, Gulbahçe Urla, Izmir, Turkey.
E-mail: [email protected]

Sukanchan Palit
Department of Chemical Engineering, University of Petroleum and Energy Studies, Energy Acres, Post
Office Bidholi via Premnagar, Dehradun 248007, Uttarakhand, India. E-mail: sukanchan68@gmail.
com, [email protected]

G. Sh. Papava
TSU Petre Melikishvili Institute of Physical and Organic Chemistry, 31 A. Politkovskaia Str., 0186
Tbilisi, Georgia
List of Contributors xv

Sh. R. Papava
TSU Petre Melikishvili Institute of Physical and Organic Chemistry, 31 A. Politkovskaia Str., 0186
Tbilisi, Georgia

Lionello Pogliani
Departamento de Química Física, Unidad de Investigación de Diseño de Fármacos y Conectividad
Molecular, Facultad de Farmacia, Universitat de València, Burjassot (València), Spain, and MOLware
SL, Valencia, Spain. E-mail: [email protected]

S. Rafiei
Department of Textile Engineering, University of Guilan, Rasht, Iran

H. Ramli
Centre of Foundation Studies, Universiti Teknologi MARA, Cawangan Selangor,
Kampus Dengkil, 43800 Dengkil, Selangor, Malaysia
Prabhat Ranjan
Department of Mechatronics Engineering, Manipal University Jaipur, Dehmi-Kalan, Jaipur 303007,
India

Olena Shyshchak
Lviv Polytechnic National University, 12, St. Bandera Str., Lviv 79013, Ukraine

Heru Susanto
Department of Information Management, College of Management, Tunghai University, Taichung,
Taiwan
L. V. Tabatadze
Food Industry Department, Georgian Technical University, 77 Kostava 0175, Tbilisi, Georgia
Department of Technology, Sukhumi State University, Ana Politkobskaia 9, 0186, Tbilisi, Georgia

Z. Sh. Tabukashvili
TSU Petre Melikishvili Institute of Physical and Organic Chemistry, 31 A. Politkovskaia Str., 0186
Tbilisi, Georgia

Paulose Thomas
Optoelectronic Lab, St. Berchmans College, Changanassery, Kerala, India

Aysun Topaloğlu
Department of Chemical Engineering, Izmir Institute of Technology, Gulbahce 35430, Urla Izmir,
Turkey

Senem Yetgin
Food Engineering Department, Kastamonu University, Kastamonu, Turkey

Gennady E. Zaikov
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygin Str., Moscow
119334, Russia
N. F. A. Zainal
Centre of Foundation Studies, Universiti Teknologi MARA Cawangan Selangor, Kampus Dengkil,
43800 Dengkil, Selangor, Malaysia
LIST OF ABBREVIATIONS

ACGH array comparative genomic hybridization

ADC azodicarbonamide
ADRs adverse drug reactions
AFM atomic force microscopy
AIDS acquired immune deficiency syndrome
ANN artificial neural network
ARDs acireductone dioxygenases
ATR attenuated total reflectance
AU-ROC area under ROC
BET Brunauer–Emmett–Teller
BL2O balanced leave-two-out
CAR chimeric antigen receptor
CaSt2 calcium stearate
CBAs chemical blowing agents
CDD charged-couple devices
CFs core functions
CO carbon monoxide
COs core orbitals
DDBJ DNA database of Japan
DFT density functional theory
DMF dimethyl formamide
DNA deoxyribose nucleic acid
DoEs design of experiments
DOP dioctyl phthalate
D–R Dubinin–Radushkevich
DRIFT diffuse reflectance infrared Fourier transform
DSC differential scanning calorimeter
DTG derivative TG
EHRs electronic health records
EMBL European Molecular Biology Laboratory
EMR electronic medical records
ENR epoxidized natural rubbers
FCC fluid catalytic cracking
FCCU fluidized catalytic cracking unit
xviii List of Abbreviations

FDR false discovery rate

FE-SEM field emission scanning electron microscopy
FIB focused ion beam
FTIR Fourier-transform infrared
FWO Flynn–Wall–Ozawa
GPC gel permeation chromatography
HAO hydroxy-acrylic oligomer
HAP hydroxyapatite
HIV human immunodeficiency virus
HMPA hexamethylphosphorotriamide
HNCO cyanic acid
HO heme oxygenase
HOMO highest occupied molecular orbital
IT information technology
K kaolinite
KAS Kissinger–Akahira–Sunose
KMTB 2-keto-4-(thiomethyl)butyrate
KoARD Klebsiella oxytoca ARD
L1O leave-one-out
LBHBs low-barrier hydrogen bonds
LDPE low-density polyethylene
Li lithium
LP linear programming
LPG liquefied petroleum gas
LSDA local spin density approximation
LUMO lowest unoccupied molecular orbital
M montmorillonite
MOEAs multiobjective evolutionary algorithms
MOO multiobjective optimization
MP methylpyrrolidone
MPP melamine polyphosphate
MSP methionine salvage pathway
MTA methylthioadenosine
N2 nitrogen
NCBI National Center for Biotechnology Information
NGS next-generation sequencing
NH2CONHNHCONH2 hydrazodicarbinamide
NH3 ammonia
NHCONHCONH urazol
List of Abbreviations xix

NMR nuclear magnetic resonance

NOM natural organic matter
NR natural rubber
PAC polyacrylate
PAN polyacrylonitrile
PBAs physical blowing agents
PCL poly(ϵ-caprolactone)
PDB protein data bank
PEO poly(ethylene oxide)
pHEMA poly(2-hydroxyethyl methacrylate)
PMA poly(methyl acrylate)
PMMA poly(methyl methacrylate)
PnBMA poly(n-butyl methacrylate)
PPO polyphenylene oxide
PPy polypyrrole
PSPD position-sensitive photo diode
PVC polyvinyl chloride
RPM revolution per minute
SaaS Software as a Service
SAM S-adenosyl methionine
SARS severe acute respiratory syndrome
SCD supercritical drying
SCF supercritical fluid
SEM scanning electron microscopy
SFOs symmetrized fragment orbitals
SP sodium perchlorate
SPEs solid polymer electrolytes
SSIRs superposing significant interaction rules
STEM scanning transmission electron microscopy
SWNT single-walled carbon nanotubes
TEM transmission electron microscopy
TEOS tetraethoxysilane
TG thermogravimetric
TGA thermogravimetric analysis
THF tetrahydrofuran
TIBO tetrahydroimidazo[4,5,1-jk][1,4]benzodiazepinone
TMOS tetramethoxysilane
UHR-SEM ultrahigh resolution-SEM
wpn water molecules per nucleotide
xx List of Abbreviations

XRD X-ray diffraction

X-RD X-ray diffractometry
XRF X-ray fluorescence
ZnSt2 zinc stearate
USPEA unsaturated/saturated poly(ester amide)s
PREFACE

Experimental techniques and methodical developments provide a detailed

yet easy-to-follow treatment of various techniques useful for characterizing
the structure and properties of engineering materials. With an emphasis
on techniques most commonly used in laboratories, this book enables
researchers and students to derive the maximum possible information from
the experimental results obtained.
Not only does this book summarize the classical theories, but also it
exhibits their engineering applications in response to the current key issues.
This timely volume provides an overview of new methods and pres-
ents experimental research in applied chemistry using modern approaches.
Each chapter describes the principle of the respective method, as well as the
detailed procedures of experiments with examples of actual applications and
demonstrates the advantages and disadvantages of each physical technique.
Thus, readers will be able to apply the concepts as described in the book to
their own experiments.
This book introduces the current state-of-the-art technology in key engi-
neering materials with an emphasis on the rapidly growing technologies. It
takes a unique approach by presenting specific materials, then progresses
into a discussion of the ways in which these novel materials and processes
are integrated into today’s functioning manufacturing industry.
It follows a more quantitative and design-oriented approach than other
texts in the market, helping readers gain a better understanding of important
concepts. They will also discover how engineering material properties relate
to the process variables in a given process as well as how to perform quanti-
tative engineering analysis of manufacturing processes.

This volume:

• Highlights some important areas of current interest in applied chem-

istry and chemical engineering
• Provides an up-to-date and thorough exposition of the present state of
the art of applied chemistry and chemical engineering
• Describes the types of techniques now available to engineers and tech-
nicians, and discusses their capabilities, limitations, and applications
xxii Preface

• Provides a balance between materials science and chemical aspects,

basic and applied research, and high technology and high volume
(low cost) composite development.
• Explains modification methods for changing of different materials
properties
• Presents and reviews the necessary theoretical and background details
• Provides a detailed description of the experiment to be conducted and
how the data could be tabulated and interpreted.

This volume presents research and reviews and information on imple-

menting and sustaining interdisciplinary studies in science, technology,
engineering, and mathematics.
Applied Chemistry and Chemical Engineering, 5-Volume Set includes
the following volumes:

• Applied Chemistry and Chemical Engineering,

Volume 1: Mathematical and Analytical Techniques
• Applied Chemistry and Chemical Engineering,
Volume 2: Principles, Methodology, and Evaluation Methods
• Applied Chemistry and Chemical Engineering,
Volume 3: Interdisciplinary Approaches to Theory and Modeling
with Applications
• Applied Chemistry and Chemical Engineering,
Volume 4: Experimental Techniques and Methodical Developments
• Applied Chemistry and Chemical Engineering,
Volume 5: Research Methodologies in Modern Chemistry and
Applied Science.
 PART I
Polymer Chemistry and Technology
CHAPTER 1

SYNTHESIS OF UNSATURATED
BIODEGRADABLE POLY (ESTER
AMIDE)S AND STUDY OF THEIR
THERMAL AND MECHANICAL
PROPERTIES
E. CHKHAIDZE1,* and D. KHARADZE2
Faculty of Chemical Technology and Metallurgy, Georgian Technical
1

University, Tbilisi, Georgia

2
Ivane Beritashvili Center of Experimental Biomedicine, Faculty of
Chemical Technology and Metallurgy, Georgian Technical University,
Tbilisi, Georgia
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.........................................................................................................4
1.1 Introduction..........................................................................................4
1.2 Synthesis of Polymers..........................................................................5
1.3 Thermal Properties...............................................................................9
1.4 Mechanical Properties........................................................................13
Keywords....................................................................................................15
References...................................................................................................15
4 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

Biodegradable poly(ester amide)s of different structures containing unsat-

urated double bonds in main chain are received: homopoly(ester amide)s
(UPEA) with 100% content of fumaric acid residues, unsaturated/saturated
poly(ester amide)s (USPEA) with <100% content of fumaric acid residues,
and saturated copoly(ester amide)s of L-leucine and L-phenylalanine with
100% content of fumaric acid residues. Their thermal properties are studied
with the purpose of determination of application area and possibilities of
cross-linking of unsaturated poly(ester amide)s using UV irradiation are
shown.

1.1  INTRODUCTION

Polymers of biomedical designation are actively used today in different

areas of medicine: as surgical, dental, orthopedical materials, in the
form of medications for capsulation, for system of targeted delivery of
medications, etc. At the same time, demand for polymer materials with
complex of specific properties rapidly grows, since it is easily possible
that these materials can possibly solve many significant problems of
medicine. Among biomedical polymers of different classes, one of the
key positions is held by AABB-structure poly(ester amide)s on the basis
of natural amino acids,1–6 which are characterized by interesting complex
of properties: high skills of biodegradation and biocompatibility with
tissues, hydrophylity, good material properties, etc. Getting of even more
diverse poly(ester amide)s with predetermined properties is possible via
their functionalization, with insertion of chemically active groups, long
hydrophilic chain into polymers, etc.7 One of the prospective ways of
polymers functionalization is represented by synthesis of macromolecules
containing unsaturated bonds both in main chain and in lateral chains.8
Addition of desirable functional groups to unsaturated bonds, as well as
reactions of multiple grafting, copolymerization, hybridization with other
unsaturated polymers, for example, unsaturated polysaccharides (acryl-
dextran, etc.), synthesis of multifunctional biodegradable hydrogels can
be implemented, as it was made by Chu and colleagues,9,10 getting of
three-dimensional biodegradable systems with introduction of unsatu-
rated bonds into biodegradable macromolecule of poly(ester amide)s is
possible, etc.
Synthesis of Unsaturated Biodegradable Poly 5

Taking into account the abovementioned, we set a goal to insert unsatu-

rated bonds into AABB-type poly(ester amide)s with the purpose of their
functionalization and respective extension of application area. Introduction
of unsaturated bonds into main chain of polymers was implemented by us
using fumaric acid—unsaturated dicarboxylic acid that was main monomer
of the work. It should be noted that due to significant place hold by fumaric
acid in polymer industry and taking into account oil price increase in the last
period, at this moment, the method of enzymatic synthesis of fumaric acid
(Rhizopus species) with glucose is elaborated. Fumaric acid received using
this method is three times cheaper compared with the same product obtained
from oil. It is also noteworthy the circumstance that fermentation process
proceeds with fixation of carbon dioxide.11
Unsaturated polyesters (polyester resins), which find extensive applica-
tion in the last period, are the most widely used in practice next to conducting
the cross-linking reaction of rubber containing unsaturated bonds. Biomedi-
cine is one of the most interesting application areas of different classes of
polymers containing unsaturated bonds. Aliphatic, unsaturated, biodegrad-
able polyesters were tested in bone tissue repair surgery—in the form of
hardening binding materials for receipt of bone prostheses. Structure of
polymeric binding materials is selected such a way so that mutually oppo-
site processes of polymer degradation/bone growth could continue until
complete recovery of tissue. Application of unsaturated biodegradable poly-
esters and polyanhydrides is possible for construction of effective medica-
tion delivery system.9,12–16
As a result of conducted researches on the basis of natural amino acids,
we received functional, biodegradable poly(ester amide)s containing
different amount of unsaturated bonds in main chain. We studied their
thermal and mechanical properties, and that allows us to identify the areas
of their application.

1.2  SYNTHESIS OF POLYMERS

For receipt of functional polymers containing unsaturated bonds in main

chain, we carried out a synthesis of di-p-nitrophenyl fumarate—bis-
electrophyllic monomer—unsaturated activated diester of fumaric acid
(Scheme 1.1) using two methods: acceptor-catalytic method in the solution
and interphase method.
6 Applied Chemistry and Chemical Engineering: Volume 4

SCHEME 1.1

Synthesis of di-p-nitrophenyl ether of fumaric acid using interphase

method gives us an opportunity to synthesize high-purity monomer with
minimum losses. For purification of received product up to polycondensa-
tion purity, only single recrystallizing turned to be enough. Di-p-nitrophenyl
ethers of saturated acids (e.g., sebacic acid) were also used by us as bis-
electrophilic monomers. Synthesis of fumaric acid and di-p-nitrophenyl
ether is described in details in our previous work.17,18 Characteristics of this
compound are given there, too.
Synthesis of di-p-toluene sulfonic acid salts of bis(α-amino acid)
α,ω-alkylene diesters was carried out by us through direct condensation
of free α-amino acids with α,ω-diols in the presence of monohydrate of
p-toluene sulfonic acid (Scheme 1.2).

SCHEME 1.2

Salts were received with high yield (75–99%). Probable structures of

obtained compounds were identified using FTIR and 1H NMR spectral and
elemental analyses.17,18
Synthesis of Unsaturated Biodegradable Poly 7

For synthesis of targeted polymers, we used method of so-called acti-

vated polycondensation.19,20 According to this method, the polycondensation
reaction implements under soft conditions that are necessary for getting rid
of early polymerization of double bonds.
Using polycondensation of obtained monomers, we got saturated
poly(ester amide)s of different structure (Scheme 1.3):

1. Unsaturated homopoly(ester amide)s on the basis of L-phenylala-

nine and unsaturated diol with 100% content of fumaric acid resi-
dues (UPEA) (V), via polycondensation of (I) and (II) compounds.
2. Unsaturated homopoly(ester amide)s with 100% content of fumaric
acid residues (UPEA) (VI a, b) on the basis of L-phenylalanine (III)
or L-leucine (IV) via polycondensation of obtained ethers with (I).
3. Unsaturated/saturated poly(ester amide)s on the basis of L-leucine
with <100% content of fumaric acid residues (USPEA) (IV) via
polycondensation of compound with (I) and ethers of di-p-nitro-
phenyl of sebacic acid.
4. Unsaturated copoly(ester amide)s on the basis of L-leucine and
L-phenylalanine with 100% content of fumaric acid residues
(co-UPEA) (III) via polycondensation of and (IV) compounds
with (I).

1.

2.

3.

4.

SCHEME 1.3
8 Applied Chemistry and Chemical Engineering: Volume 4

Synthesis and properties of each of them are described in details in

Chkhaidze et al. (2011).17
Also, it is necessary to explain polymers designations. General formula
of UPEAs, saturated homopoly(ester amide)s, is FA-[AA-x]. FA denotes
polymers obtained on the basis of fumaric acid. Polymers contain fumaric
acid residues –CO–CH=CH–CO– in main chain of polymers. AA denotes
amino acids: L-phenylalanine or L-leucine, x is the number of methylene
groups of diol and it is equal to 6, 8, and 12; for unsaturated diols, 2-butene-
diol residue is denoted by 4en.
General formula of UPEAs, polymers received on the basis of fumaric
acid and saturated acids, is FA/yk/l-[AA-x]. FA denotes fumaric acid resi-
dues, y is the number of methylene groups in saturated acids –CO–(CH2)
y
–CO–, and y = 8. AA denotes L-phenylalanine or L-leucine, x is the
number of methylene groups of diol and it is equal to 6. k and l are molar
fractions of fumaric acid and saturated acid in initial reaction mixture,
respectively.
General formula of co-UPEA, copolymers obtained on the basis of
fumaric acid, is FA-[Leu-x]k-[Phe-x]l, FA denotes fumaric acid residues,
Leu and Phe are amino acids, x is the number of methylene groups of diols,
k and l is the ratio of monomers containing leucine and phenylalanines in
terms of mol/mol. For instance, FA-Leu-12 denotes UPEA, which consists
of fumaric acid and Leu-12, FA/840/60-Leu-6 denotes USPEA, which
consists of 40 mol% of fumaric acid and 60 mol% of sebacic acid. FA-[Leu-
6]0.75-[Phe-6]0.25 denotes co-UPEA, which consists of 100 mol% of fumaric
acid, as well as 75 mol% of Leu-6 monomer (IV) and 25 mol% of Phe-6
monomer (III).
We studied properties of obtained polymers: solvability in organic
solvents, biodegradation skills (enzyme hydrolysis) using gravity method
in vitro experiments, under conditions most closely resembling to physio-
logical conditions (pH 7.4; 37°C) with enzymes α-chymotrypsin and lipase.
Reactions of polymers’ chemical transformation were conducted by us using
thioglycolic acid, 2-mercaptoethanole, and amino acid—β-alanine. All the
abovementioned is described in the work.17
It should be noted that for polymers of biomedical designation, except
the above-listed properties, it is necessary to study thermal and mechan-
ical properties, since they have significant impact on other properties
of polymers and also they determine their application area. For instance,
biodegradation of crystalline polymers proceeds at far less rates than that
of amorphous polymers. Polymers with high vitrification temperatures are
Synthesis of Unsaturated Biodegradable Poly 9

prospective compounds in the form of extracted surgical and construction

materials, while polymers with low vitrification temperatures are used in the
form of artificial leather, stent coating, for getting of medication-controlled
extraction systems, and polymers with good mechanical characteristics
are prospective generally as surgical materials, reconstructive orthopedic
surgery, for preparation of blood vessels stent, etc.

1.3  THERMAL PROPERTIES

Thermal properties of polymers were studied by us using differentiated

scanning calorimetry (DSC). Measurements were conducted with the use
of calorimeter “Perkin-Elmer DSC-7” in nitrogen medium, in the temper-
ature range 20–200°C; heating rate 10K/min. Part of work we imple-
mented by means of calorimeter “NETZSCH” DSC 200 PC” “PHOX,”
in the temperature range 20–150°C. Heating rate 10K/min. In general,
assessment of thermal properties of polymers is possible by means of
vitrification temperatures (Tg), change of specific heat capacity (Δcp),
melting temperature (Tm), and change of enthalpy (ΔH).21,22 In case of
limitation of intra- and extramolecular flexibility of polymeric chains,
their Tg increases. In its turn, Δcp shows us what conformational changes
have taken place in amorphous part and gives us an opportunity to make
certain conclusions on molecular interactions in polymers. Existence of
Tm points at formation of ordered (probably crystalline) structure in poly-
mers. Thermal characteristics of studied polymers are given in Table 1.1,
while some DSC curves are presented in Figures 1.1–1.4. Thermal char-
acteristics of polymers of all synthesized groups are given in the table.
Thermal properties of analogues of saturated structures of some of them
are also given as a comparison.
According to obtained results, we can conclude that unsaturated
poly(ester amide)s are characterized by relatively high vitrification tempera-
ture Tg in comparison with corresponding saturated poly(ester amide)s that
was anticipated and is related to increased rigidity of their chains (in other
words, less mobility).
For instance, unsaturated polyester amide FA-Phe-6 compared with satu-
rated 8-FA-Phe-6 of similar structure is characterized by ~70°C higher vitri-
fication temperature (Table 1.1, samples N2, N3). FA-Phe-6 contains double
unsaturated C=C bonds in diamide part of macromolecule, which precondi-
tion rigidity of main chain of macromolecule. In comparison with FA-Phe-6,
10 Applied Chemistry and Chemical Engineering: Volume 4

FA-Phe-4en, which contains C=C bonds both in diamide and in diester parts,
has even higher vitrification temperature (Table 1.1, sample N1).
Poly(ester amide)s on the basis of amino acid leucine are characterized
by generally more flexible chains compared with poly(ester amide)s of
similar structure, which are received on the basis of phenylalanine.17 In this
case, insertion of unsaturated bonds in amide part of polymers has no signifi-
cant impact on vitrification temperature of polymers (Tg) (Table 1.1, samples
N4, N5), while it has bigger impact on melting temperature of polymers
(increases by 50°C) (Figs. 1.1 and 1.2) and on degree of order. Though it
should be noted that as a result of second scanning, that is, repeated measure-
ment, this difference is leveled off.

TABLE 1.1  Thermal Characteristics of Homopoly(ester amide)s, Unsaturated/Saturated

Poly(ester amide)s and Copoly(ester amide)s.
No. Polymer Scan I*
Tg (°C) ΔCp (J/g*K) Tm (°C) ΔH (J/g)
1 FA-Phe-4en 109 – ~223 –
2 FA-Phe-6 92 – ~216 –
3 8-Phe-6 21.00 1.04 54.50 15.48
4 8-Leu-12 21.8 0.369 85.1 50.67
5 FA-Leu-12 22.2 0.573 137.9 30.38
6 FA-Leu-12 + phthalic anh 24.7 1.632 102.4 –
7 FA-Leu-12 + phthalic anh N6—after 3 28.1 0.91 121.3 21.74
months)
8 FA/825/75-Leu-6 32.9 1.189 – –
9 FA/840/60-Leu-6 45.4 1.873 – –
10 FA-[Leu-8]0.75-[Phe-8]0.25 27.2 2.831 – –
11 FA-[Leu-12]0.75-[Phe-8]0.25 15.5 0.201 – –
*
Scan I—I measurement.

There is no significant difference between vitrification temperature of

FA-Leu-12 blocked and unblocked with phthalimide (Table 1.1, samples
N5, N6, and N7). It should be noted that blocking of side groups was imple-
mented with the purpose of getting rid of cross-linking reaction. Certainly,
though slight rise of Tg is observed after 3-month delay of FA-Leu-12
Synthesis of Unsaturated Biodegradable Poly 11

blocked by phthalimide (Samples N6, N7), presumably due to structural

changes.
As was expected, increase of content of fumaric acid residues in unsatu-
rated/saturated polymers FA/825/75-Leu-6 and FA/840/60-Leu-6 (samples N8
and N9) caused rise of vitrification temperature of polymers (Tg) that is
expected result, since chain length increases, too. Change in specific heat
capacity (Δcp) of polymers points at the same process. Together with rise of
vitrification temperature, the specific heat capacity and degree of order of
polymers also increases.
Comparison of N10 and N11 samples of copolymers allows us to make
conclusion that increase of length of methylene chain of diol reduces vitri-
fication temperature of polymers (Tg), their specific heat capacity (Δcp) and,
respectively, increases amorphism degree.
Basically, only single value of vitrification temperature is received at the
thermogram of polymers (Table 1.1, Figs. 1.1–1.4), that is, in the synthesis
process amorphous polymers of nondomain structure are formed. Major part
of poly(ester amide)s obtained on the basis of leucine is characterized by
low vitrification temperature that is significant circumstance from the view-
point of their processing.

FIGURE 1.1  Thermogram of FA-L-Leu-12.

12 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 1.2  Thermogram of 8-Leu-12.

FIGURE 1.3  Thermogram of FA-L-Leu-12 + phthalic anh.

Synthesis of Unsaturated Biodegradable Poly 13

FIGURE 1.4  Thermogram of FA-L-Leu-12 + phthalic anh (after 3-month delay).

1.4  MECHANICAL PROPERTIES

As we mentioned earlier, for identification of application area of biomedical

polymers, the knowledge of mechanical properties of polymers together
with other abovementioned properties is important. At the same time, due
to availability of double bonds, an improvement of mechanical proper-
ties of polymers is possible via photocross-linking reaction. We selected
unsaturated/saturated polyester amide FA/825/75-Phe-6 (Mw = 69,700, Mn =
28,000, Mw/Mn = 2.49) for study of mechanical properties and determined
mechanical properties of films of mentioned polymers with 0.3–0.5-mm
thickness. Films were dried in vacuum at 50–70°C. Mechanical properties
of films were studied using Mecmesin “Multitest 1-i.” Samples in the form
of so-called doggy bone were prepared.
With the purpose of establishment of possibilities of photocross-linking
of obtained poly(ester amide)s, we conducted UV irradiation (using Intelli-
Ray 400, Shuttered UV Flood light) of unsaturated/saturated polyester amide
FA/825/75-Phe-6 without initiator and in the presence of 5% of photoiniti-
ator Darocur-1173. Young modulus E (GPa), maximum force Fmax (MPa),
breaking strength σ (MPa), and breaking elongation ε (%) prior to irradiation
and after 5-min irradiation were determined.
14 Applied Chemistry and Chemical Engineering: Volume 4

As the obtained results showed, significant change of mechanical char-

acteristics (E, Fmax, and σ) is not observed during film irradiation without
photoinitiator. In the presence of 5% of photoinitiator Darocur-1173,
improvement of mechanical characteristics of polymers takes place, and
photocross-linking of unsaturated poly(ester amide)s occurs (Table 1.2).

TABLE 1.2  Mechanical Properties of Unsaturated/Saturated Polyester Amide FA/825/75-Phe-6.

Defined Original samples Samples in the presence of photoinitiator
parameters Darocur-1173
Drying at 50°C Drying at 70°C
Prior to After Prior to After Prior to After
irradiation irradiation irradiation irradiation Irradiation irradiation
Young modu- 1.64 ± 0.09 1.55 ± 0.03 1.08 ± 0.12 2.15 ± 0.20 1.75 ± 0.05 2.35 ± 0.02
lus E (GPa)
Maximum 30.5 ± 5.5 27.0 ± 3.0 27.0 ± 3.3 49.0 ± 3.0 40.0 ± 8.0 61.0 ± 0.3
force Fmax
(MPa)
Breaking 19.0 ± 8.0 22.0 ± 2.0 36.7 ± 6.2 42.0 ± 7.0 35.0 ± 5.0 61.0 ± 0.3
strength σ
(MPa)
Breaking 185.0 ± 25.0 205.0 ± 50.0 253.0 ± 32.0 185.0 ± 5.0 60.0 ± 20.0 4.5 ± 2.0
elongation
ε (%)

Thus, on the basis of preliminary data, we can suppose that photocross-

linking of synthesized unsaturated polyester amide improves mechanical
characteristics of material that make their use prospective as surgical mate-
rials, for example, in the form of photocross-linked, biodegradable blood
vessel stent, etc.
As a result of carried out research, we received functional, biodegradable
polymers on the basis of natural amino acids containing different number of
unsaturated bonds in main chain, with good material properties, which are
prospective for getting the biodegradable materials with high mechanical
strength, for implanted artificial organs, biodegradable hydrogels, medica-
tion delivery systems, micro- and nanocapsulation, etc.
Synthesis of Unsaturated Biodegradable Poly 15

KEYWORDS

•• unsaturated/saturated poly(ester amide)s

•• homopoly(ester amide)s
•• copoly(ester amide)s
•• unsaturated biodegradable polymers
•• cross-linking

REFERENCES

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3. Okada, M.; Yamada, M.; Yokoe, M.; Aoi, K. J. Appl. Polym. Sci. 2001, 81, 2721–2734.
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Polym. Ed. 2007, 18(4), 411–438.
5. Lee, S. H.; Szinai, I.; Karpenter, K.; Katsarava, R.; Jokhadze, G.; Chu, C. C.; Huang,
Y.; Verbeken, E.; Bramwell, O.; De Scheerder, I.; Hong, M. K. Coron. Artery Dis. 2002,
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6. Defife, K.; Grako, K.; Cruz-Aranda, G.; Price, S.; Chantung, R.; Macpherson, K.;
Khshabeh, R.; Gopalan, S.; Turnell, W. G. J. Biomater. Sci. 2009, 20, 1495–1511.
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8. Lou, X.; Detrembleur, C.; Lecomte, P.; Jerome, R. e-Polymers, 2002, 034.
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L. A. M. Appl. Microbiol. Biotechnol. 2008, 78, 379–389.
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Polym. Chem. 1990, 28(5), 973–985.
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Macromol. Chem. 1986, 187(2), 341–350.
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16 Applied Chemistry and Chemical Engineering: Volume 4

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CHAPTER 2

EXPERIMENTAL DESIGN AND

PROPERTIES OF PVC FOAMS:
AZODICARBON AMIDE AND ZINC
OXIDE
FILIZ Ö. ÖMÜRLÜ and DEVRIM BALKOSE*
Department of Chemical Engineering, İzmir Institute of Technology,
Gulbahçe, Urla, Izmir, Turkey
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.......................................................................................................18
2.1 Introduction........................................................................................18
2.2 Materials and Method........................................................................22
2.3 Results and Discussion......................................................................25
2.4 Conclusions........................................................................................40
Acknowledgment........................................................................................41
Keywords....................................................................................................41
References...................................................................................................41
18 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

In this work, flexible PVC foam films were prepared using azodicarbonamid
(ADC) as chemical bowing agent and zinc oxide (ZnO) catalyst in polyvinyl
chloride (PVC) plastisols. Zinc stearate and calcium stearate were added as
thermal stabilizers for PVC. ZnSt2 and CaSt2were added to PVC as thermal
stabilizers to plastisol. Foaming and gelation of the films occur simultane-
ously during heating the plastisols. The optimum ZnO and ADC concentra-
tion were analyzed by 23 experimental design by selecting density as the
response. Design equation of density gives time as the main factor. On the
other hand, design equation of induction time gives ZnO amount as the main
factor.

2.1 INTRODUCTION

The use of polymer foams is extremely widespread in today’s technology.

Indeed, it is hard to think of going a day without coming across some sort
of polymer foam. They have a part to play almost everywhere in our life
such as disposable packaging of fast food, in sports and leisure products,
the cushioning of furniture and insulation material, in military applications,
in vehicles, in aircraft, in textiles, and in some other common applications.
For industrial foam applications, selection of convenient polymers depends
upon their properties, the economics of the foaming system and their ease
of production.
Naturally occurring polymer foams have been known for a long time,
such as sponges, cork. However, synthetic polymer foams have only been
introduced to the market over the last 50 years or so. They continue to grow
at a rapid pace because of their toughness, flexibility, resistance to chemicals
and abrasion, lightweight, excellent strength/weight ratio, superior insulating
abilities, energy-absorbing performance, and comfort features.7 Thermal
insulation, low density/lightness, and compressibility are all increased by
foaming a polymer.
Polymer foams are composed of a solid and gas phase mixed together to
form a foam, which happens too fast for the system to respond in a smooth
form. The product foam has a polymer matrix with either air bubbles or
air tunnels included in it, which is known as either closed-cell or open-cell
structure. Closed-cell foams are generally more stiff, on the other hand open-
cell foams are usually elastic.24 The open-cell foams are most suitable for car
seating, furniture, bedding, and acoustical insulation, among other uses. The
Experimental Design and Properties of PVC Foams 19

closed-cell foams are best for thermal insulation.7 There are many types of
polymeric foams, for instance; polyurethane, polystyrene foam, biodegrad-
able foam, polyolefin foams, and starch.
Polymer foams can be separated into either thermoplastics or thermosets,
which are further divided into rigid or flexible foams. Although, the thermo-
plastics can usually be broken down and recycled, thermosets are harder to
recycle since they are usually heavily cross-linked. Polymeric foams and
foam technology were explained in detail by Klemper and Sendijarevic12
and PVC foams were reviewed in detail by Wilkes et al.27

2.1.1  CHEMICAL AND PHYSICAL BLOWING AGENTS

The gas that is used in the foam is named as a blowing agent, and two types
of blowing agents can be used to expand a polymer: physical and chem-
ical. Chemical blowing agents (CBA) are chemicals that decompose to give
gaseous products in the process.24 CBA have two main advantages: they are
easy to introduce into the polymer (mixing and handling) and they are easily
processed with ordinary equipment that is to say no modification needed.
On the other hand, physical blowing agents (PBA) are gases that do
not react chemically in the foaming process. Therefore they are inert to the
polymer forming the matrix.24 PBA provide the expansion gas by under-
going changes in their physical state. These changes may include volatiliza-
tion of a liquid or release of a compressed gas to atmospheric pressure after
its combination into a polymer while under pressure. Some examples of
PBA can be given such as nitrogen, carbon dioxide, and light hydrocarbons;
moreover, each one can be used alone or in cofoaming agent.
The most popular CBA for polyolefins is certainly azodicarbonamide
(ADC) which is selected for its high gas yield 210–220 cm3 of gas per
gram of product) and the ability to match its decomposition temperature
with the polymer’s processing temperature using suitable activators (cata-
lysts or kickers), such as transition metal salts (lead, cadmium, and zinc),
polyols, urea, alcohol, amines, and organic acids. ADC decomposition
is a function of particle size, heating rate, activator type and concentra-
tion, as well as degree of dispersion of the blowing agent and activator.
ADC thermal decomposition is an exothermic process and several studies
have reported its heat of reaction. The decomposition of ADC in poly-
ethylene at high temperature (extent of reaction vs. time) produces an
S-shaped curve typical of an autocatalytic reaction.17 ADC has been used
as cross-linking and blowing agent in plastics. Both rigid and flexible
20 Applied Chemistry and Chemical Engineering: Volume 4

poly(vinyl chloride) (PVC) foams have been prepared by adding ADC as a

blowing agent. Two types of end products are obtained by decomposition
of ADC: solids such as urazol (NHCONHCONH) and hydrazodicarbon-
amide (NH2CONHNHCONH2) serve as nucleating agents; and a gaseous
mixture of cyanic acid (HNCO), ammonia (NH3), carbon monoxide
(CO), and nitrogen (N2). ADC provides foam formation by decomposing
at 195–216°C, according to the way of preparation and releasing a large
volume of nitrogen and carbon monoxide.17
PVC is a unique thermoplastic which has the ability to be produced
with wide range of properties by the choice of additive. The addition of
different level of plasticizer to PVC produces materials that have different
softnesses. This flexible material is preferred due to good chemical resis-
tance, toughness, flexibility, their ease of production, and economic
reasons.27 PVC foams widely used in wind energy, marine, road, rail, aero-
space, textile, military applications because of its excellent features, such
as light weight, sound and thermal insulation, excellent strength/weight
ratio.7,22 PVC foams can be either be obtained by physical blowing agents or
CBA. Microcellular PVC/thermoplastic foams were obtained by physical
blowing with carbon dioxide.21 The foaming parameters considerably influ-
ence the mechanical and structural and moisture absorption properties of
renewable resin precursor and residual filler modified PVC foams obtained
by high-pressure carbon dioxide.23 Rigid PVC foams were also prepared by
using CBA.3 CBA are used in producing PVC foams by gelation of plasti-
sols. The PVC plastisol composition and processing conditions effect the
foam expansion and tear strength of foams.17 Effects of plasticizers, such as
phthalate esters and mixed phthalates on foaming of PVC plastisols, were
investigated by Verdu et al.,25 Zoller and Marcilla,29–31 Yu et al. showed that
the asphalt filled hydrophobic flexible PVC foam crumps had high oil sorp-
tion capacity.28

2.1.2  PVC THERMAL DEGRADATION AND STABILIZATION

Plastisols are dispersion of PVC particles in plasticizers. PVC undergoes

thermal degradation when plastisols are heated.11 While preparing PVC
foam, PVC resin is dispersed with an appropriate plasticizer, blowing agent,
and stabilizer, and then heated to 180–200°C for simultaneous gelation and
foaming of the plastisol.7 Moreover, degradation of PVC takes place during
PVC foaming process starting at about 100°C by autocatalysis of evolved
hydrogen chloride.8 Dehydrochlorination is accompanied by polymer
Experimental Design and Properties of PVC Foams 21

discoloration going from yellow to brown and black due to formation of

conjugated double bonds as shown by eq 2.1. The dehydrochlorination of
PVC gives hydrogen chloride gas and dehydrochlorinated PVC (dePVC)
having conjugated double bonds.

PVC (s) → dePVC (s) + HCL (g). (2.1)

Different organic and inorganic compounds are used as heat stabilizers

which are based on metal soaps. Zinc soaps are useful stabilizers, however,
product zinc chloride which is a Lewis acid, accelerates dehydrochlorina-
tion after its concentration reached up to certain level.4 Zinc soaps are used
together with calcium soaps to eliminate the zinc chloride effect. CaCl2 is
formed which is not a Lewis acid. The reaction between ZnCl2 and calcium
stearate (CaSt2) is shown in eq 2.2.

ZnCl2 + CaSt 2 → ZnSt 2 + CaCl2 . (2.2)

The role of metal oxides on the thermal degradation of vinyl polymers

suggest that the kinetics of the degradation is affected by metal oxides.9 ZnO
addition increased significantly decomposition rates and a modified mecha-
nism was proposed to take into account this activation effect. ZnO added at
a low level catalyzes the decomposition of ADC, without any detrimental
effect on degradation of PVC.18 Zinc maleate/ZnO mixtures has synergistic
effect of thermal stability of PVC.13
Thermal degradation of PVC in the presence of metal oxides was inves-
tigated using a thermogravimetric (TG) method by Gupta and Visvanath.9
It follows a two-step mechanism. In the first step chlorine free radical is
formed as in the case of pure PVC, and in the second step chlorine free
radical replaces oxygen from metal oxide to form metal chloride and oxygen
free radical. Subsequently, the oxygen free radical abstracts hydrogen from
PVC. Formation of metal chloride is the rate controlling step.
In the case of transition metal oxides coated with PVC, the thermal
degradation can be correlated with the bulk properties such as the ability of
electron transfer in the transition metals to form different valence states, and
degradation may be described via an electron transfer (redox) mechanism
which proceeds through formation of HCl.9 The liberated HCl then reacts
with metal oxide, and the rate is faster at elevated temperature. Thus, the
activation energy is lower than that for the degradation of pure PVC. The
statistical investigation of the thermal stability of PVC powder was investi-
gated by Savrik et al.19
22 Applied Chemistry and Chemical Engineering: Volume 4

Response surface approach was used to optimize fusion properties of

rigid foam PVC/clay composites.15
The objective of this study is to investigate the effects of time and zinc
oxide on both ADC decomposition and foam formation. A 23 factorial design
was done for optimum foaming conditions and the response was selected as
density. Since the thermal stability was also affected, optimum conditions
for highest induction time were also investigated.

2.2  MATERIALS AND METHOD

2.2.1 MATERIALS

PVC (Petvinil, P.38/74) was the product of Petkim Co. Dioctyl phthalate
(DOP) and ADC were purchased from Merck Co. Zinc stearate (ZnSt2) and
CaSt2 taken from Baerlocher Co. and Viscobyk 5025 from BYK-Chemie
and ZnO from Ege Chemical Co. was used in this study. The PVC powder
was composed of spheres of a large particle size range from 10 nm to 20
μm.21 The particle size and the aspect ratio of ZnO was 3.86 and 4.35 µm,
respectively.15

2.2.2  PREPARATION OF THE PVC FOAM FILMS

In order to produce PVC foam films, PVC plastisol was prepared by

mixing 100 parts PVC, 80 parts DOP, 5 parts Viscobyk 5025, 1 part CaSt2,
and 1 part ZnSt2. Heat stabilizers and PVC were dried at 50°C for about 1
h before mixing. This mixture was stirred until it became a homogeneous
suspension. This sample was separated into 20 g aliquots. Four samples
were prepared having different amounts of ADC and ZnO. About 0.2 g
ADC and 0.25 g ZnO were added into the first 20 g. A total of 0.2 g ADC
and 0.25 g ZnO, 0.2 g ADC and 0.1 g ZnO, 0.4 g ADC and 0.25 g ZnO, 0.4
g ADC and 0.1 g ZnO powders were added to the second, third, fourth 20
g, respectively. The plastisol samples were cast onto glass substrate with
the aid of an automatic film applicator (Sheen 1133N) with 90 μm gap
size at a speed of 50 mm/s. Films were allowed to gel and foam in oven
(Venticell) at 190°C for 5 and 10 min to see the effect of heating time on
the foaming. The experiments were repeated one more time to optimize the
data for analysis of variance.
Experimental Design and Properties of PVC Foams 23

2.2.3  EXPERIMENTAL DESIGN

23 experiments were made to minimize the density of the films. The variables
affecting the density are ZnO amount, ADC amount, and the time of heating
at 190°C. High and low values of each variable were chosen as shown in
Table 2.1. The designs were carried out by using Design of Expert (Trial
version 8.0). The same variables were also used in optimizing the induction
time of the prepared composites.

TABLE 2.1  The Selected High and Low Values of the Variables for Minimizing the Density
of the Films.
Variable High Low
ZnO content (g/20 g plastisol) 0.25 0.10
ADC content (g/20 g plastisol) 0.4 0.2
Time (min) 10 5

2.2.4  DENSITY AND PORE VOLUME

Density of PVC foams was measured by using Sartorius density measure-

ment kit.26 Water was used as the liquid causing buoyancy. To determine the
sample’s buoyancy, floating sample was immersed by a metal sieve. The
negative weight displayed by the balance corresponded to the buoyancy
acting on the sample in the liquid. Density of foam samples was calculated
by using eq 2.3.

Wa ρ fl
ρ= + 0.0012, (2.3)
0.99983G
where G is the buoyancy force, ρfl the fluid density, ρ the foam density, and
Wa is the dry weight of foam. The percentage of the volume of pores (Vtotalpore)
of the foam samples was calculated by using eq 2.4.

ρ
Vtotalpore = (1 − ) × 100. (2.4)
ρTheoretical
Theoretical density values (ρTheoretical) were calculated from the mass of
the sample and the geometric volume of the samples.
24 Applied Chemistry and Chemical Engineering: Volume 4

2.2.4.1  CHARACTERIZATION OF THE FILMS

Scanning electron microscopy (SEM) was used to obtain PVC plastisol

foam films cell structure and to view the internal configuration of the cells.
Films were broken after immersing in liquid nitrogen (77K) and fracture
surfaces were coated with a thin gold film and examined by using SEM
(Philips XL-30S FEG).
The density of the films was measured by using “Archimedes” apparatus.
The average of four measurements was used in density determination by
taking the water density as 0.99983 g/cm3 at 25°C.
Tensile testing of the films was made according to ASTM D882. Stress-
strain diagrams for samples with ZnO and without ZnO were obtained by
tensile testing using Testometric tensile testing machine. Five samples from
each set were cut to thin strips 10 ×100 mm in size and stretched uniaxially
with a cross-head speed of 10 mm/min.

2.2.5  THERMAL GRAVIMETRIC ANALYSIS

The effect of ZnO on ADC decomposition was investigated by TG analysis

using Shimadzu TGA-51. Samples with ADC/ZnO mass ratios of 0.2:0.04,
0.2:0.08, 0.2:0.08 were prepared by through mixing of the powders Small
amount (10 mg) of powders was placed in an alumina pan for each run
and analysis were carried out with a heating rate of 5, 10, 20°C/min under
nitrogen gas flow up to 600°C. The TG analysis was also made for films
prepared by 10 min heating at 190°C. The films were heated at 10°C/min
rate from room temperature up to 600°C.

2.2.6  THERMAL STABILITY OF PVC

Thermal stability of PVC can be determined by 763 PVC Thermomat instru-

ment. It is equipped with two heating blocks each with four measuring
positions. Each block can be individually heated, therefore two sets of four
samples can be measured at two different temperatures or eight samples can
be measured at the same temperature. Also the measurements at the indi-
vidual measuring positions can be started individually. The films were cut
into 0.5 cm × 0.5 cm small squares and 0.5 g of samples was put into reac-
tion vessels. The heating blocks of PVC Thermomat were heated to 190°C.
The reaction vessels that contained PVC plastigel films were placed into the
Experimental Design and Properties of PVC Foams 25

heating blocks. HCl formed was taken up by a nitrogen gas stream and trans-
ferred into the measuring vessels.2 The deionized water absorbed HCl gas
and the change in conductivity of the solution was determined with respect
to time by the conductimeter. Therefore, the decomposition process was
monitored by measuring the conductivity of aqueous HCl solution.2
When PVC plastigels are heated in PVC Thermomat in the presence of
nitrogen gas, the conductivity of water, which nitrogen gas is passed, changes
with respect to time. The period when the conductivity starts to increase is
called as induction time, and the period when the conductivity value reaches
to 50 mS/cm is called as stability time. This value is the maximum accept-
able level of degradation.
The photographs of the films as made and after the PVC Thermomat test
were recorded by a digital camera.

2.3  RESULTS AND DISCUSSION

2.3.1  CHARACTERIZATION OF PVC FOAMS

Adhesion and cross-linking of the swollen PVC particles forming a gel and
release of the gases from ADC occur simultaneously while heating PVC
plastisols. When the temperature and heating periods were increased PVC
particles were swollen with the plasticizer and fused to each other. The gases
released by ADC were entrapped in the fused plastigel forming the porous
structure. Porous structured PVC matrix composites are obtained by this
method. The microstructures of the composites were investigated by SEM.
SEM micrographs of the fracture surfaces of the composites obtained by
immersing in liquid nitrogen are seen in Figures 2.1 and 2.2. The plastigel
film without ZnO and ADC is expected to be nonporous when heated for
10 min at 190°C. However, there were unfused PVC particles or closed air
bubbles covered with fused PVC in the film as seen in Figure 2.1. This film
had a lower density (1.139 g/cm3) than expected for a nonporous film (1.165
g/cm3) and thus it has around 2% void volume.
The pores were elliptical in shape and they had a broad size distribution
as seen in SEM micrographs of PVC foams in Figure 2.2. Their average
dimensions in width and length and their standard deviation and their aspect
ratio are reported in Table 2.2.
The maximum sized pores were obtained for the plastigel containing
0.4 g ADC and 0.25 g ZnO per 20 g of plastisol.
26 Applied Chemistry and Chemical Engineering: Volume 4

(a) (b)

(c) (d)
FIGURE 2.1  SEM micrographs of PVC plastisol film heated for 10 min at 190°C. (a) and
(b) at 100× magnification, and (c) and (d) at 1000× magnification.

(a) (b)

(c) (d)
FIGURE 2.2  SEM micrographs of PVC plastisol foam films fracture surfaces (for 10 min at
190°C) consist of these ratios: (a) 0.2 g ADC:0.25 g ZnO, (b) 0.2 g ADC:0.1 g ZnO, (c) 0.4 g
ADC:0.25 g ZnO, and (d) 0.4 ADCg:0.1g ZnO per 20 g plastisol.
Experimental Design and Properties of PVC Foams 27

TABLE 2.2  The Dimensions of the Elliptical Foams and Their Aspect Ratio.
ADC mass ZnO mass Width (µm) Length (µm) Aspect ratio
(g/20 g) (g/20 g) Average Standard Average Standard
deviation deviation
0.2 0.25 155.2 67.8 166.3 94.0 0.9
0.2 0.1 168.2 67.4 267.2 98.2 0.6
0.4 0.25 188.6 76.9 396.4 164.0 0.5
0.4 0.1 143.2 63.6 306.3 43.1 0.5

2.3.1.1 DENSITY

Plastisols and samples containing ZnO and ADC are tested by using density
Archimedes’ kit. Density of the samples was calculated using eq 2.3. Table
2.3 gives the densities and pore volume % of the films prepared by 5 and 10
min heating at 190°C. The maximum pore volume (77.42%) obtained was
for the film with 1.9% ADC and 1.2% ZnO (0.4 g ADC and 0.25 g ZnO).
This was close to the pore volume obtained by Şahin et al.18 for the plastisol
with 2% ADC and 2.5% ZnO that was heated for 12 min at 190°C.

TABLE 2.3  Density of the Composites After Heating at 190°C for 5 and 10 min.
ADC ZnO (g/20 g) Density (g/cm3) Pore volume (%)
(g/20 g) 5 min heated 10 min heated 5 min heated 10 min heated
0 0 1.139 1.158 2.23 0.60
0.2 0.25 1.161 0.315 0.34 72.96
0.2 0.10 1.160 0.386 0.43 66.87
0.4 0.25 1.164 0.263 0.09 77.42
0.4 0.10 1.156 0.467 0.77 59.91

ADC is known to promote foam formation by decomposing at

195–216°C depending on the mode of preparation and releasing a large
volume of nitrogen and carbon monoxide gas.17 Finely dispersed filler addi-
tives are known to reduce this decomposition temperature by activating
ADC and providing nucleation sites for gas evolution. The foam forma-
tion for PVC composites were related with the decomposition of ADC. The
density of the composites was lowered, since ADC gave gaseous products
that were entrapped in plastigel. However, as seen in Table 2.3, for 5 min
heating period, the foam formation did occur because there was not enough
28 Applied Chemistry and Chemical Engineering: Volume 4

time for gelation of PVC plastisol to entrap the gaseous products from the
decomposition of ADC. However, after 10 min heating, the density of the
composites drops very sharply and bubble formation within the composites
was obtained due to decomposition of ADC and confinement of the gases in
gelled plastisol.

2.3.1.2  MECHANICAL BEHAVIOR OF PVC FOAMS

Samples with and without ADC and ZnO are tested for mechanical prop-
erties using Uniaxial Tensile Testing Machine. Representative stress strain
diagrams of the samples without and with ADC and ZnO are shown in
Figure 2.3.

FIGURE 2.3  Stress–strain curves for films (a) without and (b) with 0.2g ADC and 0.25g ZnO.
Experimental Design and Properties of PVC Foams 29

Elastic modulus of the films is found from the slope of the stress strain
curve at the origin using eq 2.5.

Elastic modulus = Tensile Strength/Strain. (2.5)

According to equal assumption of the slab model, the tensile strength (σc)
of a composite equals to

σc = σ f + σ p (1 − ϕ f ), (2.6)

where φf and σp are volume fraction of filler and tensile strength of the plastic
phase, respectively.6 The filler in the present case is air in the foams and its
tensile strength is zero.
Elastic modulus of the foams can be predicted using elastic modulus of
the plastic phase and ratio of the densities of the foam (ρ) to the plastic (ρp).1

Ec = E p (ρ / ρ p ) 2 . (2.7)

The tensile strength and elastic modulus were predicted in eqs 2.6 and
2.7 and reported in Table 2.4.

TABLE 2.4  Mechanical Properties of Samples PVC and PVC Film for 10 min at 190°C.
Composition Tensile strength (Mpa) Strain Elastic modulus (Mpa)
ADC ZnO Experimental Theoretical at break Experimental Theoretical
(g/20 g) (g/20 g) (%)
0 0 600 600 355 436 436
0.2 0.25 345 162 50 690 32
0.2 0.1 333 114 55 605 48
0.4 0.25 330 75 51 647 22
0.4 0.1 238 132 36 661 70

The film without ZnO and ADC had higher tensile strength than the
foamed films as reported in Table 2.4. However, the films had higher tensile
strength values than predicted by eq 2.6. This could be attributed to the
simultaneous cross-linking of PVC by ADC during foaming process. The
modulus of elasticity values of the foamed films was also much higher than
predicted by eq 2.7. The tensile strength of the films in the present study was
nearly 10 fold higher than the films prepared in a previous study made by
Şahin et al.18 The only difference in the two studies is that using the PVC
30 Applied Chemistry and Chemical Engineering: Volume 4

dispersant Viscobyk 5025. The agglomeration of PVC particles during plas-

tisol preparation was prevented and the area of contact between plasticizer
swollen particles was higher, that made better fusion of the particles.

2.3.2  THERMAL CHARACTERIZATION OF AZODICARBONAMIDE

The effect of ZnO and ZnO concentration was studied by TGA. TG curves
of ZnO and ADC mixtures at 5 and 10°C/min rates are seen in Figures 2.4
and 2.5.

FIGURE 2.4  TG curves for mixtures with different ZnO content for 10°C/min heating rate.
The parameters on the curves are g ZnO per 0.2 g ADC.

As depicted in Table 2.5 the decomposition temperature of ADC

decreases as ZnO% increases. The mixtures with 0.04/0.2 and 0.12/0.2 ZnO/
ADC ratio started to evolve gases at 219.04°C and 188.83°C, respectively.
While N2 gas and CO are the gaseous products of ADC solid residue
consists of urazol and hydro-ADC. The solid residue also decomposes to
give gaseous products at higher temperature. ZnO has two effects in ADC
decomposition: lowering the decomposition onset temperature and leading
to complete gasification of ADC. When ZnO ratio is increased, ADC
decomposition onset temperature decreased nearly 30°C from 220°C to
190°C. Indeed, the addition of ZnO was found to accelerate the thermal
Experimental Design and Properties of PVC Foams 31

decomposition of ADC by increasing the reaction rate of the first step of

ADC decomposition by an order of magnitude using only 0.1%.17

FIGURE 2.5  TG curves for mixtures with different ZnO content for 10°C/min heating rate.
The parameters on the curves are g ZnO per 0.2 g ADC.

TABLE 2.5  Onset Temperature and the Mass Loss % at 300°C and 600°C for ZnO and ADC
Mixtures at 20°C/min Heating Rate.
ADC ZnO ADC ZnO Onset Mass loss (%)
concentration concentration mass (g) mass (g) of mass At 300°C At 600°C
(wt%) (wt%) loss/°C
83.33 16.67 0.2 0.04 219.04 60.27 78.27
71.43 28.57 0.2 0.08 200.01 42.33 58.84
62.50 37.50 0.2 0.12 188.83 43.68 59.49

The kinetics of the decomposition of ADC was investigated by Kissinger

method11 in the present study.

{ }
ln( β / Tmax 2 ) = ln AR / E + ln (1 − αmax ) n − 1 − E / RTmax , (2.8)

where β is the rate of heating, Tmax is temperature at which the rate is

maximum, αmax is the extent of reaction at Tmax, n is the order of reaction, A
is pre-exponential factor, and E is the activation energy.
32 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 2.6  TGA Results Obtained from ADC and ZnO Powders Decomposition at 5°C/
min, 10°C/min, and 20°C/min Heating Rates.
β (°C/min) ZnO (%) ADC (%) Tmax (K) Mass loss at Tmax ln(β/Tmax2)
(%)
5 16.66 83.33 496.84 63.20 −10.80
28.57 71.42 499.91 38.85 −10.81
37.50 62.50 500.26 37.19 −10.82
10 16.66 83.33 504.61 56.17 −10.14
28.57 71.42 469.96 48.46 −10.00
37.50 62.50 468.72 40.26 −9.99
20 16.66 83.33 502.76 60.27 −9.44
  28.57 71.42 480.93 42.33 −9.35
37.50 62.50 469.64 43.67 −9.30

However, no fit of the data given in Table 2.6 to Kissinge plot (eq 2.8)
shown in Figure 2.6 was obtained. This was attributed to the heterogeneous
nature of the reaction. Two solid powders were mixed and the contact surface
of the particles of ADC and ZnO were not the same at each point. The degree
of dispersion of the ADC and ZnO strongly effected the decomposition of
ADC as suggested by Robledo-Ortiz et al.17

FIGURE 2.6  Kissinger plot of ADC and ZnO powder mixtures.

Experimental Design and Properties of PVC Foams 33

2.3.3  THERMAL CHARACTERIZATION OF THE FILMS

The degradation behavior of plastisol and composites after foaming process

was investigated by TG analysis and TG curves are given in Figure 2.7a.

FIGURE 2.7  (a) TG curves and (b) Broido’s plot of plastisol 0.4 g ADC:0.25 g ZnO
polymer composite and 0.4 g ADC:0.1 g ZnO polymer composite.
34 Applied Chemistry and Chemical Engineering: Volume 4

As depicted in Figure 2.7a, ZnO addition has also a catalytic effect on

PVC thermal degradation. The onset of mass loss for dehydrochlorination
was lower for the films with ADC and ZnO than that of the plastisol. It was
225°C, 206°C, and 198°C for the plastisol, for the films with 0.4 g ADC
and 0.1 g ZnO per 20 g plastisol, and 0.4 g ADC and 0.25 g ZnO for 20 g
plastisol, respectively.
The activation energy of dehydrochlorination was found by using Broi-
do’s method shown by eq 2.9.5

ln (ln 1 / α) = − E / RT + C, (2.9)

where α is the extent of reaction, E is the activation energy of the decomposi-

tion, T is the absolute temperature, R is the gas constant, and C is a constant.
The activation energy of the mass loss was found from the slopes of the lines
in Figure 2.7b as 16, 4.2, and 3.8 kJ/mol for the plastisol, for the films with
0.4 g ADC and 0.1 g ZnO per 20 g plastisol and 0.4 g ADC and 0.25 g ZnO
for 20 g plastisol, respectively, for the mass range of 98% and 96%. Presence
of ADC and ZnO accelerated the rate of dehydrochlorination by lowering
the activation energy of the dehydrochlorination reaction.

2.3.4  THERMAL STABILITY OF THE COMPOSITES

The films prepared by heating at 190°C for 10 min had light yellow color as
seen in Figure 2.8. After PVC Thermomat test (190°C, approximately after
25 min) they were all blackened. At long heating periods at 190°C in PVC
Thermomat, PVC undergoes severe dehydrochlorination reaction and they
appeared as black due to absorption of visible light by the long sequences of
conjugated double bonds.
Representative conductivity versus time curves of PVC foam films
measured by PVC Thermomat are given in Figure 2.9. Each experiment was
made two times to observe reproducibility. The average values of the induc-
tion and stability times of the films at 190°C are reported in Table 2.7 for
films initially heated at 190°C for 5 and 10 min.
Addition of ZnO and ADC into plastisol decreased the induction time
and stability time for both 5 min heating and 10 min heating periods. PVC
was not severely degraded during foaming process since the induction times
were around 2–4 min for the foams.
PVC dehydrochlorination at high temperature has been reduced by addi-
tion of the ZnSt2 and CaSt2 heat stabilizers. Reaction of these stabilizers with
Experimental Design and Properties of PVC Foams 35

HCl greatly reduces autoaccelerating effect of HCl released by dehydrochlo-

rination. According to Balkose et al., metal soap added to PVC interacts with
HCl and decreases its degradation effect as seen in eq 2.10 and carboxylate
groups of metal soaps are exchanged with labile chlorine atoms of PVC and
form thermally stable bonds.4

(a) (b) (c) (d)

(e) (f) (g) (h)

FIGURE 2.8  The picture of the films as prepared and after PVC thermomat tests. As
prepared (a) 0.2 g ADC:0.25 g ZnO, (b) 0.2 g ADC:0.1 g ZnO, (c) 0.4 g ADC:0.25 g ZnO,
and (d) 0.4 ADCg:0.1g ZnO. After PVC thermomat test (e) 0.2 g ADC:0.25 g ZnO, (f) 0.2 g
ADC:0.1 g ZnO, (g) 0.4 g ADC:0.25 g ZnO, and (h) 0.4 ADCg:0.1g ZnO.

FIGURE 2.9  The change of conductivity of the aqueous solution with respect to time for
PVC films at 190°C for 5 min (first trial).
36 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 2.7  Average Values of Induction and Stabilization Time at 190°C for Films Initially
Heated at 190°C for 5 and 10 min.
Sample composition Induction time (min) Stability time (min)
ADC ZnO 5 min heated 10 min heated 5 min heated 10 min heated
(g/20 g) (g/20 g)
0 0 18.25 17.20 33.48 30.53
0.2 0.25 4.07 2.94 24.88 19.35
0.2 0.1 3.81 2.54 29.72 23.62
0.4 0.25 3.41 3.07 32.61 23.08
0.4 0.1 3.54 2.08 33.40 23.88

ZnSt 2 + 2HCl → ZnCl2 + HSt. (2.10)

ZnSt2 and CaSt2 are used together because of their synergetic effect. The
ZnCl2 formed by the reaction of ZnSt2 with HCl had also accelerating effect
on dehydrochlorination reaction. Thus, it was converted to inactive products
by reacting with CaSt2 as shown by eq 2.2.
ZnO is capable of neutralizing HCl forming ZnCl2 as shown in eq 2.11. It
is a fact that, when ZnCl2 concentration exceeds a certain level it also accel-
erates dehydrochlorination reaction extensively.

ZnO + 2HCl → ZnCl2 + H 2 O. (2.11)

During the decomposition of ADC, gas formation was obtained and it

acts as blowing agent. Porous PVC matrix composites are obtained. As
seen in Table 2.2, after 5 min heating, the foam formation did not occur
since there was not enough time to decompose ADC and give gaseous
products. However, after 10 min heating, the density of the composites
drops very sharply and bubble formation within the composites was
obtained. The 0.4 g ADC and 0.25 g ZnO per 20 g plastisol (1.9 wt%
ADC–1.2 wt% ZnO) and 10 min heating time should be selected for the
homogenously distributed and maximum pore formation. The induction
and stability time of composites with ADC and ZnO were lower than
that of PVC without them. This indicated that ADC and ZnO had accel-
erating effect on PVC dehydrochlorination. In the heating period of 10
min for preparation of PVC foams, ADC decomposed and even if PVC
was dehydrochlorinated, it was not to an extent that will cause a severe
discoloration.
Experimental Design and Properties of PVC Foams 37

2.3.5  DESIGN OF EXPERIMENT

To understand the optimum ADC and ZnO concentration for the foam forma-
tion 23 experimental design was applied using the response as density as
seen in Table 2.8. Equation 2.12 gives the design equation for main factors
and interaction. Figures 2.10 and 2.11 give the design cube and 3D plot of
the desirability of ADC and ZnO concentration.

TABLE 2.8  Design Table for Response Density and Variables ADC Concentration, ZnO
Concentration, and Time.
Experiment number ADC (g/20g) ZnO (g/20g) Time (min) Density (g/cm3)
1 0.2 0.10 10 0.324
2 0.2 0.25 5 1.159
3 0.2 0.10 5 1.145
4 0.4 0.25 5 1.165
5 0.4 0.10 5 1.158
6 0.4 0.10 10 0.326
7 0.4 0.25 5 1.163
8 0.2 0.25 10 0.382
9 0.4 0.10 5 1.155
10 0.4 0.25 10 0.297
11 0.2 0.25 5 1.163
12 0.2 0.25 10 0.506
13 0.4 0.10 10 0.608
14 0.2 0.10 5 1.175
15 0.2 0.10 10 0.448
16 0.4 0.25 10 0.402

Density = 2.18 − 1.07 × ADC − 1.63 × ZnO − 0.20 × time + 6.28 × ADC × ZnO
(2.12)
+0.21 × ADC × time + 0.32 × ZnO × time −1.21 × ADC × ZnO × time.
According to the density design equation the most important parameter
for the foam formation is the time. The interaction between ADC–ZnO and
time mostly affected the foam formation for the system.
The desirability approach is one of the most widely used methods for
the optimization of multiple response processes. It is based on the idea that
the “quality” of a product that has multiple quality characteristics, with one
of them outside of some “desired” limits, is completely unacceptable. The
general approach is desirability between 0 and 1. First convert the response
density is at its goal, then desirability is 1, if the response is outside of an
38 Applied Chemistry and Chemical Engineering: Volume 4

acceptable region desirability is 0. According to the desirability graph the

0.4 g ADC: 0.25 ZnO per 20 g plastisol (1.9 wt% ADC–1.2 wt% ZnO) and
10 min should be selected for the homogenously distributed foam formation.

FIGURE 2.10  Design cube—ADC and ZnO relation using the response of density.

FIGURE 2.11  3D plot of desirability—ADC and ZnO relation using the response of density.
Experimental Design and Properties of PVC Foams 39

To find optimum ADC and ZnO concentration for the thermal stability 23
experimental design was applied using the response as induction time. Equa-
tion 2.13 gives the design equation for main factors and interaction. Figures
2.12 and 2.13 give the design cube and 3D plot of the desirability on ADC
and ZnO concentration.

Induction time= 5.37 − 1.825 × ADC + 5.2 × ZnO

− 0.34533 × time − 22 × ADC × ZnO
+ 0.35833 × ADC × time - 0.16667 × ZnO × time
(2.13)
+ 1.76667 × ADC × ZnO × time.

FIGURE 2.12  Design cube—ADC and ZnO relation using the response of induction time.

According to the induction time design equation the most important

parameter for the foam formation is the ZnO amount. The interaction
between ADC–ZnO and time mostly affected the induction time for the
system. The desirability graph show that the 0.2 g ADC and 0.25 g ZnO per
40 Applied Chemistry and Chemical Engineering: Volume 4

20 g plastisol (0.98 wt% ADC–1.2 wt% ZnO) and 5 min should be selected
for longest induction time. However, since no foaming occurs in 5 min the
foams should be prepared by 10 min heating, sacrificing to a small extent in
thermal stability of PVC.

FIGURE 2.13  3D plot of desirability—ADC and ZnO relation using the response of
induction time.

2.4 CONCLUSIONS

In this work, flexible PVC foam films with elastic modulus in the range of
550 and 690 MPa were prepared using CBA ADC and ZnO additive from
PVC plastisols. ZnO was added to lower the onset of ADC decomposition
temperature nearly 20°C as shown by TG analysis. In order to prevent dehy-
drochlorination of PVC, ZnSt2 and CaSt2were added to PVC as thermal
stabilizers to plastisol. The plastisol with ADC and ZnO should be heated
at least for 10 min at 190°C to obtain the foamed films. For 5 min heating,
foam formation was not obtained. There was not enough time for decompo-
sition of ADC to give gaseous products. The other possibility is the incom-
plete gelation of the plastisol to entrap the evolved gases. However, after 10
min heating, the density of the composites was lowered very sharply and
Experimental Design and Properties of PVC Foams 41

bubble formation within the composites was obtained. PVC plastigel foam
films with elliptical cells with 143–396 µm dimensions were formed.
The optimum ZnO and ADC concentration were analyzed by 23 experi-
mental design by selecting density as the response. Design equation of
density gives time as the main factor. On the other hand, design equation of
induction time gives ZnO amount as the main factor.
Addition of ZnO and ADC into plastisol decreases the thermal stability
of the films as shown by TG analysis and PVC Thermomat tests. The onset
of the mass loss, induction time, and the stability time was lower for the
films with ADC and ZnO than that of PVC plastisol without them. Even if
dehydrochlorination was accelerated by ADC and ZnO, it was not to a high
extent to cause a severe discoloration in the 10 min heating period. Thus,
it can be concluded that flexible foam films could be obtained by using the
chemical blowing agent ADC in PVC plastisols. Foaming and gelation of
the films occur simultaneously during heating the plastisols. The foamed
films could be extensively used in packing and textile industry.

ACKNOWLEDGMENT

The authors thank Yagmur Kardeslik and Rukiye Turkay, chemical engi-
neers who graduated from Izmir Institute of Technology, for their contribu-
tion to experimental work.

KEYWORDS

•• blowing agent
•• azodicarbonamide
•• stabilizers
•• polyvinyl chloride
•• dehydrochlorination

REFERENCES

1. Alian, A. M.; Abu-Zahra, N. Mechanical Properties of Rigid PCV-clay Composites.

Polym. Plast. Technol. Eng. 2009, 48, 1014–1019.
42 Applied Chemistry and Chemical Engineering: Volume 4

2. Atakul, S.; Balkose, D.; Ulku, S. Synergistic Effect of Metal Soaps and Natural Zeolite
on Poly(Vinyl Chloride) Thermal Stability. J. Vinyl. Addit. Technol. 2005, 11, 47–56.
3. Azimipour, B.; Marchant, F. Effect of Calcium Carbonate Particle Size on PVC Foam.
J. Vinyl. Addit. Technol. 2006, 12, 55–57.
4. Balkose, D.; Gokcel, H. I.; Göktepe, E. Synergism of Ca/Zn Soaps in Poly(Vinyl Chlo-
ride) Thermal Stability. Eur. Polym. J. 2001, 37, 1191–1197.
5. Broido, A. A. Simple, Sensitive Graphical Method of Treating Thermogravimetric
Analysis Data. J. Polym. Sci. Part B: Polym. Phys. 1969, 7, 1761–1773.
6. Crawford, R. J. Plastic Engineering; Pergamon Press: New York, 1981.
7. Demir, H.; Sipahioglu, M.; Balkose, D.; Ulku, S. Effect of Additives on Flexible PVC
Foam Formation. J. Mater. Process. Technol. 2008, 195, 144–153.
8. Garcia, J. C.; Marcilla, A. Rheological Study of the Influence of the Plasticizer Concen-
tration in the Gelation and Fusion Processes of PVC Plastisols. Polymer 1998, 39,
3507–3514.
9. Gupta, M. C.; Viswanath, S. G. Role of Metal Oxides in the Thermal Degradation of
Poly(Vinyl Chloride). Ind. Eng. Chem. Res. 1998, 37, 2707–2712.
10. Jiménez, A.; Torre, L.; Kenny, J. M. Thermal Degradation of Poly(Vinyl Chloride) Plas-
tisols Based on Low-migration Polymeric Plasticizers. Polym. Degrad. Stab. 2001, 73,
447–453.
11. Kissinger, H. E. Variation of Peak Temperature with Heating Rate in Differential
Thermal Analysis. J. Res. Nat. Bur. Stand. 1956, 57, 217–221.
12. Klemper, D.; Sendijarevic, V. Handbook of Polymeric Foams and Foam Technology,
2nd ed.; Hanser Publishers: Munich, 2004.
13. Li, G. X.; Wang, M.; Huang, X.; Li, H.; He, H. Effect of Zinc Maleate/Zinc Oxide
Complex on Thermal Stability of Poly(Vinyl Chloride). J. Appl. Polym. Sci. 2015,
132(7) (Article Number 41464).
14. Moghri, M.; Khakpour, M.; Akbarian, M.; Saeb, M. R. Employing Response Surface
Approach for Optimization of Fusion Characteristics in Rigid Foam PVC/Clay Nano-
composites. J. Vinyl. Addit. Technol. 2015, 21, 51–59.
15. Ozmihci, F. O.; Balkose, D. Effects of Particle Size and Electrical Resistivity of Filler
on Mechanical, Electrical, and Thermal Properties of Linear Low-Density Polyeth-
ylene–Zinc Oxide Composites. J. Appl. Polym. Sci. 2013, 130, 2734–2743.
16. Radovanovic, R.; Jaso, V.; Pilić, B.; Stoiljković, D. Effect of PVC Plastisol Composi-
tion and Processing Conditions on Foam Expansion and Tear Strength. Hem. Indus.
2014, 68, 701–707.
17. Robledo-Ortiz, R. J.; Zepeda, C.; Gomez, C.; Rodrigue, D.; Gonzalez-Nunez, R. Non-
isothermal Decomposition Kinetics of Azodicarbonamide in High-Density Polyeth-
ylene Using a Capillary Rheometer. Polym. Test. 2008, 27, 730–735.
18. Sahin, E.; Mahlicli, F. Y.; Yetgin, S.; Balkose, D. Preparation and Characterization of
Flexible Poly(Vinyl Chloride) Foam Films. J. Appl. Polym. Sci. 2012, 125, 1448–1455.
19. Savrik, S. A.; Erdogan, B. C.; Balkose, D.; Ulku, S. Statistical Thermal Stability of
PVC. J. Appl. Polym. Sci. 2010, 116, 1811–1822.
20. Savrik, S. A.; Balkose, D.; Ulutan, S.; Ulku, S. Characterization of Poly(Vinyl Chloride)
Powder Produced by Emulsion Polymerization. J. Therm. Anal. Calorim. 2010, 101,
801–806.
21. Shakarami, K.; Doniavi, A.; Azdast, T.; Aghdam, K. M. Microcellular Foaming of PVC/
NBR Thermoplastic Elastomer. Mater. Manuf. Process. 2013, 28, 872–878.
Experimental Design and Properties of PVC Foams 43

22. Shi, A.; Zhang, G.; Zhao, C. Study of Rigid Cross-Linked PVC Foams with Heat Resis-
tance. Molecules 2012, 17, 14858–14869.
23. Singh, V. V.; Rangasai, M. C.; Singh, V. V.; Rangasai, M. C.; Bhosale, S. H.; Ghoshet,
S. B. Renewable Resin Precursor and Residual Filler Modified Poly(Vinyl Chloride)
Foam, Investigation of Microcellular Development and Moisture Absorption Behavior.
Polym. Plast. Technol. Eng. 2015, 54, 1263–1269.
24. Sivertsen, K. Polymer Foams. 3.063, Polym. Phys. 2007. http://ocw.mit.edu/courses/
materials-science-and-engineering/3-063-polymer-physics-spring-2007/assignments/
polymer_foams.pdf (accessed June 12, 2016).
25. Verdu, J.; Zoller, A.; Marcilla, A. Plastisol Foaming Process: Decomposition of the
Foaming Agent, Polymer Behavior in the Corresponding Temperature Range and
Resulting Foam Properties. Polym. Eng. Sci. 2013, 53, 1712–1718.
26. WEB 1: Sartorius Density Determination Kit User’s Manual; Sartorius AG: Goet-
tingen, 1992. https://scaleman.com/index.php/aitdownloadablefiles/download/aitfile/
aitfile_id/1414/ (accessed June 12, 2016).
27. Wilkes, C. E.; Daniels, C. A.; Summers, J. W. PVC Handbook; 2005 (Chapter 5). http://
www.hanser.de/3-446-22714-8 (accesed June 12, 2016).
28. Yu, N.; Kakhramanl, Y. N.; Gadzhieva, R. S. Sorption Propertıes of Sorbents Based on
Polyvinyl Chloride Foam. Chem. Technol. Fuels Oils 2012, 47, 464–469.
29. Zoller, A.; Marcilla, A. Soft PVC Foams: Study of the Gelation, Fusion and Foaming
Processes. III. Mixed Phthalate Ester Plasticizers. J. Appl. Polym. Sci. 2012, 124,
2691–2701.
30. Zoller, A.; Marcilla, A. Soft PVC Foams: Study of the Gelation, Fusion, and Foaming
Processes. II. Adipate, Citrate and Other Types of Plasticizers. J. Appl. Polym. Sci. 2011,
122, 2981–2991.
31. Zoller, A.; Marcilla, A. Soft PVC Foams: Study of the Gelation, Fusion, and Foaming
Processes. I. Phthalate Ester Plasticizers. J. Appl. Polym. Sci. 2011, 121, 1495–1505.
CHAPTER 3

THERMAL AND TRIBOCHEMICAL

PROCESSES IN POLYPHENYLENE
OXIDE IN THE PROCESS OF FRICTION
M. B. GURGENISHVILI*, G. SH. PAPAVA, R. G. LIPARTELIANI,
SH. R. PAPAVA, Z. N. CHUBINISHVILI, N. Z. KHOTENASHVILI,
and Z. SH. TABUKASHVILI
TSU Petre Melikishvili Institute of Physical and Organic Chemistry,
Tbilisi State University, 31 A. Politkovskaia Str., 0186 Tbilisi, Georgia
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.......................................................................................................46
3.1 Introduction........................................................................................46
3.2 Experimental Part..............................................................................47
3.3 Results and Discussion......................................................................47
3.4 Conclusions........................................................................................51
Keywords....................................................................................................52
References...................................................................................................52
46 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

Structural changes of polyphenylene oxide in the process of thermal treat-

ment and friction were studied by mass spectrometric method. It was
shown that under the terms of treatment at 300°C, destructive structuring
processes take place in a polymer. Besides, Friss regrouping takes place
that leads to branching of macromolecules and forms gel fraction. Inves-
tigation of tribochemical processes during friction showed that character
of tribochemical processes in a polymer is conditioned by the formation
of complex structure of pressed specimens containing branching, cross-
linked polymer, and low molecular fraction as a result of friction at the
border of friction surface.

3.1 INTRODUCTION

Antifriction self-lubricating polymer materials, which are obtained by tradi-

tional (polyamide. polyethylene, polycarbonate, polytetrafluorine ethylene,
polyimide, polyarylate, formaldehyde resin et al) as well as comparatively
new thermally stable polymers (polyimide, polyarylate),1 are widely used
in various spheres of technology. But alongside with the progress of tech-
nology, the demand on materials characterized by high exploitation indices
and exploited on especially high charges (P) and velocities (V), and corre-
spondingly on high heat conduction tear and wear resistant increase.2
Therefore, creation of a new, filled multicomponent system in which these
properties are well fused with good physical, chemical, and technolog-
ical properties still remains as actual theoretical and practical problem of
physics, chemistry, tribochemistry, and tribotechnology of modern polymer
materials.
Creation of multicomponent, self-lubricating antifriction material is a
complex scientific problem, which needs thorough study of the processes
going on during their processing/treatment and friction. It needs study of the
role of its separate components in order to reveal inadequate behavior of the
whole system.
As is known, at the exploitation of aggregated at high rates and high
loading of friction aggregates (even at low friction coefficient), we observe
isolation of abundant heat. If antifriction system is characterized by low heat
conduction and thermal stability, aggregate starts deformation and breaks
down because of rapid heating of friction surface. Owing to this, the sphere
of application of polymer antifriction materials is limited.
Thermal and Tribochemical Processes in Polyphenylene 47

In special literature, there are references about polyethylene oxide—a

heterochain polymer, as one of the most perspective materials. It was devel-
oped in the sixties of the last century by the American Company “General
Electric.”3 It belongs to thermoresistant polymers and possesses a series of
unique exploitation properties.

3.2  EXPERIMENTAL PART

Study of thermal stability of initial and pressed polyphenylene oxide (PPO)

was carried out by mass spectrometry. Specters were taken at the temper-
ature interval 25–500°С, after every 50°С. Energy of ionization electrons
equaled to 70 e.v.
Investigation of tribochemical processes of specimens of PPO was
performed on a device, installed in a chamber of mass spectrometer, in
immediate closeness of ionization zone,4 at the drum rotation velocity V = 1
m/s and pressure Р = 0.1 Mpa.

3.3  RESULTS AND DISCUSSION

Figure 3.1 shows that thermal destruction of the initial PPO proceeded in
two stages, reaching maximum emission of initial products at temperatures
200°С and 450°С. At 200°С, emission of xylene (m/z 106) and toluene (m/z
91) is observed. Toluene is used as a solvent for the synthesis of PPO and
is preserved in trace quantity in ready product, while xylene is present in
toluene in the form of premixes.
The main thermal gradation of PPO is observed at 450°С. It is accompa-
nied with emission of products with с m/z 122, 107, 91, 135, 242.
Comparison of the obtained results with thermal destruction of model
substances (dimethyl benzol, 2,6- and 3,5-dimethyl phenol, diphenyl
methane, diphenyl ether) showed that at such conditions, destruction of the
main chain of a polymer takes place by the formation of5:
48 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 3.1  Effect of temperature on products of destruction in initial (А) and pressed at
300°С (B) olygophenylene oxide.

Appearance of a product with m/z 135 in the specter is probably condi-

tioned by the Friss regrouping process at high temperature (450–500°С) (5)
according to a scheme:
Thermal and Tribochemical Processes in Polyphenylene 49

At the same time, at thermal destruction of purified PPO in mass specter

ion m/z 135 is not observed, which refers to high thermal stability of a
polymer.
Thus, results of the study of properties of industrial specimen of PPO
polymer showed that at thermal impact (450°С), polymer destruction takes
place in the main chain (bond phenyl-o-phenyl is destructed).

Alongside with it, in such conditions, Friss regrouping can take place
(emission of m/z 135). Low molecular admixes present in a polymer, toluene,
xylol as well as traces of dimmers, trimmers reduce thermal stability of PPO
to 200°С and can lead to changes in its structure at its treatment.
Investigation of molecular mass characteristics of industrial PPO after its
treatment by pressing at temperature 300°С showed that in this case, defi-
nite decrease of specific viscosity of a polymer from 0.47 to 0.45 dl/g and
slight increase in its molecular mass from 56,000 to 65,000 are observed
which might be conditioned by the formation of branched structure at a
polymer. After pressing, formation of gel-fraction is observed in a polymer
that amounts to approximately 4%.6
Formation of crossed structures in PPO in the process of treatment might
be conditioned at the expense of oxidation of a side methyl group as well as
recombination of free macro radicals created at thermal destruction.
50 Applied Chemistry and Chemical Engineering: Volume 4

Investigation of tribochemical processes of specimens of PPO was

performed on a device, installed in a chamber of mass spectrometer, in
immediate closeness of ionization zone,4,7 at the drum rotation velocity V =
1 m/s and pressure Р = 0.1 Mpa (Fig. 3.2).

FIGURE 3.2  Influence of friction duration on the emission of the main products of
tribodestruction from industrial specimen of polyphenylene oxide (PPO).

Investigation has shown that maximum emission of volatile products is

observed in the process of running-in in the first 5–10 min. At the increase of
duration of friction run-in, the quantity of emitted products decreases.
The main products of tribodestruction are benzyl radical—(С6Н5СН2,
m/z 91), phenyl radical (С6H5, m/z 77), xylol (С6Н4(СН3)2, m/z 106), traces
of 2,6-xylenol (С6Н3(СН3)2ОН, m/z 122), as well as the products with mass
number m/z 31 (СН2ОН) and m/z 45 (СООН), which probably appear as a
result of oxidation of methyl side groups.
At the comparison of tribo- and thermal destruction of PPO,8 we can see
that in the process of friction, in the principle the products are emitted, which
are inherent to low-temperature thermal destruction of initial PPO (m/z 106
and 91) taking place, as it was shown earlier, at 200°С.
We can suppose that initially thermally less stable products of low
molecular fractions can undergo tribodestruction and be emitted as volatile
products. At the same time, at the friction of PPO, we observe appearance
of definite amount of ions with m/z 122, m/z 107, and m/z 45 and m/z 31
in the specter, which can prove that together with tribodestruction of low
Thermal and Tribochemical Processes in Polyphenylene 51

molecular fractions, at the friction cleavage of the side methyl groups (–

СН3) takes place together with destruction in the main chain.9
While investigating the process of friction of PPO, purified by their
repeated precipitation from the solution in chloroform by acetone (Fig. 3.3),
it was proved that period of run-in, in this case, increases from 6–7 to 12–13
min.

FIGURE 3.3  Influence of duration of friction on emission of the main products from
specimens of repeatedly precipitated polyphenylene oxide.

In distinct from thermal destruction (Fig. 3.3), the main products of

tribodestruction are m/z 15 (СН3– group), m/z 91 (benzyl radical), m/z 107
(cresol), as well as small quantity of products with m/z 106 and 122. This
time, phenyl radical is absent in the specter.

3.4 CONCLUSIONS

The obtained results show that the process of friction of purified PPO is
accompanied mainly by detachment of methyl groups. The main chain at
this moment is destructed at a less degree compared with that of industrial
polymer.
Difference in tribodestruction and thermal destruction of purified PPO
is that in the process of friction, cresol radical is formed at the expense of
detachment of methyl group (m/z 15), definite amount of benzyl radical
is emitted; while at thermal destruction, the main destruction product is
52 Applied Chemistry and Chemical Engineering: Volume 4

xylenol radical (m/z 122). Apparently, this is conditioned by formation of

“secondary” thermally stable structure in PPO in the process of friction on
the surface of friction at the expense of recombination of free radicals which
are formed as a result of thermo- and mechanical effect. Absence of low
molecular fractions in a polymer, which actively participates in tribome-
chanical reactions, slows down a process of tribodestruction of PPO, which
finally leads to decrease of wear.
On the basis of the obtained results, we can suppose that character of
tribomechanical processes in industrial PPO is conditioned by complex
structure of pressed specimens which contain branched, crossed polymer
and low molecular fraction.
This structure of industrial PPO is characterized, compared with other
polyheteroarylenes,10 with lower friction coefficient, up to 120–150°С,
which makes expedient its application as a binding agent in antifriction
plastic masses.

KEYWORDS

•• polymer
•• Friss regrouping
•• tribomechanical reactions
•• mass spectrometry
•• polyphenylene oxide

REFERENCES

1. Hai, A. S. Aromatic Polyethers. Adv. Polym. Sci. 1966, 4, 496–527.

2. Korshak, V. V.; Gribova, I. A.; Krasnov, A. P.; Pavlov, S. V.; Slonimsky, G. A.; Askadsky,
A. A. Chemical Structure of Polyheteroarylene Rings and Their Wear Resistance. DAN
USSR 1985, 282(8), 654–659.
3. Conley, R. J. Studies of the Stability of Condensation Polymers in Oxygen-containing
Atmospheres. Macromolecules 1967, A1(1), 81–106.
4. Elyasherg, M. E. Expert Systems for Defining Structure of Organic Molecules by Spec-
tral Methods. Achiev. Chem. 1999, 68, 579.
5. Iachoweiz, J.; Krjszewsk, K. P. Thermal Degradation of Poly-(2,6-Dimethyl-1,4-Phen-
ylene Oxide). J. Appl. Polym. Sci. 1978, 10, 2891–2901.
Thermal and Tribochemical Processes in Polyphenylene 53

6. Kelleher, P. G.; Jassie, L. B.; Gesner, B. D. Thermal Oxidation and Photo-oxidation of

Poly-(2,6-Dimethyl-1,4-Phenylene Oxide). J. Appl. Polym. Sci. 1967, 11(1), 137–144.
7. Nekrasov, Y. S.; Zhokhov, V. E.; Aderikha, V. N.; Sorokin, D. S.; Gribova, I. A.; Krasnov,
A. P.; Korshak, V. V. A Device for Investigation of Tribochemical Processes and Rigid
Chain Polymers by Mass-spectrometry. Frict. Wear 1983, 4(1), 33–43.
8. Gurgenishvili, M. B. Development and Investigation of Antifriction Plastic Masses on
the Base of Polyphenylene Oxide. Candidate’s Thesis, Moscow, 1988, pp 33–43.
9. Popov, V. A.; Kolubaev, A. V. Analysis of Mechanisms of Formation of Surface Layers
at Friction. Frict. Wear 1997, 18(6), 818–827.
10. Korshak, V. V.; Gribova, I. A.; Krasnov, A. P.; Pavlova, S. A.; Slonimsky, G. A.;
Askadsky, A. A. Chemical Structure of Polyheteroarylene Rings and Their Wear Resis-
tance. DAN USSR 1985, 282(8), 654.
CHAPTER 4

COMPATIBILITY AND THERMAL

PROPERTIES OF POLY(ETHYLENE
OXIDE) AND NATURAL
RUBBER-GRAFT-POLY(METHYL
METHACRYLATE) BLENDS
N. F. A. ZAINAL1, C. H. CHAN2,*, and A. M. M. ALI2
1
Centre of Foundation Studies, Universiti Teknologi MARA Cawangan
Selangor, Kampus Dengkil, 43800 Dengkil, Selangor, Malaysia
2
Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM),
40450 Shah Alam, Selangor, Malaysia
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.......................................................................................................56
4.1 Introduction........................................................................................56
4.2 Experimental......................................................................................58
4.3 Results and Discussion......................................................................61
4.4 Conclusions........................................................................................73
Acknowledgment........................................................................................74
Keywords....................................................................................................74
References...................................................................................................74
56 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

Natural rubber (NR) grafted with 40 %mol poly(methyl methacrylate)

(PMMA) as side chains designated as NR-g-PMMA and poly(ethylene
oxide) (PEO) were used to prepare polymer blends by solution casting
method. Thermal stability of the PEO/NR-g-PMMA blends was investigated
by thermogravimetric analysis (TGA). The decomposition temperatures of
the blends reduce slightly at elevating amount of NR-g-PMMA. It can be
deduced that PEO has a better thermal stability as compared with NR-g-
PMMA. Thermal properties of PEO/NR-g-PMMA blends were examined
using differential scanning calorimeter (DSC). The PEO/NR-g-PMMA
blends exhibit compatibility as indicated by the depression of crystallinity
(X*) and melting temperature (Tm) of PEO at certain mass fraction of PEO
in the blends (WPEO). As for the intermolecular interactions between PEO
and NR-g-PMMA in the blends, Fourier transform infrared (FTIR) spectros-
copy was used. PEO and NR blends are immiscible, but PEO and PMMA
blends are miscible. Hence, it is interesting to elucidate the phase behavior
of PEO/NR-g-PMMA, where there may be the existence of miscible interfa-
cial region of PEO and PMMA between the PEO and NR phases.

4.1 INTRODUCTION

Natural rubber (NR), a renewable resource, is an unsaturated elastomer and

become an important material in the rubber industry, especially for the manu-
facturing of rubber tyres.1 However, due to the existence of its unsaturated
hydrocarbon and nonpolar characteristic in the chain structure, the uncured
NR suffers from limitations for practical applications. Those limitations
include low flame resistance, sensitive to heat and oxidation, limited resis-
tance to chemicals and solvents, and poor ozone and weathering performance.
Therefore, various methods have been developed to alter NR properties
through physical and chemical modifications. Improvement in certain prop-
erties through chemical modification such as oil and flame resistance, hard-
ness and tensile strength, and gas permeability has been reported.2–4 Graft
polymerization of vinyl,5–7 methyl methacrylate,8,9 and styrene8,10,11 monomers
onto NR backbone was attempted for desired properties of chemically modi-
fied NR. Besides, hydrohalogenation, halogenation, oxidation, epoxidation,
ozonolysis, hydrogenation, carbine addition, cyclization, etc. are some of the
common approaches for chemical modifications of NR in order to regulate
the physical and mechanical properties of chemically modified NR.12,13
Compatibility and Thermal Properties of Poly 57

Binary polymer blending of amorphous and semicrystalline polymers

is commonly in practice. Apart from acquiring synergistic effects of parent
polymers, blending of polymers may lead to preparation of new materials
with tunable properties for specific applications, for example, for usage as
solid polymer electrolytes (SPEs) [i.e., salt is added to polymer(s)]. SPEs
are used for ion batteries or other electrochromic devices.14–17 For polymer
blend, the term miscibility used to describe a molecularly dispersed system,
and immiscibility, on the contrary, is coexistence of phases of the individual
constituents. Compatible polymer blend is immiscible polymer blends that
may have strong intermolecular interaction or miscible phase at the interfa-
cial region of the two distinct phases of the parent polymers.
Poly(ethylene oxide) (PEO) and epoxidized natural rubbers (ENR)
are immiscible blends.18–22 PEO and NR blends are most likely immis-
cible as well. Blends of PEO and poly(methyl methacrylate) (PMMA)
are miscible.23–29 When PEO is blended with natural rubber-graft-PMMA
(NR-g-PMMA), compatible blend may be prepared because good interfa-
cial adhesion could be achieved if PEO likes PMMA-graft. Enhancement
of conductivity while retaining acceptable mechanical properties of PEO/
NR-g-PMMA-based SPEs as compared with binary system of PEO and salt
may be obtained.
SPEs with lithium salt dissolved in PEO display low ionic conductivity
(σDC ~ 10−5 S cm−1) at room temperature and prohibit them from practical
applications.30 Blending of PEO with ENR with addition of inorganic salt
enhances conductivity as compared with system with PEO and inorganic
salt at same salt content. This may be due to the preferential percolation
of inorganic salt in PEO phase in relative to ENR phase.21,31–34 However,
these studies are silent on the mechanical properties and it is expected that
the PEO/ENR-based SPEs suffer from poor mechanical properties due to
immiscibility of the systems. LiClO4-added PEO/PMMA 75/25 blend (m/m)
(a miscible system) has lower ion conductivity than that of the PEO + LiClO4
system but recorded enhanced conductivity as compared with PMMA +
LiClO4 systems at mass fraction of salt (WS) at 0.091. Li salt is more soluble
in PEO phase as compare with PMMA phase.28
The deficiencies encountered for PEO/ENR-based and PEO/PMMA-
based SPEs may be approached by blending PEO and NR-g-PMMA with
addition of inorganic salt, where PMMA-graft likes PEO. In this case,
improved interfacial adhesion between PEO phase and NR phase can be
targeted via miscible or compatible PEO/PMMA interfacial region. Perco-
lation of salt can be facilitated in PEO phase without moving to NR phase
when PEO is in excess.
58 Applied Chemistry and Chemical Engineering: Volume 4

Hence, the thermal properties and phase behavior of PEO/NR-g-PMMA

are of interest in this study as there may be the existence of interfacial region
of PEO and PMMA between the PEO and NR phases. The phase behavior–
performance relationship of ternary systems (PEO/NR-g-PMMA SPEs, i.e.,
with addition of inorganic salt) will be revealed in forthcoming publication.
This work will focus on binary blends of PEO/NR-g-PMMA, where
PMMA-graft accounts of 40 %mol of the graft copolymer. Thermal stability
of the blends was studied using thermogravimetric analysis (TGA) by esti-
mation of thermal decomposition temperature. Compatibility and thermal
properties of the blends were elucidated by using differential scanning calo-
rimeter (DSC). Fourier transform infrared (FTIR) spectroscopy was used
to study the intermolecular interaction between the polymers in the blends.

4.2 EXPERIMENTAL

4.2.1  MATERIALS AND SAMPLE PREPARATION

PEO (Thermo Fisher, Pittsburgh, USA) and NR-g-PMMA [Green HPSP

(M) Sdn Bhd, Petaling Jaya, Malaysia] were purified before the blend
preparation. For purification, PEO was dissolved in chloroform (CHCl3)
(Merck, Darmstadt, Germany) and precipitated in n-hexane (Merck, Darm-
stadt, Germany). NR-g-PMMA was purified before further used through
removal of macrogel and removal of homopolymers using selective extrac-
tion of homopolymers from the graft copolymer. The free NR homopolymer
(ungrafted NR) was extracted with light petroleum ether at 40–50°C for 24
h and the remaining product was dried at 80°C in the oven for 24 h. Subse-
quently, the residue was further extracted in acetone at 40–50°C for 24 h to
remove free PMMA homopolymer. The remaining product was dried to a
constant weight at 80°C. The characteristics of PEO and NR-g-PMMA used
in this work are tabulated in Table 4.1.
For the preparation of the blends, solution casting technique was used to
prepare free-standing PEO/NR-g-PMMA films. These films were prepared
from 2% (m/m) (m denotes mass) solutions of two polymers in tetrahydro-
furan (THF) (Merck, Darmstadt, Germany). The solution was stirred for 24 h
at 50°C until the polymers were completely dissolved. Next, the homogenous
solution was poured into Teflon dish and dried under the fume hood for over-
night at room temperature before dried at 50°C for 24 h in an oven. Then, the
film was dried again under nitrogen atmosphere at 80°C for 30 min and lastly
vacuum dried at 50°C for 48 h. All the films were kept in desiccators before
Compatibility and Thermal Properties of Poly 59

characterization. PEO/NR-g-PMMA blends at compositions (m/m) of 0/100,

20/80, 40/60, 50/50, 60/40, 80/20, and 100/0 were prepared.

TABLE 4.1  Characteristic of PEO and NR-g-PMMA Used in This Work.

Constituents PEO NR-g-PMMA
Mηa (g mol−1) 300,000
Mwb (g mol−1) 1,000,000
Mnb (g mol−1) 450,000
Tmc (°C) 65 –
ΔHref (J g−1) 188.3f
Tgd (°C) −58 −63
(−66, −2)g
Tde (°C) 374 350
Molecular structure

a
Viscosity average molar mass estimated by supplier.
b
Mass average or number average molar mass as estimated in this work by GPC.
Poly(styrene) with low polydispersity was used as standard.
c
Melting temperature by DSC as determined in this work.
d
Glass transition temperature after quench cooling by DSC as determined in this work.
e
Decomposition temperature by TGA as determined in this work.
f
Melting enthalpy adopted from Lide.35
g
Tgs values of NR-g-PMMA with 57 %mol PMMA.36
h
x = mol fraction of PMMA-graft = 0.4.
y = mol fraction of NR backbone = 0.6.

4.2.2 CHARACTERIZATION

4.2.2.1  GEL PERMEATION CHROMATOGRAPHY

The mass average (Mw) and number average (Mn) molar mass of neat poly-
mers of NR-g-PMMA was studied using a Waters gel permeation chroma-
tography (GPC) (Milford, US) coupled with Waters Styragel columns HR 3
or HR 5E CHCl3 (Merck, Darmstadt, Germany). High-performance liquid
chromatography was used as the mobile phase throughout the experiment
60 Applied Chemistry and Chemical Engineering: Volume 4

with flow rate 1.0 mL/min and solvent with sample concentration of 10.0
mg mL−1. Polystyrene standards (Easical, Darmstadt, Germany) (Mw =
665–6,989,000 g mol−1 with narrow polydispersity) with low polydispersity
were used to prepare a calibration curve.

4.2.2.2  H NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY

1

Neat NR-g-PMMA was analyzed by using 1H nuclear magnetic resonance

(NMR). 1H NMR spectrum of NR-g-PMMA was measured at 25°C on a
Bruker Avance 300 spectrometer (Switzerland). It was operated at a reso-
nance frequency of 300 MHz at point 60,000 with pulse width 10 μs and
pulse interval of 18 s at 2000–3000 scan number. Sample of NMR was
performed by using 1% m/v deuterated chloroform (CDCl3) solutions of the
rubber. The polymer solution was heated in the oven at 50°C for overnight
or until the polymer dissolved in the solvent completely where a clear solu-
tion was observed. The integrated peak areas of the NMR spectra were used
to calculate the %mol of grafted PMMA content on NR backbones using
eq 4.1. The %mol of grafted PMMA content on NR backbones is calcu-
lated using the integrated peak area assigned to methoxy protons (–OCH3)
of grafted PMMA and olefinic proton (=CH–) of NR.

%Mol P MMA of NR -g -P MMA =

( A3.5 3) × 100% (4.1)

( A3.5 / 3) + A5.1
Quantities A3.5 and A5.1 represent integrated peak areas of the methoxy
proton of PMMA at 3.5 ppm and olefinic proton of isoprene repeating unit
at 5.1 ppm, respectively. From Figure 4.1, A3.5 represents the total peak area
value of three protons in methoxy of PMMA. Therefore, A3.5 is divided by 3
to obtain the peak area value for one proton of methoxy as shown in eq 4.1.

4.2.2.3  THERMOGRAVIMETRIC ANALYSIS

Thermal stability of the PEO/NR-g-PMMA blends was studied using TGA

Q500 (TA instrument, Delware, USA). About 8 mg of each sample were
used for each experiment. All samples were heated from 30°C to 600°C in
nitrogen atmosphere at the heating rate of 10°C min−1. The activation energy
of the thermal decomposition of the sample was determined through the
semilogarithm of first derivative mass retained as the function of reciprocal
of temperature.
Compatibility and Thermal Properties of Poly 61

4.2.2.4  DIFFERENTIAL SCANNING CALORIMETER

TA Q2000 (TA Instruments, Delware, USA) equipped with RCS90 refrig-

erator cooling system (TA Instruments, Delware, USA) and nitrogen gas
purging was used to determine the values of glass transition temperature
(Tg), change of heat capacity (ΔCp), melting temperature (Tm), melting
enthalpy (ΔHm), and crystallinity (X*) of the blends in the heating cycle. The
DSC was calibrated with indium and sapphire standard. The sample was
quenched cooled to −90°C for 5 min and heated to 80°C at a rate of 10°C
min−1. Similar thermal procedure was applied in sapphire standard run and
baseline run. Quantity of Tg is taken at half ΔCp value. To determine the Cp
value of sample, the heat flow signal from the sample was compared with
the baseline of sapphire standard which is of known Cp. Both curves were
corrected by zero or baseline correction experiment whereby an empty refer-
ence and an empty sample pan were placed in the furnace. Quantity ΔCp was
estimated from the glass transition of the onset and endset of the heat flow
curve. The melting peak maximum was taken as Tm value. Quantity ΔHm is
estimated from the area corresponding to the melting endotherm.

4.2.2.5  FTIR SPECTROSCOPY

The physical intermolecular interactions of PEO and NR-g-PMMA were

examined by FTIR spectroscopy. FTIR spectrum collection was carried out
using the attenuated total reflectance (ATR) accessory with diamond crystal
window on Nicolet 6700 ATR–FTIR (Thermo Scientific, Madison, USA).
The spectra were recorded in absorbance mode in the range of 600–4000
cm−1 with 16 scans at a resolution of 2 cm−1 at room temperature (~25°C).
The sample was analyzed at three spots to ensure that the FTIR analysis was
based on a representation region of sample.

4.3  RESULTS AND DISCUSSION

4.3.1  CHARACTERIZATION OF NR-G-PMMA

Grafting of PMMA onto NR backbone can be easily verified by 1H NMR by

characterizing the extracted NR-g-PMMA after petroleum ether and acetone
extractions. A typical 1H NMR spectrum of extracted NR-g-PMMA is shown
in Figure 4.1. The absorption bands at the chemical shifts of 3.6 and 5.1
62 Applied Chemistry and Chemical Engineering: Volume 4

ppm, which indicate the signals of (−OCH3) proton of the PMMA and the
(=CH−) proton of the poly(isoprene), respectively, can be clearly observed.
The %mol of PMMA grafted onto NR obtained from eq 4.1 is 40 %mol.

FIGURE 4.1  H NMR spectra of NR-g-PMMA after extraction.

1

4.3.2  THERMAL STABILITY OF THE BLENDS

The TGA curve of %mass retained as a function of temperature is shown in

Figure 4.2. The temperature onsets of %mass retained curve as a function of
temperature (Td,onset), and the temperature of maximum decomposition rate
of the %mass retained curve (Td,inflection) of PEO/NR-g-PMMA blends are
shown in Table 4.2. Quantity T denotes temperature.
Compatibility and Thermal Properties of Poly 63

FIGURE 4.2  TGA thermograms of %mass retained curves as a function of temperature for
PEO/NR-g-PMMA blends.

TABLE 4.2  Td,onset, Td,inflection, and %mass Loss of PEO/NR-g-PMMA Blends up to 600°C.
Polymer Blends, WPEO Td,onset (°C) Td,inflection (°C) %mass Loss
1.0 374 392 96
0.8 369 389 96
0.6 368 390 97
0.5 365 389 98
0.4 362 389 99
0.2 355 383 98
0.0 350 380 99

The thermal degradation of NR-g-PMMA shows that the materials are

stable up to 165°C. Beyond that, a first minor degradation step takes place
with a low mass loss of about 2–3%, and then a second (major) degrada-
tion step occurs between 320°C and 450°C. Both quantities of Td,onset and
Td,inflection of the samples increase when the content of PEO increases. This
64 Applied Chemistry and Chemical Engineering: Volume 4

may indicate that the blends are more thermally stable with higher content of
PEO. All samples are thermally degraded at temperature 400–500°C.

4.3.2.1  TEMPERATURE DEPENDENCE OF THE RATE OF THERMAL

DEGRADATION

The temperature dependence of the rate of thermal degradation in terms

of Hoffman’s Arrhenius-like relationship is discussed. The relationship for
first derivatives of the mass retained (%) versus reciprocal of temperature is
shown in eq 4.2.

 E 
deriv. mass retained ( % ) α exp  − A  , (4.2)
 RT 

where R is the gas constant and EA is the activation energy of the thermal
degradation process of the sample. The estimation of quantities of EA can be
extracted from the slope of the semilogarithmic plots of |deriv. mass retained
(%)| against 1/T as shown in the linear region as illustrated by the solid linear
regression curve for WPEO = 0.8 in Figure 4.3.

FIGURE 4.3  Plot of ln(|deriv. mass retained|) against 1/T. Solid regression curve is after eq
4.2 for WPEO = 0.8 for the linear region.
Compatibility and Thermal Properties of Poly 65

In Table 4.3, the EA values for PEO are 59 kJ mol−1, while NR-g-PMMA
is 39 kJ mol−1. This implies that neat PEO is more thermally stable than
NR-g-PMMA. The EA values for the blends show decreasing trend with
higher content of NR-g-PMMA. Quantities of EA are in agreement with the
Td values. This suggests that blends with higher content of PEO are ther-
mally more stable.

TABLE 4.3  Activation Energy of the Rate of Thermal Degradation of PEO/NR-g-PMMA

Blends.
Polymer Blends, WPEO EA/R (K) Activation Energy, EA (kJ mol−1)
1.0 7122 59
0.8 6966 58
0.6 5744 48
0.5 5405 45
0.4 5096 42
0.2 4851 40
0 4750 39

4.3.3  COMPATIBILITY AND MELTING BEHAVIOR OF PEO/NR-

G-PMMA BLENDS

4.3.3.1  GLASS TRANSITION

One of the common experimental approaches in determining the misci-

bility or compatibility of blend systems is estimation of Tg value(s) of the
blends via thermal analysis, let us say by DSC.37 However, this approach
is applicable only for polymer pairs which have difference in Tgs for more
than 20°C.38 From DSC analysis shown in Figure 4.4, the Tg values for both
PEO and NR-g-PMMA are −58°C and −63°C, respectively. The Tgs values
of NR-g-PMMA with 57 %mol PMMA content36 are −66°C (for NR back-
bone) and −2°C (for PMMA-graft) using DSC. The Tg of PMMA-graft is
weak and sometimes it is rather challenging to be estimated precisely by
linear heating rate of the heating cycle as for this study, where the Tg value
of the PMMA-graft for the NR-g-PMMA in this study cannot be revealed
clearly.
66 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 4.4  DSC thermograms of PEO/NR-g-PMMA blends heating cycle.

TABLE 4.4  Quantities Tg and ΔCp of PEO/NR-g-PMMA.

WPEO Tg (°C) ΔCp [J/(K·°C)]
1 −58 0.131
0.8 −67 0.140
0.6 −66 0.135
0.5 −66 0.174
0.4 −64 0.205
0.2 −63 0.332
0 −63 0.387

Quantities ΔCp of the superimposed glass transition of PEO and NR-g-

PMMA in the blends are also evaluated with elevating amount of NR-g-
PMMA as illustrated in Table 4.4. If PEO and NR-g-PMMA is immiscible,
quantity ΔCp of this superimposed glass transition may be an additive quan-
tity from the quantities ΔCp of the parent polymers. ΔCp value of this super-
imposed glass transition of PEO and NR-g-PMMA in the blends is a measure
Compatibility and Thermal Properties of Poly 67

of mass fraction of the amorphous microphase of PEO and NR backbone in

the mixtures.
In molten state, PEO and NR-g-PMMA is immiscible and compatibility
of PEO and PMMA-graft most likely can be noted. Upon cooling, liquid–
solid phase separation transpires, where PEO starts to crystallize. PMMA-
graft of NR-g-PMMA may not be able to be fully rejected out from the
spherulitic growth front of PEO since PEO chain likes PMMA-graft. On the
other hand, PEO has no special affinity to NR backbone, and hence, rather
complete segregation of NR phase from PEO spherulites can normally be
observed when PEO is in excess. According to this hypothesis, the amor-
phous phase of the blends may comprise a mixture of compatible interfa-
cial region of PEO and PMMA-graft, which is neighboring of PEO and NR
backbone phases. The amorphous phase of the blends is in equilibrium with
PEO crystalline phase.
Figure 4.5 demonstrates negative deviation of additive quantity of ΔCp
for this glass transition from the quantities ΔCp of the parent polymers for

FIGURE 4.5  Change of heat capacity of the superimposed glass transition of PEO and NR
backbone in the blends. Solid curve marks the additive quantity of the superimposed glass
transition from the quantities ΔCp of the parent polymers.
68 Applied Chemistry and Chemical Engineering: Volume 4

0.2 ≤ WNR-g-PMMA < 0.8. If the quantities ΔCp is of close approximation to the
solid curve, PEO and NR-g-PMMA is immiscible and PEO is not compat-
ible with PMMA-graft. The negative deviation from the solid curve for 0.2
≤ WNR-g-PMMA < 0.8 may point that the amorphous phase of the blends may
comprise amixture of compatible interfacial region of PEO and PMMA-
graft, which is neighboring of PEO and NR backbone phases. Values of Tg
and ΔCp cannot be noted for mixture of compatible interfacial region of PEO
and PMMA-graft under the experimental condition. Hence, lower content of
PEO neighboring with NR backbone may lead to the depression of ΔCp of
this superimposed glass transition.

4.3.3.2  MELTING BEHAVIOR

DSC thermograms of PEO in blends for the heating cycle are shown in
Figure 4.6. Both of the Tm and ∆Hm were obtained from the maximum peak
and the area under the peak of the thermograms, respectively. As indicated
in Figure 4.6, a single melting of semicrystalline PEO peak in the blends is
observed. No observable melting peak for NR-g-PMMA is reported as it is
an amorphous polymer.

FIGURE 4.6  Melting endotherms of PEO in the blends after DSC.

Compatibility and Thermal Properties of Poly 69

As shown in Figure 4.7, the Tm values of PEO in PEO/NR-g-PMMA

systems show a decreasing trend when the NR-g-PMMA content increases.
As observed, there is only slight depression of the Tm when WPEO ≥ 0.6.
However, depression of Tm of PEO can be seen clearly when WPEO < 0.6. This
indicates that the system may have a mixture of compatible interfacial region
of PEO and PMMA-graft which is in agreement with the results of ΔCp of
the blends. Values of Tm of PEO obtained for PEO/NR-g-PMMA systems
depress from 66°C (WPEO = 1) to 55°C (WPEO = 0.2). Elucidation of compat-
ibility of PEO and PMMA-graft at interfacial region of the blends requires
further investigation which will be reported in forthcoming publication.

FIGURE 4.7  Melting temperatures of PEO/NR-g-PMMA blends against WPEO. Dashed

curve represents the constancy of melting temperature of PEO in the blends.

4.3.4  CRYSTALLINITY OF PEO/NR-G-PMMA BLENDS

The crystallinity (X*) of the PEO phase in the blends was determined by the
∆Hm of PEO as shown in eq 4.3;

 ∆H m 
X* =   , (4.3)
 ∆H o ×W 
ref PEO 
70 Applied Chemistry and Chemical Engineering: Volume 4

where ∆H°ref = 188.3 J g−1 is the enthalpy of 100% crystallinity of PEO.

As indicated in Figure 4.8, the X* of PEO in the blends decreases with
increasing NR-g-PMMA content. The decrease in X*is noted with elevating
content of NR-g-PMMA. This implies that the blends be compatible at the
interfacial region. This result supports the results of ΔCp and Tm which point
toward the compatible interfacial region of PEO and PMMA-graft in the
PEO/NR-g-PMMA blends.

FIGURE 4.8  Crystallinity (X*) of PEO/NR-g-PMMA blends against WPEO. Solid curve
marks the constancy of crystallinity of the blends.

4.3.5  FTIR SPECTROSCOPY

Figure 4.9 shows the FTIR spectra of neat PEO and NR-g-PMMA. The
assignment of characteristic bands of both neat PEO and NR-g-PMMA
is done based on references cited. The characteristic bands of PEO and
NR-g-PMMA and the references are tabulated in Tables 4.5 and 4.6,
respectively. It is observed that the characteristic bands of both neat PEO
Compatibility and Thermal Properties of Poly 71

and NR-g-PMMA are relatively close to the characteristic bands extracted

from the literature.

FIGURE 4.9  FTIR spectra of neat PEO and NR-g-PMMA.

TABLE 4.5  Characteristic Bands of PEO.

No. Wavenumber(s) (cm−1) Reference Wavenumber(s) Assignment Reference
from Literature (cm−1)
1 2882 2885 Vs(CH2) 39
2 1466 1466 δas(CH2) 39,40
3 1359, 1341 1360, 1343 ω(CH2) 39–41
4 1277 1278 ω(CH2) 39, 42
5 1145, 1093, 1059 1145, 1093, 1060 v(C–O–C) 39, 41
6 957 958 ρas(CH2) 39, 42
7 841 844 ρas(CH2) 43
72 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 4.6  Characteristic Bands of NR-g-PMMA.

No. Wavenumber (cm−1) Reference Wavenumber Assignment Reference
from Literature (cm−1)
1 1729 1732 v(C=O) 44
2 1376 1390 δ(O−CH3) 45
3 1146 1140 (C−O) 44
4 837 835 (=C−H) 44
5 984 990 vs(C−O−C) 45

In Figure 4.10(a), two sharp absorption bands at 1359 and 1341 cm−1
representing the crystalline phase of PEO are observed. With the addition
of NR-g-PMMA into the blends, there is a slight shifting of absorption
bands at 1341 cm−1, but no shifting of the wavenumber of absorption band
at 1359 cm−1. The absorbances of the band reduce as the content of NR-g-
PMMA increases. In Figure 4.10(b), the middle absorption bands of v(C−
O−C) mode at 1093 cm−1 corresponds to the amorphous phase of PEO,
while the two shoulders represent the crystalline phase of PEO at 1059
and 1145 cm−1. As observed, there is a slight shifting of absorption bands
of v(C−O−C) mode of amorphous phase of PEO to higher frequency from
1093 to 1101 cm−1 and become broader in shape. As for the shoulders,
only a slight shifting of the absorption bands observed at 1145 cm−1 band
and no clear shifting at 1059 cm−1. If PMMA-graft is similar to PEO, the
PEO spherulites will not be perfect and hence the crystalline structure
of PEO will be somehow affected. The shifting of absorption bands at
1341, 1145 (crystalline phase of PEO), and 1093 cm−1 (amorphous phase
of PEO) may imply the compatibility of interfacial region of PEO and
PMMA-graft. As shown in Figure 4.10(c), the decrease in the absorbance
of the C=O stretching is qualitatively proportionate to the composition
of the NR-g-PMMA in the blends with slight shifting of the wavenumber
of absorption from 1726 to 1729 cm−1. As WPEO increases, the absorption
band becomes broader in shape. The FTIR analysis shows that there is
no specific molecular interaction between PEO and NR-g-PMMA. The
compatibility of interfacial region of PEO and PMMA-graft in the blends
may be due to the entropy effects as reported in most studies of PEO/
PMMA blends.46,47
Compatibility and Thermal Properties of Poly 73

FIGURE 4.10  FTIR spectra of: (a) ω(CH2), (b) v(C−O−C), and (c) v(C=O) of PEO/NR-g-
PMMA blends.

4.4 CONCLUSIONS

PEO/NR-g-PMMA thin films were prepared using solution casting method.

From thermal stability and the activation energy of rate of thermal decompo-
sition studies, the blends show higher thermal stability with higher content
of PEO. These blends are immiscible; however, compatibility of PEO and
PMMA-graft can be noted. Based on ΔCp studies, the negative deviation
at 0.2 ≤ WNR-g-PMMA < 0.8 suggests the existence of a mixture of compatible
interfacial region of PEO and PMMA-graft in the blends. The depression of
the Tm and X* values further supports the compatibility at interfacial region
74 Applied Chemistry and Chemical Engineering: Volume 4

of PEO and PMMA-graft. Based on FTIR studies, there is no specific inter-

molecular interaction between the parent polymers; however, it point toward
only weak interaction as discussed in FTIR analysis.

ACKNOWLEDGMENT

The authors would like to express gratitude toward the Ministry of Educa-
tion Malaysia for financing the project under Research Acculturation Grant
Scheme (RAGS) [600-RMI/RAGS 5/3 (145/2014)] grant. Special thanks
to Green HPSP (M) Sdn Bhd, Petaling Jaya, Malaysia for complimentary
samples of NR-g-PMMA used in this study.

KEYWORDS

•• poly(ethylene oxide)
•• natural rubber-graft-poly(methyl methacrylate)
•• thermogravimetric analysis
•• differential scanning calorimeter
•• Fourier transform infrared spectroscopy

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76 Applied Chemistry and Chemical Engineering: Volume 4

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CHAPTER 5

THERMAL PROPERTIES AND

INTERMOLECULAR INTERACTION
OF BINARY POLYMER BLENDS
OF POLY(ETHYLENE OXIDE) AND
POLY(N-BUTYL METHACRYLATE)
H. RAMLI1, C. H. CHAN2,*, and A. M. M. ALI2
1
Centre of Foundation Studies, Universiti Teknologi MARA, Cawangan
Selangor, Kampus Dengkil, 43800 Dengkil, Selangor, Malaysia
2
Faculty of Applied Sciences, Universiti Teknologi MARA, 40450
Shah Alam, Selangor, Malaysia
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.......................................................................................................78
5.1 Introduction........................................................................................78
5.2 Experimental Part..............................................................................80
5.3 Results and Discussions.....................................................................82
5.4 Conclusions........................................................................................89
Acknowledgment........................................................................................90
Keywords....................................................................................................90
References...................................................................................................90
78 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

Poly(ethylene oxide) (PEO) and poly(n-butyl methacrylate) (PnBMA)

polymer blends were prepared via solution casting method. Thermogravi-
metric analysis (TGA) was used to determine the decomposition tempera-
ture and the thermal stability of the binary polymer blends. Decomposition
temperatures (Td) of the polymer blends were estimated from the onset of the
mass loss curves of TGA thermograms. Quantities Td of the blends increase
when the content of PEO increases indicated that the blends were more ther-
mally stable with higher content PEO. Thermal properties of PEO/PnBMA
polymer blends were investigated by differential scanning calorimeter. The
results of glass transition temperature (Tg) and change of heat capacity (ΔCp)
suggest that PEO and PnBMA are immiscible for entire blend composition.
The crystallinity (X*) and melting temperature (Tm) of the polymer blends
were estimated. There is insignificant variation of Tm of PEO in PEO/PnBMA
blends, except for high content of PnBMA in the blends. This implied that
these blends are immiscible under the experimental conditions agreed with
results of Tg and ΔCp. The values of X* of PEO in the PEO/PnBMA blends do
not deviate from the solid curve that marks the constancy of the crystallinity
of PEO in blends. Fourier transform infrared spectroscopy was used to study
the intermolecular interaction between PEO and PnBMA and suggests that
the crystalline region of PEO is not interrupted by the addition of PnBMA
at high content of PEO, only dipole–dipole interaction between PEO and
PnBMA.

5.1 INTRODUCTION

Besides the acquiring synergistic effects of parent polymers, one of the prime
motivating factors for blending of polymers is to widen and/or modify the
range of properties of existing polymers and to develop new materials with
the desired combination of properties for specific applications, for example,
as the solid polymer electrolytes (SPEs) for ion batteries or other electro-
chemical devices.1–6 Miscible blends are molecularly dispersed systems.
Characteristic for immiscible blends is coexistence of phases of the parent
constituents.
From the point of view of phase behavior, one has to distinguish
miscible and immiscible blends. Polymer pairs, especially those with high
molar masses, are generally immiscible. Therefore, most of the commer-
cial polymer blend systems are multiphase systems. The performance (e.g.,
Thermal Properties and Intermolecular Interaction 79

mechanical, transport, optical properties, etc.) of polymer blends depends

mainly on the properties of the polymeric components, phase behavior, and
the blend morphology.
The classic SPEs with lithium (Li) salt dissolved in poly(ethylene
oxide) (PEO) display low conductivity (σDC ~ 10−5 S cm−1). Most of the
binary systems of polymer and salt do not exhibit sufficient conductivity
(~10−4 S cm−1) for applications at ambient temperature. Hence, not only
homopolymers have been used as the polymer host but also polymer
blends,2,3,7,8 block copolymers,9–13 polymer composites,14–19 etc. for the
efforts to enhance the conductivity of SPEs. We focus on poly(ethylene
oxide)-blend-based SPEs.
The conductivity of some of these miscible PEO-blend-based SPEs
such as PEO/poly(methyl methacrylate) (PMMA)/Li,20 PEO/poly(methyl
acrylate) (PMA)/Li,21 PEO/polyacrylate (PAC)/Li,8,22 PEO/poly(propylene
oxide) (PPO)/Li,23 and PEO/poly(ϵ-caprolactone) (PCL)/Li24 is lower
than that of the binary PEO–salt systems.25,26 PMA, poly(n-butyl meth-
acrylate) (PnBMA), and PMMA belong to the acrylate family. PEO/PMA
blends21,27,28 and PEO/PMMA systems3,29,30 are miscible, phase separation
occurs for these systems when added with relatively high content of salt.
Conductivity of these SPEs is influenced by the phase behavior of the
systems.
Is PnBMA miscible with PEO with or without the addition of salt? Misci-
bility of PEO/PnBMA blends will have an effect on glass transition tempera-
ture (Tg). Quantity Tg may play an important role in determining the overall
physical properties of polymer blends (e.g., conductivity in the case of
SPEs). Quantity Tg of PMMA (~105°C) is higher than PnBMA (~32°C) and
lowest for PMA (~10°C). This makes PnBMA to be another potential candi-
date to be used as polymer host for SPEs. The Tg of PnBMA is lower than
PMMA, which may be important for ion transport and on the other hand, it
is higher than PMA, which may be important for appreciable mechanical
strength for PEO/PnBMA SPEs. The phase behavior–performance relation-
ship of ternary systems (PEO/PnBMA SPEs) will be revealed in forthcoming
publications.
In this study, salt-free PEO/PnBMA blends are discussed. For high molar
mass PEO and PnBMA, miscibility of the polymer blends on the molecular
scale can be assessed by thermal characterization on the thermal properties
such as quantities of Tg and melting temperature (Tm) and intermolecular
interaction using Fourier transform infrared (FTIR) spectroscopic methods.
Besides, thermal stability of the blends is studied as well.
80 Applied Chemistry and Chemical Engineering: Volume 4

5.2  EXPERIMENTAL PART

5.2.1  MATERIALS AND PREPARATION OF THE BLENDS

The characteristic of the polymers used in this chapter is listed in Table 5.1.
All polymers used were purified before the blending process. For purifica-
tion, the polymers were dissolved in chloroform (Merck, New Jersey, USA),
followed by concentration of the polymer solutions using rotary evaporator.
The pure PEO was precipitated in n-hexane (Merck, New Jersey, USA)
while PnBMA was precipitated in methanol (Merck, New Jersey, USA).

TABLE 5.1  Characteristics of PEO and PnBMA.

Characteristics PEO PnBMA
Mwa (g mol−1) 300,000 337,000
Tmb (°C) 66 –
∆Href (J g−1) 188e –
Tgc (°C) −53 32
Td (°C)
d
373 259
Source Thermo Fisher, Pittsburgh, USA Sigma-Aldrich, St. Louis, USA
Molecular structure

a
Weight-average molecular weight as determined by the suppliers.
b
Melting temperature of PEO estimated in this study.
c
Glass transition temperature estimated in this study.
d
Decomposition temperature estimated in this study.
e
Melting enthalpy of 100% crystallinity of PEO.31

PEO/PnBMA blends at compositions (w/w) of 0/100, 20/80, 40/60,

60/40, 80/20, and 100/0 were prepared via solution casting method. WPEO and
WPnBMA represent mass fraction of PEO and PnBMA in the blends, respec-
tively. Thin films of the blends were prepared from 2% (w/w) solutions of
the polymers in tetrahydrofuran (THF) (Merck, New Jersey, USA). The
solution was stirred for 24 h at 50°C until all the polymers were completely
dissolved and then was casted into a Teflon dish. The solution was air-dried
in a fume hood overnight at room temperature. The dried film was further
Thermal Properties and Intermolecular Interaction 81

dried at 50°C for 24 h in an oven. Then, the film was heated for 2 h at 80°C
under nitrogen atmosphere before it was vacuum dried for 24 h at 50°C.
All the films were kept in desiccators (with relative humidity around 40%)
before further characterization.

5.2.2  MATERIAL CHARACTERIZATION

5.2.2.1  THERMOGRAVIMETRIC ANALYSIS

Thermal stability of the blends was studied using TGA Q500 (TA Instrument,
Delware, USA). About 10 mg of each sample of the blends was heated in
nitrogen atmosphere from 30°C to 600°C at the heating rate of 10°C min−1.
The onset temperature of the mass loss curve as a function of temperature
was taken as the decomposition temperature (Td) of the sample.

5.2.2.2  DIFFERENTIAL SCANNING CALORIMETER

Differential scanning calorimeter (DSC) Q2000 (TA Instrument, Delware,

USA) was used to estimate the glass transition temperature (Tg), change
of heat capacity (ΔCp), melting temperature (Tm), melting enthalpy (∆Hm),
and crystallinity (X*) of the systems during the heating run. Before sample
analysis, the DSC was calibrated using an indium and sapphire standards.
In order to minimize the thermo-oxidative degradation, nitrogen gas was
purged throughout the analysis. About 10 mg of each sample of the blends
was annealed at 80°C and quenched cool to −90°C at the heating rate of
10°C min−1. Similar thermal procedure was applied in sapphire standard run
and baseline run. Quantity of Tg was taken at half ΔCp value. To determine
the Cp value of sample, the heat flow signal from the sample was compared
with the baseline of sapphire standard which is of known Cp. Both curves
were corrected by zero or baseline correction experiment whereby an empty
reference and an empty sample pan were placed in the furnace. Quantity of
ΔCp was estimated from the glass transition of the onset and endset of the
heat flow curve. The melting peak maximum was taken as Tm value. Quantity
ΔHm was estimated from the area corresponding to the melting endotherm.

∆H m
The X * value of PEO was estimated from the ∆H m in DSC trace, X * =
∆H ref
82 Applied Chemistry and Chemical Engineering: Volume 4

5.2.2.3  FOURIER TRANSFORM INFRARED

The intermolecular interactions of PEO and PnBMA were examined using

sampling method of attenuated total reflectance (ATR) with diamond crystal
window on Nicolet 6700 ATR–FTIR (Thermo Scientific, Madison, USA).
The sample was scanned at frequency range of 600–4000 cm−1 at a resolution
of 2 cm−1 with 32 scans. The sample was scanned at several spots to ensure
that the analysis was based on a representation region of sample.

5.3  RESULTS AND DISCUSSIONS

5.3.1  THERMAL STABILITY OF NEAT POLYMERS AND BLENDS

OF PEO/PNBMA

Figure 5.1 shows the TGA thermal decomposition profile of PEO/PnBMA

blends from 50°C to 600°C. Both neat polymers show one-step decompo-
sition process, with Td at 373°C (for PEO) and 259°C (for PnBMA) and
approximate 100% mass loss at temperature more than 400°C. The thermal
decomposition of blends proceeds in two steps, which corresponds to each
component.

FIGURE 5.1  Percent mass retained curves as a function of temperature for PEO/PnBMA
blends.
Thermal Properties and Intermolecular Interaction 83

When the normalized mass loss fraction of PEO in the blends is plotted
against its mass fraction of PEO (WPEO) (c.f. Fig. 5.2), it correlates well to
the blend composition. Besides, the percent mass loss of the blends increases
drastically when temperature exceeds 250°C. This indicates that the blends
are thermally stable up to roughly 200°C. Quantities Td of the blends increase
when the content of PEO increases indicates that the blends are more ther-
mally stable with higher content PEO.

FIGURE 5.2  Plot of normalized mass loss fraction of PEO in the blends against mass
fraction PEO. Solid curve represents normalized mass fraction of PEO = WPEO.

5.3.2  MISCIBILITY OF PEO/PNBMA BLENDS

5.3.2.1  GLASS TRANSITION TEMPERATURE

Figure 5.3 shows the DSC traces of the PEO/PnBMA blends during the
heating run. PEO has a Tg located at −53°C. When content of PnBMA is
elevating in the blends, the Tg values of PEO in the blends remain almost
constant. Quantity Tg of neat PnbMA is at 32°C. We note here, Tg of PnBMA
in the blends, especially at high content of PEO, is difficult to be estimated
as the glass transition superimposes with the start of the melting endo-
therm of PEO. Quantities ΔCp of PEO in the blends are also evaluated after
addition of PnBMA. Quantity ΔCp of PEO increases monotonously with
84 Applied Chemistry and Chemical Engineering: Volume 4

increasing WPEO. Referring to Figure 5.4, constancy of quantity ΔCp of PEO

corresponding to the content of PEO in the blends is recorded. The results
of Tg and ΔCp suggest that PEO and PnBMA are immiscible for entire blend
composition.4,6

FIGURE 5.3  DSC traces of different compositions of PEO/PnBMA blends. Dashed curves
represent Tg estimated for PEO and PnBMA.

FIGURE 5.4  Changes in heat capacity of PEO in the blends. Dashed curve marks the
constancy of change in heat capacity of PEO in the blends.
Thermal Properties and Intermolecular Interaction 85

5.3.2.2  MELTING BEHAVIOR OF PEO/PNBMA BLENDS

Quantities Tm and ΔHm of PEO in the blends are obtained from the peak
and the area under the melting endotherm, respectively, during the heating
cycle. A single melting peak of PEO is observed in the blends (see Fig. 5.5).
PnBMA is an amorphous polymer, thus it does not have melting peak.
Figure 5.6 shows the variations of Tm of PEO in PEO/PnBMA blends as
a function of mass fraction of PEO. There is insignificant variation of Tm
of PEO in PEO/PnBMA blends, except for high content of PnBMA in the
blends, where a slight depression of apparent Tm can be noticed. This implies
that these blends are immiscible under the experimental conditions. This
result is in agreement with results of Tg and ΔCp.

FIGURE 5.5  DSC traces for melting endotherms of PEO in the blends.
86 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 5.6  Apparent melting temperatures of PEO in PEO/PnBMA blends. Dashed curve
represents the constancy of apparent melting temperature of PEO in the blends.

5.3.3  CRYSTALLINITY OF PEO IN PEO/PNBMA BLENDS

The relative degree of crystallinity (X*) of PEO phase for the PEO/PnBMA
∆H m
blends is calculated from the ΔHm values in the heating cycle using X * = .
∆H ref
Quantity ΔHm is the enthalpy of fusion of the blend and ∆H ref = 188.3 J g −1

is the enthalpy of fusion of 100% crystalline PEO.31 For immiscible PEO/

PnBMA (semicrystalline/amorphous) blends, the crystallization behavior of
the PEO in the blends is expected to have close approximation as in the neat
PEO. This is due to the crystallization of PEO in the blends which takes
place within the domains of nearly neat PEO and is largely unaffected by the
presence of the amorphous PnBMA. This in principle is true for the matrix-
droplet or cocontinuous microstructures of the blends where values of Tm
and X* of PEO in the blends remain constant when the content of PEO is not
Thermal Properties and Intermolecular Interaction 87

too low. Figure 5.7 presents quantity X* of PEO in the PEO/PnBMA blends
as a function of WPEO. The values of X* of PEO in the PEO/PnBMA blends
do not deviate from the solid curve inserted in Figure 5.7. The solid curve
marks the constancy of the crystallinity of PEO in blends.

FIGURE 5.7  Crystallinity of PEO in PEO/PnBMA blends versus WPEO. Solid curve
represents constancy of crystallinity for PEO in the blends.

5.3.4  FTIR SPECTROSCOPY

Figure 5.8 illustrates the FTIR spectra of neat PEO and PnBMA. The char-
acteristic bands of both PEO and PnBMA are tabulated in Table 5.2. The
assignment of characteristic absorption bands of neat PEO and PnBMA is
done based on the references cited. The characteristic absorption bands of
the spectra of both neat PEO and PnBMA show good approximation to the
characteristic absorption bands extracted from the literature.
88 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 5.8  FTIR spectra of neat PEO and PnBMA.

TABLE 5.2  Characteristic Bands for PEO and PnBMA.

Polymer Assignment Wave number (cm−1) Reference

PEO CH2 stretching 2881 32

CH2 wagging 1359 and 1341 32
C–O–C stretching 1144, 1093, 1060 33
PnBMA CH3 stretching 2957 34
CH2 stretching 2933 and 2873 34
C=O stretching 1723 35
C–O–C stretching 1171, 1143, 1063 35

The decrease in the absorbance of the C=O stretching is qualitatively

proportionate to the composition of the PnBMA in the blends as shown in
Figure 5.9(a). However, there is no shifting of the wave number of absorp-
tion band of C=O stretching implying that the parent polymers exhibit only
dipole–dipole interaction. The center of the triplet absorption bands of
C–O–C stretching appears as a triplet at 1093 cm−1 that corresponds to the
Thermal Properties and Intermolecular Interaction 89

amorphous part of PEO while the two shoulders representing the crystal-
line phase of PEO at 1144 and 1060 cm−1 [see Fig. 5.9(b)].36,37 Overlapping
of the vibrational mode of the C–O–C shoulders of PEO at 1144 and 1060
cm−1 with the two C–O–C stretching absorption bands of PnBMA at 1143
and 1063 cm−1 predominates. The characteristic absorption bands of CH2
wagging at 1359 and 1341 cm‒1 represent the crystalline phase of PEO.4,8,36,37
It is clearly seen that there is no significant shifting of the wave numbers
of C–O–C stretching (1093 cm−1) and CH2 wagging mode (1359 and 1341
cm‒1) of PEO in the blends at high content of PEO. This suggests that the
crystalline region of PEO is not interrupted by the addition of PnBMA at
high content of PEO.

FIGURE 5.9  FTIR spectra of (a) C=O stretching and (b) C–O–C stretching and CH2
wagging of the PEO/PnBMA blends.

5.4 CONCLUSIONS

Thin films of PEO/PnBMA were successfully prepared via solution casting

method. Quantities Td of the blends increase when the content of PEO
increases indicating that the blends are more thermally stable with higher
content of PEO. The results of Tg and ΔCp suggest that PEO and PnBMA
are immiscible for entire blend composition. There is insignificant variation
of Tm of PEO in PEO/PnBMA blends, except for high content of PnBMA
in the blends, where a slight depression of apparent Tm can be noticed. This
implies that these blends are immiscible under the experimental conditions
agreed with results of Tg and ΔCp. The values of X* of PEO in the PEO/
90 Applied Chemistry and Chemical Engineering: Volume 4

PnBMA blends do not deviate from the solid curve that marks the constancy
of the crystallinity of PEO in blends. FTIR analysis suggests that the crys-
talline region of PEO is not interrupted by the addition of PnBMA at high
content of PEO, only dipole–dipole interaction takes place between PEO
and PnBMA.

ACKNOWLEDGMENT

The authors would like to thank the Ministry of Education Malaysia for
the “Research Acculturation Grant Scheme” (RAGS) (600-RMI/RAGS 5/3
(145/2014)) supporting this study.

KEYWORDS

•• poly(ethylene oxide)
•• poly(n-butyl methacrylate)
•• polymer blends
•• thermogravimetric analysis
•• differential scanning calorimeter
•• Fourier transform infrared

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24. Chiu, C. C.; Chen, H. W.; Kuo, S. W.; Huang, C. F.; Chang, F. C. Macromolecules 2004,
37, 8424–8430.
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State Ion. 1983, 11, 91–95.
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1565–1567.
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2447–2454.
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374–383.
CHAPTER 6

CROSS-LINKING OF EPOXY–
ISOCYANATE MIXTURES IN THE
PRESENCE OF HYDROXYL-ACRYLIC
OLIGOMER
OSTAP IVASHKIV1, BOGDANA BASHTA1, OLENA SHYSHCHAK1,
JOZEF HAPONIUK2, and MICHAEL BRATYCHAK1,*
1
Department of Chemical Technology of Oil and Gas Processing, Lviv
Polytechnic National University, 12, St. Bandera Str., Lviv 79013,
Ukraine
2
Department of Polymers Technology, Gdansk University of
Technology, 11/12 G. Narutowicza Str., 80233 Gdansk, Poland
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.......................................................................................................94
6.1 Introduction........................................................................................94
6.2 Experimental......................................................................................95
6.3 Results And Discussion.....................................................................97
6.4 Conclusions......................................................................................104
Keywords..................................................................................................104
References.................................................................................................105
94 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

The possibility of preparing epoxy–urethane coatings based on epoxy–isocy-

anate mixtures using epoxy resin, hydroxyl-acrylic oligomer, hardener, and
isocyanate has been considered. Stepwise method of epoxy–urethane films
formation has been developed. The effect of mixture composition, tempera-
ture, and cross-linking time on film hardness and gel-fraction content has
been established. The mixtures with optimal hardness and gel-fraction
content were analyzed by IR spectroscopy regarding functional groups
content during cross-linking at different temperatures. The reaction scheme
of three-dimensional cross-linked structure formation has been suggested.

6.1 INTRODUCTION

Polyurethane materials, as well as materials based on epoxy resins are charac-

terized by good operational properties. They are widely used for the produc-
tion of high-quality coatings, polymer concrete compositions, gums, etc.1–3
However, each of mentioned materials has own disadvantages. If we compare
epoxy and polyurethane materials, the epoxy compounds have worse abra-
sion resistance, adhesive strength relative to nonferrous metals, and aromatic
fuel tolerance. Polyurethane materials have low hardness and strength; they
are not stable relative to acid and alkali influence. To avoid abovementioned
disadvantages, the combination of both materials takes place.4
Modification of epoxy resins by isocyanate with epoxy–urethane
compounds increases the epoxy resins functionality and significantly
improves the adhesive and cohesive strength, as well as thermal resistance
of the final materials.5,6 This is a result of isocyanate and secondary hydroxy
groups interaction and formation of urethane links with high cohesion energy.7
A series of scientific works8–12 deals with the investigation of the materials
based on epoxides and isocyanate mixtures formation. In work8 it is shown
that in epoxy–isocyanate systems without catalyst, the urethane is formed at
333K due to the reaction between isocyanate and secondary hydroxy groups
of epoxy oligomers:
Cross-Linking of Epoxy–Isocyanate Mixtures 95

If the temperature is low, the system may be turned into glassy state that
makes impossible formation of epoxy–urethane materials with necessary
operational properties.
It is well known9,13 that cross-linking of epoxy resins are mostly realized
by using aliphatic amines. This fact complicates usage of compounds with
isocyanate groups because under ambient conditions these groups immedi-
ately react with amino groups of hardener and form urea groups. Thus, it is
impossible to obtain high-quality coatings. To prevent such disadvantages,
the products of isocyanate interaction and compounds containing mobile
hydrogen atom (blocked isocyanates) are used.8,12,14
On the other hand, it is known15 that coatings based on epoxy resins and
oligomers with unsaturated fragments are characterized by better perfor-
mance to compare with coatings without them.
So, in the present work, we investigate the possibility of polymer films
formation using Epidian-5 epoxy resin, diisocyanate, polyamine, and
hydroxy-acrylic oligomer (HAO) of the formula:

Such oligomer with acrylic, primary and secondary hydroxy groups

should influence the temperature of film formation and the process as itself.

6.2 EXPERIMENTAL

6.2.1 MATERIALS

Epidian-5 (Sarzyna-Ciech) with molecular weight (Mn) of 390 g/mol and

epoxy groups content of 20.0% was used as an initial epoxy resin. 4,4′-Diphe-
nylmethanediisocyanate (MDI, Suprasec 1306, Hunstman) was used as
isocyanate. Triethylenetetramine (Z-1, CEDAR) was used as a hardener.
The modifier HAO was synthesized via the reaction between hydroxy
derivative of Epidian-6 epoxy resin and acrylic acid.16 It was found for HAO
Mn 495 g/mol and hydroxyl number 351 mg KOH/g.
96 Applied Chemistry and Chemical Engineering: Volume 4

6.2.2  CROSS-LINKING OF EPOXY–ISOCYANATE MIXTURES

Epoxy–isocyanate mixtures, the compositions of which are given in

Table 6.1, were prepared by mixing HAO with MDI at room tempera-
ture for 10–15 min. The Epidian-5 was added under stirring until homo-
geneous mixture was obtained. Then Z-1 hardener was added and the
mixture was poured over previously degreased glass plates. Films forma-
tion was studied under the following conditions: first the compositions
were cured at room temperature for 24 h and then at 323 K, 343K, 363K,
383K, 403K, or 423K for 15, 30, 60, or 90 min. The structural changes
were controlled by gel-fraction content (G) of the grinded samples in
Soxhlet apparatus during their extraction by chloroform for 10 h and films
hardness (H) determined by M-3 pendulum device at room temperature
(ISO 1522).

TABLE 6.1  Composition of Epoxy–Isocyanate Mixtures.

Component Component content (mass parts)
I II III
Еpidian-5 92.5 85 70
MDI 2.5 5 10
HАО 5 10 20
Z-1 13 12 11
Note: Content of Z-1 was calculated for total amount of epoxy groups based on the ratio 20
g of epoxy groups per 14 mass parts of Z-1 hardener.

6.2.3  IR-SPECTROSCOPIC INVESTIGATIONS

IR-spectra of epoxy–isocyanate mixtures were recorded using Therma Elec-

tron Corporation-Nicolet 8700 instrument at the spectroscopic laboratory
of Gdansk Technical University. The instrument is equipped with Specac
Golden Gate adapter and diamond crystal ATR. The epoxy–isocyanate
mixtures were applied by thin layer over KBr plates and IR-spectra were
recorded. Then, the plates were placed in desiccator, held for 24 h at room
temperature and again IR-spectra were recorded. Then, the mixtures were
heated gradually at 383K (30 min), 403K (30 min), and 423K (30 min).
IR-spectra were recorded after each heating step.
Cross-Linking of Epoxy–Isocyanate Mixtures 97

6.3  RESULTS AND DISCUSSION

The results represented in Table 6.2 (mixtures I, II, and III) reveal that gel-
fraction content in the samples and film hardness depends on the mixture
composition, temperature, and cross-linking time.

TABLE 6.2  Dependence of Gel-Fraction Content and Film Hardness upon the Temperature
and Cross-Linking Time.
Mixture in Т (K) Symbol Symbol values at cross-linking time (min)
accordance 24 h under 15 30 45 60 75
with Table 6.1 ambient
conditions
І 363 H 0.58 0.86 0.91 0.92 0.92 0.99
G 77.9 92.8 94.3 93.0 93.1 94.4
383 H 0.58 0.93 0.97 0.99 1.00 1.00
G 77.9 93.3 93.4 94.8 95.5 96.5
ІІ 323 H 0.59 0.70 0.80 0.84 0.84 0.87
G 75.5 75.8 77.0 83.7 84.5 90.4
343 H 0.59 0.83 0.92 0.92 0.91 0.99
G 75.5 84.3 89.9 92.2 92.8 92.9
363 H 0.59 0.99 1.00 0.91 0.93 1.00
G 75.5 90.6 94.5 94.7 95.7 95.2
383 H 0.59 0.78 0.87 0.82 0.84 0.86
G 75.5 93.4 95.6 97.1 97.1 100.0
403 H 0.59 0.51 0.73 0.75 0.78 0.83
G 75.5 78.4 80.7 86.9 90.6 97.2
423 H 0.59 0.73 0.75 0.80 0.83 0.91
G 75.5 76.9 80.2 89.3 93.8 97.8 м
III 363 H – – – – – –
G 70.7 78.7 87.4 88.3 89.9 91.3
Note: G—gel-fraction content, %; H—film hardness, relative units.

As one can see from Table 6.2, the increase of HAO amount from 5 to 10
mass parts in the mixtures I–III practically does not change film hardness at
room temperature. At the same time, gel-fraction content slightly decreases.
To our mind, the reason is that at room temperature the functional groups of
HAO oligomer do not participate in the reactions which result in cross-linked
structures formation. Moreover, three-dimensional structures are formed at
98 Applied Chemistry and Chemical Engineering: Volume 4

room temperature due to the reaction of Epidian-5 epoxy groups with amino
groups of Z-1 hardener in accordance to the scheme:

(1)

Therefore, for the more amount of HAO and the less amount of epoxy resin
in the mixture, the less number of cross-linked structures is formed at room
temperature and gel-fraction content decreases (Table 6.2). The decrease of
hardness is not observed. Such compensation effect may be provided by the
reactions of isocyanate with primary hydroxy groups of HAO, the amount
of which increases from 2.5 to 10 mass parts in the mixtures І–ІІІ and leads
to formation of long-chain linear structures:

(2)

Due to the long carbon chain, the structures provide high hardness of
the films, that is why it does not decrease at smaller epoxy resin content in
the mixtures. However, such structures do not compensate the decrease of
gel-fraction content, since they are linear ones and do not take part in cross-
linked structures formation.
While adding Z-1 hardener to epoxy–isocyanate mixture, the residual
unreacted isocyanate MDI may react with amino groups of hardener in
accordance to the reaction:

(3)

This reaction is undesirable because it leads to instant formation of

foamed porous structures inside the epoxy matrix. The structures are brittle
and cause surface heterogeneity. The reaction (3) is improbable for the
Cross-Linking of Epoxy–Isocyanate Mixtures 99

mixtures І and ІІ since hydroxyl groups of MDI are mostly blocked by HAO
molecules according to the reaction (2).
Moreover, the reaction (1) is exothermal process and causes the mixture
heating. The result is possible reaction of HAO oligomer homopolymerization
by double bonds. The formation of linear structures with long carbon chain
also provides high hardness of the films but does not increase their gel-fraction
content. It is the additional explanation of the fact of film hardness increasing
with the increase of HAO amount in the mixtures from 5 to 10 mass parts.
Further increase of HAO amount to 20 mass parts (mixture ІІІ, Table 6.2)
leads to the negative result. It is impossible to determine films hardness,
because they become heterogeneous with nonuniform and hump-shaped
surface. At the same time, the gel-fraction content of the films decreases. To
our mind, all abovementioned may be explained by the inadmissible increase
of MDI isocyanate amount to 10 mass parts caused by the increase of HAO
amount. In other words such amount of MDI isocyanate groups could not be
completely blocked [see the reaction (2)], therefore while adding hardener
the unreacted isocyanate groups instantly react with Z-1 amino groups in
accordance with the reaction (3). Moreover, the content of epoxy resin in the
mixture (ІІІ) is much less to compare with the mixtures І and ІІ that causes
the decrease in gel-fraction content of obtained films. Thus, it is inexpedient
to increase HAO and MDI amount in epoxy–isocyanate mixtures.
The heating of mixtures І–ІІІ to 363K intensifies the reaction (1). But at
this temperature, the additional reactions involving Еpidian-5 epoxy groups
and secondary hydroxyl groups obtained via the reaction (1) as well as
secondary hydroxyl groups of HAO and Epidian-5 become possible:

(4)

(5)
100 Applied Chemistry and Chemical Engineering: Volume 4

The reactions (4) and (5) lead to the increase of cross-linked structures
density in epoxy matrix. The result is higher film hardness and gel-fraction
content of the films based on mixtures І–ІІІ (Table 6.2).
The hardness of the mixture ІІ (5 mass parts of НАО oligomer) is equal
to 0.99 relative units after only 15 min of heating at 363K and is practically
unchanged with the temperature increase. At the same time, film hardness of
the mixture I (2.5 mass parts of HAO) gradually increases from 0.86 relative
units at heating for 15 min to 0.99 relative units after 75 min of heating. The
reason is that under mentioned conditions, the intensive homopolymeriza-
tion of HAO molecules by double bonds takes place in the mixture II. As a
result, the formed long linear structures increase film hardness. At this stage,
the content of functional unsaturated bonds in HAO oligomer is almost zero
and further heating of mixture does not cause increasing of film hardness.
With the increase in heating time, gel-fraction content increases for both
mixtures (Table 6.2) confirming the partial proceeding of the reactions (4)
and (5) in the mixture І and ІІ.
The mixture ІІІ heating at 363K for 15–75 min also leads to the gradual
increasing of gel-fraction content, but it is lower to compare with gel-fraction
content of films based on mixtures ІІ and І. The reason is the low content of
epoxy resin (70 mass parts, Table 6.1) in this mixture to compare with that in
mixtures І and ІІ (92.5 and 85 mass parts, respectively).
Taking into account the obtained experimental data (H and G) for the
mixtures І–ІІІ, the films based on mixtures І and ІІ are characterized by best
properties. Therefore, we used these mixtures to study cross-linking process
at higher temperatures, at 383K in particular.
For the mixture І, the increase of heating temperature to 383K slightly
increases gel-fraction content. To our mind, the mentioned effect is achieved
due to the reactions (1), (4), and (5). Secondary hydroxyl groups of НАО
oligomer are less active than those of epoxy resin. Under the same conditions
for the mixture II, containing more НАО oligomer, the values of gel-fraction
content are considerably higher. This fact confirms our earlier assumptions
and indicates the greater role of НАО secondary hydroxyl groups (reaction
5). Higher HAO content in this mixture causes the increase of cross-linked
structures density and, as a result, higher gel-fraction content of obtained
films.
For the mixture I, the film hardness gradually increases at 383K. More-
over, after heating films for 45 min, we obtained almost maximal film hard-
ness equal to 0.99 relative units. Further increase in heating time does not
affect the film hardness.
Cross-Linking of Epoxy–Isocyanate Mixtures 101

Since the films based on mixture ІІ are characterized by high gel-fraction

content and sufficient hardness, we studied the temperature effect on cross-
linking process using this mixture.
The decrease in temperature to 343K and 323K decreases both gel-frac-
tion content and hardness (Table 6.2). Moreover, the decrease in hardness
is slight, because such temperatures are high enough for the proceeding
of the reactions (1), (2) and further HAO molecules homopolymerization,
due to which the structures providing coatings hardness are formed. At the
same time gel-fraction content sharply decreases, that indicates the intensity
decrease of the reactions (4) and (5). It means that the temperature of 323K is
not high enough to form cross-linked structures via the reactions (4) and (5).
The increase of cross-linking temperatures to 403K and 423K abnor-
mally decreases both gel-fraction content and final coatings hardness. It may
be caused by the decomposition of some structures in cross-linked matrix.
It is known that under low temperature, MDI isocyanate molecules may
react with Z-1 hardener molecules in accordance with the reaction (3). As
we mentioned before, this reaction is undesirable since it leads to the forma-
tion of foamlike structures. But if the amount of such molecules in the reac-
tion system is small, they form linear structures with reactive NH– groups.
Such groups may react at 343–363K with the residual epoxy groups of three-
dimensional cross-linked structures and graft in such a way to the general
cross-linked matrix:

(6)

If such reactions proceed till 383K, they slightly provide the increase of
gel-fraction content. However, at higher temperatures (400K and more) the
decomposition of urea bonds is possible. As a result there is a partial detach-
ment of short linear structures from general three-dimensional matrix. The
structures may be washed out by a solvent and thus cause the decrease of
gel-fraction content of obtained films.
102 Applied Chemistry and Chemical Engineering: Volume 4

To confirm the abovementioned assumptions and processing of the

mentioned reactions, IR investigations have been conducted in accordance
to the methodic described in Section 6.2.3. Mixture ІІ (Table 6.1) was chosen
as the most optimal one.
Structural changes in epoxy–isocyanate mixtures were controlled by
the absorbance bands at 918 cm−1, corresponding to asymmetric stretching
vibrations of epoxy ring, at 3400 сm−1, corresponding to the stretching vibra-
tions of hydroxyl groups, and at 1625 сm−1, corresponding to unsaturated
double bonds.
IR spectra were recorded after mixtures preparing, after keeping mixture
at room temperature for 24 h, and after heating for 0.5 h at 383K, 403K, or
424K (Figs. 6.1–6.3).
As we can see from Figure 6.1 right after mixture preparing, there is an
intensive absorbance band at 918 сm−1 that indicates high concentration of
epoxy groups in the mixture. Keeping mixture at room temperature for 24
h and its heating at 383K for 0.5 h sharply reduce the intensity of absor-
bance band that confirms occurrence of the reaction (1) with participation of
epoxy groups. Further heating (Fig. 6.1) does not influence the intensity of
absorbance band at 918 сm−1 that indicates almost total exhaustion of epoxy
groups in the system.

FIGURE 6.1  Intensity of absorption band at 918 cm−1 (a) and its change (b) after mixing
the components of mixture IІ (1), after curing it at room temperature for 24 h (2), and after
heating at 383K (0.5 h) (3), 403K (0.5 h) (4), and 423K (0.5 h) (5).

The possibility of the reaction (1) proceeding is confirmed by the results

presented in Figure 6.2. While keeping the mixture at room temperature for
24 h, we observe the sharp increase of absorbance band intensity at 3400
сm−1 characterizing the changes of hydroxyl groups concentration in the
mixture. This effect is caused by the reaction (1) at room temperature when
Cross-Linking of Epoxy–Isocyanate Mixtures 103

opening of the epoxy rings and formation of secondary hydroxyl groups

take place. Primary hydroxyl groups of HAO oligomer react with isocyanate
according to the reaction (2) and form the product with NH– groups. Char-
acteristic absorbance bands of such groups appear at 3310 сm−1 which are
very close to absorbance bands of ОН– groups.

FIGURE 6.2  Intensity of absorption band at 3400 cm−1 (a) and its change (b) after mixing
the components of mixture IІ (1), after curing it at room temperature for 24 h (2), and after
heating at 383K (0.5 h) (3), 403K (0.5 h) (4), and 423K (0.5 h) (5).

The mixture heating to 383K leads to the increase of absorbance band

intensity at 3400 сm−1 that confirms proceeding of the reactions (1), (4), and
(5). Moreover, the intensity of absorbance bands at 918 сm−1, characterizing
epoxy groups content and absorbance bands at 3400 сm−1, characterizing
hydroxyl groups content is the same within the interval corresponding to the
mixture heating from 383K to 403K for 0.5 h (Fig. 6.1а). But the increase
in temperature to 423K slightly increases the intensity of absorbance bands
at 3400 сm−1 indicating the occurrence of chemical reactions with formation
of ОН– groups.
Figure 6.3 represents the change of absorbance bands intensity char-
acterizing the variation of unsaturated double bonds concentration. While
keeping the mixture at room temperature for 24 h, the decrease of absor-
bance bands intensity at 1625 сm−1 is observed. It is the confirmation of
our assumption that at room temperature, self-heating of the mixture takes
place due to the reaction (1), followed by НАО homopolymerization relative
to the double bonds. The mixture heating to 383K intensifies this process
(Fig. 6.3). Further heating to 403K and 423K does not essentially change
the absorbance band intensity at 1625 сm−1. This fact indicates that double
bonds of HAO oligomer are almost totally exhausted at 383K and at 403K,
HAO homopolymerization is almost absent or is very slight.
104 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 6.3  Intensity of absorption band at 1625 cm−1 (a) and its change (b) after mixing
the components of mixture IІ (1), after curing it at room temperature for 24 h (2), and after
heating at 383K (0.5 h) (3), 403K (0.5 h) (4), and 423K (0.5 h) (5).

6.4 CONCLUSIONS

We synthesized new epoxy–isocyanate mixtures, consisting of Epidian-5

epoxy resin, Z-1 hardener, MDI diisocyanate, and active additive on the
basis of hydroxyl derivative of epoxy resin and acrylic acid. The Epidian-
5:MDI:HAO:Z-1 ratio of 85:5:10:12 mass parts was found to be the optimum
one. On the basis of investigated mixtures, we obtained epoxy–urethane
coatings with gel-fraction content of 93–95% and hardness of 0.99–1.00
relative units (if the temperature of coating formation was 343–363K), and
gel-fraction content of 100% and hardness of 0.86 relative units (forma-
tion temperature was 383K). It was confirmed that cross-linked structures
were formed as a result of chemical interaction of functional groups of the
mixture components.

KEYWORDS

•• epoxy–isocyanate mixtures
•• hydroxyl-acrylic oligomer
•• triethylenetetramine
•• cross-linking
•• IR-spectroscopy
Cross-Linking of Epoxy–Isocyanate Mixtures 105

REFERENCES

1. Saunders, D.; Frish, К. Khimiya poliuretanov; Khimia: Moskva, 1968; p 470.

2. Kompozitsionnye materialy na osnove poliuretanov: Per. s angl./Pod red. J. M. Buista.
M.: Khimia, 1982; p 240.
3. Lipatov, Y. S.; Kercha, Y. Y.; Sergeeva, L. M. Structura i svoistva poliuretanov; Naukova
Dumka: Kuiv, 1970; p 288.
4. Kudriavtseva, B. B. Lakorasochnye marerialy i ih primenenie. 2003, 7–8, 24–28.
5. Lapitskii, V. А.; Krytsuk, А. А. Fiziko-mekhanicheskie svoistva epoksidnyh polimerov I
stekloplastikov; Naukova Dumka: Kiev, 1986; p 96.
6. Szycher, M. Szycher’s Handbook of Polyurethanes, 2nd ed.; CRC Press: Boca Raton,
FL, USA, 2013; p 1112.
7. Smirnov, Y. N.; Valueva, L. F.; Lapitskii, V. A. Otverzshdenie epoksiuretanovyh oligo-
merov. Plasticheskie masy. 1985, 12, 41–42.
8. Morev, F.; Prokopchuk, N.; Krutko, E. Trudy BGTU 2012, 4, 88.
9. Bratychak, M. М.; Ivashkiv, O. P.; Astakhova, O. T. Dopovidi NAN Ukrainy 2014, 8, 97.
10. Takeshita, Y.; Becker, E.; Sakata, S.; Miwa, T.; Sawada, T. Polymer 2014, 55, 2505.
11. Dhevi, D. M.; Jaisankar, S. N.; Pathak, M. Eur. Polym. J. 2013, 49, 3561.
12. Kirillov, A. N. Polym. Sci. Series D 2014, 7(1), 14.
13. Moshinsky, L. Epoxy Resins and Hardeners. Structure, Properties, Chemistry and
Topology of Curing; Arcadia Press Ltd.: Tel Aviv, 1995; 370 p.
14. Bratychak, M. М.; Іvashkiv, O. P.; Astakhova, O. T.; Haponuk, Y. Ukr. Khim. Zh. 2015,
81(3), 59.
15. Jatsyshyn, O.; Astakhova, O.; Lazorko, O., et al. Chem. Chem. Technol. 2013, 1, 73.
16. Ivashkiv, O.; Bruzdziak, P.; Shyshchak, O., et al. Chem. Chem. Technol. 2015, 4, 411.
 PART II
Computational Approaches
CHAPTER 7

THE SUPERPOSING SIGNIFICANT

INTERACTION RULES (SSIR) METHOD
EMILI BESALÚ1,*, LIONELLO POGLIANI2, and
J. VICENTE JULIAN-ORTIZ2
Institut de Química Computacional i Catàlisi (IQCC) and
1

Departament de Química, Universitat de Girona, 17003 Girona,

Catalonia, Spain
2
Unidad de Investigación de Diseño de Fàrmacos y Conectividad
Molecular, Departamento de Química Física, Facultad de Farmacia,
Universitat de València, Burjassot (València), Spain, and MOLware
SL, Valencia, Spain
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract..................................................................................................... 110
7.1 Introduction...................................................................................... 110
7.2 General Framework......................................................................... 110
7.3 Application Example: Tibo Derivatives.......................................... 115
7.4 Conclusions......................................................................................132
Acknowledgment......................................................................................132
Keywords..................................................................................................132
References.................................................................................................133
110 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

The Superposing Significant Interaction Rules method is a simple rule

generator that detects molecular aggregations especially rich in molecules
tagged as being of interest under certain criterion. A series of rules are used
to rank molecular sets of congeneric families, and the procedure allows for
proposing new structures in a kind of inverse Structure-Activity Relation-
ship (SAR). An example of application is shown demonstrating how, due
to the simple arbitrary and symbolic molecular codification needed, the
method can serve to generate confidential models. As the method deals with
dichotomic properties, a special balanced leave-two-out procedure is also
considered.

7.1 INTRODUCTION

Nowadays, requirements present in both the industry and the scientific

community have being growing as long as the chemical data are expanding,
and more efficient tools are needed to mine and extract relevant information.
(Quantitative) Structure-Activity Relationship, (Q)SAR, fields are in need
to look for new, and, especially, for simple methods that give rise to reliable
models. The Superposing Significant Interaction Rules (SSIR) methodology,
first described in the work of Besalú,1 constitutes a simple procedure that,
dealing with a dichotomic molecular property, is able to rank a molecular
series of congeneric compounds. As it will be shown, the procedure can
act as an inverse (Q)SAR tool2,3 proposing new structures of interest to the
researcher. Additionally, the process allows to deal with confidential data
because the symbolic codification permits a potential (Q)SAR customer to
provide data in a masked way. The whole SAR analysis can be done without
revealing the actual nature of the compounds being investigated. Privacy
is an important issue when dealing with libraries provided by third parties
or when implementing a Software as a Service (SaaS) host.4 The secretive-
ness can be implemented across SSIR because the algorithm only needs
minimum symbolic information to be run.

7.2  GENERAL FRAMEWORK

The basic details of SSIR procedure have been described elsewhere1 and will
not be repeated here. Instead, the main leading ideal will be sketched out, but
The Superposing Significant Interaction Rules (SSIR) Method 111

to a detail enough to reproduce the example shown below. It must be said

that the primary idea to design SSIR was based on a well-known technique
in engineering: the design of experiments (DoE).5 In brief, one of the authors
had the necessity to optimize a chemical design process (peptides design)
but without the restriction to have “a priori” knowledge of responses for a
predefined set of levels combination along factors, that is, molecular resi-
dues combination along substitution sites.

7.2.1  MOLECULAR DESCRIPTION

The original field of SSIR application is the world of congeneric molecular

series. A congeneric series is described by a common molecular structure
presenting n sites of substitution that are known as factors in the language of
DoE. Each one of these sites is able to accommodate two or more substitu-
ents or residues (levels per factor). If the distinct substituents per site are
symbolically (and arbitrarily) denoted by A, B, C, …, then each compound
can be simply represented by a series of n-ordered letters or symbols as,
for example, CABD. Using this notation, the mere position of each letter
identifies the substitution site. It is worth noting that, without loss of gener-
ality, the series of codifying letters (the alphabet) can be repeated along the
distinct sites. If each site presents mi > 1 substituents (sites with a single
substituent do not enter into the combinatorial reckoning), the number of
possible residue combinations is
n
M = ∏ mi , (7.1)
i =1

where M being the theoretical number of structures in the whole virtual data-
base. Note that, normally, the researcher only holds a, usually small, fraction
of these, say N < M.

7.2.2 RULES

The way SSIR works is built on rules. A rule (or a variable) is a simple, and a
priori, random specification of molecules defining a subgroup. For instance,
the rule AXBX stands for all the structures presenting at the same time the
residue labeled A of the set of ones attached to the site number 1 and simulta-
neously the residue labeled B in the anchorage point number 3. It is said that
the rule condenses these structures. The X symbol stands here for a wild card
112 Applied Chemistry and Chemical Engineering: Volume 4

or for just “any residue” symbol. A rule can also involve negative terms, as
in the case AX BX , that is, the set of molecules presenting residue A at site 1
and, at the same time, not presenting the residue B at site 3. The former rules
are of order 2 because they inform about the allowed or not allowed residues
in only two substitution sites. The rule of order 0 XXXX virtually stands for
the whole database. The maximal rule of order is n, the number of sites. Each
rule of order n specifies a single analogue.
The generation of the rules is computationally systematic and relies on
combinatorics.6–8 The pseudocode for the generation of all the described
rules follows:

• An external single loop identifies the rules of order k with k = 1,

2, 3, … n. The theoretical final value of k is n, but usually it is not
compulsive nor necessary to explore all the possible orders.
• Next loop generates all the combinations of n sites taken within the
groups of k. A total of C (n, k) combinations are generated identifying
the sites involved in the next loop.
• The third-level loop generates all the variations of residues attached
to the previously selected combinations of sites.
• Finally, the innermost loop eventually generates the negation terms
(the above described bar notation) for each selected residue in the
previous step. As it will be seen, this loop may generate up to 2k terms.

7.2.3  QUANTIFYING THE RULE SIGNIFICANCE

In practice, despite a rule points to many virtual compounds, SSIR focuses

the attention on a < M compounds being studied by the researcher and for
those where a dichotomic property has been defined. A simple probabilistic
formula provides a factor that is treated as a p-value9,10 attached to each
rule. Let us suppose that, along known compounds, b of them are labeled as
being of interest (i.e., be active, be a drug, present a small IC50 value, and so
on). Then, if a rule condenses c analogues and d of these are of interest, the
hypergeometric probability is attached to this event (under equal or uniform
circumstances).9,10
 b   a − b
 d   c − d 
P ( d ,c;b,a ) = with d ≤ c ≤ a ≤ M and d ≤ b ≤ a ≤ M . (7.2)
 a
 c 
The Superposing Significant Interaction Rules (SSIR) Method 113

In this context, one can define the statistical significance of the rule in
terms of a p-value as the probability to condense d or more (denoted d+)
structures of interest:
min (b,c ) d −1

p (d + ,c;a ) = ∑ P (i,c;b,a ) = 1 − ∑ P (i,c;b,a ). (7.3)

i=d i = max (0 ,c + b − a )

The basic version of SSIR procedure aims to generate all the possible
rules of orders of 1, 2, 3, … and evaluates for each one the attached p-value.
Only the rules bearing a p-value lesser than or equal to a predefined threshold
or cut value, say pc, are accounted for. Once the rules are filtered by the
respective p-values, the selected ones can bear a positive or a negative vote.
A selected rule is provided with a positive vote if it condenses compounds
of interest in a higher ratio than the, p ≤ pc < 50%, neutral mode. If the rule
condenses more analogues of noninterest than the expected neutral mode
(i.e., p > 50%), there is a possibility to attach it to a negative vote if the
complementary probability is significant (1−p ≤ pc < 50%). This means that
the rule performs well-condensing structures of noninterest (this also consti-
tutes a relevant information), and that the probability factor p-value becomes

p ( d −, c; b, a ) = 1 − p ( d +, c; b, a ) + P ( d , c; b, a ) , (7.4)

where the d symbol stands for “d or less actives.”

7.2.4  THE (Q)SAR SSIR MODEL

The full series of rules that are being assigned to a positive vote consti-
tute a sort of bonus list. The malus list is formed by the set of rules having
a negative vote. Despite there are several ways to combine the rules and
votes, these possibilities will not be explored here. The basic SSIR program
version11 simply considers the direct sum of integer votes.
Once the selected rules (and their votes) are known, each molecular struc-
ture will cumulate the votes for all the significant variables condensing it.
The ultimate goal is to apply this voting scheme also over new compounds
not present in the sublibrary in order to rank them properly. For ranked or
continuous molecular property values, the resulting series of votes per mole-
cule is expected to be correlated with them. For categorical or pure dicho-
tomic properties, it is assumed that the higher the number of votes a structure
is collecting, the higher probability of being of a particular group.
114 Applied Chemistry and Chemical Engineering: Volume 4

7.2.5 CROSS-VALIDATION

If integer votes are being considered in SSIR, some cross-validation

routines are easy to be implemented. This is so because the rankings are
obtained by a mere addition of integer values. In particular, the leave-one-
out (L1O) procedure can be simulated in a fast way1: first, it is only neces-
sary to perform the full training and keep in memory the number of relevant
items attached to each rule, that is, the number of condensed structures
and the number of these that are of interest. Then, the L1O footage has not
to be explicitly reproduced. Instead, for each left-out structure, it is only
necessary to loop over the rules and, per each one, redo a simple count
of condensed and active structures that would be obtained if the model
was rebuild from scratch leaving the cross-validated structure apart. This
process allows recalculating the rule significance probability, and decide
for its vote assignation.
To the best of our knowledge, balanced leave-two-out (BL2O) cross-
validation algorithm was presented for the first time.1 The adjective balanced
comes from the fact that, at every simulated cross-validation loop, two struc-
tures are left out simultaneously, one active and another being nonactive.
This prevents to generate all the n(n−1)/2 combinations of molecular pairs
but only na × ni, that is, the product of the number of active (na) ones by the
nonactives (ni). For every generated molecular pair, a couple of prediction
votes is given that is added up. At the end of the procedure, the sum of votes
for the active and the nonactive compounds has to be divided by ni and na,
respectively (or multiplied by na and ni, respectively), setting an homoge-
neous scaling in both cases. This gives a series of comparable (and also
balanced) votes that conforms a ranking. Due to the above comments, the
BL2O procedure can be also implemented in a fast way without explicitly
generating training/testing calculations for each left-out pair, but getting the
equivalent result.
Along the BL2O cycles, it is counted for how many times an active
molecule had more votes than the nonactive companion (correct internal
classification), the times both structures received the same number of votes
(ties) and the times the active item received less votes than the nonactive one
(incorrect internal classification). As it will be seen below, this information
constitutes a classification performance parameter.
All SSIR procedures, including cross-validation protocols, are imple-
mented in our computer program SSIR.11
The Superposing Significant Interaction Rules (SSIR) Method 115

7.3  APPLICATION EXAMPLE: TIBO DERIVATIVES

The main goal of presenting this classical application example is to show the
basic SSIR footage and reveal how it is simple to obtain molecular rankings
in a systematic and reproducible way. Even more, SSIR requires a minimum
and very condensed amount of information: Apart from a dichotomic molec-
ular partition, only an arbitrary and symbolic codification of the residues is
needed. These niggling requirements encompass the ability to share the data
in a confidential manner. The reduced information needed by SSIR makes
very difficult the revelation of some of the database compounds or similar
analogues. This constitutes a valuable feature, as it is evident that there exists
an awareness for sharing chemical information in a secure way, at least at
the level of sharing databases in a protected mode from third parties.12,13
On the contrary, if some, even partial, chemical information is given (even
codified in the form of calculated indices) or some residues or additional
features are revealed, it is possible to give enough clues to disclose some of
the compounds.14

7.3.1  THE MOLECULAR SET

The molecular family chosen is a well-known set of tetrahydroimidazo[4,5,1-

jk][1,4]benzodiazepinone (TIBO) analogues consisting of 90 molecules,
the merge of training compounds listed in the work of Huuskonen15 (which
is the same as the ones in Hannongbua et al.16), and Zhou and Madura.17 In
these lists, six compounds were repeated, that is, compounds 1, 2, 36, 37,
38, and 45 in Huuskonen’s list that are same as compounds 44, 45, 3, 47, 2,
and 50 of Zhou and Madura’s article, respectively. Note that in Zhou and
Madura’s article, compounds 38 and 50 appear to be the same. A personal
communication of the authors revealed the real structure of compound 38
(X = H, Z = O, R = 2-Methylallyl, Y = 4-CHMe2, pIC50 = 4.90). Table
7.1 describes the codification dictionary of all the nonredundant training
compounds. Note that this dictionary is only known by the database owner.
The information that has to be transferred (eventually to a third party) to
apply SSIR is only the set of symbols (not the residues) and the dichoto-
mized property.
Table 7.2 lists the compounds codification according to the original
numbering of Huuskonen, Zhou, and Madura’s articles. It is worth noting
that the only information needed by the method proposed here is the
TABLE 7.1  Owner’s Dictionary Used to Codify the Compounds of References Huuskonen, Hannongbua, 15–17 Molecules Present Four Substitution 116
Sites (Labeled R1, X, R2, and R3 in Huuskonen’s and Hannongbua et al., Articles, Which Correspond to Sites Y, Z, X, and R in Zhou and Madura’s
Article, Respectively). Note that the Symbol Codification is Arbitrary, and that the Same Set of Symbols can be Repeated Along Substitution Sites.
R1 X R2 R3
Symbol Residue Symbol Residue Symbol Residue Symbol Residue
A H O O A 8-Cl A DMAa
B 5-Et S S B 9-Cl B 2-MAb
C 5-i-Pr C H C CH2CH(CH2)2
D 5,5-di-Me D 8-F D n-Pr
E 4-Me E 8-SMe E H
F 4-i-Pr F 8-OMe F CPMc
G 4-n-Pr G 8-OC2H5 G CH2CHdCH2
H 7-Me H 8-CN H CH2CO2Me
I 4,5-di-Me (cis) I 8-CHO I CH2-2-furanyl
J 4,5-di-Me (trans) J 8-CONH2 J CH2CH2CH=CH2
K 4-keto-5-Me K 8-Br K CH2CH2CH3
L 4,5-di-benzo L 8-I L CH2CH=CHMe (E)
M 5,7-di-Me (trans) M 8-C≡CH M CH2CH=CHMe (Z)
N 5,7-di-Me (cis) N 8-Me N CH2CH2CH2Me
O 5,7-di-Me (R,R;trans) O 8-NMe2 O CH2C(Br)=CH2
P 5,7-di-Me (S,S;trans) P 9-NH2 P CH2C(Me)=CHMe (E)
Applied Chemistry and Chemical Engineering: Volume 4
TABLE 7.1  (Continued)
R1 X R2 R3
Symbol Residue Symbol Residue Symbol Residue Symbol Residue
Q 4,7-di-Me (trans) Q 9-NMe2 Q CH2C(C2H5)=CH2
R 5,6-CH2C(=CHCH3)CH2(S) R 9-NHCOMe R CH2CH=CHC6H5 (Z)
S 6,7-(CH2)4 S 9-NO2 S CH2C(CH=CH2)=CH2
T 5-Me (S) T 9-F
U 5-Me U 9-CF3
V 4-CHMe2 V 10-OMe
W 4-Me (R) W 10-Br
a
3,3-dimethylallyl.
b
2-methylallyl.
c
cyclopropylmethyl.
The Superposing Significant Interaction Rules (SSIR) Method 117
TABLE 7.2  SSIR Codification of the Mixture List of Compounds of References Huuskonen, Hannongbua et al., and Zhou and Madura.15–17 118
Molecules Show Four Substitution Sites (Sites Labeled R1, X, R2, and R3 in Huuskonen’s and Hannongbua et al. Articles, Which Correspond to
Sites Y, Z, X, and R in Zhou and Madura’s Article, Respectively) that Here Have Been Codified from Left to Right.
Compound Original SSIR pIC50 Compound Original SSIR codification logIC50
number numberinga codification number numberingb
1 1 ASAA 7.34* 47 1 TSCA 7.36*
2 2 ASBA 6.80* 48 4 TSDA 8.24*
3 3 BOCB 4.30 49 5 TSEA 8.30*
4 4 COCB 5.00 50 6 TSFA 7.47*
5 5 COCA 5.00 51 7 TSGA 7.02*
6 6 DOCB 4.64 52 8 TSHA 7.25*
7 7 EOCB 4.49 53 9 TSIA 6.73
8 8 ESBB 6.17 54 10 TOJA 5.20
9 9 ESBC 5.66 55 11 TOKA 7.33*
10 10 FOCD 4.13 56 12 TSKA 8.52*
11 11 FOCB 4.90 57 13 TOLA 7.06*
12 12 GOCD 3.74 58 14 TSMA 7.53*
13 13 GOCB 4.32 59 15 TONA 6.00
14 14 HOCD 4.08 60 16 TSNA 7.87*
15 15 HOCA 4.92 61 17 TOOF 5.18
*
16 16 HOAA 6.84 62 18 TOPF 4.22
Applied Chemistry and Chemical Engineering: Volume 4

17 17 HOBA 6.79 63 19 TOQF 5.18

TABLE 7.2  (Continued)
Compound Original SSIR pIC50 Compound Original SSIR codification logIC50
number numberinga codification number numberingb
18 18 HSCD 5.61 64 20 TORF 3.80
*
19 19 HSCA 7.11 65 21 TSSF 5.61
*
20 20 HSAA 7.92 66 22 TSTA 7.60*
21 21 HSBA 7.64* 67 23 TOUA 5.23
22 22 IOCA 4.25 68 24 TSUA 6.31
23 23 ISCA 5.65 69 25 TOVA 5.18
24 24 JSCC 4.87 70 26 TSVA 5.33
25 25 JSCA 4.84 71 27 TSWA 5.97
26 26 KSBD 4.30 72 28 TOCG 4.15
27 27 LSCC 5.00 73 29 TOCB 4.33
28 28 MSCA 7.38* 74 30 TOCH 3.04
29 29 NSCA 5.94 75 31 TOCI 3.97
30 30 OOBA 6.64 76 32 TOCJ 4.30
31 31 OSBA 6.32 77 33 TOCK 4.05
32 32 POBA 5.30 78 34 TOCF 4.36
33 33 QSCA 4.59 79 35 TOCL 4.24
34 34 RSBE 5.42 80 36 TOCM 4.46
35 35 SSBE 5.70 81 37 TOCN 4.00
The Superposing Significant Interaction Rules (SSIR) Method 119
TABLE 7.2  (Continued) 120
Compound Original SSIR pIC50 Compound Original SSIR codification logIC50
number numberinga codification number numberingb
36 36 TSAA 8.34* 82 38 VOCB 4.90
37 37 TOBA 6.74 83 39 TOCO 4.21
*
38 38 TSBA 7.42 84 40 TOCP 4.54
*
39 39 TSBC 7.47 85 41 TOCQ 4.43
*
40 40 TSCC 7.22 86 42 TOCR 3.91
41 41 UOCD 4.22 87 43 TOCS 4.15
42 42 USCD 5.78 88 46 WSBF 5.66
43 43 UOCB 4.46 89 48 TSBF 7.47*
44 44 USCA 7.01* 90 49 TSCF 7.22*
45 45 TOCA 5.48
46 46 TSCB 7.58*
a
References: Huuskonen15 and Hannongbua et al.16
b
Reference: Zhou and Madura.17
*Activities marked with an asterisk (pIC50 > 6.79) mean molecule of interest (i.e., active).
Applied Chemistry and Chemical Engineering: Volume 4
The Superposing Significant Interaction Rules (SSIR) Method 121

symbolic codification and the characteristic of a compound of being or

not of interest. The pIC50 values are not needed and this also means that
the particular property or activity being studied is not revealed. The data-
base owner keeps the information presented in Table 7.1 (the real mole-
cules) and the property values, whereas the (Q)SAR modeler only needs
a reduced part of the information presented in Table 7.2 (the molecular
codification and the dichotomic labeling). SSIR procedure allows getting
a model from this minimal information, even if the modeler does not
know which kind of compounds has been dealing with. Even more, this
also applies at the final stage when new structures are being proposed:
the modeler only knows about generic “new compounds” codified in the
same manner as it was done in Table 7.2. Only the database owner is
able to decode the new proposed analogues in terms of real chemical
compounds.
The four molecular sites allow for 23, 2, 23, and 19 residues (levels) each.
SSIR program can operate in two modes, either allowing or not allowing the
generation of negation terms in rules, and this is equivalent to either consider
or not consider the pseudocode innermost loop described in Section 2. If
negation terms are not allowed, there are 67, 1533, 12,857, and 20,102 defin-
able rules of orders 1–4, respectively. The number of rules of maximal order
is the same as the number of analogues definable in the full database, M. If
negation terms are allowed, then the number of rules increases. For instance,
there are 132 rules of order 1, as 23 + 23 + 19 rules come from three resi-
dues, each one multiplied by 2 if individual negations are also considered.
This gives 130 rules. The two remaining rules are the two residues of the
second site. Note that for binary sites, there is no need to generate nega-
tions because one level is the natural negation of the other one. Even more,
for rules of order 1 involving a binary site, only one of the levels has to be
considered. This is so because this level, if significant, will bear a positive
or a negative vote, retaining all the relevant information. This information is
enough because the other level will automatically bear a negative or a posi-
tive vote, respectively, being the information wholly redundant if both rules
are to be kept.
The number of complete rules of orders 2, 3, and 4 is 5872, 91,632, and
160,816, respectively. Figure 7.1 shows the distribution of p-values (eq 7.3)
attached to the rules of order 4 (negation terms allowed).
122 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 7.1  Distribution of the negative logarithm of p-values along all the rules of order
4 for the TIBO family (representation starts at p = 0.1).

7.3.2  TRAINING AND CROSS-VALIDATION

Several calculations of training, L1O, BL2O, and predictions over the

external set have been conducted changing the cutoff p-value (pc) from
10−2 to 10−7. It is interesting to look at rules of low order, as some of them
can reveal general trends and features found in the database. For instance,
regarding the rules of order 1, only five bear p-values lesser than 0.01, if
negations are not allowed. All these rules focus on the presence of a partic-
ular residue in specific sites. Ranging from most to less significant, these
rules are: XOXX, XSXX, XXXA, XXCX, and XXAX with significances equal
to 4 10−7, 4 · 10−7, 2.6 · 10−5, 1.7 · 10−3, and 6.9 · 10−3, respectively. For the
first and third cases, the vote is negative, that is, the rule points to avoid the
specified residues at the corresponding sites.
As said above, note that the rules XOXX and XSXX, as being of order 1
for a binary (O, S) site, have the same probabilistic significance and the only
difference among them is the sign vote. Strictly, only one of the rules is to be
kept in SSIR model. Let us see it in detail. In training, rule XOXX condenses
46 of the 90 molecules, and only 3 of these 46 are actives or of interest.
According to eq 7.3, this gives a probability p(3+,46;27,90) = 0.99999998
The Superposing Significant Interaction Rules (SSIR) Method 123

to condense three or more active analogues. This is not significant. On the

contrary, the complementary success corresponds to point the attention to the
63 (i.e. 90 − 27) nonactive analogues. The XOXX rule condenses 43 (i.e. 46
− 3) of these nonactive compounds. For this case, eq 7.3 gives a significant
probability of p (43+,46;63,90) = 4 · 10−7, as stated above. The conclusion is
that rule XOXX is efficient to point to nonactive analogues and, hence, must
bear a negative vote. But as the rule is of order 1 and it involves a binary site
(O, S), the complementary rule is XSXX for which the same significant and
redundant probability values are reproduced, p ((27−3)+,90−46;27,90) = p
(24+,44;27,90) = 4 · 10−7, and points to active compounds, that is, its vote
assignation must be positive.
The variables of order 2 without negative terms generate a model
involving only 6 rules (for pc ≤ 0.01): TSXX, XSXA, XOCX, TXXA, TOXX,
and XXAA. The respective p-values are 1.2 · 10−7, 3.6 · 10−7, 7 · 10−7, 6.9
· 10−4, 1.4 · 10−3, and 7.6 · 10−3; all positive votes but the third and fifth.
Consistently, many of these rules involve combinations of terms appearing
in previous rules of order 1. Here, the moiety T at the first site appears to be
relevant. By the way, concerning the confidentiality issue notes that, in a real
example, only the database owner will know that this residue is a 5-Me(S)
group. This is the essence of SSIR method: the automation of search rules.
For some almost trivial cases, the rules could be deduced by inspection but
this can require endeavor. In general, the algorithm performs the inspection
systematically for more complicated cases involving larger databases, extra
molecular substitution points, and available residues.
Table 7.3 summarizes the representative results obtained for pc = 10−5.
The reported parameters are the Area Under ROC (AU-ROC)18,19 curves
and Spearman’s rank correlation coefficient,20 ρ, that is shown in brackets.
The procedure does not take into account any continuous experimental
activity but only the labels of being active or nonactive attached to every
molecule. Despite of that, it is worthy of mention that Spearman’s ρ pres-
ents a quite high correlation between the molecule category and the cumu-
lated votes.
The SAR models were obtained in batches of prefixed rule orders.
The table also shows how many variables are generated in each case and,
between brackets, how many of them are below the cutoff p-value. There
are no significant rules of order 3 or 4 if negations are not allowed. For the
case of order 4, as expected, none of such rules is significant because each
rule only embraces a single compound. Figure 7.2 shows the ROC for the
training model involving rules of order 3, when negation terms are allowed.
TABLE 7.3  Exploration Results Obtained for the TIBO Family of Analogues. Rank Correlation Coefficients (in Brackets) and AU-ROC Curves 124
are Given. For the BL2O the Number of Good, Tie, and Bad Classifications are Shown. For all Calculations, the p-Value Cutoff was pc = 0.00001.
Cutoff p-value = 0.00001 AU-ROC (Spearman ρ)b
Rules Negations Rules (signifi- TRN L1O BL2Oc External set predictione
order allowed cant)a TRN BL2O
1 No 67 (2) 0.786 (0.682) 0.786 (0.682) 0.712 (0.657) 1032/564/105 0.794 0.829 (0.710) (0.801)
Yes 132 (2) 0.786 (0.682) 0.756 (0.641) 0.695 (0.636) 972/624/105 0.794 0.829 (0.710) (0.801)
2 No 1533 (3) 0.899 (0.827) 0.899 (0.827) 0.899 (0.827) 1437/186/78 0.836 0.836 (0.809) (0.809)
Yes 5872 (126) 0.919 (0.832) 0.767 (0.698) 0.780 (0.709) 1459/95/147 0.888 0.937 (0.852) (0.892)
3 No 12,857 (0) – – – –
Yes 91,632 (2501) 0.928 (0.825) 0.764 (0.678) 0.796 (0.708) 1526/22/153 0.958 0.958 (0.909) (0.909)
4 No 20,102 (0) – – – –
Yes 1,60,816 (16,112) 0.927 (0.819) 0.755 (0.642) 0.767 (0.657) (0.757) 0.958 0.958 (0.905) (0.905)
1495/47/159
a
Number of rules giving p-values equal or under the cutoff along the single fitting of the training set. This number of significant ones can vary
along L1O or BL2O iterations.
b
Spearman’s rank correlation coefficient between molecule class and number of collected votes.
c
BL2O procedure needs 27 × 63 = 17,071 cycles.
d
For BL2O calculations, the number of good, tie, and bad classifications along the cycles is given in this order.
e
Predictions obtained by application of the training model (TRN) and all the collected rules along iterations in BL2O processes.
Applied Chemistry and Chemical Engineering: Volume 4
The Superposing Significant Interaction Rules (SSIR) Method 125

FIGURE 7.2  ROC curve for the training of TIBO molecules using rules of order 3 (negation
terms allowed, pc = 10−5). The small empty circle signals the best point found from the
probabilistic point of view, that is, having the lesser p-value computed according to formula
(3). The AU-ROC value is also indicated.

From the ranking imposed by previous training model, Figure 7.3 shows
the successive p-values obtained when tracing back the sorted list of mole-
cules and counting the number of active ones that are being collected in
groups of molecules sharing the same number of votes. The value inside
each circle gives the number of cumulated collected active structures.

FIGURE 7.3  Positions of 27 active TIBOs appearing in the sorted database by the model of
order 3 (negations allowed, pc = 10−5). Note the logarithmic scale in the vertical axis. The two
horizontal discontinuous lines stand for 1% and 5% significance levels.
126 Applied Chemistry and Chemical Engineering: Volume 4

For this case, 24 active structures are found in the first bloc of 33
ranked compounds and, according to formula (3), the attached probability
is p(24+,33;27,90) = 1.7 · 10−11, which is the depicted value for the point
labeled “24.” This “optimal” point of minimal p-value corresponds to
the one marked with an empty circle in Figure 7.2. Similarly, all the 27
active structures are found in the first bloc of 50 ranked compounds with
p(27+,50;27,90) = 1.6 · 10−9. Note that this efficiency has been obtained
from no knowledge of the chemical residues’ nature present in each
compound.
As said above, a fast BL2O procedure has been designed and imple-
mented throughout our SSIR program. For this case, it gives 1701 left-out
pairs or cycles (27 actives × 63 nonactive). After cumulating and scaling the
votes of rules of order 3 (negations allowed), the model is resulted to have ρ
= 0.708 and AU-ROC = 0.796. Better results are obtained for other pc values
or order rules, but this was not accompanied with better predictions over
the external set (see Section 3.3). Along the BL2O cycles, for 1526 active/
nonactive pairs, the internal classification was correct; for 22 cases, a tie in
votes was reproduced and for the remaining 153 couples, the active item
received fewer votes than the nonactive one. Note that the ratio of correct
explicit pair classifications is 0.897, an interesting value that can be treated
as an AU-ROC or efficiency parameter. This is so because it is well known
that, for a single fitting calculation, given a couple of molecules (one of
interest and the other of noninterest), the AU-ROC corresponds to the a
posteriori probability that the classifier correctly sorts the pair.21 Figure 7.4
shows the ROC for the model involving significant rules or order 3 (nega-
tion terms allowed) collected during all the BL2O iterations. The first ranked
molecules were erroneous, but the next series resulted to be very rich in
active analogues.
L1O and BL2O procedures seem to reveal that the training model is
quite unstable because the rank parameters decrease. A deeper investigation
showed that this was due to spurious borderline rules which are not signifi-
cant in training but become significant in some cross-validation cycles.
These rules became significant because the momentary extraction of some
compounds during cross-validation changed the probability assignations.
During cross-validation cycles, if only original significant training rules are
allowed to enter into local models (and, eventually, several of them will
become nonsignificant), the correlation parameters increase substantially
and artificially.
The Superposing Significant Interaction Rules (SSIR) Method 127

FIGURE 7.4  ROC curve for the BL2O cross-validation procedure of TIBO molecules using
rules of order 3 (negation terms allowed, pc = 10−5). The small empty circle signals the best
point found from the probabilistic point of view, that is, having the lesser p-value computed
according to formula (3). The AU-ROC value is also indicated.

7.3.3  TEST FOR VALIDATION

Once a ranking model is defined, prediction for new structures can be

formulated by accumulation of votes coming from the selected significant
rules. Each tested structure collects the votes of the corresponding matching
rules. This demands the training set to be provided with all the residues that
will appear in future predictions. If this condition is not met, compounds
presenting new substitutions are not properly evaluated by SSIR method.
The absence of residues will lead to the application of less rules, leaving the
counters of votes near the conservative zone of zero votes. For the particular
case of Huuskonen’s or Hannongbua et al. test set (Table 7.4), structures T6
and T7 have been treated here as equivalent because the fourth residue is not
present in training and, hence, is transparent to the training rules.
In general, the inclusion of negation terms in rules gives the best results
in both training and test/validation batches. From the collected significant
rules of orders 3 and 4 in training (Table 7.3), the predictions over the
128 Applied Chemistry and Chemical Engineering: Volume 4

external test set gave in both cases AU-ROC = 0.958. This last value was
also obtained with other tests involving pc ≤ 10−4 values. In all these cases,
the test compounds of interest are ranked first, but systematically three
compounds of noninterest (TSIA, TSWA, and TSVA) are placed in between at
positions 10–12. Figure 7.5 visualizes the result obtained when the training
model (2501 significant rules of order 3, including negations) is applied over
the external test set.

TABLE 7.4  SSIR Codification for the 24 Test Set Molecules of Reference Huuskonen15.
Lowercase Letters (a, b, c, and d) Stand for Residues Not Present in Training Set.
Compound number SSIR codification pIC50
T1 AOCA 4.9
T2 AOCB 4.33
T3 AOCD 4.05
T4 AOCa 4.43
T5 TSCA 7.355*
T6 TOCb 4.154
T7 TOCc 3.999
T8 TSDA 8.235*
T9 TOKA 7.324*
T10 TSKA 8.521*
T11 TSNA 7.865*
T12 TSFA 7.468*
T13 TSdA 7.592*
T14 TOHA 5.94
T15 TSHA 7.25*
T16 TONA 6
T17 TSVA 5.33
T18 TOVA 5.18
T19 TSWA 5.97
T20 TSIA 6.73
T21 TOLA 7.06*
T22 TSLA 7.32*
T23 TOMA 6.36
T24 TSMA 7.53*
*The 11 activities marked with an asterisk (pIC50 > 6.79) mean molecule of interest (i.e.,
active).
The Superposing Significant Interaction Rules (SSIR) Method 129

FIGURE 7.5  ROC curve for the TIBO external test set. The model included rules of order
3 (negation terms allowed, pc = 10−5). The small circle signals the best point found from the
probabilistic point of view, according to formula (3). The AU-ROC value is also indicated.

It is expected that SSIR rules generated during training have some infor-
mation content in order to (probabilistically) point to active compounds when
external sets are being considered. As an illustrative example, for this TIBO
family, the calculation with rules of order 3 without negations (pc = 0.001) only
generates a single rule during training: give a positive vote to the substructure
TSXA. Along the training set, the visual detection of such a rule is not imme-
diate. Noticeably, this single rule suffices to establish two categories in the
external test set: the analogues fulfilling or not fulfilling this pattern. Hence,
from this rule, 12 of the 24 test molecules receive a positive vote and, among
them, 9 are analogues of interest. According to eq 7.3, this results to show a
predictive significance of p(9+,12;11,24) = 0.006 for the external set.

7.3.4  INVERSE SAR: NEW ANALOGUES PROPOSALS

For the case of combinatorial analogues treatment, SSIR procedure also acts
as an inverse SAR tool22 because of its ability to suggest for new compounds.
Despite it is envisaged a direct algorithm able to generate good candidate
analogues directly from the knowledge of the selected significant rules, we
here are simply referring to a brute force procedure consisting to generate new
substituent combinations, apply the rules and select the analogues bearing a
130 Applied Chemistry and Chemical Engineering: Volume 4

maximum number of positive votes. Within this context, in general, and in

order to prevent the combinatorial explosion of possible derivatives, not all
the M analogues of eq 7.1 are to be generated in silico. In order to preserve
affinity to the multidimensional space spanned by the training compounds,
many times it only suffices to generate analogues that differ from several
training items only by a few substitutions, as it will be explained now.
The whole training database expands 20,102 TIBO analogues. For the
model of rules of order 3 (pc = 10−5, negations allowed), SSIR program was
asked for predictions of new combinatorial analogues having a high number
of votes. For exploratory purposes, only 68 compounds have been initially
considered: those having at most only one single substitution difference with
(in any site) respect to at least six training compounds. As said, these kinds
of criteria are implemented in SSIR program in order to prevent extrapola-
tions out of the molecular training domain. The SSIR answer was to synthe-
size as good candidates 24 analogues which, listed in decreasing preference
are (the brackets collect analogues with the same number of votes) TSLA,
(TSQA, TSRA, TSPA, TSOA), TSSA, TSJA, ASCA, (SSCA, VSCA, WSCA,
RSCA, KSCA, DSCA, ESCA, GSCA, BSCA, FSCA), LSCA, (PSCA, CSCA),
ESBA, OSCA, and TSCD. Note that the first ranked compound TSLA is an
active analogue present in Huuskonen’s external test set. The remaining
compounds presumably will show low activity, as all of them have nega-
tive votes. This malus list included three compounds of noninterest (TOHA,
TOMA, and AOCB) which are already present in Huuskonen’s test set. The
other low-activity test analogues AOCA and AOCD also presented nega-
tive votes, but these compounds are generated beyond the above restriction
considered to prevent extrapolations.
The generation of the training model involving rules of order 3 or 4 and
the generation of new analogues proposals only takes a few seconds on an
Intel-i7 CPU (4 GB memory) running under Windows 7. Running times
can increase substantially if the number of rules reaches the combinatorial
explosion.

7.3.5  SOME ADVANTAGES AND DRAWBACKS OF SSIR

METHOD FUTURE PROSPECTS

One of the main advantages of SSIR method relies on the fact that the data can
be processed in a systematic way and that preprocessing tasks are minimal. The
setup from scratch is fast because no conformational analysis or no elaborated
indices calculations are needed to start a computational run. The symbolic
The Superposing Significant Interaction Rules (SSIR) Method 131

treatment allows for several fields of application beyond the molecular one.
Once the symbolic descriptors and the running parameters (property-cut
parameter if dichotomization is needed, threshold p-value, rule orders being
considered, the option to include negation terms, …) are fixed, the method
can be easily reproduced. As it has been shown, simple leave-out and replace
cross-validation procedures (L1O, BL2O) can be rapidly executed.
The main drawbacks of the method open new doors for exploration and
future analysis of the SSIR characteristics and performance. As it occurs
in other methodologies, the results are depending on the balancing of the
database. Despite the method is feasible in a variety of circumstances, the
substituents’ population should be well represented along the library. Another
factor to be taken into account is the degree of library dilution: as more sites
or substitution options are present, more training molecules are presumably
needed in order to reach meaningful results. Regarding the problem of the
combinatorial explosion for the number of available rules, work is done now
in our laboratory in order to implement nonexhaustive searches of signifi-
cant rules. As it has been seen above, the test or external sets presenting new
substituents never appearing in training will presumably force conservative/
useless predictions. Furthermore, the method cannot deal with libraries of
analogues that only have one single substitution site.
There are several aspects of the method which demand more attention
as there is room for additional refinements not explored in this work. For
instance, the set of collected votes per rule can be analyzed numerically using
linear or nonlinear procedures. The collected votes per molecule and rule (and
also per range of p-values) can be interpreted as new molecular descriptors.
This idea is in turn connected with the option to merge rules of distinct order,
belonging to distinct ranges of significances or having distinct votes sign. For
instance, the series of votes can be combined by means of the construction
of linear combinations or multilinear, discriminant or partial least squares
derived weights. This panorama opens the door to transform the SAR model
into a QSAR one and related work is now in progress in our laboratory. Addi-
tionally, votes of distinct sign can be merged but with distinct weights.
Another important aspect to be investigated is the possible implementa-
tion of the false discovery rate (FDR)23 test. Standard scientific protocols
recommend filtering the selected “significant” rules according to Bonfer-
roni’s test or similar. FDR filters will reduce the number of selected rules
(this is equivalent to force the reduction of the cutoff pc value) and it is
expected to increase the quality of the model. Notwithstanding this logical
proposal, it has been stated that the implementation of FDR filters in many
cases dramatically reduces the number of rules, leading to nonpredictive
132 Applied Chemistry and Chemical Engineering: Volume 4

models. In all the calculations presented here no FDR sieve has been used.
Despite of that, in all the tests and calculations done, the performance over
the test sets was more than satisfactory. It seems that the inclusion of many
rules tends to stabilize the models, perhaps including compensatory effects.
More investigations are to be performed regarding the possibility to filter
individual rules according to its performance in cross-validation.

7.4 CONCLUSIONS

It has been described SSIR, a systematic procedure useful to rank series

of combinatorial analogues. The mathematical foundations and the algo-
rithm have been revisited and a dataset has been explored in order to reveal
the main characteristics and performance of SSIR. The method is fast for
rules of low order and can also be implemented for database ranking or
filtering purposes, and even as an inverse SAR tool. The symbolic nature of
the needed information allows manipulating the database in a confidential
manner, if needed. The BL2O procedure for cross-validation has been also
considered to check for model robustness at a cross-validation level.

ACKNOWLEDGMENT

The author acknowledges the Generalitat de Catalunya (Departament

d’Innovació, Universitats i Empresa) for the financial support given to the
QTMEM (Química teòrica i Modelatge i Enginyeria Molecular) research
group of the University of Girona (code 2014-SGR-1202). A personal
communication of J. Madura and Z. Zhou regarding a correction of a typo-
graphical error in a reference is also acknowledged.

KEYWORDS

•• Superposing Significant Interaction Rules

•• Structure-Activity Relationships
•• congeneric families
•• molecular codification
•• dichotomic properties
The Superposing Significant Interaction Rules (SSIR) Method 133

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CHAPTER 8

THE VISION OF APPLICATION OF

MULTIOBJECTIVE OPTIMIZATION
AND GENETIC ALGORITHM IN
MODELING AND SIMULATION OF
THE RISER REACTOR OF A FLUIDIZED
CATALYTIC CRACKING UNIT: A
CRITICAL REVIEW
SUKANCHAN PALIT*
Department of Chemical Engineering, University of Petroleum and
Energy Studies, Energy Acres, Bidholi via Premnagar, Dehradun
248007, Uttarakhand, India
*
Corresponding author. E-mail: [email protected];
[email protected]

CONTENTS

Abstract.....................................................................................................138
8.1 Introduction.....................................................................................138
8.2 Vision and Aim of the Present Treatise...........................................139
8.3 Scope of the Study..........................................................................140
8.4 The Need and the Rationale of This Study.....................................140
8.5 Future Recommendations of the Study...........................................141
8.6 Scientific Doctrine and Scientific Cognizance Behind Moo..........142
8.7 Definition of Moo, The Underlying Principles, and
Futuristic Vision..............................................................................142
136 Applied Chemistry and Chemical Engineering: Volume 4

8.8 What Is FCC and What are Its Fundamentals?...............................143

8.9 What Is MOO?................................................................................143
8.10 The Scientific Vision and Deep Scientific Understanding
Behind Application of GA...............................................................144
8.11 The Scientific Doctrine and the Scientific Vision Behind
Design of Riser Reactor of An FCC Unit.......................................145
8.12 The Vision, The Challenge, and the Deep Scientific
Introspection in the Design of An FCC Unit...................................145
8.13 Petroleum Refining Future, Energy Sustainability,
and the Vision for the Future...........................................................145
8.14 The Science of Application of GA in Designing
Riser Reactor of a FCC Unit...........................................................146
8.15 Application Areas in the Field of MOO..........................................146
8.16 GA and the World of Immense Challenges.....................................146
8.17 Application Areas of GA.................................................................147
8.18 The True Vision of Fccu and Its Modeling.....................................147
8.19 Riser Design in An FCC and the Progress of Science....................148
8.20 MOO: Its Vision and Difficulties....................................................148
8.21 Evolutionary MOO and the Scientific Doctrine.............................149
8.22 Fluidized Catalytic Cracking Unit in a Petroleum Refinery
and Application of Evolutionary MOO...........................................149
8.23 Visionary Scientific Endeavour in the Field of Design of a
Riser in a Fluidized Catalytic Cracking Unit..................................150
8.24 Scientific Research Pursuit in the Field of MOO...........................153
8.25 The World of Challenges, The Futuristic Vision,
and the Avenues of Research Pursuit in the Field of GA................155
8.26 Immense Difficulties and Science of Optimization........................156
8.27 Vision of Science, Energy Sustainability, and the
Future Progress of Human Civilization..........................................156
8.28 Validation of Science and Design of a Riser Reactor
in An FCC Unit...............................................................................157
8.29 Futuristic Vision of Chemical Process Modeling and
Progress Toward Future..................................................................158
The Vision of Application of Multiobjective Optimization 137

8.30 GA Applications, The Science of Optimization,

and the Vision for the Future...........................................................158
8.31 Scientific Cognizance, Scientific Vision,
and True Scientific Understanding..................................................158
8.32 Science of Scale-Up and the Path Toward Scientific Validation....159
8.33 Depletion of Fossil-Fuel Resources and a
New Visionary Future.....................................................................159
8.34 The Challenge, The Vision, and the Scientific Wisdom in
Modeling and Simulation of An FCC Unit.....................................159
8.35 Scientific Acuity, The Deep Scientific Understanding,
and Scientific Introspection............................................................160
8.36 Future Trends and Future Flow of Thoughts in the
Field Evolutionary MOO................................................................160
8.37 Conclusion......................................................................................160
Keywords..................................................................................................161
References.................................................................................................161
138 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

The world of science and technology is moving toward a newer visionary

frontier. Man’s vision, mankind’s prowess, and civilization’s progress all
will lead a long way in the true emancipation of human scientific endeavor.
In today’s scientific world, petroleum engineering science is facing an inimi-
table global crisis with the depletion of fossil fuels. Technological initiative
is the only answer to this immense crisis. Depletion of fossil-fuel resources
is a bane to human civilization. Today, human research pursuit is at its helm
at every step of human life and human civilization. Chemical process engi-
neering, chemical process modeling, and petroleum engineering science are
ushering in a new era of true realization of science. In such a crucial junc-
ture, mathematical tools such as multiobjective optimization and genetic
algorithm (GA) are opening new windows of innovation and scientific
instinct in decades to come. Fluidized catalytic cracking unit (FCCU) is a
major component in the future of petroleum refining science. Difficulties,
barriers, and challenges in petroleum refining and design of an FCCU are
overwhelming. The author with deep comprehension and unending insight
brings to the scientific forefront the barriers and difficulties in designing
a fluid catalytic cracking (FCC) unit. Scientific regeneration and scientific
fortitude are needed in the research pursuit today. The author delves deep
into the nitty-gritty’s of the design of the riser section of the FCC unit. The
riser section deserves immense importance in the pursuit of science and
engineering of petroleum refining. History of petroleum refining is ushering
in a new eon of science in today’s scientific world. The author of this trea-
tise deeply comprehends and focuses on the FCC process and instinctively
reviews recent developments in its modeling, monitoring, control, and opti-
mization. The riser unit and its design evolve immense challenges and diffi-
culties. The author pointedly focuses on modeling, simulation, control, and
optimization of this key downstream unit.

8.1 INTRODUCTION

Human civilization and scientific rigor are moving toward a newer realm
and visionary frontier. Petroleum engineering science and chemical process
engineering are witnessing immense changes and drastic challenges.
Science, engineering, and technology are in the path of renewed glory and
immense greatness. Depletion of fossil fuels has renewed scientific concern
and is devastating the petroleum engineering scenario. Scientific research
The Vision of Application of Multiobjective Optimization 139

pursuit, the scientific cognizance, and deep scientific introspection will go

a long and visionary way in the true realization and emancipation of petro-
leum engineering science and chemical process modeling. FCCU is a part of
the petroleum refinery. Energy sustainability and the global energy scenario
are at a deep distress. The need for technology initiative and application of
mathematical tools are reshaping the chemical process modeling scenario.
The author with deep and cogent insight brings to the scientific forefront
the application of multiobjective optimization (MOO) science and also the
emerging area of GA. Scientific rigor, immense scientific vision and insight
are the torchbearers of this detailed treatise. GA and its applications are the
pallbearers toward a greater emancipation of applied mathematics, chem-
ical process engineering, and chemical process modeling. Scientific vision,
scientific rigor, and the world of deep scientific understanding in the field of
chemical process modeling and simulation are opening up new avenues in
the wide path of engineering science today. In this treatise, the author repeat-
edly points out the difficulties and barriers in the design of riser unit of fluid-
ized catalytic cracking (FCC) in a petroleum refinery with deep scientific
vision and immense technological introspection.24,25

8.2  VISION AND AIM OF THE PRESENT TREATISE

The author with precision deals deeply with the MOO of the riser reactor of
the fluidized catalytic cracking unit (FCCU). The scientific truth, the scien-
tific vision, and the scientific forbearance need to be reenvisioned at every
step of its immense application. Human scientific endeavor and scientific
rigor are witnessing devastating and drastic challenges in the present decade.
The vision of petroleum engineering science is undergoing drastic changes
with the grave concern of depletion of fossil-fuel resources. Energy sustain-
ability, global energy scenario, and the progress of science and engineering
will all lead a long way in the true realization and effective emancipation
of petroleum engineering paradigm. In this present treatise, the world of
challenges and difficulties are brought to the forefront of scientific horizon
with visionary appeal and unending effectivity. The author details the basic
fundamentals of MOO, its varied applications in chemical engineering and
petroleum engineering systems, the future recommendations of the study,
and the holistic vision of the application of GA. The vision of this trea-
tise is wide and bright. The difficulties, the barriers, and the challenges of
design of an FCCU are delineated in minute details. The science of modeling
and simulation of an FCC unit, through this treatise, surpasses visionary
140 Applied Chemistry and Chemical Engineering: Volume 4

boundaries. Fluidized catalytic cracking and catalytic reactions are the heart
of a petroleum refinery. Scientific vision, the challenge to move forward, and
the instinct of scientific innovation are the pallbearers of greater advance-
ments in research in petroleum refining.24,25
Scientific vision and deep scientific understanding in the field of
modeling, simulation, control, and optimization of a riser unit of FCCU is
totally unsolved. In this treatise, the author deeply comprehends the success
of mainly the control and simulation of the riser reactor with an aim toward
global energy sustainability.24,25

8.3  SCOPE OF THE STUDY

The vision of science in today’s world and in today’s human civilization is

inspiring and in the similar vein groundbreaking. Science and engineering
is surpassing barriers of truth and understanding in today’s world. Energy
sustainability is ushering in a new eon of scientific truth and scientific
forbearance. The scope of the vision of MOO is vast and versatile. The author
deeply comprehends the success and difficulties in the application of MOO
in designing riser reactor of an FCC unit. Technological vision in today’s
world is in the midst of scientific challenges, scientific understanding, and
deep scientific questions. Scientific candor today stands in the midst of deep
distress. Modeling, simulation, and optimization of the riser reactor stand
as an important content in the success of chemical process modeling and
petroleum engineering science today. The scope of the study in the field of
application of MOO and GA is surpassing visionary boundaries. The chal-
lenge, the vision, and the application stand in the midst of deep introspec-
tion. Human science is in a state of distress. Energy sustainability and the
future of science are connected by an umbilical cord. The application areas
of GA will surely open new windows of innovation and scientific instinct in
years to come. Science is slowly and steadily opening up new frontiers of
scientific cognizance. In a similar vein, GA and bioinspired optimization are
gearing up for newer challenges and newer visionary realm.24,25

8.4  THE NEED AND THE RATIONALE OF THIS STUDY

Petroleum engineering science is moving from one drastic change toward

another. The paradigm of global energy sustainability needs to be envis-
aged at every step of human life. Depletion of fossil fuel resources has
The Vision of Application of Multiobjective Optimization 141

changed the scientific astuteness of scientific research pursuit in petroleum

engineering science. Vision of science, the progress of technology, and the
visionary era of technological validation all will lead a long way in the true
emancipation and great realization of global energy sustainability. The need
and the rationale of this study are immense and far-reaching. The author
gleans and delineates the world of scientific validation in the design of the
riser reactor in an FCCU in a petroleum refinery. The challenge, the motive,
and the paradigm of modeling, simulation, and optimization of a petroleum
refining unit are ushering in a newer visionary scientific domain in years to
come. Depletion of fossil-fuel resources is a bane to human civilization and
a disaster to scientific research pursuit. The author skillfully delineates with
deep introspection the immense difficulties and unimaginable barriers in the
modeling, simulation, control, and optimization of a petroleum refining unit.

8.5  FUTURE RECOMMENDATIONS OF THE STUDY

Designing chemical engineering systems and petroleum refining units is diffi-

cult and arduous task. The author with deep insight and wide vision informs in
a narrative the challenges in designing FCCU and futuristic vision behind it.
The scientific vision, the scientific fortitude, and the immense scientific chal-
lenges will go a long way in the true emancipation of application of MOO.
Scientific validation and scale-up of the FCC model stands as a backbone to
the futuristic vision of petroleum refining paradigm today. Scientific research
pursuit and immense scientific determination should be at that angle. The world
of challenges in the field of chemical process modeling and simulation are
revolutionizing and restructuring the avenues of science today. Future research
endeavor, the progress of science, and the forays in the domain of chemical
process engineering are opening up new eons of science and engineering.
Future of chemical process engineering and petroleum engineering
science is extremely bright. Scientific endeavor needs to be reenvisioned
with deep foresight. Future recommendations of the study should be targeted
toward greater scientific understanding in the field of applications of MOO,
bioinspired optimization, and GA. Chemical process modeling, the world of
chemical process design, and the future progress of engineering science need
to be reshaped at every step of scientific research pursuit. Future of chemical
process engineering and petroleum engineering science is bright and far-
reaching. Human scientific endeavor and scientific cognizance are in the
path of immense regeneration. Energy sustainability, ecological imbalance,
and global concern for fossil-fuel resources have urged the global scientific
142 Applied Chemistry and Chemical Engineering: Volume 4

community to devise new green technologies and newer innovations. Vision

of science in today’s world is unimaginable. Future areas of research and
future endeavor should be targeted toward the direction of holistic sustain-
able development.24,25

8.6  SCIENTIFIC DOCTRINE AND SCIENTIFIC COGNIZANCE

BEHIND MOO

Scientific doctrine and the wide world of scientific cognizance are in the
path of a newer realm and a new visionary future. MOO is opening up newer
future dimensions in the field of chemical process modeling and petroleum
refining unit designing. The vision, the challenges, and the scientific forbear-
ance are inspiring and far-reaching. MOO is revolutionizing the scientific
panorama and the ardent scientific horizon of scientific research pursuit.
Human scientific progress, immense academic rigor, and the unimaginable
challenges in the design of a riser unit in FCC unit in a petroleum refinery
are changing the scientific scenario of chemical process modeling. Scien-
tific doctrine, scientific cognizance, and immense scientific sagacity are in a
state of distress and deep turmoil. The challenge of science and engineering
needs to be reenvisioned. Scientific doctrine in today’s world of engineering
science is in a state of distress. Environmental engineering and petroleum
engineering science are ushering in a new era of scientific cognizance and
scientific introspection. The challenge, the scientific inspiration, and the
scientific doctrine need to be reshaped at each step of human life.
Scientific doctrine and scientific cognizance in today’s world of scientific
research pursuit stand in the confluence of deep scientific comprehension
and immense scientific sagacity. The challenge of human scientific research
pursuit is awesome and visionary. MOO and its application are the heart of
this treatise. The author pointedly focuses on the difficulties, barriers, and
hurdles in the successful application of MOO and GA in modeling and opti-
mization of an FCCU.

8.7  DEFINITION OF MOO, THE UNDERLYING PRINCIPLES, AND

FUTURISTIC VISION

MOO is a wide branch of applied mathematics which is surpassing vast

boundaries of science and engineering. Man’s progress, mankind’s prowess,
and the achievements of science are leading a long way in the true realization
The Vision of Application of Multiobjective Optimization 143

of applied mathematics, chemical process modeling, and the wide world of

optimization. The visionary realms of science need to be realized at every
step of human life and wide scientific forays. The underlying principles of
MOO need to be reenvisioned at every stride of scientific research pursuit.
Science and engineering of MOO is extremely complicated yet very effec-
tive. The futuristic vision of GA and bioinspired optimization is wide and
far-reaching. Science and technology are moving very fast. Chemical
process modeling and optimization is entering a new era of scientific vision
and scientific challenge. Application areas need to be restructured and reen-
visioned to the fullest scientific details. GA and bioinspired optimization are
ushering in a new era and gearing toward a newer realm in decades to come.

8.8  WHAT IS FCC AND WHAT ARE ITS FUNDAMENTALS?

FCCU stands as an important and decisive component in the design and opera-
tion of a petroleum refinery. Scientific vision, the unmitigated difficulties, and
the deep scientific introspection are the forerunners toward a greater under-
standing in the design, modeling, simulation, and control of an FCC unit.24,25
Growing demand for refinery products combined with the decreasing
quality of crude oil and tighter product specifications due to drastic envi-
ronmental constraints is forcing refiners to make definite investments and
devise innovative technologies. Fluid catalytic cracking (FCC) remains
a key unit in many refineries; it consists of a three step process: reaction,
product separation, and regeneration.24,25
Risers are considered vital parts in FCC conversion units. It is inside the
riser reactor that the heavy hydrocarbon molecules are cracked into lighter
petroleum fractions such as liquefied petroleum gas (LPG) and gasoline. The
FCC process is considered a key process in the world of petroleum industry,
since it is the main unit responsible for the profitable conversion of heavy
gas oil into commercial valuable products. There has been immense research
work done in the field of riser design and riser fundamentals. In this treatise,
the author also discusses the recent work done in the control and optimiza-
tion of an FCCU primarily the riser reactor.24,25

8.9  WHAT IS MOO?

MOO and its scientific principles in today’s scientific world stand between
deep scientific comprehension and scientific vision. The challenge of the
144 Applied Chemistry and Chemical Engineering: Volume 4

human scientific endeavor is slowly unfolding with each step of scientific

rigor. The vision of science, the progress of technology, and the ardent scien-
tific and academic rigor will lead a long and visionary way in the true real-
ization of technology and engineering.
Multivariable optimization algorithms are used in algorithms for opti-
mizing functions having multiple design and decision variable. A deep and
proper understanding of the single-variable function optimization algo-
rithms would be immensely helpful in appreciating multivariable function
optimization algorithms.24,25

8.9.1  WHAT IS GA, BIOINSPIRED OPTIMIZATION, SIMULATED

ANNEALING, AND OTHER NONTRADITIONAL OPTIMIZATION
ALGORITHMS?

GAs mimic the principles of natural genetics and natural selection to consti-
tute search and optimization procedures. Simulated annealing mimics the
cooling phenomenon of molten metals to constitute a search procedure.
Professor John Holland of University of Michigan, Ann Arbor, USA envis-
aged the concept of these GAs in the mid-1960s and published his phenom-
enal work. Bioinspired optimization mimics traditional biological sciences.
Bioinspired, short form for biologically inspired, computing is a field of
study that integrates subfields related to the topics of connectionism, social
behavior, and emergence. It is often related to the field of artificial intelli-
gence. Biologically inspired computing is a branch of natural computation.
Nontraditional optimization involves GA, simulated annealing, and bioin-
spired optimization.24–26

8.10  THE SCIENTIFIC VISION AND DEEP SCIENTIFIC

UNDERSTANDING BEHIND APPLICATION OF GA

GA and its applications are visionary yet immature. Scientific rigor and
academic prowess are at its helm at each step of human progress. GA and
bioinspired optimization in today’s scientific world are witnessing tremen-
dous changes and deep introspection. The challenge of human scientific
endeavor needs to be readdressed today. GA and application of MOO are
widely restructuring the face of chemical process engineering and chemical
process modeling.24–26
The Vision of Application of Multiobjective Optimization 145

8.11  THE SCIENTIFIC DOCTRINE AND THE SCIENTIFIC VISION

BEHIND DESIGN OF RISER REACTOR OF AN FCC UNIT

The scientific doctrine and the deep scientific vision behind the design of
a riser reactor are awesome and groundbreaking. Scientific endeavor along
with scientific fortitude need to be readdressed at each step of human civi-
lization. Petroleum engineering science in today’s scientific landscape is
witnessing drastic changes with the evergrowing concern of depletion of
fossil-fuel resources. Environmental engineering science is the other face
of the civilization’s coin today. Scientific sagacity today is at the helm of
human scientific research pursuit. Scientific vision and scientific doctrine
are unfailingly leading a long and visionary way in the true realization of
energy sustainability today. Petroleum refining needs to be reenvisioned with
each step of human scientific endeavor. Depletion of fossil-fuel resources is
changing the paradigm of research pursuit.

8.12  THE VISION, THE CHALLENGE, AND THE DEEP SCIENTIFIC

INTROSPECTION IN THE DESIGN OF AN FCC UNIT

The challenge and the vision of science in today’s scientific research pursuit
in the design of an FCC unit are widening and surpassing vast boundaries.
Today’s technology thrusts and technology introspection should be targeted
toward scientific validation. The challenge and vision of science are veri-
tably inspiring. This treatise targets the success of application of MOO in the
visionary and emerging world of optimization of the riser reactor of FCCU.
Scientific vision, scientific candor, and the world of scientific sagacity are
unfolding a newer scientific generation and scientific horizon in decades to
come.

8.13  PETROLEUM REFINING FUTURE, ENERGY SUSTAINABILITY,

AND THE VISION FOR THE FUTURE

The future of petroleum refining is moving from one paradigmatic shift over
another. Depletion of fossil-fuel resources are the vexing and burning issues of
our times. Mankind’s prowess is witnessing the test of our times as civilization
moves toward a newer world of energy sustainability. Both, energy and envi-
ronmental sustainability stand in the midst of unmitigated crisis and immense
introspection. The success of human scientific endeavor is at a state of deep
146 Applied Chemistry and Chemical Engineering: Volume 4

scientific distress. Future of petroleum refining needs to be readdressed at each

step of scientific endeavor and each step of scientific sagacity. The vision for
the future in the field of petroleum refining and design of petroleum refining
unit should be targeted toward efficiency and effectivity of the process. Cata-
lytic cracking is an energy-intensive process and the vision of modeling and
simulation should be toward immense efficiency of the process.

8.14  THE SCIENCE OF APPLICATION OF GA IN DESIGNING

RISER REACTOR OF A FCC UNIT

The science of application of GA in designing riser reactor is the crux of this

well-informed and well-observed treatise. Application of MOO and GA needs
to be readdressed and reenvisioned at each step of scientific advancement.
Riser design is the heart of petroleum refining unit. The innovative vision and
the deep challenge behind application of GA need to be deeply understood in
the path toward design, modeling, simulation, and optimization of an FCCU.

8.15  APPLICATION AREAS IN THE FIELD OF MOO

Application areas in the field of optimization are vast, versatile, and

visionary. Scientific research pursuit is at its helm at every step of human
endeavor. Scientific validation and science of scale-up need to be envisioned
at each stride of human scientific rigor. MOO has innumerable applications
in today’s world of science and engineering. Science, technology, and engi-
neering are reshaping and restructuring themselves with immediate and
urgent needs. At this critical juxtaposition of scientific reshaping, MOO
and other tools of science such as evolutionary computation are changing
the face of human scientific endeavor and civilization’s forays. Applica-
tion areas in the field of MOO and GA are immense, wide, and versatile.
Chemical process modeling paradigm is ushering in a new era of immense
scientific cognizance. Scientific history and scientific candor are witnessing
revolutionary changes with the passage of human history and time.

8.16  GA AND THE WORLD OF IMMENSE CHALLENGES

GA is regenerating itself with each step of application of optimization. The

immense challenges and barriers are in the path of reshaping. Advancements
The Vision of Application of Multiobjective Optimization 147

of science and engineering are changing the scenario of applications of

MOO. Human endeavor, the progress of technology, and the visionary world
of applied mathematics and optimization will go a long way in the true eman-
cipation of the world of today’s scientific fortitude. GA and bioinspired opti-
mization are ushering in a new world of scientific achievement. The success,
the vision, and the immense scientific challenges will lead a long way in
the true realization of MOO. The hidden questions of computational time
and the efficiency stand as strong backbone to the futuristic vision of MOO.
GA, evolutionary MOO, and bioinspired optimization are the cruxes of the
science of optimization. The challenge needs to be reenvisioned. GA and
the world of bioinspired optimization are ushering in a new eon of scientific
challenge, scientific vision, and deep scientific understanding. The candor
of science, the vision to move forward, and the immense urge to excel are
the effective pallbearers of a new paradigm in the domain of optimization.

8.17  APPLICATION AREAS OF GA

Application areas of GA are wide and far-reaching. Vision of science and

engineering in today’s human civilization are crossing wide boundaries. The
world of MOO is ushering in a new era of scientific profundity. The diffi-
culties and the barriers of application of bioinspired optimization are chal-
lenged and reenvisioned at each step of research pursuit. The challenge, the
vision, and the scientific urge to excel in the area of GA are opening up new
vistas of scientific perspicuity in years to come. Bioinspired optimization
and evolutionary MOO are the hallmarks of a new scientific generation and
a newer realm.

8.18  THE TRUE VISION OF FCCU AND ITS MODELING

FCC and its modeling are moving toward a newer phase of scientific vision
and scientific understanding. The definitions of applied mathematics are
changing with each step of scientific forays. Chemical process modeling,
simulation, and optimization are being reenvisioned with each defining
moments of the advancements of human civilization. Scientific challenges
in today’s world are at its helm and barriers need to be redefined. The
research work in the field of design of FCCU is not new yet in a latent
stage. Scientific sagacity and the world of visionary challenges are scien-
tifically inspiring and are surpassing wide boundaries. The true vision of
148 Applied Chemistry and Chemical Engineering: Volume 4

FCC is witnessing a newer realm and a purposeful vision. Modeling, simu-

lation, optimization, and control of an FCC unit stand at the heart of design
of a petroleum refining unit. Process optimization of a petroleum refining
unit in today’s world of science is surpassing visionary frontiers and is at
the helm of scientific perspicuity. The challenge and vision of optimiza-
tion and control need to be reenvisioned at each step of design of an FCC
unit in petroleum refinery. Riser modeling optimization and control stands
as a major component of the efficiency and success of catalytic cracking
process.

8.19  RISER DESIGN IN AN FCC AND THE PROGRESS OF SCIENCE

Riser design in an FCC is witnessing immense challenges. Human scien-

tific research pursuit today stands in the midst of multitudes of crossroads.
Science and engineering of optimization are passing through an eon of wide-
spread changes. The vision of energy sustainability, the grave concerns of
future of fossil-fuel resources, and the futuristic progress of science will all
go a long way in unraveling the scientific truth and scientific vision. Scien-
tific and academic rigor in the field of riser design is opening up new areas
of innovation and definitive vision. Science is a massive colossus without a
will of its own. In such a crucial juncture of scientific history and scientific
cognizance, man’s vision as well as a scientist’s prowess are reshaping and
reenvisioning the domain of petroleum engineering science.
Riser design is of vital importance in the design, modeling, and simula-
tion of an FCCU. Depletion of fossil-fuel resources and the grave concerns
for environmental and energy sustainability have urged human scientific
endeavor to devise newer innovations and newer technologies. The success
of human sustainable development will never be a mirage with the passage
of human history and time. Energy sustainability in today’s human civiliza-
tion is in the path of immense reform. Riser design is the heart of petroleum
refining process. Scientific vision and deep scientific understanding needs to
be rebuilt at each step of designing, modeling, simulation, and optimization
of a riser reactor.24–26

8.20  MOO: ITS VISION AND DIFFICULTIES

MOO and application of GA are moving toward a newer phase in this decade
of human scientific endeavor. Scientific adjudication and scientific judgment
The Vision of Application of Multiobjective Optimization 149

are entering a newer visionary era. The ultimate vision and aim of applica-
tion of MOO is to reduce the computational time in optimization. Bioin-
spired optimization and GA are changing the scientific horizon in decades
to come. MOO and applications of GA are surpassing vast and versatile
visionary frontiers. The world of challenges rests upon scientific validation,
scientific candor, and immense scientific understanding. The true defining
moment of MOO and bioinspired optimization has led to a new world of
scientific challenges and vision.

8.21  EVOLUTIONARY MOO AND THE SCIENTIFIC DOCTRINE

Evolutionary MOO and its scientific doctrine need to be reenvisioned at

each step of civilization’s destiny. The grave concern for energy and envi-
ronmental sustainability and the world of immense challenges are changing
the face of human civilization. Scientific sagacity is witnessing severe chal-
lenge. Evolutionary MOO and bioinspired optimization are moving in the
newer futuristic direction of scientific optimism and immense scientific
hope. Human scientific rigor in today’s world is in the state of definite scien-
tific vision and deep scientific understanding.

8.22  FLUIDIZED CATALYTIC CRACKING UNIT IN A PETROLEUM

REFINERY AND APPLICATION OF EVOLUTIONARY MOO

FCC and the world of energy sustainability are surpassing wide and
visionary horizons. In today’s human civilization, energy and environ-
mental sustainability are connected by an unsevered umbilical cord. The
present challenge of the human civilization lies on the successful energy
and environmental sustainability. Scientific research rigor and academic
prowess in the field of design of the riser in an FCC unit need to be reenvi-
sioned. Petroleum refining is witnessing dramatic and drastic changes. The
fascinating world of science and technology is witnessing new rigor at each
turn of the present century. Petroleum refining is moving toward a newer
and visionary scientific paradigm and a newer scientific cognizance. The
challenge of design, modeling, simulation, and optimization of a petroleum
refining unit is the vision of today and the paradigm of tomorrow. Scientific
forbearance and the difficulties and barriers are at its helm with each step
of human endeavor.
150 Applied Chemistry and Chemical Engineering: Volume 4

8.23  VISIONARY SCIENTIFIC ENDEAVOUR IN THE FIELD OF

DESIGN OF A RISER IN A FLUIDIZED CATALYTIC CRACKING
UNIT

Scientific endeavor in today’s human civilization is arduous as well path-

breaking. Petroleum refining is the backbone of many developed and devel-
oping economies. The grave concern of depletion of fossil-fuel resources
and the uncertainties of petroleum engineering science have changed the
world of scientific research pursuit. The challenges, the vision, and the prog-
ress of science are ushering a new era in chemical process modeling and the
vast domain of optimization.
Souza et al. (2007)1 discussed with lucid details a modeling and simula-
tion procedure of industrial FCC risers.1 The importance of the FCC utilities
for the petroleum industry is growing steadily and drastically as the demand
for the utilization of heavy oil increases. Therefore, there is a greater interest
of the petroleum refining industry in the development of new technologies,
which may increase the conversion, and also the quality of the gas oil into
noble products such as gasoline and LPG. For these reasons, several works
have been found in technical literature related to the catalytic cracking of
petroleum fractions. Science and engineering of the design of a riser unit of
FCC are crossing wide and visionary frontiers.1 Such studies can be divided
in two major research avenues: the fluid flow and the catalytic cracking reac-
tion schemes, both of great importance for the modeling and simulation of
an FCC unit. It can also be observed from scientific advances that there exist
countless types of models for both fluid flow and cracking kinetics, varying
from simple models to three-dimensional and three-phase models. This
work deeply focuses its attention on the riser reactor.1 It is inside the reactor
that all the cracking reactions responsible for the heavy gas oil conversion
into lighter petroleum fractions take place.1 The hot catalyst (around 700°C)
coming from the regenerator enters at the bottom of riser and is brought
into contact with a liquid stream of gas oil (around 240°C) flowing from
a number of nozzles and, almost instantaneously, is vaporized.1 This inlet
zone is characterized by the presence of turbulence and high temperature
and concentration gradients. This turbulent zone is important, but it happens
only in the few first meters of the riser, and in some sense the presence of
turbulence is not considered in its simulation.1
Another visionary area not attempted in the area of riser models is the
hypothesis that the gas oil injected in the bottom of riser is well mixed with
the catalysts.1
The Vision of Application of Multiobjective Optimization 151

In general, the fluid flow models can be classified in three categories.

First, the one-dimensional models that are normally simple to formulate and
to solve.1 They are more suitable when the interest is to explore the influ-
ence of operating conditions, test a kinetic model, or when the simulation
includes not only the riser but also other equipment such as the regenerator
and the stripper.1
The second type comprises the semiempirical models, which are usually
described as core-annulus models.1 Normally the particle fall velocity and
particle concentration are determined empirically. These models cannot
predict results for different operational conditions from those of the model
parameter estimation.1
Fernandes et al. (2005)2 discussed in details mechanistic dynamic modeling
of an industrial FCC unit. The aim of this study is to obtain a model that can
simulate the performance of an industrial FCCU in steady and dynamic state,
and will invariably be used in studies of control and real-time optimization.2
The challenge of science and engineering in FCC design is unfolding at each
step of this scientific pursuit. The model includes the riser, the stripper/disen-
gage, the regeneration system, and the catalyst transport lines.2
Llanes et al. (2008)3 drastically in a visionary review validated the use
of modeling to fine-tune cracking operations.3 Rigorous nonlinear reactor
kinetic models have traditionally been used to support refinery planning,
especially in defining linear programming (LP) submodels and operating
constraints for reactors.3 According to the authors, application of kinetic
models in engineering, operations support, and optimization are less common
due to intense efforts required to produce accurate results for each operating
scenario.3 This is an example of a refinery which uses next-generation simu-
lation tools to cost-effectively select new catalysts. This is a case history
which is written with deep comprehension and instinctive scientific imag-
ination. CEPSA’s La Rabida refinery in Spain has used nonlinear kinetic
FCC model in combination with other advanced simulation tools for several
operational studies.3 The visionary business objective of these applications
is to improve FCC unit performance in various areas and to include3:

• New catalyst selection

• Unit monitoring, troubleshooting, and optimization
• LP planning model updates
• Examining new feed scenarios

The modeling of the FCC unit is the backbone of the entire petroleum
refinery. The challenge and vision of today’s science are unimaginable. The
152 Applied Chemistry and Chemical Engineering: Volume 4

FCC model comprises a reactor–regenerator section block where all the data
related to the reaction section is introduced.3 The FCC reactor–regenerator
model seamlessly integrates with other segments of the simulation model
where downstream separation units are constructed with standard simulator
unit operations such as distillation columns, heat exchangers, drums, pumps,
compressors, and more.3
Dagde et al. (2012)4 discussed lucidly modeling and simulation of indus-
trial FCC unit and did analysis based on five-lump kinetic scheme for gas oil
cracking. The challenge and the deep scientific understanding of chemical
kinetics are slowly unfolding with each step of instinctive and innovative
scientific pursuit. Models which describe the performance of riser and regen-
erator reactors of FCC unit are presented in this treatise. The riser–reactor
is modeled as a plug-flow reactor operating adiabatically, using five-lump
kinetics for the cracking reactions. Chemical kinetics and chemical reac-
tion engineering are the forerunners toward a visionary domain of chemical
process design and chemical process modeling.4 Vision of science, the scien-
tific and academic rigor, and the march of technology will all lead a long
way in the true emancipation of holistic energy sustainability. The efficacy
of scientific modeling and simulation of an FCC unit will widen the frontiers
of science and engineering.4
Bhende et al. (2014)5 deeply discuss with cogent insight modeling and
simulation for FCC unit for the estimation of gasoline production.5 Fluidized
Catalytic Cracking
(FCC) is one of the most important processes in the petroleum refining
industry for the conversion of heavy gas oil to gasoline and diesel. Further,
valuable gases such as ethylene, propylene, and isobutylene are produced.5
This work targets the development of a mathematical model that can simu-
late the behavior of the FCC unit, which consists of feed and preheat system,
riser, stripper, reactor, regenerator, and the main fractionators.5
Ahari et al. (2008)6 discuss a mathematical model of the riser reactor in
industrial FCC unit. In this article, the author discusses and develops a one-
dimensional adiabatic model for riser reactor of an FCC unit.6 The hydro-
dynamic model was described by one general model. Simulation studies are
performed to investigate the effect of changing process variables such as
input catalyst temperature and catalyst-to-oil ratio.6
Bispo et al. (2014)7 discussed with lucid depths modeling, optimization,
and control of an FCC unit using neural networks and evolutionary methods.
Artificial neural network (ANN) stands as a major component in control
and optimization of a fluidized bed catalytic cracking reactor–regenerator
system. This innovative case study, whose phenomenological model was
The Vision of Application of Multiobjective Optimization 153

validated with industrial data, is a multivariable and nonlinear process with

strong interactions with operating variables.7
Rao et al. (2004)8 discussed industrial experience with object-oriented
modeling with an FCC case study. Process modeling and simulation has
emerged as an important tool in the advancement of chemical process engi-
neering science. There is an immediate need for refinement of advanced
modeling and simulation studies. This work researches on the framework
of one such multipurpose simulator, MPROSIM, an object-oriented process
modeling and simulation environment.8
Dasila et al. (2012)9 deeply comprehend parametric sensitivity studies in
a commercial FCC unit. A steady-state model was developed for simulating
the performance of an industrial FCC unit which was next applied to para-
metric sensitivity studies. The simulator includes kinetic models for the riser
reactor and regenerator systems.9
Souza et al. (2006)10 discussed and developed a two-dimensional (2D)
model for simulation, control, and optimization of FCC risers. A simple 2D
formulation for FCC risers has been developed. The model delineates and
approximates the mixture of gas oil, steam, and solid catalyst that flows
inside the riser reactor by an equivalent fluid with average properties. The
cracking equations are modeled by a six-lump kinetic model combined with
two energy equations.10
Pahwa et al. (2016)11 described lucidly computational fluid dynamics
(CFD) modeling of FCC riser reactor. The authors of this work present a
two-phase flow FCC riser model incorporating a four-lump kinetic scheme.
The two-phase flow (gas–solid) in the riser is modeled using the Eulerian–
Eulerian multiphase flow model.11
Varshney et al. (2014)12 effectively modeled a riser reactor in a Resid FCCU
using a multigrain model for an active matrix-zeolite catalyst. The riser reactor
is simulated using a multigrain model of the catalyst in which the amorphous
matrix as well as the embedded Y-zeolite crystals are porous and reactive. The
technology of FCC design is today entering a visionary era. The scientific vision
and the scientific cognizance are moving from one paradigm over another.

8.24  SCIENTIFIC RESEARCH PURSUIT IN THE FIELD OF MOO

Research vision is the utmost need of the hour. Sustainability and sustainable
development are the unanswered branches of human scientific endeavor.
MOO and its research domain are ushering in new future thoughts and newer
pragmatic solutions. Science of optimization and bioinspired optimization
154 Applied Chemistry and Chemical Engineering: Volume 4

are gaining new grounds. The purpose, the vision, and the immediate mission
of optimization need to be reshaped and reenvisioned at each step of futur-
istic scientific endeavor.
MOO and evolutionary techniques are changing the face of chemical
process modeling and simulation. The challenge and vision of chemical
process modeling need to be reenvisioned.
Deb et al. (2002)13 discussed a fast and elitist multiobjective GA (NSGA-
II) in a phenomenal paper. Multiobjective evolutionary algorithms (MOEAs)
that use nondominated sorting and sharing have been criticized mainly for
(1) computational complexity, (2) nonelitism approach, and (3) the need for
specifying a sorting sharing parameter. The paper deals with a nondomi-
nated sorting-based MOEA, called nondominated sorting GA II (NSGA-II),
which alleviates all the above three difficulties.13
Yapo et al. (1998)14 discussed with deep insight multiobjective global opti-
mization for hydrologic models. The development of automated (computer-
based) calibration methods has focused mainly on the selection of a single-
objective measure of the distance between the model-simulated output and
the data and the selection of an automatic optimization algorithm to search
for the parameter values which minimize the distance.14 To calibrate a hydro-
logic model, the hydrologist must specify values of its parameters in such
a way that the model’s behavior closely matches that of the real system it
represents. In some cases, the appropriate values for a model parameter can
be determined through direct measurements conducted on the real system.14
Because of the time-consuming nature of manual trial-and-error calibration,
there has been a great deal of research into the development of automated
calibration methods.14 The author rigorously brings into the scientific fore-
front the multiobjective global optimization for hydrological models.14
Marler et al. (2004)15 surveyed MOO methods for engineering. Current
continuous nonlinear MOO concepts and methods are presented. It consoli-
dates and relates seemingly different terminology and methods. In the paper,
GAs are also presented in lucid details. Discussion is provided on three
fronts, concerning the advantages and loopholes of individual methods, the
different classes of methods, and the field of MOO as a whole.15
Wang et al. (2006)16 reviewed metamodeling techniques in support of
engineering design optimization. Computation-intensive design problems
are becoming increasingly relevant in manufacturing industries. Expensive
analysis and simulation processes are the hallmarks of these processes, thus
the need of metamodeling techniques.16
Gupta (2012)17 discussed in a phenomenal paper MOO and biomimetic
adaptations of GA. Scientific vision and scientific imagination of GA are
The Vision of Application of Multiobjective Optimization 155

veritably emboldened with this endeavor. Optimization using more than one
objective function (MOO) has become quite relevant in engineering science
today. The challenge and vision of biomimetic optimization are reenvisioned
and re-enshrined in this major work. MOO provides a decision maker with
an idea of the trade-offs between noncommensurate objectives. An example
is the maximization of the profit and minimization of pollutants. Two ideas
of biological sciences, namely jumping genes (transposons) and the altruism
of honeybees, have been biomimicked to give faster adaptations of multiob-
jective GAs as well as simulated annealing.17
Kasat et al. (2002)18 deeply comprehends MOO of industrial FCC units
using elitist nondominated sorting GA. This treatise deeply discusses optimal
operation of fluidized bed catalytic cracking unit. A five-lump model is used
to characterize the feed and the products. The challenge and deep vision of
science are widening. The model is tuned using industrial data. The elitist
nondominated sorting GA (NSGA-II) is used to solve a three-objective func-
tion optimization problem.18
Kasat et al. (2003)19 dealt lucidly with MOO of an industrial fluidized bed
catalytic cracking unit (FCCU) using GA with the jumping genes operator.
The MOO of industrial operations using GAs and its variants, often requires
inordinately large amounts of computational (LPU) time. The vision, the
challenge, and the rigor of science and engineering need to be rebuilt in such
a critical situation. An adaptation to speed up the solution procedure was
the need of the hour. In this treatise, an adaptation from natural genetics is
presented in lucid details.19
Gupta et al. (2013)20 in a well-informed and well-observed treatise
discussed MOO using GA. GA is among the more popular evolutionary
optimization techniques. Its multiobjective domains and relevant versions
are useful for solving industrial problems that are more meaningful and
groundbreaking. The scientific rigor of this treatise unfolds greater visionary
areas of engineering of GA.20

8.25  THE WORLD OF CHALLENGES, THE FUTURISTIC VISION,

AND THE AVENUES OF RESEARCH PURSUIT IN THE FIELD OF GA

GA and bioinspired optimization are witnessing new challenges and

surpassing visionary scientific frontiers. The avenues of scientific research
pursuit need to have a clear-cut vision and a rigorous and purposeful mission.
Scientific and academic rigor is in the path of immense restructuring.
Research endeavor and research forays in the field of GA and bioinspired
156 Applied Chemistry and Chemical Engineering: Volume 4

optimization are seeing the newer vision of the day. Sustainability research,
sustainable development, and the wide world of chemical process modeling
are veritably ushering in a new genre of science and engineering in years to
come. Challenges are immense but options are many in the field of chem-
ical process engineering. GA and evolutionary MOO are facing tremendous
challenges with the passage of human history and time.21–23

8.26  IMMENSE DIFFICULTIES AND SCIENCE OF OPTIMIZATION

Science and engineering of optimization is moving toward a visionary realm

and a world of greater scientific understanding. The barriers and difficulties
in its application are immense and thought-provoking. The author reenvisions
the loopholes in the difficult terrains of optimization. These terrains need to
be overcome in the attainment and realization of global energy sustainability.
Bioinspired optimization in today’s scientific world is witnessing new and
unimaginable challenges. GA and bioinspired optimization are the new-gener-
ation innovative technologies which needs to be reenvisioned and re-enshrined
at each step of scientific endeavor. Design of an FCCU is an extremely diffi-
cult scientific pursuit. The challenge, the vision, and the efficacy needs to be
scientifically understood at each stride of research endeavour.21–23

8.26.1  DIFFICULTIES OF COMPUTATIONAL TIME

Computational time stands as a major component in the success of bioin-

spired optimization and application of GA. Evolutionary MOO also stands
in the midst of immense barriers with respect to computational time. Tradi-
tional optimization techniques are beset with immense difficulties such
as computational time. Thus, there is the need of improved version and
non-traditional bioinspired techniques such as GA or evolutionary MOO.
The challenge and wide vision of technology and engineering need to be
re-enshrined and rebuilt with each step of future science.21–23

8.27  VISION OF SCIENCE, ENERGY SUSTAINABILITY, AND THE

FUTURE PROGRESS OF HUMAN CIVILIZATION

The progress of human civilization today stands in the midst of immense

distress and deep scientific innovation. The challenge of sustainable
The Vision of Application of Multiobjective Optimization 157

development is revealing at each turn of decade in the present century.

Social sustainability, economic sustainability, and environmental sustain-
ability stand in the crucial juncture of human scientific rigor. Scientific
rigor and true scientific vision of bioinspired optimization and GA are the
pallbearers of a greater emancipation of energy and environmental sustain-
ability. Human scientific cognizance is witnessing the inevitable test of our
times. The author repeatedly delineates the effect and success of bioinspired
optimization and application of GA in designing FCCU.
The future progress of human civilization depends on the progress of
energy as well as environmental sustainability. Petroleum engineering
science today stands in the midst of immense disaster and intense introspec-
tion. Depletion of fossil-fuel resources and the grave concerns of ecological
balance have plunged human civilization to a deep crisis. In such a situation,
human civilization and progress of human mankind are the ultimate parame-
ters toward a greater vision of tomorrow. Sustainable development of human
civilization and human progress are in the path of immense reshaping. The
progress of science and technology is in a state of great distress with the
passage of history and time. The challenge, the vision, and the purpose of
research pursuit need to be reshaped at every stroke of a decade in the present
century in the field of energy and environmental sustainability.21–23

8.28  VALIDATION OF SCIENCE AND DESIGN OF A RISER

REACTOR IN AN FCC UNIT

Validation of science and engineering has moved to a new phase of scientific

regeneration. GA and its application in the design of the riser reactor in an
FCC unit have revolutionized and reframed the visible world of chemical
process modeling and applied mathematics. Science has moved toward a
newer path of scientific regeneration and scientific forbearance. The scien-
tific horizon of chemical process engineering and bioinspired optimization
is reframing and restructuring the world of science, engineering, and tech-
nology. The true vision of GA still needs to be explored. Human scientific
endurance is in the avenue of greater emancipation. Validation of science,
the futuristic vision of engineering, and immense scientific fortitude are the
need of the hour in the futuristic path of scientific research endeavor. Deep
scientific understanding and immense foresight are the true parameters of
human civilization today. Validation of science, the rigor of technology,
and the immense scientific foresight are the foremost parameters of human
research pursuit today.21–23
158 Applied Chemistry and Chemical Engineering: Volume 4

8.29  FUTURISTIC VISION OF CHEMICAL PROCESS MODELING

AND PROGRESS TOWARD FUTURE

Chemical process modeling is witnessing a newer visionary future. Human

scientific endeavor, the scientific urge to excel, and human mankind’s
prowess will all lead a long way in true realization of energy and environ-
mental sustainability. Vision of science and progress of chemical process
engineering in today’s world are linked by an unsevered umbilical cord.
Engineering science in today’s scientific horizon is connected to energy
sustainability in a similar umbilical cord. The world of scientific progress,
the concern for ecological balance, and the eon of scientific research pursuit
are the pallbearers of a newer visionary future.21–23

8.30  GA APPLICATIONS, THE SCIENCE OF OPTIMIZATION, AND

THE VISION FOR THE FUTURE

GA applications and its innovative scientific research pursuit are witnessing

a new restructuring and newer reenvisioning. The challenge of science, the
vast and versatile world of chemical process modeling, and the success of
realization of energy sustainability are the torchbearers of tomorrow’s scien-
tific research pursuit. Thus, the science of optimization and its immense
innovation are opening up new vistas of scientific learning and true scien-
tific understanding in years to come. A scientist’s visionary prowess, the
innovation and greatness of engineering science, and the futuristic world of
optimization in today’s world are leading a long way in successful designing
of a petroleum refining unit. MOO and application of GA are reframing the
scientific horizon of petroleum engineering science.21–23

8.31  SCIENTIFIC COGNIZANCE, SCIENTIFIC VISION, AND TRUE

SCIENTIFIC UNDERSTANDING

Scientific cognizance and scientific understanding are in the phase of new

restructuring and reenvisioning. Human scientific vision, the march of
science, and the scientific challenges are opening up wide vistas and vast
boundaries of scientific endeavor. Scientific cognizance is witnessing a real
test of times in its path toward scientific validation. Scientific validation
and scale-up are reorganizing the chemical process design scenario. The
challenge of chemical process design and modeling lies in the success of
The Vision of Application of Multiobjective Optimization 159

scientific validation and scale-up. True scientific vision and deep scientific
understanding are the bedrock of today’s pursuit of science and engineering.

8.32  SCIENCE OF SCALE-UP AND THE PATH TOWARD

SCIENTIFIC VALIDATION
Science of scale-up is entering a new phase of chemical process modeling
and simulation. Scientific validation today stands in the bedrock of immense
vision and introspection. Scale-up of a chemical process is the backbone
of chemical process engineering. Scientific validation is the crux of the
entire domain of chemical process engineering and petroleum engineering
science. Scientific truth, the immense vision, and the multitude of scientific
barriers will all lead a long way in true emancipation of petroleum engi-
neering science. Scientific validation and scale-up are the today’s visionary
avenues of science and engineering. The challenges of scale-up of chemical
processes are immense and the vision is vast and versatile. The path toward
scientific validation is opening up a new world of scientific imagination and
scientific candor in years to come.

8.33  DEPLETION OF FOSSIL-FUEL RESOURCES AND A NEW

VISIONARY FUTURE
Depletion of fossil-fuel resources is changing the face of global energy sustain-
ability. The definitive challenge, the scientific astuteness, and the deep scien-
tific introspection are widening the futuristic vision of petroleum engineering
science and chemical process modeling. The future is arduous and catastrophic.
Petroleum refining is witnessing deep crisis with respect to growing concern
of depletion of fossil-fuel resources. Upgradation of petroleum refining tech-
nology is the immediate need of an hour. Scientific vision and technological
motivation need to be reenvisioned at each step of scientific endeavor. In this
treatise, the author deeply comprehends the success of petroleum refining tech-
niques, the difficulties and the road toward energy sustainability.

8.34  THE CHALLENGE, THE VISION, AND THE SCIENTIFIC

WISDOM IN MODELING AND SIMULATION OF AN FCC UNIT

Modeling, simulation, optimization, and control of an FCC unit are the upshot
of this treatise. The author skillfully delineates the success and the definitive
160 Applied Chemistry and Chemical Engineering: Volume 4

vision in mathematical modeling and application of applied mathematics in

chemical process engineering. Growing concern of depletion of fossil-fuel
resources, the future of environmental engineering science, and the futuristic
status of global energy sustainability are the pallbearers of a greater visionary
tomorrow in the field of chemical process modeling and simulation.

8.35  SCIENTIFIC ACUITY, THE DEEP SCIENTIFIC

UNDERSTANDING, AND SCIENTIFIC INTROSPECTION

Scientific acuity and deep scientific understanding are in today’s world in

a state of immense distress and deep insight. The scientific introspection,
the grave concerns of energy sustainability, and the future of fossil-fuel
resources are dramatically changing the global scientific scenario. Human
challenges today are in the grip of immense introspection. The author repeat-
edly stresses on the future of modeling, simulation, and optimization of an
FCC unit in a petroleum refinery with a vision toward energy sustainability.
Science is a huge colossus with immense visionary implications. Future of
modeling, simulation, and optimization is showing a new path in the research
pursuit in FCC unit. Modeling, simulation, and control of riser reactor are at
the heart of refinery optimization. The author brings positively to the scien-
tific forefront the challenge and vision of design of FCC unit.

8.36  FUTURE TRENDS AND FUTURE FLOW OF THOUGHTS IN

THE FIELD EVOLUTIONARY MOO

Science and engineering of optimization is gearing for newer challenges and

newer vision. Bioinspired optimization is ushering in a new era of scien-
tific vision and scientific candor. Scientific research pursuit in today’s world
stands in the midst of deep foresight and immense introspection. The scien-
tific reality and the deep scientific understanding in the field of applica-
tion of MOO need to have a futuristic overhauling. Science, technology and
engineering science needs to gear toward a newer beginning.

8.37 CONCLUSION

Human civilization and forays into applied science are ushering in a new era
of scientific vision and deep scientific understanding. Applied mathematics,
The Vision of Application of Multiobjective Optimization 161

chemical process modeling, and science of optimization are entering a new

phase of scientific research pursuit. Global petroleum engineering concerns
and the grave future of depletion of fossil-fuel resources have urged scien-
tists and technologists to gear toward innovation and vision. The author
deeply delineates the mathematical tools in designing chemical engineering
systems and the future trends in research endeavor. Technological vision is
at the forefront of human scientific research pursuit. FCC and application
of GA in its design are the pallbearers of a new visionary era of the science
of optimization. MOO with the help of GA has a definite and purposeful
vision and that vision needs to be realized and harnessed. The difficulties,
the barriers, and the vision of the science of optimization will all lead a long
way in the true emancipation of MOO and GA. The vision of science is an
immense colossus without a definite will of its own. Petroleum engineering
science today stands in the midst of immense distress and an unending catas-
trophe. The author skillfully delineates the success, the vision, and the future
trends in the research pursuit in the domain of design of FCCU. Modeling,
simulation, and optimization of petroleum refining processes stand as a major
barrier and an unimaginable difficulty in the futuristic vision of science and
engineering. This treatise delineates the major hurdles in the design of a
FCCU and opens up new windows of innovation and scientific vision in
decades to come.

KEYWORDS

•• fluidized catalytic cracking

•• petroleum
•• vision
•• modeling
•• science
•• engineering

REFERENCES

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2. Fernandes, J.; Verstraete, J. J.; Pinheiro, C. C.; Oliveira, N.; Ramoa Ribeiro, F. In
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CHAPTER 9

A THEORETICAL STUDY OF
BIMETALLIC CuAun (n = 1–7)
NANOALLOY CLUSTERS INVOKING
CONCEPTUAL DFT-BASED
DESCRIPTORS
PRABHAT RANJAN1, TANMOY CHAKRABORTY2,*, and
AJAY KUMAR1
Department of Mechatronics Engineering, Manipal University Jaipur,
1

Dehmi-Kalan, Jaipur 303007, India

2
Department of Chemistry, Manipal University Jaipur, Dehmi-Kalan,
Jaipur 303007, India
*
Corresponding author. E-mail: [email protected].
edu; [email protected]

CONTENTS

Abstract.....................................................................................................166
9.1 Introduction......................................................................................166
9.2 Computational Details.....................................................................168
9.3 Results and Discussion....................................................................169
9.4 Conclusion.......................................................................................173
Keywords..................................................................................................174
References.................................................................................................174
166 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

Due to diverse nature of applications in the field of science and technology,

nowadays study of bimetallic nanoalloy clusters is of immense importance.
A deep insight is required to explore the structure and physicochemical prop-
erties of such compounds. Among such nanoalloy clusters, the compound
formed between Cu and Au has received a lot of attention because of their
unique electronic, optical, mechanical, and magnetic properties, which have
large application in the area of nanotechnology, material science, and medi-
cine. Density functional theory (DFT) is one of the successful approaches of
quantum mechanics to study the electronic properties of materials. Concep-
tual DFT-based descriptors have been used to reveal experimental properties
qualitatively. In this report, we have investigated the geometrical structures
and physicochemical properties of CuAun (n = 1–7) invoking DFT method-
ology. The result predicts that low-lying ground state structure of copper–
gold clusters have planar structure. The computed highest occupied-lowest
unoccupied molecular orbital (HOMO-LUMO) energy gap of Cu–Au shows
interesting odd–even oscillation behavior. A close agreement between exper-
imental and our computed bond length is also observed.

9.1 INTRODUCTION

In the recent years, nanomaterials and nanotechnology have emerged as a

new research domain in science and technology. Nanomaterials with at least
one of its dimensions in the nanometer range of 1–100 nm have various appli-
cations in the area of health care, medicine, energy, electronics, and space
industries.1 The materials with this particular size range have considerably
different property from the atomic/molecular and bulk material. However,
there are still some cases of nonlinear transition of certain physicochemical
properties, which may vary depending on their size, shape, and composi-
tion.2,3 A large number of scientific reports are available which describes
change in the optical, electronic, magnetic, mechanical, and other physico-
chemical properties of nanomaterials due to change in size and structure.4–6
Advancement of methodologies and characterization techniques has a
dependence on utilization of different compositions of nanoalloys.7–9 A deep
insight into the research of nanoalloys with proper control of their nanoscale
structures may lead to some other alternatives for high-performance devices
and technologies.1
A Theoretical Study of Bimetallic CuAun (n = 1–7) 167

The noble metal clusters can be extensively applied in various strategic

and technological areas due to its unique catalytic, magnetic, mechanical,
electronic, and optical properties.7,10–15 There are a number of examples,
where it has been seen that the combination of two or more metals enhances
the abovementioned properties.16,17 Bimetallic nanoclusters have been iden-
tified as important catalyst in fuel cell electrode reactions.18 The study based
on core–shell structure of nanocompounds is very much popular because
its properties can be tuned through suitable control of other structural and
chemical parameters. During the last few years, bimetallic nanoalloy clus-
ters such as copper, silver, and gold, have been real field of research from
experimental and theoretical point of view.19–25 Group 11 metal (Cu, Ag, and
Au) clusters exhibit the filled inner d orbitals with one unpaired electron in
the valence s shell. This electronic arrangement is responsible for reproduc-
tion of exactly similar shell effects26–30 which are experimentally observed in
the alkali metal clusters.31–33 Gold nanoclusters are very much popular due
to their potential applications in the area of fabrication technology, material
science, catalysis, biology, and medicine.34–45 In the periodic table, among
the nanoalloy clusters of group 11 elements, the compound formed between
copper and gold is very much popular due to its potential technological
applications. It has been already reported that s–d hybridization is strong in
gold as compared to copper and silver due to relativistic contraction of the d
orbitals.46–49 Studies based on first principle calculation have shown that gold
clusters with more than 10 atoms have planar structure.50–51 However, no
direct experiment has been performed on neutral gold clusters.19 It has been
already established that impurity atoms can enhance the physical and chem-
ical properties of doped gold clusters that are sensitive toward the nature of
dopant atoms. In recent years, many studies have been done on doped or
mixed gold clusters to enhance the stability and physicochemical proper-
ties of gold clusters.52–57 The nanoalloy clusters of copper–gold as a catalyst
can enhance the reaction efficiency and selectivity.58–62 Though some studies
have been performed on CuAun nanoalloy clusters, a theoretical analysis
invoking Conceptual Density Functional Theory (CDFT)-based descriptors
is still unexplored in this domain.
DFT is one of the most popular approaches for the quantum mechanical
computation of periodic systems. Due to its computational friendly behavior,
DFT is widely accepted method to study the many-body systems. DFT, which
includes electron correlation properties, has been commonly described as a
practical and effective computational tool, especially for metallic nanoclu-
sters. In the domain of material science research, particularly in supercon-
ductivity of metal-based alloys, magnetic properties of nanoalloy clusters,
168 Applied Chemistry and Chemical Engineering: Volume 4

quantum fluid dynamics, molecular dynamics, nuclear physics, DFT has

gained a huge importance.63 The study of DFT covers three major domains
such as theoretical, conceptual, and computational.64–66 Conceptual DFT is
established as an important approach to study the chemical reactivity of mate-
rials.67–69 The conceptual DFT is highlighted following Parr’s dictum “Accu-
rate calculation is not synonymous with useful interpretation. To calculate a
molecule is not to understand it.”70 We have rigorously applied conceptual
DFT-based global and local descriptors for studying physicochemical prop-
erties of nanoengineering materials and drug-designing process.71–77
In this report, we have studied a number of bimetallic nanoalloy clusters
containing copper and gold, invoking DFT-based global descriptors such
as hardness, HOMO (highest occupied molecular orbital)-LUMO (lowest
unoccupied molecular orbital) gap, softness, electrophilicity index, and elec-
tronegativity. An attempt has been made to correlate the properties of the
compounds with their computational counterparts.

9.2  COMPUTATIONAL DETAILS

In this study, we have made a theoretical analysis on the bimetallic nano-

alloy clusters of CuAun, where (n = 1–7). The 3d modeling and structural
optimization of all the compounds have been performed using Gaussian 0378
within DFT framework. For optimization purpose, the local spin density
approximation (LSDA) exchange correlation with basis set LanL2dz has
been adopted. Although LDA functionals are not so much complex but their
effectiveness is already established in manifold applications, particularly for
solid-state physics,79 where accurate phase transitions in solids80 and liquid
metals81,82 are predicted, and for lattice crystals, in which 1% precision
are successfully achieved.83 Energy minimization has been done without
imposing any restriction on molecular spin. We have adopted Z-axis as spin
polarization axis. Symmetrized fragment orbitals (SFOs) are combined with
auxiliary core functions (CFs) to ensure orthogonalization on the (frozen)
core orbitals (COs).
Invoking Koopmans’ approximation,67 ionization energy (I) and electron
affinity (A) of all the nanoalloys have been computed using the following
ansatz:

I = –εHOMO (9.1)

A = –εLU\MO (9.2)
A Theoretical Study of Bimetallic CuAun (n = 1–7) 169

Thereafter, using I and A, the conceptual DFT-based descriptors, such as

electronegativity (χ), global hardness (η), molecular softness (S), and elec-
trophilicity index (ω), have been computed. The equations used for such
calculations are as follows:

I+A
χ = −µ = , (9.3)
2
where μ represents the chemical potential of the system.

I−A
η= (9.4)
2
1
S= (9.5)
2η
µ2
ω= . (9.6)
2η

9.3  RESULTS AND DISCUSSION

9.3.1  STRUCTURE OF BIMETALLIC COPPER–GOLD

NANOALLOY CLUSTERS

In this section, low-lying geometrical structure of small copper–gold CuAun

(n = 1–7) nanoalloy clusters has been studied. A large number of isomeric
structures of copper–gold clusters have been optimized and the most stable
structures with minimum energy are shown in Figure 9.1. The most stable
structure is placed in the left and total energy of the cluster increases from
left to right. The low-lying triangular structure of CuAu2 with an apex angle
of 69.58° has Cs symmetry. A linear structure has C2v symmetry which is
having high energy than the triangular structure. CuAu3 clusters have three
isomers, showing rhombus structure is energetically more favorable than the
Y-shaped structure. We have optimized four low-lying isomers for CuAu4,
CuAu5, and CuAu6. The structure of CuAu4 indicates an early presence of 3d
geometries with Cs symmetry but it is less stable than the planar structure.
The structure of CuAu5 and CuAu6 also predicts that planar geometry
is more stable as compared to the 3d structure. For octamer of CuAu7, we
have optimized five low-lying isomers; a starlike planar structure with C2v
symmetry has been identified as the lowest energy.
170 Applied Chemistry and Chemical Engineering: Volume 4

For n = 1

For n = 2

For n = 3

For n = 4

For n = 5

For n = 6

For n = 7

FIGURE 9.1  The lowest energy and low-lying structures of CuAun (n = 1–7) nanoalloy
clusters.
A Theoretical Study of Bimetallic CuAun (n = 1–7) 171

9.3.2  ELECTRONIC PROPERTIES AND DFT-BASED DESCRIPTORS

Theoretical analysis of copper–gold bimetallic nanoalloy clusters has

been done invoking DFT methodology. The orbital energies in form of
HOMO-LUMO gap along with computed DFT-based descriptors, such as
molecular electronegativity, global hardness, global softness, and global
electrophilicity index, have been reported in the Table 9.1. It is well known
that there is a direct relationship between HOMO-LUMO energy gap and
stability of the nanoalloy clusters. Table 9.1 reveals that HOMO-LUMO
gap of the nanoclusters runs hand in hand along with their evaluated global
hardness values. As the frontier orbital energy gap increases, the hardness
value increases. The molecule having highest HOMO-LUMO gap will
be least prone to response against any external perturbation. Result from
Table 9.1 reveals that CuAu5 with C2v symmetry has maximum HOMO-
LUMO gap whereas CuAu2 with Cs symmetry possesses the lowest energy
gap. Though there is no such available quantitative data for optical prop-
erties of aforesaid clusters, we can tacitly assume that there must be a
direct qualitative relationship between optical properties of Cu–Au nano-
alloy clusters with their computed HOMO-LUMO gap. The assumption
is based on the fact that optical properties of materials are interrelated
with flow of electrons within the systems, which in turn depends on the
difference between the distance of valence and conduction band. A linear
relationship between HOMO-LUMO gap with the difference in the energy
of valence and conduction band is already reported.81 Keeping it in view,
we may conclude that optical properties of the bimetallic nanoalloy clus-
ters increase with increase in their hardness values. Similarly, the softness
data exhibit an inverse relationship with the experimental optical prop-
erties. Similar relationships are also observed between other descriptors
and HOMO-LUMO gap. The linear correlation between HOMO-LUMO
gap along with their computed electrophilicity index is lucidly plotted in
Figure 9.2. The value of regression coefficient (R2 = 0.955) supports our
predicted model.
As per the theory of cluster physics, dissociation energy and second
difference of total energy have a strong influence on the relative stability
of nanoalloy clusters. These two energies are highly sensitive quantities
and they exhibit pronounced even–odd alternation behavior for neutral and
charged clusters, as a function of cluster size.19 The similar type of oscilla-
tion behavior is also exhibited by the HOMO-LUMO gap of any particular
compound. It has already been reported that cluster with an even number
of total atoms exhibits high value of HOMO-LUMO gap as compared to
172 Applied Chemistry and Chemical Engineering: Volume 4

their neighbor cluster with odd number of atoms. The stability of the even
number electronic cluster is actually an outcome of their closed electronic
configuration which always produces extra stability. We have reported
HOMO-LUMO gap as a function of cluster size in Figure 9.3. It is distinct
from Figure 9.3 that the Cu–Au clusters containing even number of total
atoms possess higher HOMO-LUMO gap as compared to the clusters
having odd number of total atoms. So, our computed data successfully
reveal the experimental odd–even alternation behavior of bimetallic nano-
alloy clusters.

TABLE 9.1  Computed DFT-based Descriptors of CuAun (n = 1–7) Nanoalloy Clusters.

Species HOMO- Electronega- Hardness Softness Electrophilicity Symmetry
LUMO gap tivity index
CuAu 1.959 5.224 0.979 0.510 13.931 C2v
CuAu2 0.952 4.938 0.476 1.051 25.610 Cs
CuAu3 1.768 5.591 0.884 0.565 17.678 C1
CuAu4 1.033 5.331 0.516 0.967 27.507 Cs
CuAu5 2.040 5.564 1.02 0.490 15.172 C2v
CuAu6 1.306 5.496 0.653 0.765 23.130 Cs
CuAu7 1.958 5.686 0.959 0.510 16.507 C1

FIGURE 9.2  A linear correlation plot of electrophilicity index versus HOMO-LUMO gap.
A Theoretical Study of Bimetallic CuAun (n = 1–7) 173

FIGURE 9.3  Even–odd oscillation behavior of HOMO-LUMO gap and CuAun (n = 1–7)
nanoalloy clusters.

A comparative analysis has been made between experimental bond

length84–86 and our computed data of the species, namely Au2, Cu2, and CuAu.
The result is reported in Table 9.2. A close agreement between experimental
data and our computed bond length is reflected in Table 9.2.

TABLE 9.2  The Calculated Bond Lengths (Å) for the Au2, Cu2, and CuAu Species.
Species Theoretical bond length Experimental bond length
Au2 2.48 2.4784
Cu2 2.16 2.2285
CuAu 2.40 2.4286

9.4 CONCLUSION

Bimetallic nanoalloy clusters have received a lot of attention due to their

wide range of technological applications. In this report, geometrical struc-
ture and physicochemical properties of copper–gold nanoalloy clusters have
been systematically investigated by using DFT methodology. The study
predicts that lowest energy structure of most stable isomers has planar struc-
ture. The result reveals that HOMO-LUMO gap of this nanoclusters runs
hand in hand along with the computed hardness. Due to nonavailability of
any quantitative benchmark, the optical property of copper–gold nanoalloy
174 Applied Chemistry and Chemical Engineering: Volume 4

clusters has been assumed to be exactly equivalence of its HOMO-LUMO

gap. Here, our evaluated data reveal that optical property of these nanocom-
pounds maintains a direct relationship with computed global hardness and
inverse relationship with computed softness. This trend is consistent with
other experimental facts also. The value of regression coefficients of model,
obtained between electrophilicity index and HOMO-LUMO gap, success-
fully supports our approach. The nanoalloy clusters also exhibit interesting
odd–even oscillation behavior, showing that even number of atoms in clus-
ters is more stable as compared to their neighbor odd number of clusters.
From our study, we can claim that CuAu5 is the most stable cluster among
the reported systems. The calculated bond lengths for the species Au2, Cu2,
and CuAu are numerically very close to the experimental value, which
supports efficacy of our analysis.

KEYWORDS

•• electronic properties
•• nanoalloy clusters
•• copper–gold
•• odd–even oscillation

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 PART III
Clinical Chemistry and Bioinformatics
CHAPTER 10

BIOCHEMISTRY APPS AS ENABLER

OF COMPOUND AND DNA
COMPUTATIONAL:
NEXT-GENERATION COMPUTING
TECHNOLOGY
HERU SUSANTO1,2,*
1
Department of Information Management, College of Management,
Tunghai University, Taichung, Taiwan
2
Computational Science, Research Center for Informatics, The
Indonesian Institute of Sciences, Jakarta, Indonesia
*
Corresponding author. E-mail: [email protected]; susanto.net@
gmail.com

CONTENTS

Abstract.....................................................................................................182
10.1 Information System........................................................................182
10.2 Information Technology.................................................................183
10.3 Bioinformatics................................................................................185
10.4 Bioinformatics Application in Progress.........................................186
10.5 The Commercialization of Bioinformatics....................................193
10.6 Advantages.....................................................................................194
10.7 Future Direction of Bioinformatics................................................198
10.8 Conclusion.....................................................................................199
Keywords..................................................................................................200
References.................................................................................................200
182 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

In today’s society, bioinformatics research is putting a great emphasis on

answering “when,” “what if,” and “why” questions with the help of infor-
mation technology. Researchers had argued that it could be the key factor in
facilitating and attaining an efficient decision-making in medical research.
With the current deluge of data, computational methods have become indis-
pensable to biological investigations. Originally developed for the analysis
of biological sequences, bioinformatics now encompasses a wide range of
subject areas, including structural biology, genomics, and gene expression
studies. Additionally, nowadays biological data are proliferating rapidly.
With the advent of the World Wide Web and fast Internet connections, the
data contained in these databases and a considerable amount of special-
purpose programs can be accessed quickly and efficiently from any location
in the world. As a consequence, computer-based tools now play an increas-
ingly significant role in the advancement and development of biological
research. This study investigates the role of information technology in
enabling science as well as the consequences and implication of technology
in supporting medical research and bioinformatics.

10.1  INFORMATION SYSTEM

Information system is a part of information technology. It has been well

defined in terms of two perspectives: one relating to its purpose, the other
relating to its structure. From a functional perspective, an information
system (IS) is a technologically implemented medium for the purpose of
recording, storing, and disseminating linguistic expressions, as well as for
supporting inference-making. While from a structural perspective, an IS
consists of a collection of people, processes, data, models, technology, and
partly formalized language, forming a cohesive structure which serves some
organizational purpose or function. In an organization, a convenient and
fastest way to deal with large amount of data to organize and analyze the
enormous information is by using IS. Many big companies, such as eBay,
Amazon, and Alibaba, also use information system. Information is widely
used in any organization nowadays. IS is a software that is used to collect,
store, and process data. It is also used to spread information and feedback
will be provided for it to meet an objective. Data are raw facts that are used
for reference. Information, however, is a collection of data that can be used
to answer question as well as for problem-solving. The primary purpose of
Biochemistry Apps as Enabler of Compound 183

IS is to collect raw data and transform it to information that will be benefi-

cial for decision-making.
The three main roles of an IS are to support competitive advantage
decision-making, business decision-making, and business processes opera-
tions. For each role, it has its own level where it operates. For supporting
competitive advantage and decision-making, it works on a strategic level,
while to support business decision-making, it works on tactical level and to
support business process and operations, it works on operational level. IS
does not have only one type. In fact, it varies depending on the usage of the
information in an organization. Decision support system is one type of IS.
Often, it is used for decision-making where the system analyzes and works
on existing data which will project statistical prediction and data model.
Transaction process systems allow multiple transactions such as collecting,
processing, storing, displaying, modifying, or canceling transaction at one
time. Management information systems mainly focus on processing the data
from transaction process, in order to make it useful for business decisions
according to specific problems. Office automation systems are concerned
with office tasks as it will control the organization’s flow of information.
Executive information systems create conceptual information, such as stra-
tegic and tactical decisions, to satisfy the senior management. Expert system
is said to be a set of computer programs that can imitate human expert. In
science, it is difficult to find the results of relationships between genetic
variability, diseases, and treatment responses, where it usually comes out as
uncertain and inconsistent.
However, there are systems such as Fuzzy Arden Syntax or the probabi-
listic OWL reasoner Pronto that can be used to increase the size of the clas-
sical rule engines. Such systems are examples of decision support systems.
It must be associated with specialists and international bodies so it would
affect the clinical practices efficiently. Based on these findings, the system
we visualized must be directly interconnected with the IS of the hospital so
there is existing workflow when handling information gathered from elec-
tronic patient records and clinical laboratories.

10.2  INFORMATION TECHNOLOGY

Information technology (IT) is a computer technology that consists of hard-

ware, software, computer network, users, and the internet. IT enables organi-
zation to collect data, make their work organized, and analyze data that help
them achieve their objectives. IT personnel mainly focus on certain area, such
184 Applied Chemistry and Chemical Engineering: Volume 4

as business computer network, database management, information security,

software development, and science fields. In bioscience, IT is generally used
for automated data collection, statistical study of data, internet-accessible
shared databases, modeling and simulation, imaging and visualization of
data and investigation, internet-based communication among researchers,
and electronic dissemination of research results. For instance, the use of IT
for automated gene sequencers, which utilizes robotics to process models
and computers to manage, store, and retrieve data, has made possible the
rapid sequencing of the human genome, which in turn has resulted in first
time expansion of genomic databases. Shared internet-accessible databases
are important in paleontology; and models as well as databases are signifi-
cantly used in population biology and ecology; and genomics is influencing
many fields in biology. Furthermore, IT can be a distinct tool from the other
scientific tools, for instance microscopes or physics accelerators, which are
commonly used in the scientific process, such as data gathering. Addition-
ally, IT supports hypothesis formation that is the first stage to gather obser-
vations about the problem examined in a biological study, and also research
design, collection of data, data analysis, and communication of scientific
result.7
In other science fields, IT also helps in analyzing subsurface creations,
mapping, and modeling complex systems. For example, seismic data used
to measure earthquakes were traditionally recorded on paper or film but
today they are recorded digitally, making it possible for the researchers to
analyze the data swiftly. Furthermore, internet-connected system allows
many researchers to obtain and contribute data to address a large problem.
In several areas of sciences, imaging and visualization has become impor-
tant because it can give clear modeling that helps the researchers understand
biological system such as tissues, organisms, and cells.
The role of IT toward software is that it helps the software to commu-
nicate with the hardware to input data, process data, and give the output.
The communication and interaction between software and hardware can
be defined when collecting and processing a signal detected by laboratory
equipment, for example, charged-couple devices (CDD) in spectrophotom-
eter that is used to measure the amount of light reflected or absorbed from
a sample object and other devices that can be connected to a computer via
an analog to digital connector. Computer-aided algorithms are being used
to examine the behavior of thousands of genes at a time and are creating
a foundation of data for building integrated models of cellular processes.
Molecular biologists and computer scientists have experimented with
various computational methods established in artificial intellect, including
Biochemistry Apps as Enabler of Compound 185

knowledge-based and expert systems, qualitative simulation, artificial

neural networks, and other mechanical learning techniques. These methods
have been applied to problems in data analysis, creation of databases with
advanced retrieval capabilities, and modeling of biological systems. Prac-
tical outcomes have been obtained in finding active genes in genomic
sequences, assembling physical and genetic maps, and predicting protein
structure. IT has been proven to have conspicuously great impacts on
different areas of bioscience.

10.3 BIOINFORMATICS

Bioinformatics is the application of computer technology in managing any

biological information and their managements. This application is exten-
sively being used to analyze specifically biological and genetic informa-
tion based on living things, both in plants and animals. Essentially, it has
been used in many applications such as studying human disease, managing
biological information, information systems for molecular biology manage-
ment, and other related fields. In other words, in biology, it conceptualizes
the study of molecules and constitutes informatics techniques, a combina-
tion of computer science, applied math, and statistics in the sense of physical
chemistry.
Previously, the use of traditional methods for studying diseases mostly
observed single factors, but the present technologies help in studying
multiple factors at the same time, together with each and every possible
thousands of variables. Bioinformatics methods are also being used to study
the fundamental molecular biology of the disease and move toward person-
alized medicine, which involves understanding these diseases and shifting to
new and more fitting treatment regimes.
The purpose of studying bioinformatics is to organize any biological data
in a specified database which will help researchers to access or even enter
any new related information. Bioinformatics is also a useful tool in devel-
oping the resources with the aid of data analysis, and this tool is able to
develop, implement computational algorithms, and other software tools that
help in understanding, interpreting, and analyzing any biological data that
serve the humankind in a meaningful manner. Moreover, the computational
tools are efficient in interpreting the results of biological research or can be
applied during protein, cell, and gene research, in discovery and develop-
ment of any new drugs or even during developing herbicide-resistant crop
combination.1,6
186 Applied Chemistry and Chemical Engineering: Volume 4

The essence of bioinformatics application simply involves melding

biology with computer science, the use of genomics information in under-
standing human disease, and the identification of new molecular targets
for drug discovery on a large scale. The uses of bioinformatics are mostly
in analyzing biological and genetic information which is associated with
biomolecules on a large scale, disciplines related to molecular biology, from
structural biology, genomics to gene expression studies applied to gene-
based drug discovery, and development of genomic information resulting
from the Human Genome Project. Experts and researchers, furthermore,
apply bioinformatics in studying the sequences of genomes which appeared
both in plants and animals in the field of agricultural studies with the
advancement in genomics technologies throughout the years from 1950s
until now. Genome sequencing apparently involves genetic databases for
patients; next-generation sequencing (NGS) technology allows researchers
to study complex genomics research, analyze genome-wide methylation or
DNA–protein interactions, and study microbial diversity in the environment
and in humans.8,11,15

10.4  BIOINFORMATICS APPLICATION IN PROGRESS

Grid infrastructures and next-generation computing technology played an

important role in the recent decade in supporting scientific, computer-based
analysis. However, the increasing complexity of bioinformatics resulted in
finding new solutions to speed up computational time. Grid infrastructure
is not completely satisfactory in terms of providing services and managing
data that are reliable for presenting bioinformatics.
Another key issue is represented by the fact that the grid is offering poor
chances to customize the computational environment. In fact, it is quite
common in computational biology to make use of relational databases and/
or web-oriented tools to perform analyses, store output files, and visualize
results, which are difficult to exploit without having administration rights on
the used resources. Another related problem derives from the huge amount
of bioinformatics packages available in different programming environ-
ments that typically require many dependencies and fine-tuned customiza-
tions for the various users. Here, the cloud computing offers a new solution
to this limitation.18
The reason why the cloud computing is the best solution is that unlike
in-house computing infrastructure, cloud computing is delivered over the
internet. Cloud computing provides cheap, reliable, and large-scale data
Biochemistry Apps as Enabler of Compound 187

where a small organization can get the same information as a well-funded

organization. Bioinformatics grew with an increasing use of the internet,
which allows creation and sharing of large biological data and offers rapid
publication of research results. The internet also provides the researchers an
access to a complex supercomputing system such as grid infrastructure.

10.4.1  GENOMICS, BIOMEDICINE, AND MICROBIOLOGY

Genomics is a large-scale data acquisition using technological advancements

which involves genome structures, evolution, and variations.12 Genomics
origin can be traced back as far as to the 19th century to the work of Gregor
Mendel. However, in the middle of the 19th century, the progress of IS
and IT was not as advanced as it is today. It is important to remember that
genomics is an essential area of bioinformatics, as well as understanding its
roles in the milestones of biological and molecular discovery, for instance,
the Human Genome Project, an international scientific research project with
goals to determine what makes up human DNA and its physical and func-
tional characteristics, understanding heredity, understanding diseases, its
role in pushing the innovation in genomic technologies, and many more.
Another view on genomics is that the main concept of genome informatics
was to analyze, process, and interpret all aspects of DNA in order to come
up with a more defined and accurate information on biological structure
and components of DNA.3 All things considered, genomics is evolving duly
because IT and IS keep on improving throughout the years. Owing to this,
the world is progressing at a much faster pace, namely, in biomedicine and
microbiology, and the knowledge that it brought, had been or is still being
used to broaden our views on molecular mechanisms in spreading, treating,
and curing diseases, and preventing the development of diseases.
Almost every year, new drugs are being discovered or improved to better
serve their purpose in curing, treating, and preventing health issues all around
the world. Bioinformatics acts as the main agent for its progression due to
its vast collection of advanced tools for managing a large volume of data, as
well as to help interpret, predict, and analyze clinical and preclinical data. As
biological technologies progress, so do the data they produce and this often
leads to a massive boom in database collection. Useful data could be proven
to be useless without a proper system or tools to access them accurately
and thus it is imperative to have computational tools that can search and
integrate significant information. Development of bioinformatics resources
has shown that it is essential in screening valuable data for effective drug
188 Applied Chemistry and Chemical Engineering: Volume 4

solution in a profitable and timely manner. As an example, array compar-

ative genomic hybridization (ACGH) method has been used globally for
DNA analysis on normal and pathological clinical samples to check for the
DNA copy number gain and loss across the chromosomes.10 In addition, the
current proteomic analysis that uses mass spectrometry (MS)-based tech-
nology is progressively used for identifying molecular network targets and
is responsible for many discoveries in profiling correlations in the pathogen-
esis of certain human illnesses. Through this analysis and method, integra-
tion of the connections between proteomics and metabolomics platforms can
increase the dynamic and potency of the drug treatment solution.17
Adverse drug reactions (ADRs) are often caused by all-purpose drugs
that exist in today’s market. Most people would prefer this type of drugs
due to their economic status and often due to their state of living. Personal-
ized medicine could provide the needed solution to these circumstances. Yan
argued that through the development of pharmacogenomics and systems
biology, personalized medicine could aid in the advancement of reduc-
tionism-based and disease-centered curative methods to systems-based,
correlative, and human-centered care.19 Developing further understanding
between genotypes and phenotypes from analyzed data of genomic studies
through data integration methods helps connect an efficient clinical and
laboratory data flow. By implementing a translational informatics support
into data mining techniques, knowledge discovery, and electronic health
records (EHRs), better diagnostic and treatment selection can lead to a more
suitable medication for the right people. A good translational bioinformatics
will aid in establishing a powerful platform to connect various knowledge
scopes for translating numerous biomedical data into predictive and preven-
tive medicine.19 Altogether, this will bring about an ideal personalized medi-
cine that is less costly, with reduced errors and risks, diminished ADRs, and
that overcomes the therapeutic obstruction.
According to Wu, Rice, and Wang, cancer is one of the most prevalent
and profound diseases that can occur at anytime and anywhere in the body.19
Its development is explained as an uncontrollable genetic mutation of cells
in the body of organisms whereby it drastically affects the metabolism, loss
in genes, and promotion of invasive tumor growth, metastases, and angio-
genesis.14 Multiple factors such as the period, severities, drug resistance,
cell origins, locations, and affectability can be the causes for poor diagnoses
and therapy results for the patient with cancer. However, over the years, the
results from advanced and accurate clinical bioinformatics and uses of new
systems clinical medicine have helped improve the results of cancer treat-
ment and diagnosis all around the world. Adoptive immunotherapy (gene
Biochemistry Apps as Enabler of Compound 189

therapy) is commonly used for cancer treatment, it uses the technology of

genetic modification whereby T cells with antitumor antigen receptors (TCR)
or chimeric antigen receptors (CAR) are used, duly because they can target
antigens expressed on tumor cells.13 In recent times, the use of semantic
web technology has enabled better understanding of high throughput clin-
ical data and established quantitative semantic models gathered from Corvus
(data warehouse providing systematic interface to numerous forms of omics
data) rooted from systematic biological knowledge and by application of
SPARQL endpoint.4 In addition, application of new biomarker strategies in
cancer bioinformatics has become more popular in monitoring progress of
the disease and its response to therapy. It is expected to coordinate with clin-
ical informatics which includes patient inputs, such as complaints, history,
therapies, symptoms and signs, medical examinations, biochemical analysis,
imaging profiles, and other valid inputs. On the whole, the expected result
would provide more accurate interpretable signatures and therefore helps in
better diagnosis and cancer solutions for specific patients.
The world’s population is continuously booming and is expected to
reach 11 billion by the year 2100 and this brings about new challenges in
managing disease outbreaks. A rise of infectious diseases by new viruses and
drug-resistant bacteria are the tendencies of disease outbreaks. Over the last
two decades alone, new virus strains have kept the world in constant fear of
deadly outbreak threats: swine flu pandemic, SARS (severe acute respira-
tory syndrome), HIV (human immunodeficiency virus) and AIDS (acquired
immune deficiency syndrome), malaria, tuberculosis, and, more recently,
Zika virus. Steps in bottling more outbreaks have been initiated throughout
the globe but more importantly, the sharing of knowledge on how it came
to be and the proper exploitation methods to discover the viruses’ weak-
nesses has proven to be a better front in battling outbreaks. Next-genera-
tion genome sequencing has aided the advancement of biotechnologies and
tools by providing new insight into viral distinctiveness, allowing in-depth
sampling and providing bigger capacity for automation, and thus enabling
new data interpretation on what could be done or changed to the charac-
terization of viral quasi-species.9 Kijak et al. named their bioinformatics
package Nautilus, which runs on several operating systems, and it represents
new sets of tools to support better data analysis, facilitating the application
of next-generation sequencing and allowing better insight on HIV genome
characterizations throughout the population and its evolution.9 Nevertheless,
the rapid occurrences of antimicrobial resistance in microorganisms cannot
be diminished simply by continuous biological studies but this requires
a global understanding in public to always keep a hygienic environment,
190 Applied Chemistry and Chemical Engineering: Volume 4

in practice, as well as awareness, wherever and whenever they are. This

method is the main preventative method for, generally, all kinds of microbial
infections, duly because producing a constantly evolving medicine and treat-
ment to fight against rapidly evolving antimicrobial-resistant illnesses will
take higher health care expenditures and is time-consuming for all sides. The
risk of death from resistant microorganisms is much higher than that of the
same nonresistant microorganisms.

10.4.2  BIOLOGICAL DATABASE

Database is seen as a major tool for storing biological data for public use.
Relational database concept of computer science and information retrieval
concept of digital libraries are implemented to fully interpret biological data-
base. Gene sequence, attributes, textual descriptions, and ontology classifi-
cation are stored in biological database. The data mentioned are categorized
as semistructured data that later can be displayed in table form, key delim-
ited record, and XML structure. The common method of cross-referencing
is often used by database accession number.
A biological database can be defined as the collection of biological data
obtained during live-experiment and computation operation and analysis.
Biological data should be organized properly to enable easy data operations
such as manipulation, deletion, and calculation. The aim of the database
must follow two principles: data should be accessible and it can be used in
both single- and multiuser system environment.
Databases, generally, can be grouped into primary, secondary, and composite
databases. Primary database includes data that are gathered during experiment
such as nucleotide sequences and three-dimensional structures. It is often
called archival database. The data gathered are resulted from experiments by
researchers all around the world. Primary database includes GenBank, DDBJ,
and SWISS-PROT. Secondary database is derived from analysis of the first-
hand (primary) data such as sequences and secondary structure. The results
of secondary database are usually in the form of conserved sequences, signa-
ture sequences, and active site residues of protein. Curated database is another
term for secondary database. Some of the databases were created and hosted
by the researchers themselves at their own laboratory such as SCOP, CATH,
and PROSITE, which were developed in Cambridge University, University
College of London, and Stanford University, respectively.
The first database was created in 1956, after the insulin protein sequence
became available; insulin was the first protein to be sequenced. The content
Biochemistry Apps as Enabler of Compound 191

of the insulin sequence includes just 51 residues which characterized the

sequence. Four years after the discovery of insulin protein sequence, the first
nucleic acid sequence of yeast tRNA with 77 bases was discovered in 1960.
Three-dimensional structure was studied as well as the first protein structure
database with only 10 entries was created in 1972. Currently, the Protein
Data Bank (PDB) has grown to store more than 10,000 entries.
Since protein sequence databases were maintained by individual labora-
tories, SWISS-PROT protein sequence, which was categorized as consoli-
dated format database, was started in 1986. Database functionality was
expanded not only with the capabilities of handling data and sophisticated
queries facilities but also by implementing bioinformatics analysis function
in modern databases.
Similar to general databases, biological database can also be catego-
rized into two groups: sequence structure databases and pathway databases.
Sequence structure databases mainly focus on nucleic acid sequence and
protein sequence, whereas pathway databases focus on protein.

10.4.3  SEQUENCE DATABASES

Sequence databases are categorized as the most frequently used databases

and some of them are marked as the best biological databases. GenBank is
one of the examples of widely used sequence databases. GenBank focuses
on DNA and protein sequence.
GenBank is classified as one of the most widely used sequence biolog-
ical databases. The name refers to the DNA sequence databases of National
Center for Biotechnology Information (NCBI). GenBank data are mainly
made up of sequences submitted by individual laboratories and data inter-
change from international nucleotide sequence databases, European Molec-
ular Biology Laboratory (EMBL) and DNA database of Japan (DDBJ).16

10.4.4  STRUCTURE DATABASES

To be able to completely understand the protein function, knowledge of

protein structure and molecular interaction and mechanism must be under-
stood thoroughly. The PDB is the worldwide repository of experimentally
classified protein structures, nucleic acids, and complex assemblies, including
drug–target complexes.5 The PDB was created in Brookhaven National
Laboratories in 1971. It mainly contains information on molecular structure
192 Applied Chemistry and Chemical Engineering: Volume 4

of macromolecules from x-ray crystallography and nuclear magnetic reso-

nance (NMR) method. Currently, Research Collaboratory for Structural
Bioinformatics plays a huge role in maintaining PDB. One of the features of
PDB is that it mainly allows user to display and present data either in plain
text or through a molecular viewer using JMOL.

10.4.5  PATHWAY DATABASES

The growth of metabolic databases through metabolic study pathway will

fulfill the need and enhance the development of system biology. One of the
popular pathway databases is KEGG. KEGG refers to the Kyoto Encyclo-
pedia of Genes and Genomes. KEGG database is the center of information
for system analysis of gene function and connecting genomic information
with higher order functional information. KEGG consists of three databases,
namely, PATHWAY, GENES, and LIGAND. PATHWAY database is respon-
sible for storing the higher order functional information. This information
includes the computerized knowledge on molecular interaction networks.
These data are often encoded by coupled genes on the chromosome which
are crucial for predicting gene functions. GENES database consists of the
collection of gene catalogs and sequences of genes and proteins produced
by the Genome Project. The third database, LIGAND, keeps the information
regarding chemical compounds and chemical reactions which are important
for cellular processes.

10.4.6  PREVENTION AND TREATMENT OF DISEASES

Bioinformatics is a scientific discipline that deals with obtaining, analyzing,

distributing, processing, and storing biological information. It uses scientific
knowledge, such as algorithm and computer science, in order to understand
the biological significance of a wide variety of data. With this, it enables
researchers to find new strategies to look for clues in the prevention and
treatment of diseases. Bioinformatics has turned into a key ingredient with
the alliance of genomics, proteomics, and drugs in today’s world.
In fact, bioinformatics owes its creation to the need to handle large amounts
of data produced by these “-omic” technologies (genomics, proteomics,
and, more recently, metabolomics). The information is generated by high-
performance methods such as gene sequencing, DNA microarrays, and mass
spectroscopy. Bioinformatics can be called a transverse activity because it is
Biochemistry Apps as Enabler of Compound 193

applicable to all the subsectors of biotechnology and life sciences. However,

its main application is biomedicine. Bioinformatics manages and decodes
“-omic” data and it facilitates the translational medicine concept by helping
to distribute information throughout the entire health care value chain. This
covers the discovery and analyzing of genes, the protein structures coded by
these genes, and the design of molecules and drugs to counter these proteins,
up to their clinical application, which is where bioinformatics plays a leading
role in the development of specific medicine.

10.4.7  DRUG DISCOVERY

Traditionally, pharmaceutical companies were interested only in intro-

ducing new drugs when any well-known pharmaceutical company had been
successful in developing them. However, in today’s society, companies have
invested heavily in approaches that can speed up the development process.
The pressure of producing drugs in short period of time with a high standard of
safety has resulted in extremely enhancing interest of the researchers in bioin-
formatics. Bioinformatics involves identification of biological candidate and
could be the storage of information. Drugs only can be produced if the drug
target is studied and identified. For example, human genome sequence infor-
mation can be found in the system, which can help in drug-making process.

10.5  THE COMMERCIALIZATION OF BIOINFORMATICS

The success of development in combining both computer technology and

biomedicine has helped scientists to become more efficient and productive
with the ability to predict the upcoming trend of biosolution with the help of
bioinformatics. With the bioinformatics technology being widely exploited,
the opportunity for commercialization is unquestionable. However, many
investors were reluctant to invest in bioinformatics sector due to its history
of investment during the late 1990s which resulted in high losses. Despite
the losses, in 2002, Philip Green, biologist in the University of Washington,
wanted to decipher human genome with more accurate reading of DNA
letters. Celera-made machine was the only tool he used which was supplied
by Applied Biosystems. Due to the lack of functionality of this software,
he then designed his own software to cater to the needs of his project. As a
result, Green’s innovation is categorized as industry standard and its source
code is available for free.
194 Applied Chemistry and Chemical Engineering: Volume 4

The advancement of technology played a huge role in the success of

bioinformatics, where computer tools are being used for managing biolog-
ical information and computational biology is used to identify the molecular
components of living things. The involvement of computer technology in
biological area also introduces the studies of principle and operation of data
manipulation and data analysis of biomolecules, structure, or composition of
various materials, such as nucleic acids and, gene products, such as proteins.
Research and data gathering in biological field involves laboratory experi-
ments where mathematical operations and computation are used to obtain
meaningful information from meaningless data, especially in genomics.
Computers have been used as the backbone in bioinformatics and have even-
tually become one of the major tools in storing biological data and compare
them with the existing data set. This provides important useful inputs, which
biologists usually gather during their hands-on laboratory experiment, to
computer-user/researcher and saves a lot of time and resources. Cost of labo-
ratory has been cut down with the use of computer and software, where most
of the operations and experiments are performed via computer with the help
of special-purpose software.
The popularity of using open-source software has increased over the
years, which has affected bioinformatics companies. Open-source software
can be defined as computer software freely available to the public. In general,
it is free software which can be freely copied, distributed, modified, and
manufactured. Characteristics of open source are as follows: there should
be no discrimination to people, groups, or endeavor; the license distribution
should be costless and general to every product; and the license must be
restriction-free with respect to other software and technology neutral. The
Linux system is one of the great examples of open-source software with
a major success. Bioinformatics firms find it hard to gain profit due to this
open-source software movement.

10.6 ADVANTAGES

Bringing together large data sets of medical data and tools to analyze the
data offers the potential to enhance the research capabilities of medical
researchers, who could use this vast source of biological and clinical data to
discover and develop new treatments and better understand illnesses. Phar-
maceutical companies could use the biomedical data to create drugs targeted
at specific populations. Furthermore, health care providers can use the data
to better inform their treatments and diagnoses.2
Biochemistry Apps as Enabler of Compound 195

Etheredge, as cited in a study by Castro,2 claimed that applying infor-

matics to health care creates the possibility of enabling “rapid learning”
health applications to aid in biomedical research, effectiveness research,
and drug safety studies. For example, using this technology, the side effects
from drugs newly introduced to the market can be monitored in real time,
and problems, such as those found with the recently withdrawn prescription
drug Vioxx, can be identified more quickly. Moreover, the risks and benefits
of drugs can be studied for specific populations yielding more effective and
safer treatment regimens for patients.
Etheredge concluded that using rapid learning techniques not only can
improve patient safety but also can lead to substantial improvements in the
quality and cost of care by turning all of the raw digital data into knowl-
edge where these rapid learning health networks can enable doctors and
researchers to better practice evidence-based medicine. Evidence-based
medicine is the use of treatments judged to be the best practice for a certain
population on the basis of scientific evidence of expected benefits and risks.
Bioinformatics deals with computer management and analysis of
biological information: genes, genomes, proteins, cells, ecological systems,
medical information, robots, and artificial intelligence, as there are many
applications of bioinformatics resulting from the combination of computer
and biology. The evolution of technology helps in supporting bioinformatics
in discovering diseases and applications in forensics using software pack-
ages and bioinformatics tools, for example, the evolution of technology
such as Illumina NGS to provide accurate sequencing. NGS technology can
provide valuable and useful information for a better understanding of health
and diseases.
Bioinformatics can also be useful in determining the order of the four
chemical building blocks called bases that make up the DNA molecule.
This is because the sequence provides scientists data regarding what kind of
genetic information is carried in a particular DNA segment. Moreover, the
sequence data can highlight the changes in a gene that may cause disease.

10.6.1  FORENSIC DNA AND BIOINFORMATICS

Bioinformatics and forensic DNA analysis are fundamentally characterized

by studies in both law and biology and draw their techniques from statis-
tics and computer science, which facilitates solving problems in law and
biology. It could be useful to identify a victim and suspect with personal
relatedness to other individuals; these are the two major focuses of forensic
196 Applied Chemistry and Chemical Engineering: Volume 4

DNA analysis. It is a common event in forensic analysis, especially by crime

and investigation unit or CSI, to look at close connections, for example,
paternity disputes, suspected incest case, corpse identification, alimentary
frauds (e.g., OGM, poisonous food, etc.), semen detection on underwear
for suspected infidelity, insurance company fraud investigations when the
actual driver in a vehicle accident is in question, criminal matters, and autop-
sies for human identification following accident investigations. All of these
problems may be solved by using bioinformatics methods.
Also, genetic tests have been widely used for major catastrophic events
such as terrorist attacks, airplane crash, and tsunami disaster. It can be used
for mass fatality identification and forensic evidences. Personal identifica-
tion relies on identifiable characteristics, as the human body has a personal
identity that is unique biologically (such as blood, saliva, and DNA), physi-
ological difference (such as fingerprints, eye irises, and retinas, hand palms,
and geometry and facial geometry), behavioral difference (such as body
posture, habits, signature, keystroke dynamics, and lip motion), and also on
the combination of physiological and dynamical characteristics such as the
voice.
Hence, genetic testing results are integrated with the information collected
by multidisciplinary teams composed of medical examiners, forensic pathol-
ogists, anthropologists, forensic dentists, fingerprint specialists, radiologists,
and experts in search and recovery of physical evidence. Officers could have
access to the personal information, where biological data can be obtained
from hospital records and behavioral data may be collected from banks
or office document such as fingerprint or signature just by looking at the
database.
Therefore, the application of genetic testing in large-scale tissue
sampling and long-term DNA preservation plays an important role in mass
fatalities which have recently occurred. Thus, DNA has become the most
important personal identification characteristics because all genetic differ-
ences, whether being expressed regions of DNA (genes) or some segments
of DNA, are characteristic of a person. DNA possesses coding pattern of
inheritance that can be monitored and used as marker.

10.6.2  CANCER AND BIOINFORMATICS

According to the Cancer Research UK (2012), cancer is one of the leading

causes of death worldwide with 14.1 million cases of cancer recorded and
about 8.2 million deaths from cancer estimated in 2012. A leading cause
Biochemistry Apps as Enabler of Compound 197

of cancer is malignant growth or tumor which is caused by abnormal and

uncontrolled division due to the changes in DNA of cell by mutation. Also,
errors in the genes may cause this abnormal behavior to be cancerous. These
changes occur when exposed to a certain type of cancer-causing substances.
In the post-genomics era, age holds phenomenal promise for identifying
the mechanistic bases of organismal development, metabolic processes, and
diseases. Bioinformatics research will lead to a wide understanding of the
regulation of gene expression, protein structure determination, compara-
tive evolution, and drug discovery. Presently, two-dimensional gel protein
pattern can be easily analyzed using bioinformatics technology, where these
software applications possess user-friendly interfaces that are incorporated
with tools for linearization and merging of scanned images.
New techniques and new collaborations between computer scientists,
biostatisticians, and biologists are required in today’s research. There is a
need to develop and integrate database repositories for the various types of
data being collected, to develop tools for transforming raw primary data into
forms suitable for public dissemination or formal data analysis, to obtain and
develop user interfaces to store, retrieve, and visualize data from databases,
and to develop efficient and valid methods of data analysis.
Cancer DNA sequencing using NGS provides better information and
requires less time compared with normal gene sequencing using gel struc-
ture. With NGS, researchers can perform whole-genome studies, targeted
gene profiling, and tumor-normal comparisons. Therefore, it is easy to detect
tumor and DNA fragments with detailed quantitative measurements from
the database.
Furthermore, the prediction of genes is likely to be linked to newly devel-
oped diseases or modified version of an old disease that evolves or mutates.
The use of bioinformatics can easily recognize related genes that have any
similar function or characteristic of the original gene, such as the similarity
in percentage of DNA sequence. The biggest challenge is to identify enor-
mous markers of DNA, as the application of molecular links to diseases
will continue to face technological as well as biological and algorithm chal-
lenges. The human body consists of very complicated and diverse features
because it is continually evolving and responding to changes.
As for using bioinformatics to replicate, the structure of new DNA struc-
ture provide a challenge in technology; this is because, unlike cells, other
interrelationships may not be visible through the microscopic view. Thus,
the already designed computer frameworks or databases may not cope with
the expansion in network-level measurements and information.
198 Applied Chemistry and Chemical Engineering: Volume 4

10.7  FUTURE DIRECTION OF BIOINFORMATICS

Bioinformatics makes the information accessible and shareable in compar-

ison with traditional biological records, with the help of developing tools
that make it easy to send, receive, and share information. For example, elec-
tronic medical records (EMR) reduce the chances of error that are caused
by obstruction and other researcher’s conflicts during the manual data entry
processing after paper-based data collection. Besides that, it also supports
elimination of the manual task of extracting data from charts or filling out
specified data sheets. The data stored can be obtained directly from the EMR.
By referring to the EMR, the researchers do not need to examine or observe
the task again. Bioinformatics has grown rapidly and diversified into subdis-
ciplines, such as cheminformatics in chemistry; neuroinformatics, which is
related to gathering data across all scales and neuroscience levels to under-
stand the complex function of brain and work toward treatments for brain-
related illness; and immunoinformatics, which uses informatics techniques
to study molecules of the immune system.
Usually, the organizations, such as Antigen Discovery, Rasa Life Science
Informatics, and LabCentrix, use bioinformatics to store large amount of
data, or in other words, big data, which contain both structured and unstruc-
tured data that are hard to process if the organization uses traditional data-
base and software techniques. Examples of big data are patient information,
types of disease, and DNA. Hence, by applying bioinformatics, this can be
done easily as it can store huge amount of data.
Bioinformatics interface seems to be unattractive, the designing of the
tools has to be user-friendly, where people can easily understand it and use
it. A user-friendly interface can make the researchers analyze the information
more efficiently and effectively to convert the information into knowledge.
Other than that, the users must be properly trained to use bioinformatics
tools to prevent difficulties. This would be a tough situation for developing
regions, as training and knowledge is required along with time and financial
support.
Bioinformatics is important, yet the biggest challenge being faced by
the molecular biology society nowadays is to make sense of the wealth of
data that have been produced by the genome sequencing projects. With the
advent of new tools and databases in molecular biology, researchers are now
enabled to carry out research not only at genome level but at proteome, tran-
scriptome, and metabolome levels. Therefore, incisive computer tools must
be improved to accept the extraction of meaningful biological information.
Biochemistry Apps as Enabler of Compound 199

10.8 CONCLUSION

In conclusion, the bioinformatics has wide applications from single tradi-

tional methods in handling genomic studies to more advanced method-
ologies toward the improvements in biological studies. Understanding the
vast collection of bioinformatics tools and technologies that exist to serve
different purposes is also vital to the advancement in IT. Bioinformatics
helps in improving the ways of biological research and provides innovative
ways, for instance, the use of databases to store any biological information
with the help of more advanced software tools and computational algorithm.
These databases, which are being stored in the computer memory, are mostly
related to microorganisms. In business studies, the research on scientific
fields gives opportunities for businesses to broaden their chances of making
profits, for instance, the invention of new medicines, drug developments,
and so forth.
In the world of biomedicine and microbiology, IT through bioinfor-
matics has provided numerous resources and tools for new drug discovery,
and personalized and preventive medicine. Moreover, the success in cancer
treatment via gene therapy is also gradually increasing, owing to the NGS
techniques and technologies. This increase in treatment success is observed
not only for cancer but also for other known diseases such as HIV and
AIDS.
On the other hand, databases are also being widely used in bioinfor-
matics applications. The relational database concept of computer science
and information retrieval concept are implemented to fully interpret
biological database. The aim of the database is basically to be accessible
and be useful in both single- and multiuser system environment. There
are several types of databases provided for different purposes such as
for protein development, human brain studies, diseases, drug discoveries
and development, and also for agricultural studies, in both plants and
animals. These data can be considered highly accessible and reliable for
other researchers and scientists. Furthermore, it has data integration and
even they can add new findings or even update, as it is most liked and
easy to use. Scientists and researchers are also being trained in handling
databases.
Finally, bioinformatics applications are widely being used for more
advanced technological developments, there are pros and cons not only in
biological manner but also in business manner. As stated, these are being
handled properly and their usage is being improved throughout the years.
200 Applied Chemistry and Chemical Engineering: Volume 4

KEYWORDS

•• physical chemistry
•• bioinformatics
•• computational methods
•• biological investigations
•• sequence database
•• structural biology
•• genomics

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2161-1025.1000e120
CHAPTER 11

ADSORBENTS FOR DNA

SEPARATIONS
SENEM YETGIN1 and DEVRIM BALKOSE2,*
1
Food Engineering Department, Kastamonu University, Kastamonu,
Turkey
2
Chemical Engineering Department, Izmir Institute of Technology,
Izmir, Turkey
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.....................................................................................................204
11.1 Introduction....................................................................................204
11.2 Silica, Alumina, and Hap...............................................................206
11.3 Materials and the Method..............................................................218
11.4 Results and Discussion..................................................................219
11.5 Conclusions....................................................................................226
Keywords..................................................................................................227
References.................................................................................................227
204 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

DNA can easily be adsorbed to positively charged surfaces as well as to

negatively charged surfaces by electrostatic bridges with the water of hydra-
tion of charged cations. The functional groups and the pore structure and
surface charge are all the important parameters for DNA adsorption. DNA
adsorption to alumina, clay, silica, single-walled carbon nanotubes (SWNT),
metals, organic and bioorganic molecules, polypyrrole (PPy)–silica nano-
composite particles, polymers and hydrogels, poly-L-lysine-immobilized
pHEMA, and HAP are reviewed in this chapter. The experimental results for
preparation and characterization of silica, alumina, and HAP are reported in
detail.

11.1 INTRODUCTION

Adsorption is a widely used DNA purification technique in biological anal-

ysis. The main parameters affecting the adsorption process are its size, shape,
polarity, and chemical structure of the substance wanted to be removed. DNA
is a biopolymer and it structurally depends on nucleotide sequence and has
been known to bind many classes of substances—alumina, clay, and silica,
including single-walled carbon nanotubes (SWNT) as biosensor,72 metals,
organic and bioorganic molecules such as drugs. Under most environmental
conditions, DNA molecules are negatively charged, and they can easily be
adsorbed to positively charged surfaces such as the edges of clay minerals29
as well as to negatively charged surfaces such as the surfaces of clays by
electrostatic bridges with the water of hydration of charged cations.38,47 It
should be noted that DNA double helix form has been affected by physical
adsorption of the DNA on a surface, which also influences its denaturation.2
Some composites were also reported as DNA adsorbents such as polypyr-
role (PPy)–silica monocomposite particles,57,58 polymers, and hydrogels.61
Polypyrrole is a conductive polymer, stable and biocompatible compared
with other polymers.33 Its good thermal and mechanical stability let its use in
biological areas such as biosensor design. Composite form of it, with DNA
absorbable material, makes them acceptable for DNA adsorption. There-
fore, polypyrrole–silica nanocomposites (untreated and amine or carboxylic
powder acid functionalized) were studied at neutral pH in sodium phosphate
buffer by Saoudi and coworkers. 57,58 DNA adsorption was measured to be 32
and 22 mg/g for the aminated silica sol and the aminated PPy–silica particles,
respectively, and 6.5 mg/g for the carboxylated particles. DNA adsorption
Adsorbents for DNA Separations 205

is not applied only for purification of DNA but also for therapies of autoim-
mune diseases. DNA-immobilized supports, such as polymeric adsorbent,
have been used. Amount of immobilized DNA on the material is directly
related to antibody removal rate. For instance, poly-L-lysine-immobilized
poly(2-hydroxyethyl methacrylate) (pHEMA) membrane was used for that
purpose.61 At 4°C from phosphate-buffered salt solution, maximum DNA
adsorption was obtained as 5849 mg/m2.
Different surfaces used in DNA adsorption are listed in Table 11.1. Glass,
silica, polylactic acid, functionalized polystyrene, polypyrrole powders, soil,
gold, montmorillonite, kaolinite, goethite, gibbsite, and allophane are some
of the adsorbents used for DNA adsorption.

TABLE 11.1  DNA Adsorption onto Different Surfaces.

Adsorbent DNA type Reference
Glass Escherichia coli DNA Hu- Vogelstein and
man spleen DNA Gillespie68
Silica particles or diatoms DNA and RNA from, e.g., Boom et al.6
human serum and urine
Polymerized poly-L-lactic acid film Plasmid DNA Jiang et al.26
surface
Poly-L-lysine immobilized poly(2-hy- Calf thymus Şenel et al.61
droxyethyl methacrylate)
Polypyrrole (PPy)-silica monocomposite Calf thymus DNA Saoudi et al.58
Positively charged amidine functional- Double stranded DNA Hodrien et al.25
ized polystyrene microspheres extracted from herring
Chemically synthesized polypyrrole Calf thymus Saoudi et al.58
powders
Soil Calf thymus DNA Ogram et al.43
N-methylpyridinium terminated gold Type XIV from herring testes Aslanoğlu et al.3
Silica beads were packed into glass PCR-amplifiable DNA Breadmore et al.7
microchips
Montmorillinite Salmon sperm DNA Saeki et al.56
Kaolinite Salmon sperm DNA Saeki et al.56
Silica Salmon sperm DNA Saeki et al.56
Goethite Salmon sperm DNA Saeki et al.56
Gibbsite Salmon sperm DNA Saeki et al.56
Synthetic allophane Salmon sperm DNA Saeki et al.56
Naturel allophane Salmon sperm DNA Saeki et al.56
206 Applied Chemistry and Chemical Engineering: Volume 4

A detailed review about preparation and characterization of adsorbents

namely silica, alumina, and hydroxyapatite (HAP) will be made in the
following section. Experimental results will be reported for representative
commercial samples.

11.2  SILICA, ALUMINA, AND HAP

11.2.1 SILICA

Nucleic acids are readily adsorbed on silica and on a glass surface under
chaotropic solution conditions.6,9 DNA adsorption by silica was exten-
sively investigated.20,39,40 Silica offers a quick and less chemical purifica-
tion. Therefore, silica, the most commonly used matrix for solid-phase
extraction, was shown to effectively bind DNA when it was used to purify
DNA from agarose gels.68 Silica is extensively used in commercial DNA
purification. Silica-based kits are the most common method of nucleic
acid purification for PCR. A typical spin column comprises a nearly
5-mm-diameter and 1-mm-thick glass fiber disc (membrane), or other
form of silica, filled in a polypropylene tube.30Spin column was designed
to allow centrifugation or vacuum suction to facilitate flow through the
porous silica membrane. Silica-based DNA extraction kits are widespread,
produced by companies such as Clontech (Nucleo Spin), Mo Bio Labo-
ratories (UltraClean BloodSpin), Qiagen (QiaAmp), Promega (Wizard),
Epoch Biolabs (EconoSpin), and Sigma-Aldrich (GenElute). Promega
products are available for plasmid, genomic, and fragment/PCR product
purification. Promega has sold and supported silica-based DNA purifica-
tion systems for nearly two decades.
According to some studies, DNA molecules bind to OH groups on the
edge of phyllosilicates such as montmorillonite37,46 as seen in Figure 11.1(a)
and (b). DNA adsorption in soils using montmorillonite as adsorptive particle
has been investigated by several researchers.28,50 Adsorption mechanism in
Figure 11.1(c) represents DNA molecules associated with the surface, which
negatively charged materials via a bridging of cations.28,46 Divalent cations
such as Mg2+ and Ca2+ support binding about 100 times greater than monova-
lent cations such as Na+, K+, and NH+4.19According to Figure 11.1(d), DNA
molecules directly bind to solid organic surface. On the contrary, Saeki
and Sakai55 proved that organic matter addition decreased the adsorption
capacity of DNA on the soil material.
Adsorbents for DNA Separations 207

FIGURE 11.1  Conceptual figures of DNA adsorptions.

DNA adsorption by silica was controlled by three effects (1) weak elec-
trostatic repulsion forces, (2) dehydration, and (3) hydrogen bond forma-
tion.40 The presence of a monovalent cation such as Na+ neutralizes the nega-
tive charges on the phosphate backbone of DNA, reducing the electrostatic
barrier between DNA and silica. Therefore, DNA adsorption capacity is
increased.
Mao et al.37 have also indicated that it is possible to form hydrogen bonds
between the phosphate groups in DNA and the silanol groups on the surface
of silica (Fig. 11.2). This hydrogen bond formation has a weak and additive
effect on adsorption. Melzak et al.40 reported that intermolecular electrostatic
forces between DNA and silica surface strongly disfavors adsorption at low
ionic strength. The adsorption capacity as a function of ionic strength can
be explained by electrostatic double-layer repulsion between the DNA and
the natural organic matter (NOM) layer.42 Silica adsorption capacity of DNA
was found to be greater than that of montmorillonite.56 The solution chem-
istry and the type of surface will influence the amount of DNA adsorbed.
208 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 11.2  Proposed binding of DNA to silanol groups on the silica surface. (Reproduced
from Environmental Health Perspectives, 1994; 102(suppl 10):165–171).

Consequently, there are other important situations where both adsorption

and denaturation of DNA occur simultaneously. For example, adsorption
of plasmid and chromosomal DNA on microcrystalline silica surface and
the effect of ionic strength, temperature, pH, DNA size, and conformation
on the adsorption phenomenon were reported by Melzak et al.40 Adsorp-
tion isotherms pointed out those three effects: (1) shielded intermolecular
electrostatic forces, (2) dehydration of the DNA and silica surfaces, and (3)
intermolecular hydrogen bond formation in the DNA–silica contact layer.
These three effects mentioned above make the dominant contributions to
the overall driving force for adsorption. For instance, adsorption of DNA
from Bacillus subtilis, calf thymus, and salmon sperm on montmorillonite,
kaolinite, and silica increased with an increase of ionic strength or a decrease
of pH.40
Adsorption of DNA onto bare silica under high ionic strength and chaotic
solution conditions is supported.7 High ionic strength serves to protect the
negative surface, reducing the electrostatic repulsion between the nega-
tive DNA and the surface of the silica, while the mono- and divalent salt
dehydrates the silica surface and DNA, thus promoting hydrogen bonding
between the DNA molecules and the protonated silanol groups.
Solberg and Landry 63 focused on mesoporous silica material to find its
gene therapy potential. Ammonium ion containing chemicals was found to
Adsorbents for DNA Separations 209

be two to three times more effective in cross-link between DNA and meso-
porous silica surface than mono- or divalent cations
Adsorbed DNA was 100 times more resistant against DNase I than
was DNA free in solution. Khanna and Stotzky 28 reported that the protec-
tive effect of clays—montmorillonite (M) and kaolinite (K)—against the
activity of nucleases did not eliminate the transforming ability of bound
DNA. In order to determine clay–DNA complexes x-ray diffractometry
(X-RD) and transmission (TEM) and scanning electron microscopy (SEM)
were used. The results figured out possible place of the DNA bound and the
adsorption process. SEM images showed that the binding of this DNA was
mainly on the edges of M and K, although some binding was also apparent
on the planar surfaces.29 Extension from the edges of the clays enables the
unbound end of DNA to interact with receptor sites on competent cells
and result in their transformation; and binding on clays alters the electron
distribution and/or conformation of DNA, which reduces its hydrolysis by
nucleases.
Recently, there has been an increasing interest in methodology of DNA
extraction for the synthesis of microchips and biosensors. Silica solid phase
is also most commonly and easily adaptable to microdevices. Since stan-
dard procedures are time-consuming, microdevices are preferable. Price et
al.52 reviewed DNA microchips. They concluded that DNA purification by
microchips is related to the availability of equipment, reagents, and sample,
as well as the balance between speed, extraction efficiency, and quality.
Approximately 5 × 10−7 dm3 bed volume filled silica resin was used in
a microchip DNA purification device by Tian et al.65 Sol–gel-derived silica
adsorption was used in DNA purification on microchips under chaotropic
conditions and was described in many studies. Breadmore et al.7 used a
tetraethoxyorthosilicate-based sol–gel to immobilize the silica beads in a
microdevice, and also showed effective extraction of DNA from only 0.2 µL
of whole blood sample. Figure 11.3 shows the microchip channel filled with
silica beads which was immobilized with sol–gel method. They improved
DNA purification from blood in less than 15 min.
Different oxide forms of iron are used in the studies in biological appli-
cations that focus on magnetic bioseparation, biological labeling, and diag-
nostics contrast enhancement agents for magnetic resonance imaging, tumor
hyperthermia, and drug carrier design.64 Magnetic particles are also used
in DNA purification method. Magnetic separation is also a good way to
shorten both adsorption and separation steps. In DNA purification method,
magnetic silica microspheres are used. They consist of magnetic nanopar-
ticles uniformly dispersed in a silica matrix where there are large amounts
210 Applied Chemistry and Chemical Engineering: Volume 4

of hydroxyl groups on their surfaces. These groups interaction efficiency

can be enhanced with silanol, epoxide, diol, and carboxyl groups. Chao
et al.10 tested over 100 ng/µL concentrated calf thymus DNA adsorption
behavior onto silica-coated magnetic particle with modified surfaces. As a
result, surface-modified magnetic particles are promising materials to DNA
purification.

(a) (b) (c)

FIGURE 11.3  Microchip packed with silica particles (a) 1× magnification, (b) 10×
magnification, (c) cross section of packed channel at 500× magnification. (Reprinted with
permission from Breadmore, M. C.; Wolfe, K. A.; Arcibal, I. G.; Leung, W. K.; Dickson,
D.; Giordano, B. C.; Power, M. E.; Ferrance, J. P.; Feldman, S. H.; Norris, P. M.; Landers,
J. P. Microchip-Based Purification of DNA from Biological Samples. Anal. Chem. 2003, 75,
1880–1886. © 2016) American Chemical Society.)

Silica is one of the commonly used adsorbents and support materials for
scientific research. It is mainly found in soil material.41 Adsorption of DNA
onto soil, variable-charged minerals, humic substance, and organomineral
complexes are the most frequently used materials understanding the DNA
extraction from soil as model solid surfaces. DNA of various organisms
has an advantage to adjust its activity and susceptibility to biodegrada-
tion. Saeki et al.54 also emphasized that the presence of oxide minerals
in soil enhance DNA adsorption. Silica is one of them. Higher number
of cross-linking sites on the surface of silica enables it higher attachment
rate occurred by hydroxyl groups that easily form hydrogen bonding with
amine groups.

11.2.1.1  SILICA AEROGELS

Aerogels have been used in a wide range of applications as listed in Table

11.2, such as catalytic supports, thermal insulation in solar window systems,
acoustic barriers, supercapacitors, refrigerators, hydrophobic adsorbents for
nonpolar compounds, Cerenkov radiation detector media in high energy
physics, or inertial confinement fusion targets for thermonuclear fusion
reactions.14,49 Ru et al.53 studied drying of silica aerogels and xerogels by
conventional and CO2 and ethanol supercritical drying (SCD) methods.
Adsorbents for DNA Separations 211

TABLE 11.2  Identification of Aerogel Properties and Features with Their Applications.
Property Features Applications
Thermal Best insulating solid Architectural and appliance insulation,
conductivity Transparent portable coolers, transport Vehicles,
High temperature pipes, cryogenic, skylights, space
Lightweight vehicles and probes, casting molds
Density/porosity Lightest synthetic solid Catalysts, sorbers, sensors, fuel storage,
Homogeneous ion exchange targets for ICF, X-ray
High specific surf. area lasers
Multiple compositions
Optical Low refractive index solid Cherenkov detectors, lightweight optics,
Transparent light guides, special effect optics
Multiple compositions
Acoustic Lowest sound speed Impedance matchers for transducers,
range finders, speakers
Mechanical Elastic Energy absorber, hypervelocity particle
Lightweight trap
Electrical Lowest dielectric constant Dielectrics for ICs, spacers for vacuum
High dielectric strength electrodes, vacuum display spacers,
High surface area capacitors

Silica aerogels, which are synthesized through the association of a chem-

ical step, called as “sol–gel” chemistry. Physical step is a particular way of
drying the wet gel at supercritical conditions.

11.2.1.1.1  Sol–Gel Process

The sol–gel process is a wet-chemical technique widely used for producing

promising materials in scientific areas such as material science and ceramic
engineering. Special property of sol–gel method is its capability to convert
the molecular precursor to the product. It makes possible to control the
process and structural composition. This method is used primarily for the
fabrication of materials (typically metal oxides) starting from a colloidal
solution (sol). Sol is a colloidal suspension which consists of particles
having sizes less than 1000 nm. Thus, the gravitational force become negli-
gible and short-time forces, such as wander walls and surface charge forces,
are the main forces acting on the particles. A gel is described as a solid
molecular three-dimensional network that included a liquid network of the
same size and shape. Chemical step has three general reversible reactions:
212 Applied Chemistry and Chemical Engineering: Volume 4

hydrolysis–esterification, alcohol condensation–alcoholysis, and water

condensation–hydrolysis as indicated in Figure 11.4. In the first reversible
reaction, alkoxide groups (OR) are replaced with hydroxyl groups (OH).
Then condensation reaction occurs rather than hydrolysis or alcoholysis.

FIGURE 11.4  Hydrolysis and condensation for silicon alkoxides.

These reversible reaction rates define the generally assumed product

structures. According to this, relative slow hydrolysis and fast conden-
sation rates are resulted as controlled precipitation. Expected products
from different hydrolysis and condensation reaction rates are reported by
Legrand.35 Colloids and sols were obtained if both rates are slow for hydro-
lysis and condensation. On the other hand, if both reactions are fast, colloidal
gels and precipitates are obtained.
Hydrolysis starts with water. However water and alkoxysilanes such
as tetraethoxysilane (TEOS) and tetramethoxysilane (TMOS) are partially
immiscible. Additional solvent is needed to homogenize the mixture. There-
fore, alcohols, acetone, dioxane, and tetrahydrofuran are the solvents added
to this mixture.
Adsorbents for DNA Separations 213

In the sol–gel process, a sol is first formed by mechanically mixing a

liquid alkoxysilane precursor, such as TEOS, deionized water, a solvent,
and an acid or alkaline catalyst at ambient conditions. During this step, the
alkoxysilane groups are transformed to silanol groups by acid catalysis.
Several important papers have investigated the significance of the chem-
ical parameters such as the nature of the starting alkoxide,1,13 the hydrolysis
ratio (water:alkoxide molar ratio), the cosolvent,8 and the catalysis condi-
tions that determine the kinetics and mechanisms of the hydrolysis and
condensation reactions.16 Some attention has also been devoted to the influ-
ence of the processing factors such as the reaction temperature, the ageing
period and conditions, the washing solvent, and the drying conditions.

11.2.1.1.2  Gel and Gelation

A gel is composed of solid and liquid phases which are independent of each
other. A wet gel was prepared by two-step process which was developed
by Brinker et al..8 The first step involves acid (hydrochloric) catalysis of
the hydrolysis of tetraethyl orthosilicate (TEOS). The second step involves
condensation polymerization of the silanol groups resulting from the hydro-
lysis reaction. The condensation reaction is reserved by the acid added in
the first step; thus, the second step includes the addition of ammonium
hydroxide to neutralize acid.

11.2.1.1.3  Drying of the Gels

Three main routes are commonly used for drying5:

1. Freeze-drying (which needs to avoid the triple point)

2. Evaporation (which implies crossing the liquid–gas equilibrium
curve)
3. SCD (which needed to avoid the critical point)

Depending on the drying process, gel is named differently. Drying of the gel
is a critical step. A xerogel is the result of that liquid evaporation at ambient
temperature and pressure (it often retains the same form as the original gel
with up to 90% shrinkage).
An aerogel is the result of the removal of the liquid part without damaging
the solid structure (often by supercritical removal). During SCD, especially
214 Applied Chemistry and Chemical Engineering: Volume 4

under high pressure and high temperature, not only drying but also super-
critical extraction and the chemical reaction of alcogel component occurs.
This drying process, discovered by Kistler (1931),31 involves removal of the
solvent from wet gel.34 This process preserves the texture of the dry mate-
rial. In practice, it strongly reduces the pore collapse. SCD is consisted in
heating a gel in a device such as autoclave, until the pressure and temper-
ature exceeded the critical temperature Tc and critical pressure Pc of the
liquid entrapped in the gel pores. Aerogel shows very high surface area and
important nanoporosity. This is provided by the absence of capillary forces.
The surface forces attracting the liquid and solid phases were not present,
since only the gas phase and the solid existed above critical temperature.
Shrinkage of the gels during drying is driven by the capillary pressure, P,
which can be represented by eq 11.1. Capillary force can also be measured
by contact angle as represented in eq 11.2.

γ lv
P= (11.1)
(r p −δ )
2 γ xCosθ
P = , (11.2)
rp

where γlv is the surface tension of the pore liquid, rp is the pore radius, which
can be represented by eq 11.3, and δ is the thickness of a surface adsorbed
layer.8

2V p
rP = , (11.3)
Sp

where Vp and Sp are pore volume and surface area, respectively. When
liquid evaporates from the pores of a gel, a concave (meniscus) forms. At
the moment that the liquid/vapor meniscus enters a pore, the walls will
be covered with a film of adsorbed liquid and then capillary pressure will
increase according to eq 11.1 attracting the walls of the capillary closer to
each other.
By transforming the solvent into a supercritical fluid (SCF), the surface
tension disappears along with the capillary pressure gradient built up in the
pore walls, avoiding the potential collapse of the pore volume due to the
capillary force. SCD in organic solvents, which are usually alcohols, leaves
the pores without damaging and the resulting materials are generally hydro-
phobic since their surfaces are covered with alkoxy groups.49
Adsorbents for DNA Separations 215

It is important that during SCD, mass transport and heat transfer occur
simultaneously. Therefore, homogenizer solvent should be selected care-
fully. The most commonly used SCFs and their properties are given in Table
11.3. SCFs are highly compressed gases which combine properties of gases
and liquids in same conditions. Figure 11.5 is the phase diagram of a pure
substance in a two coordinate system: pressure (P) and temperature (T). For
every substance, there is a value of T and P where liquid phase and gaseous
phase have the same density. They are the coordinates of the so called crit-
ical point, which ends the liquid–vapor coexistence curve. The area corre-
sponding to temperature and pressure beyond the critical point coordinated
is the supercritical region. The fluid in this region is called as a SCF. Subra
and Justin have reported that SCF can transfer heat and mass better than
gases do.

FIGURE 11.5  P-T plane phase diagram of a pure substance.

216 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 11.3  Properties of Some Supercritical Fluids.

Fluid Formula Critical constant
Pressure (MPa) Temperature (°C)
Carbon dioxide CO2 7.36 31.1
Freon 116 CF3CF3 2.97 19.7
Ethanol C2H5OH 6.36 243
Methanol CH3OH 7.93 240
Nitrous oxide N2O 7.24 36.4
Acetone (CH3)2O 4.66 235
Water H2O 22 374
(Reprinted with permission from Pierre, A. C.; Pajonk, G. M. Chemistry of Aerogels and
Their Applications. Chem. Rev. 2002, 102, 4243–4265. © 2002 American Chemical Society.)

Adsorption of calf thymus DNA to a silica aerogel, a mesoporous silica

gel, and a silica wafer was investigated by Yetgin and Balkose (2015).71
Silica aerogel was synthesized from TEOS by supercritical ethanol drying
process. The DNA adsorption capacity of silica aerogel was nearly two times
of that of the mesoporous silica gel due to its macroporous structure and its
higher silanol content. Silica aerogel was found to be a very promising mate-
rial for DNA adsorption.

11.2.2 ALUMINA

Alumina, also called aluminum oxide, is the only solid oxide form of
aluminum. It has the chemical formula Al2O3. It is commonly referred to as
alumina (α-alumina) or corundum which is the naturally occurring alumina.
Alumina materials have been technologically significant ceramic materials
throughout human history. Type of α-alumina has hexagonal close-packed
structure while γ-alumina type signifies cubic close-packed crystalline form.
In a hexagonal unit cell, the sides that provide depth and width to the cell are
equal, and are at an angle of 120° to each other. c is at angles of 90° to sides
“a” and “b.” The hexagonal parameters for α-Al2O3 are c = 1.297 nm and a
= 0.475 nm, with c/a = 2.73.36
α-phase alumina, also called corundum, is the only thermodynami-
cally stable oxide of aluminum and is the final product of the calcination
process. Calcination order can be defined as follows: gibbsite → boehmite
(γ-AlOOH) → γ-alumina (γ-Al2O3) → δ-alumina (δ-Al2O3) → θ-alumina
(θ-Al2O3) → α-alumina. Metastable Al2O3 phases transform toward stable
α-alumina by calcination procedure.
Adsorbents for DNA Separations 217

Zeta potential measurement has identified that the α-alumina has isoelec-
tric point at nearly pH 9.1.51
Alumina has a melting point nearly 2000°C. Therefore, it is used as
insulator or refractory material. It is used in orthopedic and dental implants
surgery.24 Furthermore, it is used as catalytic support material in reaction
engineering.
Alumina is also classified as nonbioactive material.44 It has been used
in orthopedic surgery because of its high biocompatibility.27 Its adsorption
capacity of DNA was studied and already published by Chattoraj and Upad-
hyay in 1968 and reported as a review by Chattoraj and Mitra.11 Alumina
has been also tested on DNA and RNA purification. DNA and RNA were
also denaturized with heat and acid presence. Adsorption isotherm was
found to fit Langmuir equation in linear form. Therefore, authors concluded
that denaturized DNA and RNA were adsorbed by alumina more than their
native form. Alumina adsorbed 0.25 and 0.75 mg amount of DNA and RNA,
respectively at pH 6.5 with maximum 10 mg/cm3 concentration.

11.2.3 HYDROXYAPATITE

HAP’s chemical formula is Ca10(PO4)6(OH)2 which is the main mineral

element of teeth and bones and belongs to calcium phosphates family.
Different techniques are used for HAP powder production. HAP’s
morphology, stoichiometry, and level of crystallinity change with prepara-
tion technique, which define biomaterial-phase thermal stability, mechan-
ical stability, and dissolution behavior. HAP has lattice parameters a = b
= 0.934 nm, c = 0.687 nm, α = β = 90°, γ = 120°, and hexagonal crystal
structure with the space group P63/m.48 Ca/P ratio is an important ratio
which defines properties of calcium phosphate mineral such as acidity and
solubility.66 Lower Ca/P ratio represents larger acidity and solubility of the
mixture, for example, Ca/P < 1. These properties change while increasing
the Ca/P ratio to the value of 1.67. The Ca/P ratios of tetracalcium phosphate
(Ca4P2O9), HAP (Ca10(PO4)6(OH)2), α-tricalcium phosphate (Ca3(PO4)2), and
β-tricalcium phosphate (Ca3(PO4)2 are 2, 1.67, 1.5, and 1.5, respectively.66
HAP has been used clinically for many years. HAP has good biocompat-
ibility in bone contact as its chemical composition is similar to that of bone
material. HAP shows excellent biocompatibility with hard tissues and also
with skin and muscle tissues.23 Synthetic HAP is a very important biomaterial
used for several applications in medicine as a bulk ceramic, implant coating
materials, ceramic coating, or as one of the components of composites.
218 Applied Chemistry and Chemical Engineering: Volume 4

Porous HAP was used for cell loading. Ohgushi and Caplan 44 applied HAP
for cell loading, drug carrier for controlled drug release based on adsorption/
desorption properties,30 most extensively for hard tissue scaffolds, affinity
chromatography analysis for DNA binding for protein purification,19 and
the separation of ssDNA and dsDNA by chromatography12 or both of them
such as plasmid DNA and protein adsorption.59 This can be explained by
positively charged pairs of calcium ions and six negatively charged oxygen
atoms which are associated with triplets of crystalline phosphates placed
onto the surface. It is possible that amino and guanidinyl groups of proteins
can attach to phosphate ions of HAP, and DNA’s phosphate part can attach
to calcium ions.
HAP has osteogenic cell proliferation capacity onto implant surface,
therefore should be investigated of surface interaction on coated material or
smooth surface. Therefore, coating is main usage area of HAP. In practice,
HAP surface can be formed on either HAP thin film or HAP pellet forms.62
Sol–gel deposition technique is a well-known film formation procedure. Sol
or particulate sol can be used. The final form can be obtained by dip or spin
coating. In dipping process, substrate such as inert glass film contacts with
the dip solution for a few seconds. HAP pellet can be prepared from powder
form. For instance, Şimsek 62 compacted HAP powder in a stainless steel
die with 1-cm internal diameter under 160 MPa pressure. All pellets were
sintered different temperatures between 800°C and 1300°C for 2 h. The sol–
gel approach affords conditions for the synthesis of HAP films. HAP film
can also be prepared directly from sol or indirectly from particulate sol solu-
tions. Ozcan and Çiftçioğlu prepared particulate sol route HAP thin film.45
Yetgin 70 prepared HAP pellets by sintering and examined the AFM image
of calf thymus DNA which was placed on its surface by dropping and drying
of a DNA aqueous solution.

11.3  MATERIALS AND THE METHOD

11.3.1 MATERIALS

Silica (SiO2), alumina (Al2O3), and HAP [Ca10(P04)6(OH)2] were examined

as adsorbents for calf thymus DNA. Silica (Sigma-Aldrich-Silicagel, Grade
7744 pore size 60 Å, 70–230 mesh), alumina from Seydişehir, Turkey, and
HAP supplied by Sigma-Aldrich (23093-6) were characterized for this
purpose.
Adsorbents for DNA Separations 219

11.3.2  CHARACTERIZATION OF SILICA, ALUMINA, AND HAP

The characterization of the adsorbents included the determination of the

functional groups, pore size, surface area, and chemical composition. The
adsorbents used in this study were characterized by x-ray fluorescence
(XRF) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, x-ray
diffraction (XRD), and physical adsorption of nitrogen.
Elemental analyses were made by XRF method. XRF analyses were
carried out by using Spectro IQ II on the opaque surfaces of the pellets
prepared by heating the mixture of lithium tetraborate and sample at 1100°C
and cooling to room temperature.
FTIR spectroscopy is used to obtain information about functional groups
present in a material using KBr disc method. Shimadzu 8601 FTIR spectro-
photometer was used to obtain the spectra.
Philips X’Pert Pro diffractometer was used to investigate phase structure
of the adsorbents and crystalline form of the component present in the adsor-
bent samples. The operating conditions were 45 kV and 40 mA, Cu Kα radia-
tion, λ = 0.154 nm. The registrations were performed in the range over 2θ
values of 5–70° with a scan speed of 0.06°/s. The data were collected with
X’Pert data collector. The collected data were analyzed by X’Pert Graphics
& Identify software.
Specific surface area, pore diameter, and pore volume of the adsorbents
were obtained by using the physical adsorption of nitrogen technique at 77
K, using Micromeritics ASAP 2010.

11.4  RESULTS AND DISCUSSION

The elemental composition of silica, alumina, and HAP which was deter-
mined by XRF analysis is given in Table 11.4. While the silica gel contained
80.77% silica, alumina contained 82.38% alumina. Both samples contained
free and bound water that was lost during heating for sample preparation.
HAP’s theoretical Ca/P value of 1.67 was obtained in freshly prepared
sample, but during heating at 1000°C for sample preparation for XRF anal-
ysis, volatile components such as water and phosphoric acid were removed
decreasing P content. Thus the molar ratio of Ca/P was found as 2.0 from the
analysis indicating HAP was transformed to tetracalcium phosphate during
sample preparation for XRF analysis.
220 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 11.4  Composition (Mass, %) of Representative Adsorbents by XRF.

Na Mg Al Si P Ca Fe Cu
Silica 0.02 0.55 0.46 37.75 0.02 0.13 0.09 0.28
Alumina 1.11 1.16 43.61 0.001 0.01 0.06 0.09 0.25
HAP 0.21 0.27 0.66 0.68 9.84 26.69 0.08 0.23

Table 11.5 shows the main vibration bands of silica related to FTIR spec-
trum. The peak at 3400 cm−1 is related to the hydrogen-bonded ν O–H mode
of residual silanol (Si–OH) groups and of adsorbed water.15 Low-intensity
peak at 1630 cm–1 is related to bending vibration of water.14 The weak band
near 970 cm–1 was assigned to the oscillating oxygen atoms in the silica
network, including silanol groups and broken Si–O–Si bridges.14 The peak
at 1080 cm−1 wavenumber is related to Si–O–Si bond tensile strain.

TABLE 11.5  Assignments of the Main Infrared Bands in the FTIR Spectrum of Silica Gel.
Wavenumber (cm−1) Assignment Reference
~460 ρSi–O–Si Fidalgo and Ilharco15
800 vaSi–O–Si Fidalgo and Ilharco15
950 Si–OH stretching vibration Fidalgo and Ilharco15
~1080 Asymmetric stretching vibration of Fidalgo and Ilharco15
the Si–O bond Fidalgo and Ilharco17
1600 Bending vibration of H2O Balkose et al.4
δH–O–H mode Fidalgo and Ilharco17
3400 Hydrogen bonded –OH stretching Balkose et al.4

However, it is reported that perfect silica surface such as quartz has no

free surface hydroxyl groups.65 On the other hand, acid treatment of silica
hydrolyzes the surface, and increases the concentration of surface silanol
groups.41In Figure 11.6, FTIR spectrum of silica gel is seen. It clearly shows
that the silica gel contains OH groups, H2O, and SiO2.
The XRD diagram of silica gel shown in Figure 11.7 has no crystal-
line diffraction peaks indicating that it was totally amorphous and not
crystalline.
The FTIR spectrum of alumina shown in Figure 11.8 had peaks related
with water (at 1600 cm−1) and hydrogen-bonded OH groups (3464 cm−1) and
Al–O stretching vibrations (1014 cm−1).
Adsorbents for DNA Separations 221

FIGURE 11.6  FTIR spectrum of silica gel.

FIGURE 11.7  X-ray diffraction diagram of silica gel.

FIGURE 11.8  FTIR spectrum of Alumina from Seydişehir, Turkey.

222 Applied Chemistry and Chemical Engineering: Volume 4

The XRD diagram of the alumina from Seydişehir, Turkey is seen in

Figure 11.9. X’Pert Graphics & Identify software of XRD pattern and
obtained data for α-alumina were listed in Table 11.6. The observed peaks
and the peaks of α-alumina had the same 2θ values.

FIGURE 11.9  XRD pattern of Alumina from Seydişehir, Turkey (Cu Kα radiation was used).

TABLE 11.6  The Observed and the X-ray Diffraction Peaks of α-Alumina.
Observed 2θ, ° JCPDS # (75-1865) 2θ, °
25.6 25.546
35.14 35.105
37.74 37.734
41.65 41.619
43.36 43.302
52.64 52.486
57.45 57.423
59.73 59.670
61.35 61.056
66.40 66.434
68.19 68.126
76.70 70.756

FTIR spectrum of HAP is shown in Figure 11.10. Bands at 3400 and

1600 cm−1 belong to hydrogen-bonded OH stretching vibrations and bending
vibrations of water, respectively. The bands at 1092 and about 1040 cm−1
were assigned to the components of the triply degenerated asymmetric P–O
Adsorbents for DNA Separations 223

stretching mode.60 The bands at 601 and 571 cm−1 are related to components
of the triply degenerate O–P–O bending mode and the bands in the range
462–474 cm−1 are also connected to the components of the doubly degen-
erate O–P–O bending mode.17

FIGURE 11.10  FTIR spectrum of HAP from Sigma Aldrich.

The XRD diagram of HAP is shown in Figure 11.11. The observed peaks
were analyzed by X’Pert Graphics & Identify software and the obtained data
are listed in Table 11.7. Joint Committee on Powder Diffraction Standards
(JCPDS) numbers which are known to identity of the x-ray powder diffrac-
tion patterns were also obtained by this software. The HAP sample had all
the peaks related to HAP which was reported in JCPDS 09-0432.

FIGURE 11.11  XRD pattern of HAP from Sigma Aldrich.

224 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 11.7  The Observed and Expected X-ray Diffraction Peaks of HAP. (Source: JCPDS
number 09-0432 by Wu et al.69)
Observed 2θ JCPDS # (09-0432) 2θ
10.79 10.820
16.90 16.741
21.70 21.819
22.77 22.902
25.77 25.879
28.05 28.126
28.79 28.966
31.64 31.773
32.05 32.196
32.78 32.902
39.05 39.204
40.27 40.452
41.82 42.029
46.54 46.711
49.30 49.467
50.29 50.490
63.15 63.011
63.88 64.078

11.4.1  SURFACE CHARACTERISTICS OF SILICA, ALUMINA,

AND HAP

The surface characteristics of the adsorbents can be determined by nitrogen

gas adsorption at 77 K. In Figures 11.12–11.14, the nitrogen gas adsorption
isotherms of silica, alumina, and HAP are seen. Silica, alumina, and HAP
isotherms were all of the Type IV of the UIPAC classification. Hysteresis
loop is formed by adsorption/desorption isotherms due to condensation and
evaporation of liquid nitrogen from mesopores and depends upon the shape
and size of pores.22 Hysteresis cycle was commonly observed for materials
with interrelated pore networks with different size and shape. The isotherms
of silica, alumina, and HAP have hysteresis loops, which are consistent with
the presence of mesopores. Relative pressure of (P/P0) greater than 0.6 is
associated with capillary condensation in mesopores, which is character-
istic of type IV isotherms.53 Single-point, BET, and Langmuir surface areas,
Adsorbents for DNA Separations 225

average pore diameter, total pore volume, and micropore volume of the
adsorbents are listed in Table 11.8. Silica had the higher surface area, total
pore volume, micropore volume, and pore diameter than alumina and HAP.

FIGURE 11.12  Nitrogen adsorption and desorption isotherms of Silica at 77 K.

FIGURE 11.13  Nitrogen adsorption and desorption isotherms of Alumina at 77 K.

226 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 11.14  Nitrogen adsorption and desorption isotherms of HAP.

TABLE 11.8  Surface Characteristics of the Adsorbents.

Properties Silica Alumina HAP
Single point surface area (m /g)
2
556 106 68
BET surface area (m /g)
2
571 108 69
Langmuir surface area (m2/g) 787 148 96
Average pore diameter (nm) (4V/A by BET) 5.5 5.7 6.2
Single point total pore volume (cm3/g) 0.79 0.16 0.11
Max micropore volume (cm3/g) 0.20 0.04 0.03

11.5 CONCLUSIONS

Adsorption of DNA was made for DNA purification, biosensor develop-

ment, and gene transfer purposes. DNA can easily be adsorbed to positively
charged surfaces as well as to negatively charged surfaces by electrostatic
bridges with the water of hydration of charged cations. DNA adsorption
to alumina, clay, silica, SWNT, metals, organic and bioorganic molecules,
polypyrrole (PPy)–silica nanocomposite particles, polymers and hydrogels,
poly-L-lysine-immobilized pHEMA, and HAP are reviewed in this chapter.
The preparation and characterization of silica, alumina, and HAP were
Adsorbents for DNA Separations 227

reviewed in detail. Experimental results are reported for the silica, alumina,
and HAP samples which were used in calf thymus DNA adsorption in our
further studies. OH functional groups that are potential bonding sites for
DNA were present in all three adsorbents. The silica gel sample had highest
surface area, total pore volume and micropore volume, and the pore diam-
eter among the three adsorbents under investigation. The functional groups
and the pore structure and surface charge are all the important parameters
for DNA adsorption.

KEYWORDS

•• adsorbents
•• DNA purification
•• silica
•• gelation
•• polypyrrole

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61. Şenel, S.; Bayramoglu, G.; Arıca, M. Y. DNA Adsorption on a Poly-L-lysine-Immobi-
lized Poly(2-hydroxyethyl methacrylate) Membrane. Polym. Int. 2003, 52, 1169–1174.
62. Şimşek, D. Preparation and Characterization of HA Powders—Dense and Porous HA
Based Composite Materials. Master Thesis Izmir Institute of Technology, Materials
Science and Engineering, Izmir, 2002.
63. Solberg, S. M.; Landry, C. C. Adsorption of DNA into Mesoporous Silica. J. Phys.
Chem. B 2006, 110, 15261–15268.
64. Souza, K. C.; Mohallem, N. D. S.; Sousa, E. B. M. Mesoporous Silica-Magnetite Nano-
composite: Facile Synthesis Route for Application in Hyperthermia. J. Sol–Gel Sci.
Technol. 2010, 53, 418–427.
65. Tian, H.; Huhmer, A. F. R.; Landers, J. P. Evaluation of Silica Resins for Direct and Effi-
cient Extraction of DNA from Complex Biological Matrices in a Miniaturized Format.
Anal. Biochem. 2000, 283, 175–191.
Adsorbents for DNA Separations 231

66. Vallet-Regi, M.; Gonzalez-Calbet, J. M. Calcium Phosphates as Substitution of Bone

Tissues. Prog. Solid State Chem. 2004, 32(1–2), 1–31.
67. Vandeventer, P. E.; Lin, J. S.; Zwang, T. J.; Nadim, A.; Johal, M. S.; Niemz, A. Multi-
phasic DNA Adsorption to Silica Surfaces Under Varying Buffer, pH, and Ionic Strength
Conditions. J. Phys. Chem. B 2012, 116(19), 5661–5670.
68. Vogelstein, B.; Gillespie, D. Preparative and Analytical Purification of DNA from
Agarose. Proc. Natl. Acad. Sci. U. S. A. 1979, 76, 615–619.
69. Wu, C. H.; Wang, T. W.; Sun, J. S.; Wang, W. H.; Lin, F. H. A Novel Biomagnetic
Nanoparticle Based on Hydroxyapatite. Nanotechnology 2007, 18, 165601.
70. Yetgin, S. DNA Adsorption on Silica, Alumına and Hydroxyapatite and Imaging of
DNA by Atomıc Force Microscopy. PhD Dissertation, Izmir Institute of Technology,
Izmir, 2013.
71. Yetgin, S.; Balkose, D. Calf Thymus DNA Characterization and its Adsorption on
Different Silica Surfaces. RSC Adv. 2015, 5, 57950–57959.
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CHAPTER 12

ADSORPTION OF DNA ON SILICA,

ALUMINA, AND HYDROXYLAPATITE
SENEM YETGIN1 and DEVRIM BALKOSE2,*
1
Food Engineering Department, Kastomonu University, Kastomonu,
Turkey
2
Chemical Engineering Department, Izmir Institute of Technology,
Izmir, Turkey
Corresponding author. E-mail:[email protected]
*

CONTENTS

Abstract.....................................................................................................234
12.1 Introduction....................................................................................234
12.2 Materials and Methods...................................................................244
12.3 Results............................................................................................246
12.4 Conclusions....................................................................................260
Keywords..................................................................................................261
References.................................................................................................261
234 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

The equilibrium and kinetics of DNA adsorption on silica, alumina, and

hydroxylapatite (HAP) powder as a function of pH and MgCl2 concentra-
tion were investigated. The adsorption isotherms of DNA on silica, alumina,
and HAP were fitted to Langmuir model better than Freundlich model and
Dubinin–Radushkevich model. Higher correlation coefficients were obtained
with pseudo-second-order model than the pseudo-first-order reaction model
in adsorption kinetics of DNA. The DNA adsorption to the external surface
of the particles was very fast kinetically and accomplished within about 15
min. After that, intraparticle diffusion mechanism becomes dominant. Intra-
particle diffusion coefficient decreased significantly in the order of alumina,
silica, and HAP. The kinetic models, reaction, and diffusion models showed
that adsorption at the external surface was dominant at initial stages of the
DNA adsorption and it was followed by slower intraparticle diffusion.

12.1 INTRODUCTION

Adsorption is one of the most widely used techniques for removal of pollut-
ants from contaminated media or desired substance in solution. Solid-phase
extraction method is one of the useful extraction techniques for DNA puri-
fication based on adsorption. Immobilization of DNA onto solid particles,
beads, or column is known as solid-phase extraction method. DNA is a nega-
tively charged biopolymer. This charge defines interaction possibilities with
surface. DNA can be attached to positively charged surfaces easily.
The forces between the surface and DNA might be repulsive or attractive.
The adsorption phenomenon depends on the interaction between the surface
of the adsorbent and the adsorbed species. Attractive interactions lead to
adsorption. The interaction may be due to: chemical bonding, hydrogen
bonding, hydrophobic bonding, Van der Waals force, and electrostatic inter-
action.17 DNA adsorbed at the silica surface depends on solution pH, ionic
strength, electrolyte type, and valency and conformation of DNA (linear,
plasmid, supercoiled).1,11,14,19
Surface charge is one of the important parameters to understand electro-
static interaction between DNA and solid surface. In the double helix struc-
ture, the bases exist in a highly hydrophobic environment inside the helix,
while the outer, negatively charged backbone allows the dsDNA molecule
to interact freely with the hydrophilic environment. General idea is about
DNA that is not adsorbed by same charged surface due to the electrostatic
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 235

repulsion. It is reported that based on the physicochemical circumstance

DNA has superior adsorption onto different hydrophilic and hydrophobic,
inorganic and organic solid surface because of its surface active character-
istic.3 DNA is surface active due to its preferential adsorption from solu-
tion to different hydrophilic and hydrophobic, inorganic and organic solid
surfaces depending upon physicochemical conditions.
Adsorption process is defined by isotherm. The adsorption isotherm is the
relationship that shows the distribution of adsorbate between the adsorbed
phase and the solution phase at equilibrium. Adsorption isotherms are essen-
tial for the description of how adsorbate concentration interacts with adsor-
bents and are useful in optimizing their use. Therefore, empirical equations
are important for adsorption data interpretation and predictions. The Lang-
muir and Freundlich isotherms are the most frequently used models used in
data evaluation.
Possible electrostatic and hydrophobic mechanisms for the adsorption of
DNA in solutions containing monovalent salt are discussed and compared
with the observations in divalent salt.10 Also, other parameters that effect
DNA adsorption have been classified as; base composition, ionic strength,
pH, DNA chain length, and DNA concentration.4

12.1.1  SORPTION ISOTHERM METHOD: ADSORPTION

EQUILIBRIA

The adsorption isotherm is the relationship that shows the distribution of

adsorbate between the adsorbed phase and the solution phase at equilibrium.
Adsorption isotherms are essential for the description of how adsorbate
concentration interacts with adsorbents and are useful in optimizing their
use. Therefore, empirical equations are important for the adsorption data,
interpretation, and predictions. A wide variety of other adsorption models
have been formulated over the years. Freundlich, Langmuir, and Brunauer–
Emmett–Teller (BET) are the most useful models; they figure out adsorption
profile despite the fact that they are old adsorption models. These funda-
mental adsorption equation’s general equilibrium constants were analyzed
on the basis of equilibrium concentration. Langmuir and Freundlich differs
in that while Langmuir expression explains monolayer adsorption process.
Freundlich can explain multilayer adsorption process. BET equation is
a theoretical expression of adsorption and is commonly used in the gas-
phase adsorption process for finding the monolayer adsorption capacity of
an adsorbent.
236 Applied Chemistry and Chemical Engineering: Volume 4

12.1.1.1  LANGMUIR MODEL

The Langmuir equation is based on a kinetic approach and assumes a

uniform surface, a single layer of adsorbed material at constant temperature.
The model is useful when there is no strong specific interaction between the
surface and the adsorbate. Thus, single adsorbed layer forms and no multi-
layer adsorption occurs. It also assumes that the surface is homogeneous and
adsorption energy is constant over all sites. Adsorption occurs at specific
homogeneous sites within the adsorbents and there is no interaction between
the sorbate molecules that are bound to the next active sites. The Langmuir
equation has the following form:

Q°bCe
qe =
1 + bCe (12.1)

where, qe is the amount adsorbed at equilibrium, Ce is the equilibrium

concentration, b and Qo are Langmuir coefficients related to the energy of
adsorption and the maximum adsorption capacity, respectively. Langmuir
equation can be described by the linearized form as follows:

1 1 1
= +
qe Q° bQ°Ce (12.2)

The linear Langmuir plot can be obtained by plotting 1/qe versus 1/Ce.
The coefficients Qo and b can be evaluated from the intercept and slope,
respectively.

12.1.1.2  FREUNDLICH MODEL

The Freundlich model is an empirical equation, which assumes that the

adsorbent has a heterogeneous surface composed of adsorption sites with
different adsorption potentials and energy. The model equation is as follows:

qe = K f Ce 1/ n (12.3)

where qe is amount adsorbed at equilibrium and Ce is the equilibrium concen-

tration. Kf and n are equilibrium constants (temperature dependent) related
to adsorption capacity and intensity, respectively. Graphically, a plot of qe
versus Ce gives the adsorption isotherm. The linearized form of Freundlich
sorption isotherm is:
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 237

1
log qe = log K f + log Ce (12.4)
n
A plot of log qe versus log Ce gives a linear graph. The coefficients Kf and n
can be calculated from the intercept and slope, respectively.
The dimension of Kf depends on the value Ce while the exponent “n” is
dimensionless. Adsorbent total adsorption capacity increases resulting in Kf
parameter increase. The n value might vary along adsorption process and is
related to the adsorption efficiency and also to the energy of adsorption.

12.1.1.3  DUBININ–RADUSHKEVICH MODEL

Dubinin–Radushkevich (D–R) equation is widely used for description of

adsorption in microporous materials, where adsorption process follows a
pore-filling mechanism. Instead of surface layering, in pore filling mech-
anism the chemical potential is a function of adsorbed amount. Dubinin–
Radushkevich equation can be represented in eq 12.5.5 This model is based
on the assumptions of a change in the potential energy between the adsorbate
and adsorbent phases and a characteristic energy of a given solid. Adsorption
energy value has a clue about the type of sorption, whether it is physical or
chemical.
The linear plot of ln qe versus ε2 are used to define sorption energy
constant (K) and maximum adsorption capacity based on D–R isotherm
(qm), respectively. Then adsorption energy (E) is obtained by the use of
sorption energy constant with eq 12.7. Units of the isotherm formula param-
eters are Ce (ng/µL), qm is the maximum adsorption capacity based on D–R
isotherm (µg/g), and K is the constant related to the sorption energy (mol2/
kJ2), therefore, E has kJ/mol unit. If the value is lower than 8 kJ/mol, adsorp-
tion is defined physical. Between the values of 8 and 16 kJ/mol, sorption is
chemically controlled.6

qe = qm e
( − K ε ) (12.5)
2

 1
ε = RT 1 +  (12.6)
 Ce 

1
E= (12.7)
2K
238 Applied Chemistry and Chemical Engineering: Volume 4

where, ε is Polanyi potential, R is the gas constant (8.314 × 10–3 kJ/mol K),
and T is the temperature (K), where E is the mean adsorption energy (kJ/
mol).

12.1.2  ADSORPTION KINETICS

Adsorption is one of the most widely used technique to remove pollutants

from contaminated media or desired substance in solution. Several system
variables should be considered. For instance, initial concentration, sorbent
particle size, solution temperature, solution pH, and agitation have a greater
effect on the sorption of solutes in reaction controlled sorption processes. As
a result, the correlation coefficients between experimental and theoretical
data will provide the ‘best fit’ model. Some kinetic models are involved
in adsorption reaction models; the pseudo-first-order equation, the pseudo-
second-order equation, or diffusion model; the Elovich equation and intra-
particle diffusion model.
Sorption rate is described by three main series of resistances due to
external mass transfer, intraparticle diffusion, and reaction. The first one
occurs through transport of adsorbate molecules from the bulk solution to
the adsorbent external surface. The second is the diffusion of the adsorbate
from the external surface into the pores of the adsorbent.
When adsorption is performed, thermodynamic and kinetic parts should
be involved to get more details about its performance and mechanisms.19 To
determine the kinetic performance of a given adsorbent has great significance
for the small application as much as adsorption capacity of used adsorbent.
The cost and performance of a product or the mode of application are the
concerns in controlling the efficiency of this process. Therefore, the sorption
capacity and required contact time are the two most important parameters.
Adsorption is not only to remove substance from solution but also is a
fundamental parts of a reaction mechanism. Reaction mechanism requires
the adsorption of each reactant on the catalysis surface. Therefore, adsorp-
tion kinetic is important. Chemical kinetics is a useful way of describing
the reaction pathway and time needed to reach equilibrium. In other words
in kinetics analysis, the solute uptake rate, which determines the residence
time required for completion of adsorption reaction, may be established. The
dependence of the sorption kinetics on the physical and chemical charac-
teristics of the adsorbent is obvious and affects the mechanism. Numerous
studies were carried out in formulating a general expression to analyze
the kinetics of adsorption on solid surfaces for the liquid–solid adsorption
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 239

system. Adsorption rate covers a series of resistance resulted from diffusion

and reaction steps.

12.1.2.1  REACTION MODELS

12.1.2.1.1  The Pseudo-First-Order Equation

Scientists have proposed mathematical models to describe adsorption data,

which can generally be classified as adsorption reaction models and adsorp-
tion diffusion models. In 1898, Lagergren presented the first-order rate
equation for the adsorption of oxalic acid and malonic acid onto charcoal.10
Lagergren kinetics equation may have been the first one in describing the
adsorption of liquid–solid systems based on solid capacity. Lagergren rate
equation is one of the most widely used sorption rate equations for the sorp-
tion of a solute from a liquid solution. It is represented in the following
formula. 6

dqt
= k ( qe − qt ) (12.8)
dt
where: qt is the adsorption capacity at time t, qe is the adsorption capacity at
equilibrium, and kl is the rate constant of pseudo-first-order adsorption.
It can be linearized after taking integration and applying boundary condi-
tions for t = 0 to t = t. The integrated form becomes:

kl
log( qe − qt ) = log( qe ) − t (12.9)
2.303
When the log (qe−qt) versus t plot is drawn, the slope gives the kl/2.303 and
the intercept gives the log qe. This model assumes that the rate of change of
adsorbate uptake with time is related to the difference in saturation concen-
tration and the amount of solid uptake with time.5

12.1.2.1.2  The Pseudo-Second-Order Equation

A pseudo-second-order model describing the adsorption kinetic may be

expressed in the following form:

dq
= K 2 ( qe − q ) (12.10)
2

dt
240 Applied Chemistry and Chemical Engineering: Volume 4

where, qe: adsorbate amount per unit weight of adsorbent amount at equi-
librium, K2: the rate constant of pseudo-second-order adsorption. It can be
linearized by taking integration and applying the initial conditions.

t 1 1
= + t (12.11)
q K 2 qe2 qe
If t/q versus t is plotted, slope gives the 1/qe and the intercept gives the
1/K2qe2. This model assumes that the sorption process is a pseudo-chemical
reaction process. The driving force is difference between the average solid
concentration and the equilibrium concentration. Also, the overall sorption
rate is proportional to the square of the driving force.5

12.1.2.2  DIFFUSION MODELS

Adsorption and desorption rate in porous material is generally defined trans-

port within the pore structure rather than surface kinetic.20 Diffusion models
derived from Fick’s law of mass transport as represented in eq 12.12. It is
important that in this equation, mass transport not only depends on concen-
tration. Because it is known that for any transport mechanism, true driving
force is the gradient of the chemical potential (µ). The adsorption process
only be independent of the adsorbate concentration in case of thermody-
namically ideal system.21

∂C
F = −D (12.12)
∂x
Adsorption process includes fluid film diffusion, intraparticular diffu-
sion, and mass action. Mass action can be neglected because of high rate for
kinetic study in physisorption processes. Consequently, adsorption process
is predominantly controlled by film diffusion or intraparticular diffusion.
Adsorption kinetics is described by many models: The two-resistance
models such as the film-solid model, the film-pore model, and the branched
pore model give detailed analysis of the adsorption dynamics.
Distinction of kinetic and diffusion control mechanism generally is not
simple. It is a general idea that if system reaches equilibrium within 3 h, the
process is usually kinetic controlled. If process takes place above 24 h it is
diffusion controlled. Either diffusion or kinetic control adsorption equilibria
when the duration of the process between 3 and 24 h. A more suitable quan-
titative approach to distinguish between kinetic and diffusion rate control
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 241

can be performed by the square root of contact time analysis according to

equation.
However, these models include complex partial differential equations
solution and their solution needs computer programs aid and extensive
computer time.12 Mathews and Webber 13 intraparticle diffusion models are
the two most widely used models for studying the mechanism of the adsorp-
tion without complex solution and computer program.

12.1.2.2.1  External Mass Transfer: Mathew–Weber Model

This model assumes that only external film diffusion is the main driving
force during the initial sorption period and controls the sorption process.
In other words, the film diffusion controls the adsorbate uptake rate in the
initial stages, followed by particle diffusion in the latter stages. The model
formula is given in eq 12.13.

Ct
ln = − k f St (12.13)
C0

where, Ct is the concentration of adsorbate in the solution at time t, C0 is

the initial concentration of adsorbed in the solution, kf is the external mass
transfer coefficient (m/s), t is the time, and S is the surface area for mass
transfer (m−1). The initial slope of the linear plot of ln Ct/C0 versus t is used
in the determination of the external mass transfer coefficient (kf).

12.1.2.2.2  Intraparticle Diffusion: Weber–Morris Model

This model was derived from the Fick’s second law. According to this, the
effects of the external mass transfer resistance can be ignored, the direction
of the diffusion is radial, and the intraparticle diffusivity is constant. This
model was used to calculate the intraparticle diffusion rate constant. The
model equation is given below.

qt = kd t 0.5 (12.14)

A plot of the amount of adsorbed, qt, against the square root of time,
t , gives a straight line plot of slope kd, a diffusional rate parameter. This
0.5

straight line, passing through the origin, indicates intraparticle diffusion

control.8 It can be seen from eq 12.14 that if intraparticle diffusion is the rate
242 Applied Chemistry and Chemical Engineering: Volume 4

limiting step, then a plot of q versus t0.5 will give a straight line with a slope
that equals kd and an intercept equal to zero.
The approximate solution of the diffusion equation for qt/q0 <0.6 is
shown in eq 12.15.
1/ 2
qt 6  Dt 
=  2 (12.15)
q0 πr 

12.1.2.2.3  Micropore Diffusion

For a spherical particle at constant surface concentration for short time and
long time periods can be written in eqs 12.16 and 12.18, respectively by
integrating eq 12.17.

mt D 
1/ 2
 1 ∞  nr  D t
= 6  2t   + 2∑ ierfc  c  − 3 c2  (12.16)
m∞ r   π  Dc t  rc 
n =1


∂q  ∂ 2 q 2 ∂q 
= D 2 +  (12.17)
∂t  ∂r r ∂r 

mt 6  π2 D t 
= 1 − 2 exp  − 2 c  (12.18)
m∞ π  rc 

In literature, a variety of studies focused on developing a formula

to be used in analyzing the kinetics of adsorption on solid surface. To
identify the exact mechanism, it is necessary to carry out experiments.
Therefore, determination of DNA adsorption kinetics requires adsorption
experiments.
DNA adsorption onto silica coated natural organic matter (NOM) surface
kinetic was found 120 mg/dm3 supercoiled and the linear plasmid DNA by
QCM-D by Nyugen and Chen 15. Their result also revealed that adsorption
took place within 20 min for Ca2+ and 40 min for Mg2+ cations. Just, 7 mM
Na+ ion positively affects DNA adsorption capacity when both divalent
cations are present. They concluded that adsorption was mainly controlled
by specific bridging between the DNA phosphate groups and NOM carboxyl
groups. Additionally, same group reported that kinetics of DNA adsorption
to NOM-coated silica surfaces depended on ionic strength, and that DNA
adsorption was significant at moderately high ionic strength.16 Adsorption
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 243

kinetic measurements were performed by quartz crystal microbalance device

which is sensitive for any little change in the amount mass.
Kinetics model of DNA adsorption onto silica surface was reported by
Vandeventer et al.22 Their model schematic representation can be seen in
Figure 12.1. According to the study, DNA can loosely or tightly bind to
available silica surface sites.

FIGURE 12.1  Kinetic model representation of DNA adsorption to silica. (Reprinted

with permission from Vandeventer, P. E.; Lin, J. S.; Zwang, T. J.; Nadim, A.; Johal, M. S.;
Niemz, A. Multiphasic DNA Adsorption to Silica Surfaces Under Varying Buffer, pH, and
Ionic Strength Conditions. J. Phys. Chem. B 2012, 116(19), 5661–5670). © 2016 American
Chemical Society.)

“A” represents bulk DNA in solution, and “S” denotes the available
surface binding sites. “B” and “C” represent DNA tightly and loosely bound
to the surface through multiple binding sites or a single binding site, respec-
tively. Assumed adsorption pathway is given in eqs 12.19–12.21.

k 1→

A + nS ← B (12.19)
k2
k 3→

B ← C + (n − 1) S (12.20)
k4
k 3→

B ← C + (n − 1) S (12.21)
k4
Experiments were performed with Sigma Aldrich silica particles and
MagPrep silica particles (MagPrep silica particles (70912) from Merck)
as a function of time by using different buffer solution at pH 5 such as in
6 M sodium perchlorate (SP), acetic acid containing 400 mM K+ (AA),
244 Applied Chemistry and Chemical Engineering: Volume 4

glycine containing 400 mM KCl (GL), or sodium citrate containing 400

mM KCl. MagPrep beads and Sigma Aldrich silica particle were used in
different amounts. Tubes loaded with 250 μg magnetic beads were filled
with 100 ng/μL salmon sperm DNA in 150 μL of the buffer under investi-
gation. Aldrich silica was used 3–6 mg amount 200 ng/μL salmon sperm
DNA for experiments using sodium perchlorate buffer or 80 ng/μL for
all other buffers. Sodium perchlorate buffer solution has great effect on
DNA adsorption on both types of silica material as seen in Figure 12.2.
Buffer ions play a role in the DNA adsorption process further than simply
adjusting the pH.

FIGURE 12.2  (a) DNA adsorbed to silica (mass per unit area) at pH 5 and (b) total DNA
adsorbed to 250 μg of MagPrep silica particles as a function of buffer (gray). (Reprinted with
permission from Vandeventer, P. E.; Lin, J. S.; Zwang, T. J.; Nadim, A.; Johal, M. S.; Niemz, A.
Multiphasic DNA Adsorption to Silica Surfaces Under Varying Buffer, pH, and Ionic Strength
Conditions. J. Phys. Chem. B 2012, 116(19), 5661–5670). © 2016 American Chemical Society.)

In the present study, adsorption equilibrium and kinetics of calf thymus

DNA on silica, alumina, and hydroxyapatite from aqueous solutions at
different pH values is aimed to be investigated. Calf thymus DNA adsorp-
tion was determined by using Nano Drop method for this purpose. The fit
of experimental data to different adsorption and kinetic models was investi-
gated by linear regression analysis.

12.2  MATERIALS AND METHODS

12.2.1 MATERIALS

Calf thymus DNA was used and supplied by Sigma Aldrich (D1501) and it
is used in adsorption experiments. Zeta potential measurements by Yetgin
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 245

and Balkose 24 showed that calf thymus DNA in aqueous solutions had
isoelectric point near pH 2 value and their particle size ranged from 300 to
800 nm and it was 490 nm on the average. As adsorbent, alumina (Al2O3),
silica (SiO2), and hydroxyapatite (HA) (Ca10(P04)6(OH)2) were used. HAP
had Ca/P mass ratio of 2.71.23. Silica (Sigma Aldrich-Silicagel, Grade 7744
pore size 60 Å, 70-230 mesh) and alumina was obtained from Seydişehir in
Turkey and hydroxyapatite was supplied by Sigma Aldrich (23093-6). The
average particle sizes of silica, alumina, and hydroxyapatite was 162 and
59 µm, and 102 nm, respectively.23 Their pore sizes are 5.7, 5.5, and 6.2 nm
for alumina, silica, and hydroxyapatite, respectively. The BET surface area
values were 108, 571, and 69 m2/g for alumina, silica, and hydroxyapatite,
respectively.23

12.2.2 METHODS

12.2.2.1  ADSORPTION EXPERIMENTS

Before the adsorption experiment, all adsorbents were dried at 120°C for
18 h under vacuum. In order to the control the adsorption of buffer solu-
tion, adsorbents were controlled free of DNA. Blank control of UV analysis
is done as in the following to adsorbent surface and release of ingredients
from the adsorbent to buffer solution 1.5 cm3 buffer was equilibrated with
0.0075 g of adsorbent. UV spectrum of the supernatant was taken. The DNA
concentration has been estimated at 260 nm using a standard curve obtained
by measuring absorbance of a series of solutions of known DNA concen-
trations by spectrophotometric method. This method is applied by Nano-
Drop 2000 (Thermo Scientific ND 1000). DNA solutions were prepared in
10–20–40–60–80–100 ng/µL range for obtaining the calibration curve. The
following buffer solutions in Table 12.1 were prepared to obtain solutions
with pH values 2–9.
Stock solutions of DNA were diluted with pH buffer solutions to obtain
the 10–100 ng/µL concentration range. Subsequently, 0.0075 mg of adsor-
bent (SiO2, Al2O3, and HA) was added to the 1.5 mL DNA solutions to get
a solid to liquid ratio 5 g/dm3, and DNA concentration of the supernatant
was measured after mixing at 100–200 rpm by Fine PCR mixer incubator at
25°C for 24 h. Cation addition effect was tested by adding 0.5 and 20 mM
MgCl2 into the DNA stock solution at pH 5.
246 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 12.1  The Buffer Solutions with Ionic Strength 0.001 M.

pH Buffer type
2 Glycin-HCl
3 Potassium hydrogen phthalate-HCl
4 Potassium hydrogen phthalate-HCl
5 Acetate
6 Acetate
7 Phosphate buffer
8 Phosphate buffer
9 Phosphate buffer

12.2.2.2  ADSORPTION KINETICS

In total, 0.008 mg of adsorbent (SiO2, Al2O3, or HAP) was added to the 1.6
mL 100 ng/µL DNA concentration solutions to keep a solid to liquid ratio 5
g/dm3. Kinetic measurements were carried out at 25°C under constant stirred
conditions for maximum 3 h by Fine PCR mixer incubator. About 2–4 µL
supernatant sample was taken at each time interval. Separated samples were
stored in clean Eppendorf tubes until analyses. Data were collected for each
pH with respect to time.
For the control of adsorption of buffer solution to adsorbent surface and
release of ingredients from the adsorbent to buffer solution, 1.5 cm3 buffer
was equilibrated with 0.0075 g of adsorbent and blank measurement was
done by taking the UV spectrum of the supernatant. The DNA concentration
has been estimated at 260 nm using a standard curve obtained by measuring
absorbance of a series of solutions of known DNA concentrations by spec-
trophotometric method. This method was applied again by Nano Drop 2000
(Thermo Scientific ND 1000).

12.3 RESULTS

12.3.1  ADSORPTION EQUILIBRIUM

Charging of solid surfaces in aqueous environments is change with the pH of

the aqueous solutions. DNA molecule is negatively charged due to phosphate
groups when the pH is above the isoelectric point. Therefore, surface charge
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 247

inevitably influences adsorption phenomena considering the role played in

electronic interaction. Therefore, pH 5 is the optimum value that figures out
influence of other parameters on adsorption process, which is away from
DNA isoelectric point (pH 2) and thus, makes the DNA stable. Structural
or chemical properties might impact on DNA purification method. Adsorp-
tion isotherms of DNA on silica alumina and hydroxyapatite are shown at
different pH values.
The isoelectric point of DNA used in the present study was at pH 2.24 The
isoelectric points of silica, alumina, HAP were reported to be 2,22 9,18 and
89, respectively. DNA is negatively charged above pH 2. Since silica surface
is also negatively charged above pH 2, the adsorption of DNA should be
due to hydrogen bonding, Van der Waals attractions between silica and
DNA. Alumina and DNA had opposite surface charges between pH 2 and
9, thus ionic attractions play an important role on adsorption on alumina.
The surface charge of HAP is positive up to pH 8. Thus, ionic attractions
between DNA and hydroxyapatite had a great contribution to the adsorption
on HAP. DNA adsorption isotherms for silica, alumina and hydroxyapatite
at different pH values are seen in Figures 12.3–12.5.

FIGURE 12.3  DNA adsorption on Silica at different pH values.

248 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 12.4  DNA adsorption on Alumina at different pH values.

FIGURE 12.5  DNA adsorption on HAP at different pH values.

Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 249

Cation addition was also tested by adding MgCl2 into the DNA stock
solution. Also, 0.5 and 20 mM MgCl2 were tested. Adsorption isotherms
about this situation are shown in Figures 12.6 and 12.7, respectively.
Consequently, adsorbents adsorption capacities were enhanced. Mg2+ ions
help the DNA adsorption onto the surface as a bridge. Approximately 3
mg/g adsorption capacity of HAP is greater than fine organic clay minerals
and montmorillonite (1 mg/g) reported in Cai et al.2 at 0.5 mM MgCl2
concentration and with 25 g/dm3 solid to liquid ratio. However, at 20 mM
MgCl2 concentration clay minerals, DNA adsorption capacities are greater
than HAP. It should be considered that their initial concentration is 200 µg
salmon sperm DNA in 400 µL tris buffer, which is higher than this study’s
initial concentration.

FIGURE 12.6  Adsorption on Silica, Alumina, and HAP at pH 5 with 0.5mM MgCl2.

As a summary, Figure 12.8 shows the adsorption capacity of all adsor-

bents at pH 2–9. HAP has always higher adsorption capacity than silica
and alumina. The results indicate that there is significant potential for the
removal of DNA from aqueous solution using HAP as an adsorbent. Nano
sized HAP which has Ca/P mol ratio of 2.0 is promising adsorbent for DNA
purification. DNA’s phosphate part can easily attract calcium ions.
250 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 12.7  DNA adsorption on Silica, Alumina, and HAP at pH 5 with 20mM MgCl2.

MgCl2 addition enhanced the adsorption capacity as shown in Figure

12.9. As the divalent cation molarity increase from 0.5 to 20 mM, adsorp-
tion capacity was enhanced but not proportionally.

FIGURE 12.8  Calf thymus DNA removal % by Silica Alumina and HAP versus pH values.
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 251

FIGURE 12.9  Calf thymus DNA removal % by Silica Alumina and HAP versus divalent
cation addition at pH 5.

12.3.1.1  ADSORPTION ISOTHERMS

Sorption isotherms data shown in Figures 12.3- 12.5 can be subject to the
Langmuir (eq 12.2) and Freundlich (eq 12.3) plots. The Langmuir plots
yielded two important parameters: Langmuir monolayer capacity, Qo, giving
the amount of DNA required to occupy all the available sites in unit mass
of the adsorbent, and the Langmuir equilibrium parameter, b, related to the
equilibrium constant. The Freundlich model gives parameters Kf and n.
Parameters of Langmuir and Freundlich models for adsorption of DNA at
different values are shown in Table 12.2. The regression coefficients were
not different for Langmuir and Freundlich models. Negative Qo and b values
were found for silica at pH 3 and pH 5 with MgCl2 and alumina at pH 9 with
high regression coefficients indicated, the adsorption did not fit to Langmuir
model. The negative n value found for Alumina at pH 8 shows the Freun-
dlich model was not followed. Freundlich model regression coefficients
were lowered when MgCl2 was added.
252 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 12.2  Parameters of Langmuir and Freundlich Models for Calf Thymus DNA
Adsorption Isotherms.
pH Adsorbent Langmuir Freundlich
R2
Qo b R2
Kf n
2 Silica 0.992 4347.8 0.0022 0.932 127.7 1.41
Alumina 0.967 7142.8 0.0344 0.964 437.03 1.66
HAP 0.997 9090.9 0.0125 0.984 188.67 1.35
3 Silica 0.982 −3333 −0.0058 0.878 0.064 0.404
Alumina 0.996 40000 0.0019 0.993 95.37 1.083
HAP 0.997 30703 0.0045 0.992 157.3 1.096
4 Silica 0.909 76.16 0.3730 0.942 23.98 14.81
Alumina 0.909 16826 0.0093 0.997 16.74 1.06
HAP 0.999 70338 0.0711 0.72 305.8 0.89
5 Silica 0.995 584.79 0.747 0.959 408.9 11.21
Alumina 0.861 172.4 0.988 0.88 258.8 2.07
HAP 0.772 8333 0.0201 0.79 364.1 1.68
6 Silica 0.912 524.1 0.094 0.934 104.3 2.83
Alumina 0.912 524.1 0.094 0.883 142.9 3.59
HAP 0.928 3333 0.011 0.986 27.7 1.04
7.4 Silica – – –
Alumina 0.785 6.48 0.072 0.776 1.288 3.32
HAP 0.811 101 0.125 0.947 19.15 2.668
8 Silica 0.914 6.39 0.201 0.835 1.47 1.232
Alumina 0.991 20.37 0.093 0.769 250.1 −15.52
HAP 0.968 169.49 0.129 0.947 420.8 3.087
9 Silica 0.857 60.79 0.068 0.764 7.0 1.973
Alumina 0.624 −5000 −0.029 0.893 813.8 1.612
HAP 0.936 1449.2 0.072 0.875 204.8 2.158
pH 5 and 0.5 mM MgCl2 Silica 0.9 −357.1 −0.012 0.651 6.86 1.07
Alumina 0.86 1111 0.281 0.849 464 4.89
HAP 0.959 2500 0.222 0.962 796.3 3.40
pH 5 and 20 mM MgCl2 Silica 0.915 −714.2 −0.011 0.909 464.1 4.87
Alumina 0.817 1666.7 0.055 0.571 228.14 2.24
HAP 0.712 5000 0.042 0.823 2335 7.8

Dubinin–Radushkevich(D-R) model eq 12.5 was also applied to obtained

experimental data. Parameters of qm, K, and energy (E) were determined
and listed in Tables 12.3–12.5. Regression coefficients of D–R isotherm
models for silica alumina and HAP were lower than 0.92, 0.97, and 0.95,
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 253

respectively. Model parameter could not be obtained at some pH values such

as for silica at pH 8, alumina at pH 5, and HAP at pH 3. Furthermore, no
reliable data were obtained in the presence and absence of MgCl2 at pH 5
for silica. It should be noted that D–R adsorption isotherm is formulated for
microporous materials. Silica has the highest micropore volume among to
all adsorbents. All energy values were lower than 8 kJ/mol therefore, DNA
adsorption on silica, alumina, and HAP were all physical adsorption.

TABLE 12.3  Dubinin–Radushkevich Parameters for Silica at 25°C.

pH value qm (ng/mg) K (mol2/kJ2) R2 E (kJ/mol)
2 1.3 × 1010 2.440 0.92 0.453
4 4.49 × 102 0.057 0.86 2.972
5 5.1 × 103 0.304 0.23 1.282
6 6.06 × 103 0.432 0.74 1.076
9 1.2 × 107 1.929 0.65 0.509
20 mM MgCl2 9.1 × 106 1.504 0.91 0.557

TABLE 12.4  Dubinin–Radushkevich Parameters of Calf Thymus DNA for Alumina at 25°C.
pH value qm (ng/mg) K (mol2/kJ2) R2 E (kJ/mol)
2 2.3 × 10 8
1.741 0.97 0.536
4 1.31 × 105 0.455 0.80 1.048
6 2.44 × 104 0.631 0.87 0.890
7 6.32 × 103 0.780 0.88 0.801
8 8.39 × 103 0.611 0.97 0.904
9 4.12 × 105 0.631 0.91 0.890
0.5 mM MgCl2 4.8 × 103 0.234 0.79 1.463
20 mM MgCl2 1.91 × 104 0.444 0.60 1.061

TABLE 12.5  Dubinin–Radushkevch Parameters of Calf Thymus DNA for HAP at 25°C.
pH value qm (ng/mg) K (mol2/kJ2) R2 E (kJ/mol)
2 4.3 × 106
1.075 0.95 0.682
4 5.45 × 104 0.135 0.94 1.925
5 5.2 × 103 0.138 0.95 1.903
6 1.08 × 1010 2.509 0.95 0.446
7 3.39 × 103 0.222 0.73 1.499
8 1.65 × 104 0.377 0.86 1.151
9 1.17 × 104 0.374 0.82 1.156
0.5 mM MgCl2 9.12 × 103 0.210 0.83 1.544
254 Applied Chemistry and Chemical Engineering: Volume 4

It is known that DNA adsorption is possible because DNA has negative

charge due to the phosphate backbone above its isoelectric point, it can make
hydrogen bond with the solid surfaces and there are Van der Waals attractions
between DNA and the surfaces. Calf thymus DNA used in the adsorption exper-
iment had an isoelectric point less than pH 2.2. Zeta potential measurement
showed that the α-alumina has isoelectric point at nearly pH 9.1.18 The isoelec-
tric points of silica, alumina, and HAP were reported to be 2, 9, and 8, respec-
tively. DNA was negatively charged above pH 2.2. Since the silica surface was
also negatively charged above pH 2, the adsorption of DNA on silica should
be due to hydrogen bonding and Van der Waals attractions. Alumina and DNA
had opposite surface charges between pH 2 and 9, thus ionic attractions play an
important role on adsorption of DNA on alumina. The surface charge of HAP
was positive up to pH 8. Thus, ionic attractions between DNA and hydroxyapa-
tite had a great contribution to the adsorption of DNA on HAP.

12.3.2  ADSORPTION KINETICS

12.3.2.1  PSEUDO-FIRST- AND SECOND-ORDER MODELS

Experimental data show that those adsorptions occurred in short time. Equi-
librium was generally achieved within 15 min as seen in Figures 12.10–12.18
that show the amount adsorbed DNA versus time curves for silica, alumina,
and hydroxyapatite at pH 2, pH 5, and pH 8. Pseudo-first-order (eq 12.8)

FIGURE 12.10  Pseoudo first order and second orders model fits for adsorption of DNA to
silica from pH 2 solution.
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 255

and pseudo-second-order (eq 12.11) model constants were determined by

nonlinear regression analysis of the experimental adsorbed amount (q) versus
time (t) data. In Figures 12.10–12.18 first-order model fits by nonlinear regres-
sion are shown. The first- and second-order model constants are reported in
Table 12.6, Table 12.7, and Table 12.8 for silica, alumina, and hydroxyapa-
tite, respectively. High correlation coefficients were obtained with pseudo-
second-order reaction than the pseudo-first-order reaction model.

FIGURE 12.11  Pseoudo first order and second orders model fits for adsorption of DNA to
silica from pH 5 solution.

FIGURE 12.12  Pseoudo first order and second orders model fits for adsorption of DNA to
silica from pH 8 solution.
256 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 12.13  Pseoudo first order and second orders model fits for adsorption of DNA to
alumina from pH 2 solution.

FIGURE 12.14  Pseudo first order and second orders model fits for adsorption of DNA to
alumina from pH 5 solution.
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 257

FIGURE 12.15  Pseoudo first order and second orders model fits for adsorption of DNA to
alumina from pH 8 solution.

FIGURE 12.16  Pseoudo first order and second orders model fits for adsorption of DNA to
HAP from pH 2 solution.
258 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 12.17  Pseoudo first order and second orders model fits for adsorption of DNA to
HAP from pH 5 solution.

FIGURE 12.18  Pseoudo first order and second orders model fits for adsorption of DNA to
HAP from pH 8 solution.
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 259

TABLE 12.6  The Reaction Model Parameters of Calf Thymus DNA on Silica at 25°C.
pH Pseudo first-order Pseudo second-order
qe (ng/mg) k1 1/min R2 qe, ng/mg k2, g/(mg.min) R2
2 8615 0.731 0.78 8821 1.46 × 10 −4
0.83
3 899 0.529 0.74 932 7.65 × 10−4 0.72
4 5605 0.010 0.94 8270 8.95 × 10 −7
0.94
5 2647 0.130 0.48 2750 1.66 × 10 −4
0.86
7.4 8449 0.495 0.89 8713 8.5 × 10−5 0.93
8 2483 1.992 0.59 2561 7.1 × 10 −4
0.63

TABLE 12.7  The Reaction Model Parameters of Calf Thymus DNA on Alumina at 25°C.
pH Pseudo first-order Pseudo second-order
qe (ng/mg) k1, 1/min R 2
qe (ng/mg) k2, g/(mg.min) R2
2 11420 0.876 0.87 11839 1.47 × 10 −4
0.96
3 2356 0.043 0.99 2635 2.28 × 10 −5
0.99
4 15973 0.026 0.98 19185 1.44 × 10−6 0.96
5 3175 0.297 0.77 3271 1.31 × 10 −4
0.78
7.4 6461 0.102 0.88 6672 3.27 × 10−5 0.91
8 2810 0.876 0.94 2872 4.3 × 10 −4
0.96

TABLE 12.8  The Reaction Model Parameters of Calf Thymus DNA on HAP 25°C.
pH Pseudo first-order Pseudo second-order
qe (ng/mg) k1, 1/min R 2
qe (ng/mg) k2, g/(mg.min) R2
2 14592 1.04 0.92 15333.9 1.42 × 10−4 0.91
3 8594 3.67 0.89 8664.7 1.18 × 10 −3
0.91
4 14157 11.05 0.82 14442.1 1.35 × 10 −3
0.91
5 7961 0.133 0.84 8574.7 2.1 × 10−5 0.91
7.4 4779 0.197 0.88 5132.4 5.4 × 10 −5
0.83
8 1283 0.029 0.72 1524.7 1.8 × 10−5 0.86

12.3.2.2  INTRAPARTICLE DIFFUSION

The initial stage of DNA adsorption was defined as kinetically very fast and
completed within about 15 min. After that, mechanism of intraparticle diffu-
sion becomes dominant. Diffusivity of DNA in the adsorbents was calcu-
lated by using the solution of the diffusion equation for the long time period
260 Applied Chemistry and Chemical Engineering: Volume 4

and is shown in Table 12.9. R2 values range obtained between 0.62 and 0.93
for Silica, 0.47 and 0.84 for Alumina, and 0.15 and 0.84 for HAP, as reported
in Table 12.8. Long-time diffusion coefficient—in other word intraparticle
diffusion rate was decreased significantly in the order of alumina, silica,
and HAP. The average pore diameter of alumina (5.7 nm) was greater than
that of silica (5.5 nm). Diffusion coefficient of DNA in alumina was deter-
mined to be nearly 10 times than in silica. HAP has the highest average pore
diameter value (6.2 nm) and on the contrary the smallest particle size (100
nm) in all adsorbents. Therefore, diffusion is not expected in HAP, thus the
diffusivity 10−20 m2/s is very low.

TABLE 12.9  Diffusivity of DNA in Silica, Alumina, and HAP at 25°C.

pH Silica Alumina HAP
D (m2/s) R2 D (m2/s) R2 D (m2/s) R2
2 7.8 × 10−15
0.75 2.5×10−14
0.86 5.2 × 10−19
0.87
3 5.3 × 10−16
0.45 – – 9.6 × 10−21
0.88
4 1.5 × 10−15 0.82 1.5×10−14 0.56 7.34 × 10−20 0.90
5 7.3 × 10−16
0.73 1.1×10−14
0.66 8.2 × 10−20
0.89
7.4 2.5 × 10−15 0.75 1.5×10−14 00.87 6.2 × 10−20 0.94
8 – – 1.6×10−14
0.74 6.2 × 10−20
0.57

12.4 CONCLUSIONS

DNA is adsorbed to the surfaces by ionic bonds, by Van der Waals attrac-
tions and by hydrogen bonds. Calf thymus DNA used in the adsorption
experiment had an isoelectric point less than pH 2.2. The isoelectric points
of silica, alumina, and HAP were reported to be 2, 9, and 8, respectively.
DNA was negatively charged above pH 2. Since the silica surface was also
negatively charged above pH 2, the adsorption of DNA on silica should
be due to hydrogen bonding and Van der Waals attractions. Alumina and
DNA had opposite surface charges between pH 2 and 9, thus ionic attrac-
tions play an important role on adsorption of DNA on alumina. The surface
charge of HAP was positive up to pH 8. Thus, ionic attractions between
DNA and hydroxyapatite had a great contribution to the adsorption of
DNA on HAP.
Enhancements of the adsorption capacities of adsorbents were obtained
with the addition of MgCl2. The adsorption capacity of DNA on adsorbents
increased when divalent cation molarity was changed from 0.5 to 20 mM.
Adsorption of DNA on Silica, Alumina, and Hydroxylapatite 261

The adsorption isotherms of DNA on silica, alumina and HAP were

fitted to Langmuir model better than Freundlich model and Dubinin–Radu-
shkevich model. Higher correlation coefficients were obtained with pseudo-
second-order model than the pseudo-first-order reaction model in adsorption
kinetics of DNA. The DNA adsorption to the external surface of the particles
was very fast kinetically and accomplished within about 15 min. After that,
intraparticle diffusion mechanism becomes dominant. Intraparticle diffusion
coefficient decreased significantly in the order of alumina, silica, and HAP.
The kinetic models, reaction, and diffusion models showed that adsorption
at the external surface was dominant at initial stages of the DNA adsorption
and it was followed by slower intraparticle diffusion.

KEYWORDS

•• adsorption
•• DNA
•• silica
•• alumina
•• hydroxylapatite

REFERENCES

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Specific Binding and Combing of DNA. Biophys. J. 1997, 73, 2064–2070.
2. Cai, P.; Huang, Q.; Jiang, D.; Rong, X.; Liang, W. Microcalorimetric Studies on the
Adsorption of DNA by Soil Colloidal Particles. Colloids Surf. B Biointerfaces 2006,
49, 49–54.
3. Chattoraj, D. K.; Mitra, A. Adsorption of DNA at Solid–Water Interfaces and
DNA–Surfactant Binding Interaction in Aqueous Media. Curr. Sci. 2009, 97(10),
1430–1438.
4. Dias, R. S.; Lindman, B. DNA Interactions with Polymers and Surfactants; John Wiley
& Sons: New Jersey, 2008.
5. ……Do, D.D. Adsorption Analysis: Equilibria and Kinetics. Imperial College Press,
London, 1998
6. Erdoğan, B. C.; Ülkü, S. Cr(VI) Sorption By Using Clinoptilolite and Bacteria Loaded
Clinoptilolite Rich Mineral. Microporous Mesoporous Mater. 2012, 152, 253–261.
7. Ho, Y. S.; Mckay, G. Research Note the Sorption of Lead (Ii) Ions on Peat. Water Res.
1999, 33(2), 578–584.
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8. Ho, Y. S.; Ng, J. C. Y.; Mckay, G. Kinetics of Pollutant Sorption by Biosorbents Review.
Sep. Purif. Methods 2000, 29(2), 189–232.
9. Komulski, M. pH Dependent Surface Charging and Points of Zero Charge IV. Update
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10. Lagergren, S. About the Theory of So-Called Adsorption of Soluble Substances. Kung-
liga Svenska Vetenskapsakademiens. Handlingar 1898, 24, 1–39.
11. Lorenz, M. G.; Wackernagel, W. Bacterial Gene Transfer by Natural Genetic Transfor-
mation in the Environment. Microbiol. Rev. 1994, 58(3), 563–602.
12. Malash, G. F.; El-Khaiary, M. I. Piecewise Linear Regression: A Statistical Method for
the Analysis of Experimental Adsorption Data by the Intraparticle-Diffusion Models
Chem. Eng. J. 2010, 163, 256–263.
13. Mathews, A. P.; Weber, W. J. Effects of External Mass Transfer and Inter-particle Diffu-
sion on Adsorption. Phys. Chem. Waste Water Treat. AIChE Symp. Ser. 7 1976, 3, 91–98.
14. Melzak, K. A.; Sherwood, C. S.; Turner, R. B. F.; Haynes, C. A. Driving Forces for
DNA Adsorption to Silica in Perchlorate Solutions. J. Colloid Interface Sci. 1996, 181,
635–644.
15. Nguyen, T. H.; Chen, K. Role of Divalent Cations in Plasmid DNA Adsorption to Natural
Organic Matter-Coated Silica Surface. Environ. Sci. Technol. 2007, 41, 5370–5375.
16. Nguyen, T. H.; Elimelech, M. Adsorption of Plasmid DNA to a Natural Organic Matter-
Coated Silica Surface: Kinetics, Conformation, and Reversibility. Biomacromolecules
2007, 8, 24–32.
17. Parida, S. K.; Dash, S.; Patel, S.; Mishra, B. K. Adsorption of Organic Molecules on
Silica Surface. Adv. Colloid Interface Sci. 2006, 121, 77–110.
18. Polat, M; Sato, K.; Nagaoka, T.; Watari, K. Effect of pH and Hydration on The Normal
and Lateral Interaction Forces between Alumina Surfaces. J. Colloid Interface Sci.
2006, 304, 378–387.
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tion Kinetic Models. J. Zhejiang Univ. Sci. A. 2009, 10(5), 716–724.
20. Romanowski, G.; Lorenz, M. G.; Wackernagel, W. Adsorption of Plasmid DNA to
Mineral Surfaces and Protection against DNase I. Appl. Environ. Microbiol. 1991, 7,
1057–1061.
21. Ruthven, D. Principles of Adsorption and Adsorption Processes; John Wiley and Sons:
New York, 1984.
22. Vandeventer, P. E.; Lin, J. S.; Zwang, T. J.; Nadim, A.; Johal, M. S.; Niemz, A. Multi-
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CHAPTER 13

THERMAL BEHAVIOR OF SODIUM

SALT OF CALF THYMUS DNA
AYSUN TOPALOĞLU1, GÜLER NARIN2,*, and DEVRIM BALKÖSE1
Department of Chemical Engineering, Izmir Institute of Technology,
1

Gulbahce 35430, Urla Izmir, Turkey

2
Department of Chemical Engineering, Uşak University, Uşak, Turkey
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.....................................................................................................264
13.1 Introduction....................................................................................264
13.2 Materials and Methods...................................................................271
13.3 Results and Discussion...................................................................273
13.4 Conclusions....................................................................................300
Keywords..................................................................................................301
References.................................................................................................302
264 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

Dehydration, melting, and thermal degradation of sodium salt of calf thymus

DNA in dry state were investigated. For investigation of kinetics of reactions
taking place during the nonisothermal heating, thermal gravimetric analysis
(TGA) data recorded at different heating rates were analyzed using various
model-free isoconversional methods. Differential scanning calorimetry
(DSC) analysis was performed both in open and hermetically sealed cells.
Melting temperature of the DNA was higher in the sealed cells (110°C) than
in the open cells (80°C). The residues formed after the DNA was repeat-
edly heated and cooled in sealed DSC cells were analyzed by transmittance
Fourier transform infrared (FTIR) spectroscopy. These residues were also
analyzed by scanning electron microscope (SEM) for the morphological
changes. The original fibrous form of the DNA turned to a black residue
during heating to 175°C in the hermetically sealed cells with upper pressure
limit of 0.3 MPa. Microbubbles indicating the intumescence characteristic
of the DNA were observed on the surface of the residues. In the transmission
FTIR spectrum of the residue obtained by heating the DNA to 600°C under
nitrogen flow, bands characteristics for inorganic phosphates were detected.
The DNA was also analyzed in situ by diffuse reflectance infrared Fourier
transform (DRIFT) spectroscopy during heating/cooling under vacuum. The
results were discussed based on the effects of heating rate and reaction atmo-
sphere on the intumescence behavior of the DNA.

13.1 INTRODUCTION

Deoxyribose nucleic acid (DNA) molecule is the storage site for genetic infor-
mation and fulfils the replication of that information during the cell division.1
DNA is a biopolymer composed of repeating units of nucleotides. A nucleo-
tide unit consists of the segment of the backbone of the molecule which holds
the chain together and also a nucleobase (purines and pyrimidines) which
interacts with the other DNA strand in the helix. Alternating phosphate and
sugar (deoxyribose) molecules form the backbone of the DNA strand. The
sugars are linked together by phosphodiester bonds between the third and fifth
carbon atoms of the adjacent sugar rings. The helix of the DNA is held by
two forces: hydrogen bonds between nucleotides and base-pairing interaction
of the nucleobases. DNA has been investigated for various applications like
DNA-based drugs, recombinant DNA for the production of industrial micro-
organisms, biosensor development, environmental monitoring, and so on.2–5
Thermal Behavior of Sodium Salt of Calf Thymus DNA 265

Since there is a close correlation between the biological function of DNA

and its structure, understanding the relation of water to DNA is of both prac-
tical and fundamental importance. The stability and conformational integ-
rity of DNA are largely controlled by the interactions with the surrounding
water molecules.6–8 Two factors are mainly responsible for the stability of
the DNA double helix: base-pairing between complementary strands and
stacking between adjacent bases.9 Water is essential to the stabilization of
the secondary and tertiary structures, thereby biologically active structures
of DNA. DNA has been shown to exist in a variety of secondary structures
or conformations such as right-handed double-helical A, B, C, and D forms
and the left-handed double-helical Z form.8 One of the important factors in
determining the conformation of DNA is the degree of hydration. At high
relative humidity (≥90%), DNA fibers or films adopt the B conformation at
room temperature. As the relative humidity is reduced to a certain threshold,
the decrease in hydration leads to the transformation of B-DNA into other
conformations, depending on the DNA sequence and the nature of the coun-
terions involved.10 There are two kinds of hydration shells around DNA: the
water molecules which hydrate the DNA helix up to a relative humidity of
about 80% form the tightly bound primary hydration shell (about 20 water
molecules per nucleotide that hydrate the phosphate, sugar, and base) while
those which adsorbed at higher humidities form the more loosely bound
secondary hydration shell.11 In the primary hydration shell, at least 11–12
water molecules per nucleotide (wpn) that are directly bound to the DNA are
incapable of crystallization to ice upon cooling to temperatures well below
0°C.12 These tightly bound water molecules in the primary shell constitute
an integral part of the stability of DNA-ordered structures. These water
molecules are difficult to remove and their removal leads to the collapse of
the double helical structure of DNA. In the absence of water, the ordered
conformation is lost and base stacking is destroyed.13–18 All three molecular
subgroups in DNA (the heterocyclic bases, deoxyribose, and the diesterified
phosphate groups) provide sites where water molecules can be adsorbed.11
Presumably, specific water–DNA interactions arise primarily from hydrogen
bonding to the groups on the edges of the bases facing the grooves of the
double helix and to a lesser extent from hydrogen bonding to the sugars and
phosphate groups.8
The structural changes during the melting of DNA include disruption
of base pairs, unstacking of the bases, and disordering of the deoxyribose–
phosphate backbone.19 It is known from infrared (IR) spectroscopic studies
that the structural changes of DNA induced by dehydration are reversible
upon rehydration.14,15 Duguid and coworkers used differential scanning
266 Applied Chemistry and Chemical Engineering: Volume 4

calorimetry (DSC) and laser Raman spectroscopy to probe the energetic

and structural changes that accompany melting of the B form of DNA of
160 base pair fragments of calf thymus DNA in solution. Raman bands
diagnostic of purine and pyrimidine unstacking, conformational rearrange-
ments in the deoxyribose–phosphate moieties, and changes in environment
of phosphate groups have been identified. Melting behaviors of the sepa-
rate Raman markers (834, 1240, and 1668 cm−1) have been correlated with
one another over the temperature interval 11–93°C. From the DSC results,
the standard thermodynamic parameters (vant Hoff enthalpy and effective
number of base pairs in a cooperative melting) were obtained and correlated
with the localized structural changes monitored by Raman spectroscopy.
The changes observed in specific Raman band frequencies and intensities as
a function of temperature revealed that thermal denaturation was accompa-
nied by disruption of Watson–Crick base pairs, unstacking of the bases, and
disordering of the B-form backbone. These three types of structural change
were highly correlated in the temperature range of 20–93°C.19
There are relatively few published works on the thermal stability of
nucleic acids at low hydration.20–25 Falk and coworkers investigated hydra-
tion of solid calf thymus DNA (NaDNA) gravimetrically as a function of
relative humidity at 21°C. The Brunauer–Emmett–Teller (BET) model
fitted the data between 0% and 80% relative humidity. It was found that
two molecules of water are strongly bound to each phosphate group with
energy about 8.4 kJ, higher than that for the adsorption of water molecules.
Above 75% relative humidity, the water molecules hydrate the C=O groups
and ring nitrogen atoms fill the grooves of the DNA helix. This process is
completed by about 80% relative humidity and further hydration of DNA is
accompanied by swelling. All exposed hydration sites are probably filled at
this point.13
From the frequency and intensity changes of infrared bands of solid
films of calf thymus LiDNA and NaDNA as a function of relative humidity,
Falk and colleagues defined five preferred hydration sites. These sites have
different binding affinities for the water of hydration. The PO2−Na+ groups
(phosphate groups of the phosphodiester backbone) become hydrated
at relative humidity below 65% (about six water molecules are adsorbed
completing the hydration of the phosphate group), while the hydration of
the bases begins at higher relative humidities. Above 65% relative humidity,
the C=O groups and the ring nitrogen atoms became hydrated. The strength
of hydrogen bonding is greatest for the first water molecules adsorbed and
decreases thereafter, approaching the strength of hydrogen bonding of liquid
water.23
Thermal Behavior of Sodium Salt of Calf Thymus DNA 267

Falk and coworkers investigated polarized infrared and ultraviolet

spectra of oriented films of the NaDNA as a function of relative humidity. It
was concluded that DNA films were stable in the B configuration at relative
humidity values as low as 75% and that at still lower humidities a revers-
ible transition occurs to a disordered form in which the bases are no longer
stacked one above another and are no longer perpendicular to the axis of the
helix. The loss of base stacking upon drying suggested that the B configura-
tion of DNA was stabilized by the stacking of the bases in the presence of
water.14
In another study, Falk and colleagues measured the width of OH
stretching infrared absorption band (3400 cm−1) of water bound to solid calf
thymus DNA as a function of temperature. It was found that the first 10 water
molecules per base pair in the primary hydration shell do not freeze into an
ice-like state at temperatures down to −150°C. An additional intermediate
layer of about 3 wpn crystallizes with difficulty and tends to supercool if the
cooling rate is high.24
Lee and coworkers investigated thermal denaturation of salmon testes
NaDNA at low water contents (1–12 wpn) as a function of temperature using
DSC and IR spectroscopy in the temperature range from −10°C to 160°C.
The samples with different moisture contents (1–12 wpn) were analyzed by
DSC in closed cells. The DSC curves demonstrated a sharp endothermic
maximum near 90°C in the first DSC scan for the sample with 12 wpn. This
peak became broader, less intense, shifted to lower temperatures as the initial
wpn of the DNA decreased (up to 6.3 wpn), and eventually vanished at 3.3
wpn due to the loss of ordered structure upon dehydration, as confirmed
by the IR data. During the second scan, this endothermic maximum was
replaced by a step increase in the heat flow curve for the samples with
3.3–4.7 wpn. DNA thermal denaturation in the 3.3–12 wpn range was irre-
versible but structural disruptions caused by dehydration were fully revers-
ible. The calorimetric manifestation of the glass transition was established
for denatured DNA at low hydration.22
Abdurakhman and coworkers studied effects of hydration on the struc-
ture of poly(dG)–poly(dC) DNA using infrared spectroscopy. The water
content of the samples reduced as temperature increased and reached a very
low value of about 0.1 wpn above 120°C. As humidity was lowered to 0%,
the water content decreased to 1 wpn. The molecular vibrations, which char-
acterize the backbone structure and base stacking and pairing, indicated that
the samples maintained an A-form double helical structure at all the values
of water content. The disorder in the base stacking was observed as a result
of the decrease in the water content. Denaturation at high temperatures above
268 Applied Chemistry and Chemical Engineering: Volume 4

100°C was reversible with the decreasing temperature. At high temperature,

the disorder was accompanied by denaturation, where the changes in the
backbone occurred.25
Whitson and coworkers measured the enthalpy of desorption of the
water of primary hydration bound to wet-spun films of CsDNA at 59% rela-
tive humidity by DSC as 30.88 kJ/mol H2O. The net activation energy for
desorption of this water from CsDNA was calculated as 60.8 kJ/mol H2O
from the DSC data by the Kissinger method.26
Hoyer and coworkers performed DSC experiments on desorption of
water from poly(A) or DNA in the region of less than 10 water molecules
per base pair. A broad endothermic transition centered near 70°C in the DSC
thermogram was interpreted as being due to desorption of the water of hydra-
tion. For hydrations above 10 water molecules per base pair, the enthalpy of
the desorption was the same as that for bulk water (about 41.9 kJ/mol) and
increased to about 126 kJ/mol at two water molecules per base pair.27
Marlowe and colleagues performed DSC experiments on hydrated wet-
spun films of calf thymus Cs, K, and NaDNA (with about eight water mole-
cules per base pair) to study effect of counterions on binding of the water of
primary hydration. Two prominent features were revealed by DSC: a broad
endothermic transition near 75°C due to desorption of the primary water of
hydration and a sharp exothermic transition near 240°C due to pyrolysis of
the sample. The temperatures of both transitions increased with the increasing
heating rate. The DNA films which were heated at a scan rate of 10°C/min to
180°C once yielded crystalline diffraction patterns indicating that A-DNA-
like helices were preserved (even at very low relative humidity). But heating
to 180°C thrice destroyed the double helical structure of DNA as well as the
crystallinity of the sample.18
Lavalle and coworkers measured the water content and swelling of wet-
spun films of calf thymus Na, K, Rb, and CsDNA as a function of rela-
tive humidity. The water content of the films was independent of coun-
terion species. The A to B transition occurred at different relative humidity
values implying that the intermolecular interactions were quite different in
the DNAs with different counterions. The swelling experiments revealed
that the intermolecular bonds changed in a very similar manner up to 84%
relative humidity. Dramatic and irreversible changes were observed in the
dimensions of the films above 84% relative humidity.10
Understanding of DNA degradation is important for studies that use or
target DNA, as well as for biomedical applications such as thermal targeting
of DNA in cancer cells. Such targeting can be achieved, for example, by
using localized heating with gold nanoparticles.28 Knowledge on DNA
Thermal Behavior of Sodium Salt of Calf Thymus DNA 269

degradation can also be used in obtaining purines and pyrimidines. The

sublimation of adenine, cytosine, guanine, and thymine from λ-DNA was
tested under reduced pressure (0.13 kPa) at temperatures above 150°C. With
the exception of guanine, ~60−75% of each base was sublimed directly (not
acid hydrolyzed prior to heating) from the λ-DNA and recovered on a cold
finger of the sublimation apparatus after heating to 450°C.29
Thermal degradation of pUC19 and pGY1 plasmids,28 λ-DNA,290 herring
sperm DNA,30,31 and NaDNA from salmon testes22 were previously investi-
gated. Karni and coworkers found that under dry conditions, degradation of
pGY1 and pUC19 plasmids occurs in a linear manner, starts at about 130°C
with complete degradation at around 190°C. Upon heating of the plasmids
to 170–200°C, aggregates of short DNA fragments were formed resulting
from incomplete degradation. After heating at 210°C, these fragments were
destroyed (complete degradation). Degradation of DNA in solution was
studied using a pressure system that prevents evaporation of the water. DNA
degradation occurred between 100°C and 110°C, much lower than under
dry conditions. This degradation temperature was lower than the boiling
temperature of water, a temperature range in which DNA does not degrade
when pressure is not applied. This result indicates that applying pressure (1
or 1.3 MPa) to a DNA solution greatly increases the sensitivity of DNA to
heating. It is possible that the pressure weakens the chemical bonds between
the atoms within the DNA molecule. Another possibility is that the exposure
to oxygen within the compressed air that was used to create the pressure
damaged the DNA and made it more sensitive to heat-induced degradation.
They could not determine the degradation of DNA in aqueous solution using
this method, since applying pressure on the DNA solution caused the DNA
to be more sensitive to heat and to degrade already above 90°C.28
Recently DNA was investigated as a novel green natural alternative to
organohalogen flame retardants. DNA’s fire retardant activity is related to
its intumescent-type thermal behavior. When an intumescent material is
subjected to a heat flow, it develops a multicellular foamed carbonaceous
shield (char) on its surface. This shield acts as a physical barrier able to limit
the heat, fuel, and oxygen transfer between flame and polymer, leading to
flame extinguishment.32,33
The intumescent behavior of DNA is due to its structure containing phos-
phate groups (produce phosphoric acid), deoxyribose units (act as a carbon
source, dehydrates to form char and release blowing gases), and nitrogen-
containing bases (release ammonia). Supramolecular assembled structure
of DNA in which the three components are molecularly organized is also
important for its “all-in-one” intumescent fire retardant behavior.30
270 Applied Chemistry and Chemical Engineering: Volume 4

Thermal degradation of DNA from herring sperm occurred through a

number of steps following the removal of adsorbed water (completed until
150°C). In the first degradation step (150−200°C), two sharp weight losses
were detected and a small amount of combustible volatiles were produced.
The chemical modifications involved in thermal degradation of DNA were
followed by the attenuated total reflectance (ATR) spectra of the residues
after heating at selected temperatures in the range of 180–600°C. In the
attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectra
of the residue heated to 180°C, changes in intensities/frequencies of the
bands at 3000 cm−1 (OH stretching vibrations), 890 cm−1 (sugar–phosphate
vibrations), 1260 cm−1 (PO2− asymmetric stretching), 1430–1475 cm−1 (base-
sugar vibrations), and 1660 cm−1 were observed. Water, CO2, and isocyanic
acid evolved in the 50−180°C range under air while OH groups appeared in
the residue. The DNA underwent a significant physical modification at this
stage: the original white DNA powder grains were blown to hard, blackish/
red closed cells which is the typical behavior of intumescent fire retardant
materials. At higher temperatures (180−230°C), the closed cells formed at
180°C disrupted likely due to increasing pressure of the gases trapped in the
cells. DNA from herring sperm transformed into a multicellular, foamed,
thermally insulating material at a relatively low temperature (160−200°C)
as compared with an intumescent model compound, pentaerythritol diphos-
phate (300−350°C). Furthermore, on heat exposure, the intumescent residue
was converted into a highly thermally stable ceramic-like material which is
resistant to thermal oxidation unlike organically derived intumescent chars
and hence preserved the intumescent fire barrier properties.30 It was also
shown that DNA can promote char formation either when coated on cotton
fabrics31–34 or on thick films of ethylene vinyl acetate copolymers.35
Very recently DNA was investigated as a flame retardant additive for
melt-compounded formulations with low-density polyethylene (LDPE) and
compared with LDPE compounded with melamine polyphosphate (MPP),
one of the industry standard intumescent FR additives for plastics. DNA
showed a much greater compatibility with the LDPE matrix than MPP.
Biochemical characterization of heat-treated DNA revealed that DNA under-
goes denaturation, fragmentation, and oxidation at 145°C.36
Using as a flame retardant agent requires bulk amounts of DNA, thus
the major drawback is the cost. However, advances in DNA extraction from
large-scale sources as well as its “all-in-one” intumescent formulation make
DNA competitive intumescent fire retardant material.
In the present study, dehydration, melting, and thermal degradation
kinetics of sodium salt of calf thymus DNA in dry state was investigated.
Thermal Behavior of Sodium Salt of Calf Thymus DNA 271

Kinetics of the reactions causing mass loss during the nonisothermal

heating in the 15−200°C range was investigated using various model-free
isoconversional methods. DSC analyses were performed both in open
and hermetically sealed cells at different heating rates. The residues of
the sealed cell DSC analysis, repeatedly heated/cooled in the temperature
range of 10−175°C, were analyzed by transmission IR spectroscopy. The
morphological changes in these residues were examined by scanning elec-
tron microscopy. Evolution of the IR bands during heating of the DNA
under vacuum was followed by in situ diffuse reflectance infrared Fourier
transform (DRIFT) spectroscopy.

13.2  MATERIALS AND METHODS

13.2.1 MATERIALS

Sodium salt of calf thymus DNA in fiber form from Sigma Aldrich (D1501)
was used in the experiments as received. It is referred to as DNA further
in the chapter for simplicity. It was stored at 4°C in refrigerator till it was
used. The DNA from calf thymus is 41.9 mole% G–C and 58.1 mole% A–T
with 2.94 wpn. The water content as received was measured as 11 wt% by
thermal gravimetric analysis (TGA).

13.2.2 METHODS

13.2.2.1  THERMAL GRAVIMETRIC ANALYSIS

Thermal gravimetric analysis of DNA was made by heating the samples

(5–10 mg) at 5, 10, and 15°C/min rates from 20°C to 600°C in Setaram
Labsys TGA under nitrogen gas flow.

13.2.2.2  DSC ANALYSIS

DSC analyses of DNA under nitrogen flow in open aluminum pans and in
hermetically sealed aluminum cells were performed using Shimadzu DSC
50 and TA instrument DSC Q10, respectively. The DNA samples were
analyzed by heating at 5, 10, and 15°C/min rates in open pans from room
temperature up to 600°C.
272 Applied Chemistry and Chemical Engineering: Volume 4

The DNA in hermetically sealed cells was heated at 5, 10, and 15°C/min
rates from 10°C up to 175°C, kept at this temperature for 10 min, then cooled
to room temperature at 5, 10, and 15°C/min rates and heated to 175°C again
at the same rate.

13.2.2.3  TRANSMISSION FOURIER-TRANSFORM INFRARED (FTIR)

ANALYSIS

FTIR spectra of the DNA as received, heated up to 600°C in open DSC cells
and heated–cooled–reheated in hermetically sealed cells, were taken with
KBr pellet technique using Shimadzu FTIR-8400. Two milligrams of DNA
was mixed with 200 mg KBr and the mixture was pressed into 1-cm diam-
eter pellets under 6 ton forces.

13.2.2.4  DIFFUSE REFLECTANCE INFRARED FOURIER TRANSFORM

(DRIFT) SPECTROSCOPY ANALYSIS

DRIFT spectra were recorded using a praying mantis diffuse reflection

attachment (Harrick Scientific Products Inc.) equipped with a high-
temperature, low-pressure reaction chamber fitted with CaF2 windows
(HVC-DRP, Harrick Scientific Products Inc.), and FTS 3000 MX spec-
trophotometer (Digilab Excalibur Series). We placed 0.1 g DNA in the
sample holder and after taking its spectrum at room temperature and 101.3
kPa pressure, the sample chamber was evacuated down to 0.1 Pa pres-
sure and heated up to 175°C at 2°C/min rate under vacuum. The DRIFT
spectrum of the sample was obtained at different temperatures during
its dynamic heating. The sample chamber was cooled to room tempera-
ture under vacuum and opened to room atmosphere (25°C, 60% relative
humidity). The DRIFT spectrum of the sample after exposure to the atmo-
sphere was also recorded.

13.2.2.5  SCANNING ELECTRON MICROSCOPY

Microphotographs of DNA samples before and after the DSC analysis in

hermetically sealed cells were taken by scanning electron microscope
(Quanta FEG-250, FEI). The samples were coated with gold before the
analysis.
Thermal Behavior of Sodium Salt of Calf Thymus DNA 273

13.3  RESULTS AND DISCUSSION

13.3.1  THERMAL CHARACTERIZATION OF CALF THYMUS DNA

13.3.1.1  THERMAL GRAVIMETRIC ANALYSIS

A polymer undergoes physical changes (such as glass transition and melting)

and chemical changes (such as thermal degradation to smaller molecular
mass fragments) on heating. While there are no mass losses for the glass
transition and melting, the mass decreases as temperature increases if vola-
tile molecules are formed on heating the polymer.
A general reaction can be written for dehydration and thermal degrada-
tion of a polymer even if it is much more complicated:

A(s) → B(s) + C(g),

for which the rate can be expressed as

d (1 − α)
= − k (T )(1 − α) , (13.1)
n

dt
where α is the conversion (extent of reaction), t is the time, k(T) is the reac-
tion rate constant, T is the absolute temperature, n is the reaction order, and
(1 − α)n represents the reaction model describing the dependence of the rate
on the fraction of solid remaining unreacted as the reaction proceeds and
referred as f(α). The conversion is defined as

mo − mT
α= ,
mo − m f (13.2)

where m0 is the initial mass of the sample, mT is the mass of the sample at
time t, and mf is the final mass of the sample. For a nonisothermal thermo-
gravimetric analysis under constant heating rate, that is, β = dot/dt, eq 13.1
becomes
dα k (T )
= f ( α) . (13.3)
dT β
Substituting k(T) by the Arrhenius expression, eq 13.3 yields

dα A  E 
= exp  − a  f ( α) , (13.4)
dT β  RT 
274 Applied Chemistry and Chemical Engineering: Volume 4

where A is the pre-exponential factor, Ea is the apparent activation energy,

and R is the universal gas constant. The activation energy is denoted as
apparent activation energy since the activation energy derived from thermo-
gravimetric data is the sum of activation energies of chemical reactions and
physical processes. Integrating eq 13.4 up to conversion α at the temperature
T gives
α T T
dα A  Ea  A  Ea 
∫ f ( α) = g ( α) = β ∫ exp  − RT  dT ≈ β ∫ exp  − RT  dT
0 To 0
(13.5)
AEa x
exp ( − x ) AEa
= ∫ dx = p ( x) ,
Rβ 0
x2 Rβ

where T0 is the initial temperature, g(α) is integral form of the reaction

model, and p(x) is the temperature integral for x = Ea/RT which does not
have analytical solution. If T0 is low, the lower limit of the integral on the
right-hand side of eq 13.5 can be approximated to be zero.
The Arrhenius parameters (A and Ea) together with the reaction model,
f(1 − α), are called the kinetic triplet. These parameters can be estimated
by model-free and model-fitting analysis methods. The isoconversional
model-free methods allow the apparent activation energy to be determined
as a function of the conversion without presumption of the reaction model.
These methods assume that the reaction rate at a given conversion is only a
function of the temperature. The most common isoconversional model-free
kinetic methods used in evaluating activation energy are integral Flynn–
Wall–Ozawa (FWO) and Kissinger–Akahira–Sunose (KAS) methods and
differential Friedman method.

13.3.1.1.1  FWO Method

This method, suggested independently by Flynn and Wall,37 and Ozawa,38

uses Doyle’s39 approximation of p(x) yielding

 AEa  Ea
lnβ = ln   − 5.331 − 1.052 . (13.6)
 R g ( α)  R T

For a constant conversion, the plot lnβ versus 1/T from the data at different
heating rates gives a straight line from the slope of which the apparent acti-
vation energy can be obtained.
Thermal Behavior of Sodium Salt of Calf Thymus DNA 275

13.3.1.1.2  KAS Method

KAS method40,41 is based on the Coats–Redfern42 approximation of p(x) for

20 < x < 50,
exp ( − x )
p ( x) ≅ . (13.7)
x2
From eqs 13.5 and 13.7 it follows that

 β  AR  Ea
ln  2  = ln  − . (13.8)
T   Ea g ( α)  RT
Thus, for constant conversion, the plot ln(β/T2) versus (1/T) gives a straight
line whose slope can be used to calculate the apparent activation energy.

13.3.1.1.3  Friedman Method

The differential isoconversional method suggested by Friedman43 is based

on eq 13.4 in logarithmic form and leads to

  dα   Ea , α
ln  βi    = ln  Af ( α) − , (13.9)
  dT  α,i  RTα,i

where subscripts i and α designate a given value of heating rate and extent
of conversion, respectively. The subscript α,i designates values related to a
given conversion, and i is an ordinal number of the experiment conducted at
the heating rates, βi. This method leads to the activation energy for a given
value of α by plotting ln(βi (dα/dT)) against 1/T.

13.3.1.1.4  Kissinger Method

Another model-free method is the Kissinger method, which is based on

determination of the kinetic parameters by the shift of the peak maximum40:

 β  AR  Ea
ln  2  = ln  − , (13.10)
 Tp   Ea  RTp

where Tp is the peak maximum temperature.

276 Applied Chemistry and Chemical Engineering: Volume 4

Figure 13.1 shows the TG curves recorded at different heating rates. The
integrated and partial mass losses are given in Table 13.1. The mass loss in
the 15–200°C range corresponds to elimination of water from the structure
since it was heated under nitrogen gas flow. When DNA is heated in air, CO2
and isocyanic acid are released, besides water, in this temperature range.31
The mass loss in the 200–400°C and 400–600°C ranges correspond to pyrol-
ysis of DNA and volatilization of DNA bases, respectively.30

TABLE 13.1  Partial and Integrated Mass Losses for DNA.

Heating rate (°C/min) Mass loss (%)
15–200°C 200–400°C 400–600°C Total
5 11.1 28.8 8.7 48.6
10 11.1 29.4 8.2 48.7
15 12.8 30.5 7.3 50.6

FIGURE 13.1  Thermogravimetric curves for DNA at different heating rates.

The derivative TG (DTG) curves (Fig. 13.2) showed mainly three peaks:
a broad peak in the 25–200°C range, sharp second (200−250°C), and third
(250−400°C) peaks. The maximum rate of mass loss increased with the
increasing heating rate and the peak maxima shifted gradually to higher
temperatures as the heating rate increased from 5°C to 15°C/min (from
51.4°C to 92.7°C, from 219.3°C to 235.6°C, and from 270.0°C to 318.3°C
for the first, second, and third peaks, respectively).
Thermal Behavior of Sodium Salt of Calf Thymus DNA 277

FIGURE 13.2  DTG curves for DNA at different heating rates under nitrogen flow.

The calf thymus DNA contains 11.1 wt% water initially corresponding to
2.94 wpn. This initial water content corresponds to the tightly bound water
molecules in the primary shell and constitutes an integral part of the DNA-
ordered structure. Variation of the water content of the DNA with tempera-
ture during heating up to 220°C under nitrogen flow is shown in Figure 13.3.
The water content of the DNA at the temperature of the maximum mass
loss rate was calculated as 2 wpn for all the heating rates. This wpn corre-
sponds to about 21% relative humidity according to the relationship given
by Lavalle and coworkers.10

1
FIGURE 13.3  Variation of the water content of the DNA with temperature during the TG
analysis.
278 Applied Chemistry and Chemical Engineering: Volume 4

The first peak in TG curves was analyzed using different kinetic models
by assuming that this peak is due to desorption of the water from the DNA.

13.3.1.1.5  FWO Method

The FWO plots obtained for the temperature range of 15–200°C are presented
in Figure 13.4. The lines have fairly equal slopes at low conversions but the
slope has changed at high conversions (α > 0.70). The apparent activation
energy values obtained by FWO method were in the range of 37.15–99.38
kJ/mol with the average value of 47.26 kJ/mol as reported in Table 13.2.

FIGURE 13.4  FWO plots.

TABLE 13.2  Average Activation Energies for the Individual Conversion Ranges.
FWO KAS Freidman
α ≤ 0.7 α > 0.7 α ≤ 0.7 α > 0.7 α ≤ 0.7 α > 0.7
Average Ea (kJ/mol) 39.70 66.06 35.96 62.85 41.67 70.58
Standard deviation (kJ/mol) 2.29 29.53 2.41 30.74 3.05 29.20

13.3.1.1.6  KAS Method

In accordance with the KAS method (eq 13.8), the ln(β/T2) versus 1/T plots
for the temperature range of 15–200°C gave straight lines (Fig. 13.5) from
which the apparent activation energies were determined in the range of
Thermal Behavior of Sodium Salt of Calf Thymus DNA 279

33.32–97.56 kJ/mol with the average value of 43.72 kJ/mol as reported in

Table 13.2.

FIGURE 13.5  ln(β/T2) versus 1/T plots (KAS method).

13.3.1.1.7  Friedman Method

Plotting of ln(βi(dα/dT)) against 1/T (Fig. 13.6) gives a series of lines with
high correlation coefficients (R2 > 0.879) yielding the apparent activation
energies in the range of 38.41−102.36 kJ/mol as reported in Table 13.2.

FIGURE 13.6  Friedman plots.

280 Applied Chemistry and Chemical Engineering: Volume 4

The dependence of activation energy, obtained from TG data in the

15–200°C range, on conversion for the three isoconversional methods (FWO,
KAS, and Friedman) is shown in Figure 13.7. The apparent activation ener-
gies calculated by the different methods are compatible with each other and
followed the similar trend with the conversion. The slight discrepancies in
the apparent activation energies determined by the different methods are
attributed to the assumptions in the derivation of the model equations.44

FIGURE 13.7  Dehydration activation energies of DNA as a function of conversion

calculated from the isoconversional model-free methods (15–200°C).

Ea is found to vary with the extent of conversion indicating complexity

of the dehydration reaction and reflects the changing mechanism (multistep
mechanism) during the course of the reaction. The variation of activation
energy as the reaction proceeds in homogenous state can be attributed to
control of the reaction rate by several elementary steps, each having unique
activation energy.45 On the other hand, in an elementary solid-state reac-
tion (heterogeneous reaction), the activation energy might vary with conver-
sion due to heterogeneous nature of the solid sample, which might cause a
systematic change in the reaction kinetics due to product formation, crystal
defect formation, intracrystalline strain, or other similar effects. Kinetic
complexities can also result from physical processes (e.g., sublimation,
localized melting, adsorption–desorption, diffusion of a gaseous product,
melting, particle size, and morphology effects, etc.) that have different acti-
vation energies.46 In the present study, the initial water content of the DNA
Thermal Behavior of Sodium Salt of Calf Thymus DNA 281

was 2.94 wpn as shown in Figure 13.3 and it is expected that removal of the
water will result in a fully denaturized DNA at 175°C. These transformations
might result in formation of solid products on the DNA surface having a
different energy barrier to the vaporizing water molecules. Thus, the rate of
dehydration might be controlled by the rate of diffusion of structural water
molecules across this barrier.
In the observed Ea versus α curves, two regions exist: for α ≤ 0.70, where
Ea is almost constant and for > 0.70, where Ea increases with the conversion.
The averaged activation energies over each conversion range are reported in
Table 13.2 together with the standard deviation values. For α ≤ 0.70 (corre-
sponding to the final temperatures of 93.5°C, 104.4°C, and 121.8°C for 5°C,
10°C, and 15°C/min heating rates, respectively) with fairly constant activa-
tion energy with conversion, the volatilization of the structural water in DNA
double helix can be assumed to follow a single-step reaction. This conver-
sion range corresponds to 70 wt% of the total mass loss in the 15–200°C
range and the final water content of 0.88 wpn.
The experimental values of Ea for the conversion below 0.70 are expected
to reflect the energy barriers to volatilization of primary shell hydration water
from DNA, thus Ea is dependent on the strength of interaction between water
and DNA. The averaged activation energies over the conversion range of α
≤ 0.7 are slightly lower than the activation energy of bulk water vaporization
(43.20 kJ/mol). This implied that vaporization of the strongly bound water
molecules is at least partially limited by diffusion. The difference between
the activation energies for vaporization of water from DNA and of bulk
water (2–8 kJ/mol) is comparable to the hydrogen bond energy (5–10 kJ/
mol) which would be the typical mechanism of interaction between water
and DNA.47 The increasing dependence of Ea on α observed for α > 0.7 might
reflect concurrent (parallel, simultaneous) reactions.48

13.3.1.2  DSC ANALYSIS OF DNA IN OPEN AND HERMETICALLY

SEALED CELLS

DSC thermograms recorded using open aluminum cells during heating of

DNA up to 600°C under nitrogen flow are shown in Figure 13.8. There are
mainly two peaks in these curves: an endothermic peak (with maximum at
Tm) belongs to melting and dehydration of DNA, and an exothermic second
peak (with maximum at Td) due to pyrolysis of DNA. For 5°C/min heating
rate, another exothermic peak was detected at 341.3°C (with enthalpy of
325.5 J/g).
282 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 13.8  DSC curves for heating DNA in open cells under nitrogen flow.

One broad endothermic peak was detected in the DSC thermograms

acquired in the hermetically sealed cells during the first heating to 175°C
(Fig. 13.9). The transition has started at room temperature but has not
completed at 175°C. The temperatures corresponding to the peak maxima
(Tm) are 113.6°C, 112.9°C, and 114.3°C for 5°C, 10°C, and 15°C/min
heating rates, respectively. These Tm values are higher than those detected in
the DSC curves recorded using the open cells. At the end of the first heating,
DNA was cooled at the same rate to 10°C and then reheated up to 175°C
(second heating). The endothermic peak observed in the first scan is absent
in the second scan thermogram indicating irreversibility of the transition
occurred during the first scan.
The DSC thermograms presented here are similar to those obtained by
Lee and coworkers for salmon testes NaDNA with initial water content of 12
wpn. They detected a sharp endothermic transition between 70°C and 100°C
with maximum near 90°C in the first DSC scan in hermetically sealed pans
during heating up to 140°C. Complete absence of the endothermic peak in
the second scan thermogram indicated irreversibility of the thermal denatur-
ation of DNA in solid state. In contrast, the endothermic peak reappeared in
the second scan when the DNA solution was heated, implying reversibility
of the denaturation in solution.22
In another study, reappearance of the endothermic peak during the second
scan was observed by Marlowe and coworkers for wet-spun film of NaDNA
after the sample was exposed to 75% relative humidity after the first heating
Thermal Behavior of Sodium Salt of Calf Thymus DNA 283

at 180°C. If the sample was kept under dry atmosphere after the first scan,
no transition was observed during the subsequent scan. The broad peak was
assigned to dehydration of the DNA. Heating to 180°C once yielded crystal-
line diffraction patterns but thrice destroyed the double helical structure and
crystallinity of the DNA.18

FIGURE 13.9  DSC curves for the analysis in hermetically sealed cell with heating up to
175°C, cooling to 10°C, and then reheating (second heating) to 175°C at different rates. The
arrows indicate the direction of temperature change.

The extent of reactions taking place in the open and sealed cells during
the DSC analyses in the temperature range of 15−200°C as a function of
temperature was calculated from the ratio of the integrated area until the
corresponding temperature to the total area of the peaks was detected in the
DSC thermograms. Since the transition observed for the sealed cell during
the first heating had not been completed at the final temperature (175°C), the
upper end of the peaks were simulated numerically and the total area was
calculated by numerical integration. According to this simulation, the endo-
thermic transition in the sealed cell completed at around 200°C independent
of the heating rate.
The extent of reactions taking place during the TG, open cell, and sealed
cell DSC analyses as a function of temperature is shown in Figure 13.10. As
seen in these plots, the extent of reactions followed the same trend during the
TG and open cell DSC analyses up to the extent of reaction of about 0.7 for
5 and 10°C/min heating rates (Fig. 13.10a and b). After this limit, the reac-
tions in the open DSC cells proceed faster with the increasing temperature.
284 Applied Chemistry and Chemical Engineering: Volume 4

FIGURE 13.10  Extent of reactions as a function of temperature for TG, open cell, and
sealed cell DSC analyses at the heating rate of (a) 5°C/min, (b) 10°C /min, and (c) 15°C/min.

Effect of heating rate on the temperature sensitivity of the reaction

rates for the TG, open cell, and sealed cell DSC analysis can be seen in
Figure 13.11. The extent of reaction in the sealed DSC cell is slightly
Thermal Behavior of Sodium Salt of Calf Thymus DNA 285

sensitive to temperature while those occurring during the open cell DSC and
TG analyses are highly temperature dependent.

FIGURE 13.11  Effect of heating rate on the extent of reactions for (a) TG, (b) open cell,
and (c) sealed cell DSC analyses.
286 Applied Chemistry and Chemical Engineering: Volume 4

Denaturation (melting) and dehydration of DNA double helix in open

cells can be represented by eq 13.11:
heat
hydrated DNA double helix → DNA single strand + H 2 O(g) . (13.11)

In open cell, the water desorbed from DNA is carried away from the system
by the flowing nitrogen gas. On the other hand, during the sealed cell DSC
analyses, the water bound to the DNA is released as in the open cell but
vapor–liquid equilibrium is established in the cell (Fig. 13.12). The amount
of water released above the saturation limit condenses in the cell on the
sample. When the vapor pressure of released water reaches 0.3 MPa (at
around 135°C), the water vapor starts to escape from the cell. After that, the
pressure in the cell remains constant at 0.3 MPa. Thus, the reaction occur-
ring in closed cells can be written as

heat
hydrated DNA double helix → DNA single strand + H 2 O(g) + H 2 O(l) . (13.12)

FIGURE 13.12  The hypothetical (predicted from the TG data) and saturation pressures of
water vapor in the sealed DSC cells.

Considering the water desorbed from DNA consumed an average heat of

vaporization of 2.24 kJ/g water (average value for the temperature range of
10–200°C) and knowing the amount of water desorbed from the TG anal-
yses, the enthalpy change of melting of DNA in the open and sealed DSC
Thermal Behavior of Sodium Salt of Calf Thymus DNA 287

cells (∆Hm) was calculated by subtracting the enthalpy change of vaporiza-

tion of water (ΔHvap) from the calorimetric enthalpy change (∆Hcal) and is
given in Table 13.3. The calorimetric enthalpy corresponds to the area under
the first endothermic peaks.

TABLE 13.3  Tm and Enthalpy Changes Calculated from the Open and Hermetically Sealed
Cell DSC Analyses.
Heating Open cells Hermetically sealed cells
rate Tm (°C) ΔHcal ∆Hm Td (°C) ΔHd Tm (°C) ΔHcal ∆Hm
(°C/min) (J/g) (J/g) (J/g) (J/g) (J/g)
5 73.3 280.5 34.9 230.0 −171.3 113.6 534.1 297.2
10 82.9 385.8 140.2 238.9 −97.1 112.9 458.1 222.8
15 89.3 418.5 172.9 244.6 -117.9 114.3 538.6 266.5

Higher heat of melting (∆Hm) values were obtained at higher heating

rates in the open cells. The ∆Hm values determined in the present study from
the open cell DSC analyses are in good agreement with values given in the
literature. Duguid and coworkers19 reported heat of melting value for calf
thymus DNA as 41.0 J/g. Spink and coworkers49 showed that DNA with
A–T base pairs and G–C base pairs has 50.5 J/g and 76.8 J/g heat of melting,
respectively, in ethylene glycerol.
The calculated ∆Hm values were higher for the hermetically sealed cell
than those for the open cell indicating that there were other endothermic
reactions besides melting and dehydration of DNA during heating in the
sealed cells. Under the 0.3 MPa pressure in the sealed cells, formation of
short DNA fragments as a result of incomplete degradation of the DNA
is possible.28 Heating of DNA powder from herring sperm (<50 base pair
degraded) in the solid state in hermetic pans at 145°C caused complete dena-
turation and formation of individual free nucleotides and single-stranded
DNA oligomers.36 Also incomplete degradation of DNA in solution at
temperatures above the melting temperature caused formation of DNA frag-
ments.50 The formation of these fragments also involves enthalpy changes
that might lead to the higher heat of melting values found.

13.3.1.3  KISSINGER ANALYSIS

As mentioned above (Section 13.3.1.1), the temperature at which the

maximum mass loss occurs (Tp) in the DTG curves increased with the heating
288 Applied Chemistry and Chemical Engineering: Volume 4

rate signifying that the reaction is thermally activated (kinetics limited).18

The three mass loss peaks in the DTG curves of DNA (see Fig. 13.2) were
analyzed by the Kissinger method. The Kissinger plots given by eq 13.10
are shown in Figure 13.13 and the calculated activation energies are given
in Table 13.4.

TABLE 13.4  Activation Energies for the DTG Peaks by the Kissinger Method.
Temperature Correlation Tp (°C) Ea (kJ/mol)
range coefficient (R2) 5°C/min 10°C/min 15°C/min
15−200°C 0.862 63.4 73.1 92.6 30.55
200−270°C 1.000 219.6 229.3 235.5 135.69
250−400°C 0.986 273.3 296.4 317.3 57.92

FIGURE 13.13  Kissinger plots for DNA (from DTG data).

The activation energy of the first mass loss step which is attributed to
dehydration is lower as compared with the pyrolysis steps at higher temper-
atures. Furthermore, the activation energy of the first step is lower than
those previously calculated by the isoconversional methods for degree of
conversion below 0.70. The correlation coefficient of the first step is low as
compared with those at higher temperatures. This is resulted from the broad-
ness of the peak and consideration of only the peak maxima by the Kissinger
method.
As given in Table 13.3, the maxima of the endothermic and exothermic
peaks shifted to higher temperatures with the increasing heating rates for
Thermal Behavior of Sodium Salt of Calf Thymus DNA 289

the open cell DSC analyses. On the other hand, shift in the peak maximum
temperature was less prominent for the sealed cells. The Kissinger plots for
the peaks detected in the DTG, open cell, and sealed cell DSC thermograms
in the 15−200°C range are shown in Figure 13.14 and the activation energies
calculated are given in Table 13.5.

TABLE 13.5  Activation Energies for the First Peaks in the DTG, Open Cell, and Sealed
Cell DSC Thermograms by the Kissinger Method.
Thermal analysis method Correlation coefficient (R2) Ea (kJ/mol)
DTG 0.862 30.55
Open cell DSC 0.999 66.06
Sealed cell DSC 0.117 342.24

FIGURE 13.14  Kissinger plots for the peaks detected in the DTG, open cell, and sealed cell
DSC thermograms in the 15−200°C range.

The activation energy determined from the DTG data by the Kissinger
method is the average value for the dehydration in the 15–200°C tempera-
ture range. However, we detected two regions in this temperature range by
the isoconversional methods as given in Table 13.2. The activation energy
determined from the open cell DSC data by the Kissinger method is in good
agreement with that determined by the isoconversional methods for the
conversions above 0.7. This value also agrees well with the values reported
for the desorption of primary hydration water from hydrated wet-spun films
of calf thymus CsDNA (58 and 61 kJ/mol).18,26
290 Applied Chemistry and Chemical Engineering: Volume 4

The linearity of the Kissinger plot for the sealed cell DSC data was
extremely low indicating that the reactions taking place in these cells are
not kinetics limited.18 Furthermore, if multiple reactions having different
activation energies occur simultaneously, the temperature dependence of
the overall rate (observed as a single transition in the DSC curve) cannot
be fit by a single kinetic equation. Also if the transition has several steps
comprising the chemical reaction step, heat, and mass transfer steps, and
so on, depending on the experimental conditions, one of these steps can
be the rate limiting step. Moreover, for our case, the static atmosphere
and high water vapor pressure in the sealed cells might lead to diffusion
hindrance and back reactions further complicating the problem. Besides,
the Kissinger method assumes that the reaction rate is maximum at the
peak maximum temperature (Tp). Thus, the Kissinger plot is linear only
if the reacted fraction at the maximum reaction rate is independent of
the heating rate.51 However, there is no evidence for the Tp values in the
sealed cell DSC thermograms to be the temperatures where the reaction
rate is maximum. Also from the sealed cell DSC data, the reacted frac-
tions at the peak maxima are 0.42–0.46, that is, not independent of the
heating rate.
The Kissinger plots for the second peaks in the DTG and open cell DSC
thermograms (200−270°C) are shown in Figure 13.15 and the activation
energies calculated from these plots are given in Table 13.6.

TABLE 13.6  Activation Energies for the Second Peaks in the DTG and Open Cell DSC
Thermograms by the Kissinger Method (200–270°C).
Thermal analysis method Correlation coefficient (R2) Ea (kJ/mol)
DTG 0.999 135.96
Open cell DSC 0.999 154.45

In this temperature range, the DNA undergoes pyrolysis. The correlation

coefficients are high suggesting that the complexities are not valid for this
temperature range. The values found here are close to that reported for wet-
spun films of calf thymus CsDNA (Tp of around 240°C) as around 183 kJ/
mol.18
The discrepancies in the activation energies calculated using the data
from the different thermal methods imply occurrence of different reac-
tions under the experimental conditions and that the thermal analyses are
performed in the temperature range of interest.
Thermal Behavior of Sodium Salt of Calf Thymus DNA 291

FIGURE 13.15  Kissinger plots for the second peaks in the DTG and open cell DSC.

13.3.2  MORPHOLOGICAL CHARACTERIZATION OF UNHEATED

AND HEATED CALF THYMUS DNA

Morphological changes occurred during the sealed cell DSC analyses

(repeatedly heated/cooled between 10°C and 175°C at different heating/
cooling rates) were deduced based on the SEM micrographs of the resi-
dues. SEM micrographs for the native and heated/cooled DNA samples are
shown in Figure 13.16. The native form of the calf thymus DNA is in the
form of a bundle of parallel fibers, each fiber having 0.05−0.2 µm diameter
(Fig. 13.16a).
The heating/cooling at 5°C/min caused the fibrous structure to be trans-
formed into a congealed block of melted polymer. Thick fibers and DNA
fragments were also observed. No indication for the intumescence action
has been observed for this residue (Fig. 13.16b). Formation of the fragments
as a result of incomplete degradation of the DNA under the high pressure in
the cell was discussed above (Section 13.3.1.2) and suggested as a possible
reason for the higher melting enthalpies from the sealed cell DSC data. The
DNA residue formed after heating/cooling cycles at 10°C/min rates in the
sealed DSC cell exhibited the typical behavior of intumescent fire retardant
materials: microbubbles were formed on the fibers (Fig. 13.16c). In the
micrograph of the DNA residue formed after heating/cooling cycles at 15°C/
min, the bundles of parallel fibers reappeared. Densely packed microbubbles
292 Applied Chemistry and Chemical Engineering: Volume 4

with diameter less than 0.1 µm can be seen on a bundle of about 1 µm

diameter (Fig. 13.16d). The samples have become blackened after heating
at 175°C, indicating degradation accompanying the morphological changes.

FIGURE 13.16  Scanning electron micrographs of DNA: (a) before heating, after two
heating/cooling cycles between 10°C and 175°C in hermetically sealed DSC cells at a rate of
(b) 5°C/min, (c) 10°C/min, and (d) 15C/min (scale bar 2 µm for all images).

The morphological changes observed by SEM can be explained by

entrapment of the gases released from DNA in the molten DNA.30,31 This
behavior involves transition of DNA from a solid to a viscous liquid on
heating, with simultaneous thermal decomposition of weak chemical struc-
tures that produce the blowing gases. The thermally induced bond scission
is however limited, leading to a stable macromolecular structure, which
is essential to the viscoelasticity required by the blowing action.30 DNA
is transformed from a solid to a viscous liquid with simultaneous thermal
Thermal Behavior of Sodium Salt of Calf Thymus DNA 293

decomposition of weak chemical structures that produce the blowing gases.

In 50−180°C range, Alongi and coworkers30 detected CO2 and isocyanic acid
besides water as volatiles by TG-FTIR upon degradation of herring sperm
DNA in air. In the present study, during heating in the sealed cell under high
pressure of water vapor, formation of volatiles as a result of degradation of
DNA besides water is possible. These volatiles (blowing gases) have to be
trapped and to be diffused slowly in the viscous, melt, degraded DNA in
order to exhibit the intumescent behavior. The viscoelastic melt, degraded
DNA expands as volatiles are produced and at the same time, cross-linking
reactions and charring cause the matrix to harden and to produce highly
porous char.52
DNA has a significant weight loss between 10°C and 175°C (around 11
wt%) due to desorption of the primary shell hydration water under nitrogen
flow. The change of the reaction kinetics for the extent of reaction above 0.7
(above 94°C for 5°C/min) was resolved by the isoconversional analysis of
the TG data as discussed before (Section 13.3.1.1).

13.3.3  TRANSMISSION FTIR AND DRIFT SPECTROSCOPY

13.3.3.1  TRANSMISSION FTIR

Transmittance IR spectra of the native DNA and residue after the DNA was
heated to 600°C under nitrogen flow are shown in Figure 13.17. The IR
vibrations for the native DNA were detected at 960, 1018 (shoulder), 1063,
1089, 1240, 1375, 1425, 1490, 1535, 1653, 1693, 2191, 2930 cm−1 (shoulder)
and a broad band in the 2400–3700 cm−1 region with maxima at 3440 cm−1.
The IR spectrum of the residue is very different from that of the native
DNA. The bands in the spectrum of native DNA were replaced by 520, 756,
775, 900, 995, 1107, 1170, 1240, 1315, 1620, and 1700 cm−1 bands in the
spectrum of the residue. These bands cannot be associated to an organic
structure but rather to an inorganic ceramic-like material rich in phosphate
and nitrogen as in the case of melamine phosphate thermal degradation.53
A broad band in the 1800–3700 cm−1 region detected in the spectrum of the
residue can be assigned to N–H and C–H stretching vibrations. The broad
band at 3440 cm−1 can be assigned to OH groups with a possible contribution
from residual water not removed.
Upon heating to 175°C, DNA produced an expanded cellular carbon
structure derived from the dehydration of sugar units (probably induced by
reacting with phosphate groups) and swollen by the released gases formed
294 Applied Chemistry and Chemical Engineering: Volume 4

from the nitrogen bases. Following breaking of the weak C−N sugar-base
bonds at the beginning of the degradation, unsaturated sugar–phosphate
chains are formed. Above 400°C, cross-linking reactions take place between
the phosphorous and nitrogen-based condensates involving acidic phos-
phorous and basic nitrogen groups. As a result thermally stable P–N-based
structure is formed.30

FIGURE 13.17  Transmittance IR spectra of the native DNA and residue after the DNA
heated to 600°C under nitrogen flow.

The thermal resistance of the intumescent char is important in terms of

its fire retardant performance. A higher amount of char formed may indicate
a lower amount of volatile species released during the thermal degradation
of a polymer. On heating to 600°C, calf thymus NaDNA produced a residue
of about 50 wt% according to the TG analysis. If only Na+ and phosphate
ions remained after the pyrolysis, the residue would be 35 wt%. Thus, it
can be concluded that there are other carbonized species in the residue
besides phosphates. During cross-linking reactions between phosphorous
and nitrogen-based condensates above 400°C, carbon may be trapped and
thermally stabilized in the P–N-based structure.30
From SEM micrographs (Fig. 13.16), it was seen that DNA exhibited
intumescent behavior upon heating to 175°C in the sealed cells as a result
of melting and degradation, and release of water was assumed to be the
major volatile product. The chemical transformations occurred in the DNA
during the sealed cell DSC analysis were followed by the transmittance IR
spectroscopy.
Thermal Behavior of Sodium Salt of Calf Thymus DNA 295

Transmittance IR spectra of the native DNA and of the DNA that was
repeatedly heated/cooled in the sealed DSC cells at different rates are shown
in Figure 13.18. Specifically, the bands in the 1500–1800 cm−1 region are
assigned to base stacking and pairing and those at 1060 cm−1 and 1089 cm−1
to backbone conformation.22 In preparing KBr pellets for the samples, 2 mg
DNA was used. Considering errors in weighing of the samples, the band
intensities were normalized by the intensity of 1234 cm−1 band. This band is
due to the PO2− asymmetric stretching vibrations and is largely invariant to
temperature, thus it is used as a standard for intensity normalization.22
Heating of DNA in the sealed cell led to slight increase in the inten-
sities of 1089 cm−1 (PO2− symmetric stretching vibration) and 1063 cm−1
(C−O stretching vibration of the phosphodiester) bands (Fig. 13.18a). These
changes imply conformational changes in the deoxyribose–phosphate back-
bone. The normalized absorbance of 1089 cm−1 band is a good measure of
thermal denaturation of DNA. These bands are primarily assigned to vibra-
tional modes of the ordered deoxyribose–phosphate backbone and are highly
sensitive in frequency and intensity to DNA melting.
The position of 1234 cm−1 band did not change after heating to 175°C (Fig.
13.18b). This band is due to the asymmetric PO2− stretching vibrations. Not
the intensity but the frequency of this band is known to be strongly dependent
on the water content of the DNA: at high water content, it appears at 1220
cm−1 and linearly shifts to a higher frequency with the decreasing water.10
Intensity of the bands in the range of 1400−1500 cm−1 (vibrations for
coupling between base–sugar entities) increased in the spectra after the DNA
was heated/cooled at 175°C at 15°C/min rate (Fig. 13.18c). The bands in this
range became less prominent and band at 1480 cm−1, which is assigned mainly
to purine imidazole ring vibrations,54,55 disappeared in the spectra of the sample
heated/cooled at 5°C/min. Alongi and coworkers detected a small intensity
increase at 1430−1475 cm−1 in the spectra of herring sperm DNA heated in
air at 180°C and interpreted this as an indication of chemical modifications
involved in the degradation step concerning the intumescent behavior. The
bands at 1260, 1060, 1006, and 960 cm−1 also lost intensity after the heating.30
For 5°C/min rate, the bands in the 1550−1750 cm−1 region, which are
assigned to double-bond in-plane vibrations of the bases (e.g., C=O, C=N,
and C=C), were replaced by a single band (Fig. 13.18d) probably due to
condensation of bases after breaking of the weak C−N sugar–phosphate
bonds at low heating rate. In the literature, shifting of the 1653 cm−1 band to a
lower frequency was attributed to conversion of carbonyl groups (C−O) into
C=N bonds upon the condensation.30 This band is sensitive to base stacking
and pairing.22 Thus, the observed changes in the intensity can be interpreted
 296

FIGURE 13.18  Transmission FTIR spectra of the native and heated DNA in the spectral regions of (a) 1000–1160 cm−1, (b) 1150–1350 cm−1,
(c) 1300–1500 cm−1, and (d) 1500–1800 cm−1. The legend given in (a) is valid for the others.
Applied Chemistry and Chemical Engineering: Volume 4
Thermal Behavior of Sodium Salt of Calf Thymus DNA 297

as disruption of stacking and pairing of bases. The decrease in the intensity

of this band was attributed to rupture of hydrogen bonds between the base
pairs (as during melting of DNA).19 No such effects were observed for the
residues obtained at 10°C and 15°C/min.
The band at 877 cm−1, which is assigned to sugar–phosphodiester vibra-
tions, has a higher intensity in the spectrum of the residue obtained at heating
rate of 15°C/min (Fig. 13.19a). This is due to conversion of carbonyl groups
(C−O) into C=N bonds during the bases condensation reactions. It was also
reported that disruption of hydrogen bonding between water molecules and
polar groups of the sugar–phosphate backbone upon heating the DNA solu-
tion might produce the band at 872 cm−1.19

FIGURE 13.19  Transmission FTIR spectra of the native and heated DNA in the spectral
regions of (a) 700–1000 cm−1 and (b) 2400–4000 cm−1. The legend given in (a) is valid for (b).

The intensity of 3440 cm−1 band decreased gradually with the increasing
heating rate (Fig. 13.19b). The intensity of this band is strongly dependent
on the water content and has been used as a measure of water content of
DNA.11 The lower intensity of this band in the spectra of residues obtained
at higher rates might suggest evolution of higher amounts of water. This
is in good agreement with the more prominent intumescence character-
istic of the residue obtained at 15°C/min observed in the SEM micrograph
(Fig. 13.16d). However, the higher intumescent action for this residue cannot
be explained only by the amount of water released. Since the overall intu-
mescent process of DNA depends on the competing reactions through which
298 Applied Chemistry and Chemical Engineering: Volume 4

its thermal degradation takes place, the chemical structure of the char may
have an important effect on its foaming behavior.56
As a consequence, the intumescent behavior of the DNA observed by
the SEM analysis is accompanied by the structural modifications (upon
dehydration, melting and degradation) as deduced from the transmittance IR
spectra of the residues. The effect of heating rate on these structural changes
was also interpreted from these spectra.

13.3.3.2  DRIFT SPECTROSCOPY ANALYSIS

Effect of evacuation and heating under vacuum on the structural vibrations

of the DNA was examined through the in situ DRIFT spectroscopy analysis.
Variations in the normalized intensities of 1089, 1653, and 3440 cm−1 bands
in the DRIFT spectra with temperature under vacuum are shown in Figure
13.20. Also variations in the normalized band intensities with evacuation
and heating during the in situ DRIFT spectroscopy analysis are shown in
Figure 13.21.

FIGURE 13.20  Variation of the normalized intensities of 1089 cm−1, 1653 cm−1, and 3440
cm−1 bands during the in situ DRIFT spectroscopy analysis under vacuum.

The intensity of 1089 cm−1 increased upon evacuation at room tempera-

ture and continued to increase gradually with the temperature; although small
Thermal Behavior of Sodium Salt of Calf Thymus DNA 299

fluctuations are apparent. Upon cooling and exposure to the room atmosphere
(60% relative humidity) after the heating, the intensity continued to increase
(irreversible changes in deoxyribose–phosphate backbone). Semenov and
coworkers reported that the intensity of this band is strongly dependent on
the water content and decreases under nitrogen flow at room temperature.57

FIGURE 13.21  Variation of normalized intensities of 1089 cm−1, 1653 cm−1, and 3440 cm−1
bands with evacuation and heating during the in situ DRIFT spectroscopy analysis.

Slight loss of intensity was observed for 1653 cm−1 during heating under
vacuum which recovered its initial value upon exposure to the room atmo-
sphere (60% relative humidity), indicating reversibility of the changes in
stacking and pairing of the bases upon increase in the relative humidity. As
stated before, the loss in the intensity can also be attributed to rupture of
hydrogen bonds between base pairs (as during melting of DNA).19
The 3440 cm−1 band also lost intensity upon evacuation and heating as
a function of temperature continuously due to removal of the water. Upon
exposure to the room atmosphere (60% relative humidity), the band gained
its initial intensity as a result of adsorption of water. The normalized inten-
sity of 3440 cm−1 band is positively correlated with that of 1653 cm−1 band
and negatively with that of 1089 cm−1 (not shown).
The recovery of the initial intensities of the 3440 and 1653 cm−1 bands
upon exposure to the atmosphere and irreversible intensity loss for 1089
300 Applied Chemistry and Chemical Engineering: Volume 4

cm−1 band indicates that the bases were restacked and repaired upon hydra-
tion of the DNA but the backbone conformation was irreversibly destroyed.
Thus, the endothermic transition observed in the DSC thermograms recorded
during the first heating in the sealed cell is not due to denaturation upon loss
of the hydration water, but due to the thermal degradation of the DNA.
The intensities of the 1089, 1653, and 3440 cm−1 bands are more temper-
ature sensitive under vacuum than under water vapor of 0.3 MPa pressure.
Thus, higher enthalpies are required in order to modify the sugar–phos-
phate backbone conformation, base stacking, and pairing as well as water
content of the DNA under the pressure as reflected by the higher melting
enthalpies for the sealed cells (Table 13.3). Also during the heating under
dynamic evacuation, any gases evolved are continuously removed from the
sample. This may affect the intumescence process and thus fire-retardant
performance of the DNA. Loss of structural water is strongly affected by the
external pressure. Presence of water vapor on the sample leads to a decrease
in the dehydration rate as compared to that in vacuum, that is, an increase in
the activation energy for dehydration. The presence of water vapor affects
not just the dehydration but the subsequent thermal reactions, and hence the
characteristics of the residue produced.58

13.4 CONCLUSIONS

The intumescent behavior of Na salt of calf thymus DNA fibers was inves-
tigated for the first time. The thermal denaturation and dehydration kinetics
of sodium salt of calf thymus DNA was investigated using the nonisothermal
thermogravimetric data obtained at three different heating rates. The mass loss
of DNA due to dehydration was 11% and the remaining mass at 600°C was
50% at 10°C/min heating rate. By the application of the model-free methods,
the average apparent activation energy in the temperature range of 15–200°C
was found to be dependent on the conversion, indicating the complexity of the
dehydration reaction and reflects the changing mechanism (multistep mecha-
nism) during the course of the reaction. On the observed Ea versus α curves,
two different regions exist: for α ≤ 0.70, where Ea approximately does not
change with conversion and α > 0.70, where Ea increases with the conversion.
For α ≤ 0.70 (corresponding to the final temperatures of 93.5°C, 104.4°C,
and 121.8°C for 5°C, 10°C, and 15°C/min heating rates, respectively) with
fairly constant activation energy with conversion, the volatilization of the
structural water in DNA double helix can be assumed to follow a single-step
reaction. The averaged activation energies over this conversion range were
Thermal Behavior of Sodium Salt of Calf Thymus DNA 301

determined as 39.70 ± 2.29, 35.96 ± 2.41, and 41.67 3.05 kJ/mol using FWO,
KAS, and Freidman methods, respectively. These activation energy values
are slightly lower than the activation energy of bulk water vaporization
implying diffusion-controlled vaporization. For α > 0.70, the corresponding
average activation energies were found to be 66.06 29.53, 62.85 ± 30.74, and
70.58 ± 29.20 kJ/mol, respectively. The Kissinger method indicated 30.55,
135.69, and 57.92 kJ/mol activation energy for the 15−200°C, 200−270C,
and 250−400°C ranges, respectively. The approach described in the present
study allowed the determination of the activation energy values for the
dehydration and degradation steps for DNA. The DSC analysis of DNA in
open cell and hermetically sealed closed cells indicated higher melting peak
maximum (Tm), 110°C, than that in open cell, 80°C. The heat of melting value
of DNA in the sealed cell is higher than heat of melting value of open cell for
5°C/min heating rate which are 297.2 and 37.9 J/g, respectively. For 10°C/
min and 15°C/min heating rate, the heat of melting value of DNA sealed cell
experiments was also higher than that measured in open cell. Since it was
thought that DNA degradation will occur at higher temperatures, heating was
carried out only up to 175°C in closed cells. However, the first peak in sealed
cell experiments was not completed during heating up to 175°C. By the
application of Kissinger method to the DSC curves, the R2 values of 0.99 and
0.12 were obtained for the endothermic first peak in open and sealed cells,
respectively. When DNA was heated, morphology of the fibers was changed
and thicker and irregular fiber structures with swollen bulbs were formed.
However, when DNA was cooled, the exothermic crystallization peak could
not be seen. Both the transmission FTIR and DRIFT spectroscopy analysis
showed that normalized 1653 and 3440 cm−1 band intensities decreased as
DNA lost water besides melting up to 175°C. The water loss (denaturation)
caused the intensity of 1089 cm−1 band to increase.

KEYWORDS

•• calf thymus DNA

•• dehydration
•• degradation
•• activation energy
•• in situ DRIFT spectroscopy
302 Applied Chemistry and Chemical Engineering: Volume 4

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 PART IV
Special Topics
CHAPTER 14

ENVIRONMENTAL ENGINEERING,
MEMBRANE TECHNOLOGY AND
NOVEL SEPARATION PROCESSES: A
BROAD SCIENTIFIC PERSPECTIVE AND
A CRITICAL OVERVIEW
SUKANCHAN PALIT*
Department of Chemical Engineering, University of Petroleum and
Energy Studies, Energy Acres, Bidholi via Prem Nagar, Dehradun
248007, Uttarakhand, India
*
Corresponding author. E-mail: [email protected];
[email protected].

CONTENTS

Abstract.....................................................................................................309
14.1 Introduction...................................................................................309
14.2 The Goal of the Study................................................................... 311
14.3 Environmental Engineering Science, Membrane Science,
and Global Water Crisis................................................................312
14.4 Global Water Crisis and Arsenic Groundwater Contamination....314
14.5 Technology Initiatives and Technological Vision in the
Field of Water Technology............................................................315
14.6 Scientific Vision, Scientific Cognizance,
and the Path Toward Progress.......................................................315
14.7 Vision of the Application of Membrane Science..........................315
14.8 Scientific Doctrine of Membrane Science....................................316
308 Applied Chemistry and Chemical Engineering: Volume 4

14.9 Membrane Science: Current Trends and Future Challenges.........317

14.10 Vision of Science, The World of Challenges and the
Research Pursuit in Novel Separation Processes..........................317
14.11 Technology Initiative in Developed and Developing
Countries and Future of Global Water Scenario...........................318
14.12 Global Water Crisis and Arsenic Groundwater Contamination....318
14.13 Vision and Challenges to Move Forward in
Environmental Engineering Science.............................................319
14.14 The World of Visionary Frontiers and the Progress of
Membrane Science........................................................................319
14.15 Barriers, Difficulties, and the World of Challenges......................320
14.16 Vision of Science, Scientific Imagination, and the
Avenues of Science Forward........................................................320
14.17 Novel Separation Processes and the Future of Science
and Engineering............................................................................321
14.18 Future Directions and Future Challenges in the
Emancipation of Science and Technology....................................321
14.19 Future Vision and Future Flow of Thought..................................322
14.20 Conclusion....................................................................................322
Keywords..................................................................................................323
References.................................................................................................323
Environmental Engineering, Membrane Technology 309

ABSTRACT

The world of science and technology is moving toward a newer and visionary
realm at a rapid pace. Vision of science is entering a new era. Environmental
engineering science in a similar vein is undergoing paradigmatic change.
Environmental regulations, stringent environmental restrictions, and the
futuristic vision has urged scientific domain to devise new and innovative
technologies. Membrane science is an innovative technology which needs
to be reorganized and redefined. Grave concerns, inimitable disaster and
environmental sustainability has plunged human civilization to an unwanted
catastrophe. Environmental disaster is bane to human progress. Mankind’s
progress, civilization’s prowess, and the path toward future progress will
pave the way toward newer technologies and will surpass visionary fron-
tiers. Membrane science in today’s world has an unsevered umbilical cord
with industrial wastewater treatment and drinking water treatment. Global
water technology scenario is at a deep distress. Developed as well as devel-
oping nations are witness to the crisis of groundwater contamination. At this
critical juncture of history and time, scientific advancement and applica-
tion of membrane science are the vicious and vehement parameters toward
the immense and innovative growth of human civilization. The author, with
a deep and cogent insight, delineates the utmost importance of membrane
science in the progress of environmental engineering science. The trea-
tise also delineates the hidden scientific truths of the immense potential of
membrane science, fouling and concentration boundary layer.

14.1 INTRODUCTION

The world of environmental engineering and chemical engineering is

moving drastically toward a newer and innovative era. Grave concerns
and effective environmental restrictions are the torchbearers of the future
of industrial wastewater treatment and drinking water treatment. Advance-
ment of science and technology and the vision to excel has urged the human
civilization and the scientific domain to aim for new innovations. History
of science and engineering are boon to human civilization and human prog-
ress. Challenge, vision, and the scientific endurance are opening up new
chapters in the application of membrane science in environmental engi-
neering science. The challenge of science needs to be revisited and reen-
visioned. Membrane science and its classification are surely and inevitably
changing the face of scientific endeavor. Since the scientific endeavor of
310 Applied Chemistry and Chemical Engineering: Volume 4

Loeb–Sourirajan model in membrane technology, the world of science has

revolutionized and reenvisioned. Concentration boundary layer is the next
domain of scientific endeavor which needs to be reshaped and restructured.
Ground water remediation is the next primordial issue which needs to be
targeted vehemently. Arsenic groundwater contamination is a bane to human
civilization and human progress. The author cautiously addresses with deep
comprehension to the challenges behind the application of membrane tech-
nology in environmental engineering science. The challenges and future
trends need to be evaluated by the scientific community vehemently and
intensely. History of science is ushering in a new and insightful beginning.
Challenges, vision, and barriers in the application of membrane science will
surely bring forward in the scientific forefront a new generation of scientific
vision and scientific truth.21
Today, membrane separation processes stands in the midst of deep
comprehension and wide scientific vision. The environmental engineering
paradigm in today’s world is undergoing drastic changes and the future
perspectives are surely bright and far-reaching. Human scientific progress,
the wide vistas of challenges and the wide future of research pursuit will
go a long way in the true evolution of a newer scientific era. This present
century is the century of innovative science and technology. The challenge
of science and technology and its vision are gearing human mankind toward
a positive horizon.21,22

14.1.1  VISION OF THE PRESENT TREATISE

The present treatise explores and delineates with cogent and effective insight
the scientific truth and scientific vision behind membrane science and tech-
nology. Scientific cognizance and vision of science are the torchbearers to
a new realm and new era. The treatise redefines the hidden truth behind
the application domain of membranes. Loeb–Sourirajan model defined the
application domain of membrane science and thus ushered in a new innova-
tive area of science.1 The years after its discovery were truly far-reaching and
scientifically ground breaking. Purpose and aim of this treatise is visionary
and the challenge veritably groundbreaking. Groundwater treatment, indus-
trial wastewater treatment, and global drinking water scenario is undergoing
a drastic and vicious challenge. Global water initiative is a primordial issue
which needs to be targeted with utmost importance. The author with lucid
details delineates the future trends in the application of membrane science in
alleviating global water crisis.1–4
Environmental Engineering, Membrane Technology 311

The author with great scientific vision and cogent scientific insight
unfolds the intricacies of membrane separation processes and the future of
global water shortage. In today’s world, global water shortage and environ-
mental sustainability have an unsevered umbilical cord. More devastating
crisis is looming large over the scientific horizon. The vision of this trea-
tise unfolds the immense potential of membrane separation processes and
novel separation processes. Its application to environmental engineering
science is delineated and discussed in details. The author rigorously eluci-
dates the scientific vision and the scientific greatness behind membrane
science and novel separation processes with an extended view toward
global water crisis. Technological initiative and technological vision in
today’s human civilization is surpassing wide and versatile frontiers. The
author repeatedly focuses on environmental engineering techniques with a
positive vision. The future of membrane technology will veritably open up
newer innovative areas.

14.2  THE GOAL OF THE STUDY

The mission, goal, and aim of the study is to address the grave cause of
industrial water pollution. Challenge needs to be redefined and reenvisioned.
Membrane science is the next generation technology. Man’s vision, mankind’s
prowess, and civilization’s progress are opening windows of innovation in
environmental engineering science. The treatise analyses the immense scope
and potential of membrane science in the future of environmental science.
Goals of human mankind with respect to environmental engineering science
and application of membrane science needs to be reshaped. The world of
environmental engineering is ushering in a new and vibrant era. History of
human mankind is also moving toward a visionary era. Loeb–Sourirajan
model defined the entire path of human scientific endeavor in membrane
science. The author skillfully rewrites vision and history of science in the
path toward progress in membrane. Scientific challenge, scientific truth, and
scientific vision will all go a long way in the emancipation of membrane
science and technology. The aim and objective of this scientific endeavor
targets is the application of membrane science in solving global water crisis.
Science, engineering, and technology are ushering in a new era of scien-
tific truth and vision. Global water crisis is moving from one definite and
visionary perspective to another.
312 Applied Chemistry and Chemical Engineering: Volume 4

14.3  ENVIRONMENTAL ENGINEERING SCIENCE, MEMBRANE

SCIENCE, AND GLOBAL WATER CRISIS

Global water crisis and global water shortage are the primordial issues
which need to be addressed at this critical juncture of history and time. Envi-
ronmental engineering science is veritably witnessing dramatic and drastic
challenges. Challenges in the path toward progress, scientific vision, and
scientific validation are the order of today’s technological era. Scientific
validation from the laboratory to the common mass and human society needs
to be vehemently and intensely addressed and targeted. Global water crisis is
a bane and a catastrophe to the human civilization. Mankind’s history, civili-
zation’s prowess and the road toward progress will all lead a long way in the
emancipation of engineering and science of membrane separation processes.
Scientific cognizance, scientific doctrine, and the immensely vital domain
of scientific validation are the veritable pallbearers of a new dawn of human
civilization. Vision of technology needs to be revalidated at every step of
human progress.

14.3.1  VISIONARY SCIENTIFIC ENDEAVOUR IN THE FIELD OF

MEMBRANE SEPARATION PROCESSES

The scientific world of today is witnessing vicious challenges. Membrane

separation processes are one of the primordial challenges in the allevia-
tion of global water crisis. The author with deep and cogent comprehen-
sion elucidates the present trends in research in the field of membrane
science and the future directions and success. Technology initiative and
scientific endeavor are the pillars of modern science. Water technology
needs to be revamped with the course of human history. Provision of basic
human needs, need to be the prime focus of future scientific research
pursuit. Loeb–Sourirajan model11 revolutionized the science and tech-
nology of membrane separation processes. Cheryan (1998)11 elucidated in
a visionary treatise the past, present, and future trends of the application
of ultrafiltration and microfiltration. The phenomenon of osmosis, which
is the transport of water or solvent through a semi-permeable membrane
(defined as a membrane that is permeable to solvent and impermeable to
solutes), has been known since 1748, when Abbe Nollet observed that
water diffuses from a dilute solution to a more concentrated one when
separated by a semi-permeable membrane.11 Cheryan11 touches upon
Environmental Engineering, Membrane Technology 313

performance and engineering models of membrane separation processes

and the crucial domain of fouling and cleaning. Process design of diafiltra-
tion–continuous, discontinuous and dialysis stands as a major and critical
point of his research. The research also encompassed upon applications of
ultrafiltration and microfiltration.
Chen et al. (2013)12 discussed in details in a study on dynamics of ultra-
filtration membrane materials preparing and its uses in drinking water treat-
ment. The ultrafiltration membrane technology as a new water treatment
technology can be used in a large scale depending largely on membrane
material itself and also depending on the membrane production conditions
and process. This treatise reviews the development and current and future
trends of preparing ultrafiltration membrane material, and analyzes deeply
its application prospects in water treatment of drinking water. This paper
veritably surpassed visionary boundaries. Commercialization process of
preparing ultrafiltration membrane materials and polymer membrane has
got unprecedented research and development. The membrane material such
as bisphenol A type of cellulose derivatives (PSF), polysulfone polyether
sulfone (PES), polysulfone amide (PSA), ployvinylidene fluoride (PVDF)
and polyacryonitrile (PAN), have extensively promoted the development of
ultrafiltration membranes.
Ahmed et al. (2010)13 dealt lucidly in a review fabrication of a polymer-
based mixed matrix membrane. This short review delineates the main and
promising areas of research in gas separation, by considering the materials
for membranes, the industrial applications of membrane separations, and
finally the opportunities for integration of gas separation units in hybrid
systems for the intensifications of the process.
Cath et al. (2006)14 reviewed forward osmosis, its principles, appli-
cations, and recent trends of its development. This paper is a visionary
treatise which deals extensively and lucidly the wide world of a modern
domain of membrane science-forward osmosis. Osmosis is a physical
phenomenon known for long decades. After 1960s, attention was on
osmosis through synthetic materials. Osmosis as it is known now as a
forward osmosis which has new applications in separation processes for
waste water treatment, food processing, and seawater desalination. The
success of membrane science and desalination are extremely relevant to
the present and future of human scientific pursuit. A state of art has been
attempted considering physical principles and applications of forward
osmosis.
314 Applied Chemistry and Chemical Engineering: Volume 4

14.4  GLOBAL WATER CRISIS AND ARSENIC GROUNDWATER

CONTAMINATION

Arsenic groundwater contamination is creating unimaginable environmental

havoc in developing and developed world. Human scientific endeavor and
the futuristic scientific vision is at a deep distress. Global water crisis and
scientific challenges are the pallbearers of future technological initiatives
and scientific vision.11 Arsenic and heavy-metal groundwater contamination
are ravaging the human mankind and in a similar vein the world of chal-
lenges needs to be revamped and veritably readdressed. Water crisis needs to
be alleviated. In today’s human civilization, arsenic groundwater contamina-
tion and global water crisis have an unsevered umbilical cord. The success
and efficacy of scientific endeavor wholly and veritably lies on effective
and determined scientific validation and scientific vision. Global water chal-
lenges are in deep distress and unending whirlpool. In such a crucial junc-
ture, technological and scientific visions are the pallbearers of the future.
Both developed and developing nations are ensconced with this ravaging
environmental disaster. Science and technology of water initiatives needs to
be effectively restructured with the active participation of the civil society.
With this aim and objective in mind, the scientific domain will surely move
toward true emancipation of water technology and science.11

14.4.1  ARSENIC GROUNDWATER CONTAMINATION AND

THE FUTURE OF GLOBAL WATER SHORTAGE

Arsenic groundwater contamination and its effective remediation are the

primordial issues facing progress of human mankind today.1–5 Developed
and developing countries are in a deep and questionable distress with every
step of human progress. Bangladesh and West Bengal state of India are the
major regions of the developing economies in such a highly distressful condi-
tions. Heavy metal contamination is a vexing question which looms large
in the midst of scientific horizon. The world of challenges, the immense
difficulties and the inimitable disaster questions the pursuit of science and
technology. History of science is in the midst of immense catastrophe. Civil
society decisions, the burgeoning urge to excel and the question of scientific
validation will go a long way in alleviating the concern and the inimitable
arsenic contamination crisis. Membrane science and its applications are the
inevitable pallbearers to a new dimension of scientific hope and scientific
cognizance.1–5
Environmental Engineering, Membrane Technology 315

14.5  TECHNOLOGY INITIATIVES AND TECHNOLOGICAL

VISION IN THE FIELD OF WATER TECHNOLOGY

The world of water technology is slowly gearing toward newer visionary

initiatives. Developed and developing nations are in the whirlpool of envi-
ronmental devastations and inimitable crisis. Arsenic groundwater contami-
nation is a burning example. Vision of science has no answers. Bangladesh
and the state of West Bengal in India, for centuries are bearing the immense
burden of heavy metal groundwater contamination.11 Technology initiatives
need to be reenvisioned with each step of human life. As human mankind
moves toward the third decade of twenty first century, the need for scientific
and technological validation are enhanced. Science in today’s world is a
colossus without a will of its own. In such a crucial juxtaposition, the efforts
and the scientific urge to excel should move toward effective validation of
science. Water technology and water science in a similar vein need to totally
focused toward human needs and the effective validation of science.11

14.6  SCIENTIFIC VISION, SCIENTIFIC COGNIZANCE, AND THE

PATH TOWARD PROGRESS

Scientific vision in the domain of membrane science and technology is

inspiring and far-reaching. Innovations, scientific instinct and scientific vali-
dation needs to be reenvisioned. Mankind’s prowess, civilization’s progress,
and the vistas of science are the torchbearers to a new scientific genera-
tion and a newer scientific realm.6–9 History of science and technology is in
the midst of immense disaster and pessimism with the burgeoning environ-
mental crisis. Environmental disasters and its causes and concerns will inev-
itably pave the way toward a new dimension of scientific pursuit. Scientific
validation is the answer to the grave concerns and the impending crisis.10
Advancements in science and technology in today’s world of scientific
vision depends wholly on scientific validation. In such a crucial juxtaposi-
tion, membrane science is the only answer to the wide gamut of environ-
mental engineering problems.11,21,22

14.7  VISION OF THE APPLICATION OF MEMBRANE SCIENCE

The vision of the application of membrane science in environmental engi-

neering science is absolutely wide and far-reaching.11 Environmental
316 Applied Chemistry and Chemical Engineering: Volume 4

regulations and stringent restrictions has urged the future scientific genera-
tions and scientific domain to scale visionary heights. Membrane science
and its varied technologies are the plausible technologies for tomorrow. In
today’s scientific endeavor, technology is diverse. Advancement of science
and technology relies intensely and vehemently on scientific vision and
strong scientific understanding. History of human civilization is taking a
definitive turn. The challenge for the future is groundbreaking and replete
with scientific fortitude. Membrane and water treatment is evolving into
new future directions and future dimensions. History of human scientific
endeavor and the progress of science is moving toward a definitive direc-
tion along with emancipation of engineering. Chemical engineering, process
engineering and environmental engineering is in a world of immense and
intense rationalization and optimization. History of human civilization and
human scientific endeavor is in today’s scientific world is taking a defini-
tive turn and a visionary turnaround. The world of scientific fortitude and
scientific understanding is witnessing a devastating as well as an effec-
tive environmental engineering paradigm. Environmental catastrophes are
rebuilding environmental engineering techniques and paradigm. Man’s
vision is emboldened at every step of human history and human scientific
endeavor. Mankind is steadily moving toward a new era of effective envi-
ronmental engineering frontier. The frontiers of science and engineering of
membrane separation processes are surpassed and the world of challenges
are overcome at its utmost. Water technology and environmental engineering
technologies in today’s world have an umbilical cord. The success of envi-
ronmental sustainability will move toward alleviating global water crisis.
Effective water science, the vision to excel and the visionary frontiers of
membrane science will evolve into new future dimensions of holistic science
and technology.21,22

14.8  SCIENTIFIC DOCTRINE OF MEMBRANE SCIENCE

The doctrine of membrane science is undergoing drastic challenges and vehe-

ment changes.11 History of environmental engineering science is witnessing
visionary changes and environmental sustainability is the ultimate goal of
human civilization.11 At such a crucial juxtaposition, a scientist’s vision as
well as the intense scientific understanding behind environmental engineering
techniques are vehemently emboldened. Membrane science is ushering in a
new dawn of scientific era. Separation phenomenon in chemical engineering
frontiers is a hallmark toward the future of scientific endeavor. Desalination,
Environmental Engineering, Membrane Technology 317

industrial wastewater treatment, and provision for clean drinking water are
the pallbearers to a new scientific understanding and vision.11,21,22

14.9  MEMBRANE SCIENCE: CURRENT TRENDS AND FUTURE

CHALLENGES

Current trends and future challenges in the field of membrane science are
of utmost importance to the growth of science and engineering. History
of human mankind is witnessing a glorious scientific rebirth and scien-
tific rejuvenation with the progress of scientific endeavor in membrane
science. Membrane fouling, phenomenon of concentration boundary layer
and the effectivity of separation phenomenon are the veritable hallmarks
of future scientific research pursuit. Reverse osmosis and desalination are
the hallmarks of reenvisioning of membrane technology. Future of global
water crisis is grave and vehemently disastrous.11 Current trends of effec-
tivity of membrane separation phenomenon are evolving into new dimen-
sions of research pursuit. Membrane fouling is a vexing and challenging
issue. Future challenges and future direction of membrane science should
be effectively toward alleviating and wiping global water crisis. Advance-
ment in science and technology and challenges of the future will lead a long
way in the ultimate emancipation of membrane separation phenomenon.11
Membrane science in today’s scientific world has an umbilical cord with
alleviation of global water crisis. Man’s vision, the visionary path toward
scientific progress and the civilization’s advancement are the hallmarks
toward a new era of environmental engineering paradigm. Current trends in
the advancement of membrane science are targeted toward greater emanci-
pation toward global water crisis which veritably includes desalination and
industrial wastewater treatment. Challenges are surmounting at every step of
human scientific endeavor. Yet the urge and vision to excel has propelled the
human scientific pursuit to scale one visionary height over another.

14.10  VISION OF SCIENCE, THE WORLD OF CHALLENGES AND

THE RESEARCH PURSUIT IN NOVEL SEPARATION PROCESSES

Vision of science in today’s scientific world is undergoing remarkable

challenges. Human scientific vision, scientific rigor and ardor are drasti-
cally changing the scientific landscape. Man’s prowess and civilization’s
immense and wide vision needs to be reshaped with respect to scientific
318 Applied Chemistry and Chemical Engineering: Volume 4

research pursuit. Novel separation processes and membrane science are

transforming the scientific horizon. Scientific endeavor, the vision of tech-
nology initiatives and the world of challenges are the pallbearers of energy
and environmental sustainability. Scientific research pursuit and the world
of chemical process engineering are revolutionizing the scientific domain.

14.11  TECHNOLOGY INITIATIVE IN DEVELOPED AND

DEVELOPING COUNTRIES AND FUTURE OF GLOBAL WATER
SCENARIO

Technology initiative in developed and developing countries in the domain

of water technology are changing the face of global science. True eman-
cipation and true realization of environmental sustainability are the need
of the hour. The greatness and the glory of membrane science needs to be
reenvisioned. Global water scenario is witnessing a disastrous crisis with
the burning issue of arsenic groundwater pollution. Global water technology
is in the midst of a deepening crisis in the developed as well as developing
world. Science and technology has no constructive answers. Human science
and vision is endangered. Global arsenic groundwater remediation needs
to be effectively addressed. Human scientific vision stands as a primordial
issue in the future path of human civilization.

14.12  GLOBAL WATER CRISIS AND ARSENIC GROUNDWATER

CONTAMINATION

Arsenic groundwater contamination is a veritable bane to human civili-

zation.5–8,11 Progress of science and environmental engineering in today’s
world in a state of distress as well as in a state of reenvisioning. Ground-
water remediation needs to be reshaped and revitalized with every step of
human progress. Developing and developed economies are entangled in
water shortage crisis and ground water contamination. Newer innovative
technologies needs to be envisioned with progress of scientific endeavour.11
Provision of clean drinking water and industrial wastewater treatment stands
tall in the midst of immense optimism as well as deep introspection.10,11 In
Bangladesh and the state of West Bengal, India, groundwater contamination
is playing havoc to the human civilization. Concern, challenges and barriers
has opened up new vistas of scientific hardships in years to come in the field
of arsenic groundwater remediation. History of human challenges is having
Environmental Engineering, Membrane Technology 319

a new beginning with the grave concern of the world’s largest unsolvable
environmental disaster.10,11 Bangladesh and West Bengal still today remains
in a murky state of affairs with the drinking water crisis. The challenge is
absolutely insurmountable and disastrous. Science has met with a disastrous
failure at every step of human progress in the path of arsenic groundwater
remediation. Human mankind’s future targets, the world of immense chal-
lenges and the march of science are the primordial issues which needs to be
tackled with utmost importance in future.11,21,22

14.13  VISION AND CHALLENGES TO MOVE FORWARD IN

ENVIRONMENTAL ENGINEERING SCIENCE

Industrial wastewater treatment is witnessing a new dawn in the present

century. Environmental engineering science in a similar vein is evolving
toward a newer future dimension at every step of life and human civiliza-
tion.11 Membrane science stands as the utmost answer and the plausible solu-
tion toward global water crisis and controlling industrial pollution. Vision
and challenges to move forward are immense and retrogressive. At such a
critical juncture of science, history and time, the evolution and emancipation
of new and innovative technologies are of utmost importance to the prog-
ress of membrane separation phenomenon. The wide world of membrane
science needs to be reenvisioned and restructured carrying with the legacy
of Loeb–Sourirajan model.11 Loeb–Sourirajan model has left an indelible
impact to the future of environmental engineering science. Drinking water
treatment, industrial pollution control and the future of environmental engi-
neering science are in questionable times and in a state of immense distress.
History of human civilization needs to be restructured and reshaped at every
step of human progress.11

14.14  THE WORLD OF VISIONARY FRONTIERS AND THE

PROGRESS OF MEMBRANE SCIENCE

Science and engineering in today’s world are surpassing visionary frontiers.

Scientific vision and scientific candor are in the path of new rejuvenation.
Membrane science is a veritable pillar of novel separation process. Loeb–
Sourirajan model had revolutionized and rebuilt the membrane science
scenario. Scientific progress in today’s world is at a deep distress due to
ecological imbalance and frequent environmental catastrophes. The vision
320 Applied Chemistry and Chemical Engineering: Volume 4

of science is undergoing tremendous metamorphosis. Water science and

technology is advancing toward a newer regeneration. Technological vision
needs to be reshaped with the passage of history due to the serious environ-
mental issues. Thus novel separation processes and membrane science are
primordial issues of this century11 Science and engineering of membrane
separation processes are surpassing visionary frontiers. Human scientific
endeavor in today’s world is at its zenith.

14.15  BARRIERS, DIFFICULTIES, AND THE WORLD OF

CHALLENGES

Scientific challenges and scientific vision are vast and versatile. Science
is witnessing vicious challenges. The effectivity of membrane separation
process stands as a primordial issue. Fouling stands as other major impedi-
ment. The world of scientific truth is beckoning toward a newer vision
and newer goal. Barriers and difficulties are running riot in the scientific
research pursuit domain. Yet the goal and vision needs to be reshaped and
reenvisioned with each step of human history and time.11
Barriers and difficulties in the progress of membrane science are vast and
versatile. Scientific understanding and scientific rigor are at its helm with
the passage of human history and time. Fouling and concentration polariza-
tion stands as a major impediment to the success of membrane separation
phenomenon. Research endeavor and scientific validation are the torch-
bearers of tomorrow’s success of membrane science. The author in this trea-
tise stresses study on the immense importance of novel separation processes
such as membrane science in the path of environmental engineering science
validation. Success of scientific rigor, the immense progress of engineering
in this century and the wide world scientific understanding all will lead a
long way in the successful validation of membrane separation processes.15–20

14.16  VISION OF SCIENCE, SCIENTIFIC IMAGINATION, AND

THE AVENUES OF SCIENCE FORWARD

Vision of science and scientific imagination are in the road toward newer
vision and newer hope. Scientific fortitude and scientific forbearance needs
to be reenvisioned in such difficult human era. Man’s visions as well as civi-
lization’s prowess are moving toward newer future direction and a visionary
eon. This is an age of scientific sagacity and immense scientific cognizance.
Environmental Engineering, Membrane Technology 321

Global water crisis is at a state of immense disaster. The road forward and
the progress of human civilization is in the midst of unimaginable crisis
with the growing concern of ecological imbalance and at the same time the
apprehension of environmental catastrophes. Membrane science is changing
the scientific horizon. Man’s immense instinctive vision, civilization’s move
forward and the world of challenges has redefined the paradigm of environ-
mental engineering science. The target of human civilization, the progress of
scientific endeavor and the urge of the civil society should be geared toward
a newer environmental engineering paradigm.11

14.17  NOVEL SEPARATION PROCESSES AND THE FUTURE OF

SCIENCE AND ENGINEERING

Novel separation processes needs to be redefined with each foray into civi-
lization’s history and time. Membrane science and membrane separation
processes are in the process of new scientific regeneration and a new scien-
tific imagination. The vision of science in today’s world is veritably awe-
inspiring. Technological vision is challenged. Novel separation processes
today stands as a major pillar of environmental engineering paradigm.
Human scientific endeavor is in the midst of deepening crisis. Yet the future
of science and engineering needs to be reenvisioned. Loeb–Sourirajan model
revolutionized the concept of diffusion process in membranes. The discov-
ered theory and the subsequent research pursuit are the torchbearers of a new
visionary scientific age.11,15–17

14.18  FUTURE DIRECTIONS AND FUTURE CHALLENGES IN THE

EMANCIPATION OF SCIENCE AND TECHNOLOGY

Future directions and future dimensions of research in the field of membrane

science are surpassing wide and visionary frontiers. The main crux of the
research endeavor should be greater application toward alleviation of global
water crisis. Membrane separation phenomenon should be of utmost impor-
tance to the avenues of progress in water technology and environmental
engineering science. Science and its application are entering into an abso-
lutely visionary era. History of science and technology and its legacy are in
a revolutionary phase in the present century. The world of challenges has
shrunken with new innovations and newer scientific instincts. The eman-
cipation of science is visible and revealed at every step of human scientific
322 Applied Chemistry and Chemical Engineering: Volume 4

endeavor. Progress of civilization with the advances of environmental engi-

neering are ushering in a new dawn of scientific growth and a new direction
toward emancipation of science.11,18–20

14.19  FUTURE VISION AND FUTURE FLOW OF THOUGHT

Future vision of membrane science and future flow of thoughts in environ-

mental engineering science needs to have a definite direction.11 Global water
crisis, groundwater remediation, and the future of membrane science are the
hallmarks and definite yardsticks to the scientific progress.11 Arsenic ground-
water remediation is the hallmark toward a greater emancipation of science
and engineering. Man’s scientific progress, civilization’s prowess, and the
world of challenges have given way to newer windows of innovation and the
effective avenues of environmental engineering science. Vistas of science are
beyond imagination and beyond comprehension. Groundwater remediation
remains as a single yardstick to the progress of science and technology. The
world of water technology is in a grave crisis. In such a visionary juncture,
application of science and engineering such as membrane science remains
entrenched in scientific frontier. The history of science is ushering in a new
beginning with the evolution of new technologies in membrane separation
processes.11

14.20 CONCLUSION

History of human scientific endeavor is moving through a difficult and

distressful era.11 A scientist’s vision is emboldened at every step of human
progress. Membrane science and the paradigm of environmental engineering
science is surpassing wide and visionary frontiers. The question of envi-
ronmental sustainability is a vexing issue in the future of human mankind.
Environmental devastation along with stringent restrictions is the hallmarks
of the present environmental engineering paradigm. Membrane separation
phenomenon is moving toward a newer direction and a visionary realm.11
The success of science is befitting to the progress of human civilization.
Mankind’s history, civilization’s legacy and the path of environmental regu-
lations have urged the scientific community to yearn for innovation and
scientific instinct. Challenges for tomorrow and the vision for the future have
propelled human society to look for green chemistry. In such a juxta posi-
tion, green environmental engineering techniques will surely enhance the
Environmental Engineering, Membrane Technology 323

scientific vision and scientific truth. Scientific forbearance and the world of
challenges needs to be restructured with the evolution of new environmental
engineering paradigm.11 The future vision of membrane science will inevi-
tably enhance the civilization’s growth and mankind’s prowess.11Membrane
science in today’s world will open up new doors of scientific innovation in
years to come.
Science and engineering are moving fast toward a new visionary frontier.
Environmental engineering science is witnessing drastic changes in its path
toward true realization of environmental sustainability. This treatise will be a
pallbearer toward the future world of membrane science and environmental
engineering science. Progress of engineering, the grave concerns of human
civilization and the scientific forbearance to excel will all lead a long and
definite way in the true emancipation of membrane science.

KEYWORDS

•• membrane
•• environment
•• water
•• arsenic
•• global
•• shortage

REFERENCES

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How to Avoid Them: A Review. Sep. Purif. Technol. 2008, 63, 251–263.
2. Matsuura, T. Progress in Membrane Science and Technology for Seawater Desalina-
tion—A Review. Desalination 2001, 134, 47–54.
3. Sidek, N. M.; Ali, N.; Fauzi, S. A. A. The Governing Factors of Nanofiltration Membrane
Separation Process Performance—A Review. In UMTAS, Empowering Science Tech-
nology and Innovation Towards a Better Tomorrow; 2011; pp 241–248.
4. Hong, S.; Elimelech, M. Chemical and Physical Aspects of Natural Organic Matter
(NOM) Fouling of Nanofiltration Membranes. J. Membr. Sci. 1997, 132, 159–181.
5. Hilal, N.; Mohammad, A. W.; Atkin, B.; Darwish, N. A. Using Atomic Force Micros-
copy Towards Improvement in Nanofiltration Membranes Properties for Desalination
Pretreatment—A Review. Desalination 2003, 157, 137–144.
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6. Hilal, N.; Zoubi, A.; Darwish, N. A.; Mohammad, A. W.; Abu Arabi, M. A Compre-
hensive Review of Nanofiltration Membranes: Treatment, Pretreatment, Modeling and
Atomic Force Microscopy. Desalination 2004, 170, 281–308.
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Company Inc.: USA, 1998.
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Preparing and Used in Drinking Water Treatment. Int. J. Environ. Sci. Dev. 2013, 49(4),
343–385.
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Membrane—A Short Review. Int. J. Basic Appl. Sci. 2010, 10(2), 17–27.
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and Recent Developments. J. Membr. Sci. 2006, 281, 70–87.
15. Palit, S. Filtration: Frontiers of the Engineering and Science of Nanofiltration—A Far-
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Kharissova, O. V., Kharisov. B. I., Eds.; Taylor and Francis: USA, 2016; pp 205–214.
16. Palit, S. Advanced Oxidation Processes, Nanofiltration, and Application of Bubble
Column Reactor, Nanomaterials for Environmental Protection; Boris, I. K., Oxana, V.
K., Rasika Dias, H. V., Eds.; Wiley: USA, 2015; pp 207–215.
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Technol. 2015, 14(4), 817–825.
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CHAPTER 15

A COMPARATIVE STUDY ON
ELECTROCENTRIFUGE SPINNING
AND ELECTROSPINNING PROCESS
AS TWO DIFFERENT NANOFIBER
CREATION TECHNIQUES
S. RAFIEI*
Department of Textile Engineering, University of Guilan, Rasht, Iran
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.....................................................................................................326
15.1 Introduction....................................................................................326
15.2 Experimental Study by Focusing on Flow Rate for
Both Devices..................................................................................332
15.3 Results and Discussion..................................................................335
15.4 Conclusion.....................................................................................338
Keywords..................................................................................................339
References.................................................................................................339
326 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

In this study, centrifugal and electrical forces have been employed simul-
taneously for nanofiber production, and the effect of adding the centrifugal
force to the electrical forces on the nanofiber diameter and production rate
has been investigated in detail.

15.1 INTRODUCTION

When the diameters of polymer fibers are shrunk from micrometers to

submicro or nanometers, several new characteristics emerge, including a
very high ratio of surface area to volume, flexibility in surface function-
alities, and superior mechanical performance (e.g., stiffness and tensile
strength). These unique properties make these polymeric fibers ideal candi-
dates for many important applications.1–3
Although several methods have been proposed for nanofiber manu-
facturing so far, an efficient and cost-effective procedure of production is
still a challenge as debated by many experts. Electrospinning has been the
most successful method to produce nanofibers so far. It is a well-known and
prominent procedure which is based on electrostatic force that provides the
possibility for spinning nanofibers from many kinds of polymers using melt
or solution spinning.4–6
The use of mechanical methods to apply high rates of tension to a polymer
solution or melt is only possible for polymers with high extension ability, to
prevent uneven transmission of tension and stress concentration. In order to
apply high rates of tension to a polymer solution or melt, methods which can
apply even distribution of stress during the tension process are required. When
the centrifugal force acts upon a substance, the particles of that matter will
experience a force proportional to their distance from the center of rotation.
Thus, this force can be used to apply high rates of tension on a polymer solu-
tion. During the tension process, if the polymer solution has sufficient viscosity,
it will be stretched as a string, transforming to a polymeric fiber after drying.7,8
Electrocentrifuge spinning or has been recently introduced as a benefi-
cial method for nanofiber production. It is necessary to specify the effec-
tive parameters on nanofiber production and diameters. In this research, the
effective parameters on the process and the influence of each parameter on
fibers diameter are addressed. Also the fiber production capability of electro-
centrifuge technique is compared with that of the conventional electrospin-
ning method.9–11
A Comparative Study on Electrocentrifuge Spinning 327

15.1.1 NANOFIBERS

Nanofibers are defined as fibers with diameters less than 100 nm which
can be produced by different methods such as melt processing, interfacial
polymerization, electrospinning, electrocentrifuge spinning, and antisol-
vent-induced polymer precipitation.5 The fibers which are produced by
these methods have a very high specific surface area, unusual strength, high
surface energy, surface reactivity, and high thermal and electric conduc-
tivity that could be used in products by special application. These unique
properties make the polymeric nanofibers ideal candidates for many impor-
tant applications, such as, nanofiltration,12 nanocatalysis, tissue scaffolds,13
protective clothing, filtration, nanoelectronics,14 high-performance nanofi-
bers,15,16 drug delivery systems, wound dressings, and composites. Although
several methods have been proposed for nanofiber manufacturing so far, an
efficient and cost-effective procedure of production is still a challenge and is
debated by many experts.17–20

15.1.2  ELECTROSPINNING METHOD

Electrospinning is an efficient and simple mean of producing nanofibers

by solidification of a polymer solution stretched by an electric field.21 It is
a well-known and prominent procedure based on electrostatic forces that
provides the possibility for spinning nanofibers from many kinds of poly-
mers using melt or solution spinning.22,23
In typical electrospinning process, an electrical potential is applied
between droplets of polymer solution or melt, held through a syringe needle
and a grounded target; afterwards the electrostatic field stretches the polymer
solution into fibers as the solvent is evaporating. During the process the
polymer jet undergoes instabilities, which together with the solution proper-
ties, determines the morphology of the forming nanosized structures obtained
onto the collector. The electrical forces elongate the jet thousands of times,
causing the jet become very thin. Ultimately, the solvent evaporates or the
melt solidifies, and a web containing very long nanofibers is collected on the
target. The fiber morphology is controlled by the experimental design and
is dependent on solution properties and system conditions such as conduc-
tivity, solvent polarity, solution concentration, polymer molecular weight,
viscosity, and applied voltage.4,24
To overcome various limitations of the typical electrospinning method,
researchers have applied some modifications to the original setup.24,25 Some
328 Applied Chemistry and Chemical Engineering: Volume 4

of these reformed techniques which have been done by now include: elec-
trospinning using a collector consists of two pieces of electrical conduc-
tive plates separated by a gap, collecting spun nanofibers on a rotating thin
wheel with sharp edge, fabricating aligned yarns of nylon 6 nanofibers
by rapidly oscillating a grounded frame within the jet26 and finally using
a metal frame as a collector to generate parallel arrays of nanofibers.27
Matthews et al.26 have applied a rotating drum to collect aligned nanofibers
at a very high speed up to thousands of revolution per minute (RPM). In
another approach, Deitzel et al.28 used a multiple field technique which
can straighten the polymer jet to some extent. Luming et al.29 used this
technique to collect aligned nanofibers by increasing the surface velocity
of the drum.
Increasing the production rate of nanofibers has always been one of the
most important challenges of researchers. Most efforts in this point have
been focused on increasing the number of nozzles.30 Yarin et al. introduced
the concept of “upward needleless electrospinning of multiple nanofibers”.31
A similar idea was discussed by Liu and He32,33 by the name of “Bubble
electrospinning” method.

15.1.3  CENTRIFUGAL FORCE

In Newtonian mechanics, the term centrifugal force is used to refer to an

inertial force (also called a ‘fictitious’ force) directed away from the axis of
rotation that appears to act on all objects when viewed in a rotating reference
frame. The concept of centrifugal force can be applied in rotating devices
such as centrifuges, centrifugal pumps, centrifugal governors, centrifugal
clutches, etc., as well as in centrifugal railways, planetary orbits, banked
curves, etc., when they are analyzed in a rotating coordinate system.34
Centrifugal force is an outward force apparent in a rotating reference
frame; it does not exist when measurements are made in an inertial frame of
reference. All measurements of position and velocity must be made relative
to some frame of reference. For example, if we are studying the motion of an
object in an airliner traveling at great speed, we could calculate the motion
of the object with respect to the interior of the airliner, or to the surface of the
earth. An inertial frame of reference is one that is not accelerating (including
rotation). The use of an inertial frame of reference, which will be the case for
all elementary calculations, is often not explicitly stated but may generally
be assumed unless stated otherwise.35,36
A Comparative Study on Electrocentrifuge Spinning 329

In terms of an inertial frame of reference, centrifugal force does not

exist. All calculations can be performed using only Newton’s laws of motion
and the real forces. In its current usage, the term “centrifugal force” has no
meaning in an inertial frame. In an inertial frame, an object that has no forces
acting on it travels in a straight line, according to Newton's first law. When
measurements are made with respect to a rotating reference frame, however,
the same object would have a curved path, because the frame of reference
is rotating. If it is desired to apply Newton's laws in the rotating frame, it
is necessary to introduce new, fictitious, forces to account for this curved
motion. In the rotating reference frame, all objects, regardless of their state
of motion, appear to be under the influence of a radially (from the axis of
rotation) outward force that is proportional to their mass, the distance from
the axis of rotation of the frame, and to the square of the angular velocity of
the frame. This is the centrifugal force.37,38
In order to apply high rates of tension to a polymer solution or melt,
methods which can apply even distribution of stress during the tension
process are required. When the centrifugal force acts upon a substance, the
particles of that matter will experience a force proportional to their distance
from the center of rotation. Thus, this force can be used to apply high rates
of tension on a polymer solution. During the tension process, if the polymer
solution has sufficient viscosity, it will be stretched as a string and trans-
formed to a polymeric fiber after drying.

15.1.4  CENTRIFUGAL SPINNING METHODS

Hooper patented the centrifugal spinning in 1924. Classical centrifugal

spinning involves supplying centripetal force using a rotary distribution
disc with side nozzle holes. The rotation shears the spinning dope, clas-
sically thermoplastic materials, for instance, molten mineral or glass to
form fibers such as mineral wool. Recent advances in centrifugal nanos-
pinning have demonstrated the potential of this technique for nanofibers
production. The initial work done merging electrospinning with centrifugal
concepts indicated a competitive edge compared with the technique alone
in terms of its ability to produce homogeneous nanofibers of below 100 nm
in size and a simultaneous one-step post-spin draw possibility to enhance
molecular alignment and fiber crystallinity for improved tensile strength of
the resultant fiber.8,9
Nanofibers which are produced by traditional electrospinning usually
have a wide diameter distribution, whereas the fiber diameter has an
330 Applied Chemistry and Chemical Engineering: Volume 4

important effect on the performance of nanofiber mats in many important

applications. Several of variables can influence the electrospun nanofiber
diameter, diameter uniformity, and nanofiber quality such as volumetric
charge density, distance from nozzle to collector, initial jet/orifice radius,
relaxation time, viscosity, concentration, solution density, electric poten-
tial, perturbation frequency, and solvent vapor pressure. Furthermore, fiber
diameter is increased with increasing the surface tension and flow rate, but is
decreased with increasing the electric current. Solvent–polymer interactions
critically influence the diameter and morphology of the electrospun fibers.
One method for obtaining finer nanofiber is to reduce the concentration of
the polymer solution. Also, it has been found that with the increase in elec-
trical conductivity of the polymer solution, there is a significant decrease in
the electrospun nanofiber diameter. Also, the control of the process parame-
ters such as applied voltage and temperature can influence electrospun nano-
fiber diameter. The diameter of the nanofibers is increased by increasing the
electrospinning voltage.2,39
Although all these approaches can influence nanofiber diameter, there are
some limitations due to the addition of unwanted components, insufficient
and difficult controllability, and strict thinning effect. Therefore, it is neces-
sary to provide a method that can fabricate nanofibers with high uniformity
and fineness without any additional procedures.

15.1.5  CENTRIFUGAL ELECTROSPINNING

Centrifugal electrospinning has been attempted and the setup typically

comprises of rotary spinnerets similar to centrifugal spinning. In 2006,
centrifugal electrospinning using a rotary spinneret was reported by
Dosunmu et al. using a porous ceramic tube spinneret and by Andrady et al.
using a rotatable spray head with four individual extrusion elements, which
in turn can be made of bundles of multiple nozzles.
Reiter Oberflachen technik GmbH developed the Hyper Bell centrifugal
electrospinning technology, which was subsequently acquired by Dienes
Apparatebau GmbH. A centrifugal electrospinning unit with three spin heads
currently supplied by Dienes Apparatebau is able to increase the throughput
of conventional nozzle electrospinning by a thousand fold with a minimum
achievable nanofibers diameter of 80  nm. Coupling centripetal force with
electrostatic force, highly aligned poly(lactic acid) (PLA) electrospun fibers
with improved modulus of 3.3 GPa (PLA in chloroform and tetrahydrofuran)
were produced.
A Comparative Study on Electrocentrifuge Spinning 331

15.1.6  CENTRIFUGAL NANOSPINNING

A spinning method using only centripetal force to produce nanofibers was

recently developed. Force spinning by FibeRio Technology Corporation
achieved a minimum as-spun fibers diameter of 45 nm. The first polyethylene
oxide (PEO) nanofibers obtained by force spinning demonstrated homoge-
neity with an average diameter of 105–300 nm. Furthermore, aligned PLA
nanofibrous scaffolds were prepared using a similar method by Badrossamay
et al.35 under the name ‘‘rotary jet-spinning,’’ and were used to seed cardio-
myocytes in mice. The result showed good tolerance of the nanofibers, and
the cell seedings successfully developed into pulsating multicellular tissues.
The temperature, rotational speed of the spinneret, and collection distance
are the parameters influencing the geometry and morphology of centrifu-
gally spun nanofibers.
Centrifugal nanospinning is a versatile method that overcomes many
of the limitations. The process offers higher productivity and simplicity in
an equipment setup without the complication of high voltage in up scaled
processing and the material constraint on electrical conductivity or relative
permittivity compared to electrospinning. Nevertheless, centrifugal nanos-
pinning is an extrusion process limited by challenges related to the material
properties and the designs of the spinneret, which can lead to large differ-
ences in fiber quality and productivity. The fiber diameter in a single PLA
sample can vary from 50 to 3.5 mm. The degree of complexity in the spin-
neret design is also proportional to the cost incurred. Although centrifugal
nanospinning is a facile technique to generate three-dimensional scaffolds
with a moderately high degree of uniaxial alignment, formation of more
complex three-dimensional nanostructures with functionalized nano features
or alignment of fibers in more than one direction may be difficult and has yet
been demonstrated with this technique to date.
There has been much research and progress in the development of
various designs and modification to the electrospinning process over the last
century. Nevertheless, there are still many areas where further refinement
of the process will be welcomed. To begin with, although there are several
setups designed to achieve fiber alignment, there is still a serious short-
coming in getting highly aligned nanofibers over a large area of substan-
tial thickness. Generally, a drum collector is not able to get highly aligned
fibers even though it is able to get a larger area of fibrous mesh. Aligned
nanofibers have been shown to induce cell elongation and proliferation in
the direction of the fiber alignment. The ability to fabricate highly aligned
fibers in large quantity over a large area will allow more investigation in
332 Applied Chemistry and Chemical Engineering: Volume 4

cellular response to the fiber alignment in terms of gene expression and cell
interaction. Typically, electrospun assemblies are in a two-dimensional form
and in the case of yarn a one-dimensional form. The only three-dimensional
electrospun structure with significant length, width, and height is a fibrous
tube. However, researchers have yet found a way to consistently fabricate a
solid three-dimensional structure through electrospinning. With the ability
to fabricate three-dimensional structure, other applications such as bone
replacement scaffold can be considered. Recently, Smit et al. and Khil et al.
demonstrated the fabrication of continuous yarn made out of purely nanofi-
bers. However, the spinning speed of 30 m min−1 is still much slower than
that of the industrial fiber spinning process, which runs from 200 to 1500 m
min−1 for dry spinning (Gupta & Kothari, 1997). Yarn made out of electro-
spun fibers has many applications, especially when fabricated into textiles.
However, for electrospun yarn to be adopted by the textile industry, its yarn
spinning speed has to be improved significantly.
Although Sun et al. made a breakthrough in the electrospinning process
by creating controlled pattern using electrospun nanofibers, the small volume
of solution that can be spun at one time significantly reduced the practicality
of the process. An advantage of electrospinning is its ability to spin long
continuous fibers at high speed. However, it is still not possible to form
highly ordered structures rapidly. Arrayed nanofiber assemblies created thus
far are based on arranging aligned nanofibers with very little control on the
distance between each fiber.
In the following experimental part of this study, besides exploring the
effects of centrifugal force on the nanofibers diameter, the fiber produc-
tion capability of electrocentrifuge technique is compared with that of the
conventional electrospinning method.

15.2  EXPERIMENTAL STUDY BY FOCUSING ON FLOW RATE FOR

BOTH DEVICES

15.2.1  MATERIALS

Commercial polyacrylonitrile (PAN) polymer powder with Mw = 100,000

g/mol and Mn = 70,000 g/mol was supplied by Polyacryl, Iran. The used
solvent was Dimethyl Formamide (DMF) from Merck Company. The
polymer solutions of PAN in DMF with the concentration of 13–16 wt%
were prepared using a digital scale (Libror AEU-210, Shimadzu) with accu-
racy to gage of 0.0001 g. Dissolving and stirring of mixture was performed
A Comparative Study on Electrocentrifuge Spinning 333

with constant speed at room temperature after that, the solution was kept on
70°C for 2 h to complete the dissolution.
Scanning electron microscopy (SEM) images were used to measure
the nanofibers, diameter of different samples using a field-emission scan-
ning electron microscope (Philips SEM, XL-30). At least 100 fibers were
chosen to compare each sample layer and diameter with the image scale. The
average of the results was applied as the diameter of fibers produced within
the process.
In order to measure the flow rate, 0.3 + X mg of solution with four decimal
places accuracy was poured into the needle container. Then the needle was
located into the centrifuge apparatus and centrifugal action was continued
until the solution weight run to 0.3 − X mg. The difference between the two
weights indicates the amount of pumped solution in grams. By measuring
the density of solvent and polymer into account, the volume of pumped solu-
tion can be calculated.

15.2.2  ELECTRO CENTRIFUGE METHOD AND SETUP

Figure 15.1 represents a schematic picture of the centrifuge apparatus. In

order to exert centrifugal force, a rotating disk with capability of controlling
speed in the range of 0–10,000 rounds per min has been used. A tube with
an inner diameter of around 4 mm is eccentrically placed within the cylinder
body as polymer container which is connected to a needle with geometric
characteristics of 0.165 mm inner diameter, 0.3 mm outer diameter, and
17 mm of length as nozzle. The assembly of the polymer solution container
and the nozzle inside the disk reduces the effects of air stream on the nozzle
tip during the rotation. The intense impact between the air and the needle
causes the polymer solution to dry at the needle tip and block the flow of the
polymer solution through the nozzle.
The centrifuge method for PAN solution with the concentration of 12–16
wt% at a rotational speed in the range of 0–9540 rpm can produce defected
nanofiber with drop sprinkling and bead. To improve the centrifuge method
in order to obtain intact nanofibers, electrical force was used simultaneously.
A high voltage power supply was used to apply an electrostatic force
which is able to generate DC voltages up to 22 kV. A metallic cylinder of
26.6 cm diameter and 10 cm height which is connected to a negative elec-
trode of high voltage supply was used as the fiber collector and the nozzle
was connected to the positive electrode as shown in Figure 15.2. The
distances between the disk center and the needle tip and the interior surface
334 Applied Chemistry and Chemical Engineering: Volume 4

of the collector cylinder and the needle tip are 5.3 and 8 cm, respectively.
Only 0.30 mL of the volume of the container is filled up by the solution in
all experiments.37,38
Applying centrifugal force causes the polymer solution to flow out of the
nozzle. A jet is formed at the nozzle exit, if the viscosity of the solution will
be high enough; then the electrical and centrifugal forces elongate the jet
thousands of times and it becomes very thin. Ultimately, by the evaporating
the solvent, very long nanofibers are collected on the interior surface of the
collector

FIGURE 15.1  Schematic of centrifuge spinning setup: (a) axle of rotation, (b) polymer
solution container, (c) nozzle tip, and (d) cylinder.

FIGURE 15.2  Schematic of electrocentrifuge setup: (a) axle of rotation, (c) nozzle tip, (d)
cylinder, (e) collector, and (f) polymeric jet.
A Comparative Study on Electrocentrifuge Spinning 335

15.2.3  THEORY OF FLOW RATE

It should be noted that the flow rate is controlled only by the centrifugal force
in the present experimental setup. When the free surface of the polymer solu-
tion in the container and the nozzle tip are at the same atmospheric pressure,
the pressure within the container increases as the centrifugal force is exactly
equal to the pressure loss across the nozzle due to the viscosity effect, that
is, ΔP1,2 = ΔP2,3. On the other hand, the pressure rise in the container can be
estimated as:

1
( )
L0
∆P1,2 = ∫ ρl ω2 dl or ∆P1,2 = ρ L0 2 − x0 2 ω2 , (15.1)
x0 2
where ρ is the liquid density, L0 is the distance between the center of rotation
and the nozzle entrance, x0 is the distance between the center of rotation and
the liquid free surface, and ω is the angular speed.
Equation 15.1 shows that the pressure loss across the nozzle depends on
the length of the liquid column (L0 – x0)within the container. Since the flow
rate is also proportional to the same pressure difference, we can control the
flow rate by changing x0 and ω.

15.3  RESULTS AND DISCUSSION

Electrical forces which are known as Columbus and external field forces play
the drawing role in electrospinning method. The electrocentrifuge method has
been established with the intention of adding centrifugal force to the above
forces. Therefore, the effect of centrifugal force on the production rate and
fiber diameter is a matter of importance and has been investigated in this study.

15.3.1  EFFECT OF ROTATIONAL SPEED AT CONSTANT FLOW

RATE ON THE NANOFIBER DIAMETER

In order to investigate the effect of rotational speed at the constant flow rate
on the fibers’ diameter, fibers were produced from a 15 wt% solution at five
different quantities of the solution. For each run, the rotational speed was
adjusted by trial and error in a way that the flow rate in all rotational speeds
remains unchanged (1.2140 mL/h). As reported in Table 15.1 the obtained
results reveal that the fibers, diameter increases by increasing the rotational
speed at the constant flow rate. This can be interpreted in this way that by
336 Applied Chemistry and Chemical Engineering: Volume 4

increasing the rotational speed, the aerodynamic effects of the air stream
formed in between of rotating cylinders become more prominent around the
fiber. As the velocity of the air flow increases, the polymer jet gets dry before
it can be elongated further by the centrifugal force. Therefore, it seems that
at every flow rate there is a rotational speed in which the minimum fiber
diameter can be spun.

TABLE 15.1  Nanofiber Diameters Using Different Rotational Speeds at a Constant Flow
Rate 1.2140 mL/h.
Nanofiber diameter (nm) Rotational speed (rpm) Nanofiber production method
344 6360 Electrocentrifuge
396 7950 Electrocentrifuge
470 9540 Electrocentrifuge
352 0 Electrospinning

15.3.2  COMPARISON BETWEEN THE NANOFIBER

PRODUCTION RATES IN ELECTROSPINNING AND
ELECTROCENTRIFUGE SPINNING SYSTEMS

Before comparing the two systems of electrocentrifuge and electrospinning,

it is essential to know that all the effective variables (excluding the centrif-
ugal force) of the two systems have the same conditions.
The variation of surface tension cannot be significant when the polymer
concentration is in a range of 13–16%, and, therefore, we assume that this
parameter is constant for all experiments. Comparisons between the two
systems are made at two different applied voltages of 10 and 15 kV, and for
13, 14, 15, and 16 wt% solutions of PAN at the same conditions. The most
effective voltage which is possible to be applied to an 8 cm gap is equal to
15 kV. At higher voltage, the surrounding air will be ionized, which results
the generation of electric current between the positive and negative poles.
The setup parameters are exactly the same for both systems, except for the
flow rate. In the electrospinning system, a syringe pump provides the neces-
sary flow rates, while in the electrocentrifuge system the flow rate is adjusted
by the centrifugal force. For the specified parameters, the mean diameter of
the nanofibers obtained from the two systems was in a range of 200–600 nm.
Figure 15.3 shows typical SEM images of nanofibers produced from a 15
wt% polymer solution with a rotational speed of 6360 rpm and an average
diameter of 410 nm.
A Comparative Study on Electrocentrifuge Spinning 337

FIGURE 15.3  SEM images of nanofibers produced by electrocentrifuge method with 6360
rpm and 0.3 cc polymer solution in container: (a) low magnification (2000×) and (b) high
magnification (6000×).

Keeping other parameters constant, by increasing the flow rate to a

specific limit, bead formation and drop sprinkling occur in electrospinning.
The flow rate of the solution at the beginning of the bead formation is defined
as the maximum rate of solution pumping for electrospinning. However, in
the electrocentrifuge case, by increasing the rotational speed the flow rate
of the solution will increase when other parameters are constant. Therefore,
the production rate of fibers by the electrocentrifuge system is calculated by
measuring the solution flow rate at the maximum possible rotational speed
that leads to the production of fibers which are free of defects and beads. The
increase in the production rate of fibers by the electrocentrifuge method is
defined as the ratio of flow rates of the two systems when the produced fibers
have the same diameter.
As it can be seen, the electrocentrifuge method can increase the rate of
fiber production to a large extent. For the concentration of 16 wt%, the rpm
of 9540 is not the maximum possible rotational speed and it is feasible to
produce fibers with this concentration at higher velocities. This case was not
investigated here due to the apparatus limitations.
Table 15.2 shows a decline in the production rate index as the concentra-
tion of the polymer solution are increased in constant voltage. The observa-
tions show that at a constant rotational velocity and applied voltage, upon
increasing the concentration, the flow rate decreases and the production rate
of the electrocentrifuge system rapidly approaches that of the electrospinning
method. Interestingly, increasing the applied voltage reduces the production
rate when other parameters are constant. The effect of the centrifugal force
on the increase in production rate is more prominent for lower voltages due
to the lower electrospinning production rate in that range (Table 15.3).
338 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 15.2  Effect of Polymer Concentration on the Production Rate at Constant Voltage
of 15 kV.
Production rate Polymer solution Rotational speed Nanofiber production
percent concentration (wt%) (rpm) method
1200 13 6360 Electrocentrifuge
723 14 7950 Electrocentrifuge
450 15 9540 Electrocentrifuge
195 16 – Electrocentrifuge
197 13 0 Electrospinning

It can be concluded from the experiment that at lower polymer concentra-

tions, the centrifugal forces are more effective. For example, at the concen-
tration of 13 wt% and voltage of 10 kV, the production rate is 12 times larger
than that of the conventional electrospinning approach.

TABLE 15.3  Effect of Applied Voltage on the Production Rate in Constant Concentration
of 13%.
Production rate Applied voltage (kV) Rotational speed Nanofiber production
percent (rpm) method
187 10 6360 Electrocentrifuge
444 12 7950 Electrocentrifuge
678 14 9540 Electrocentrifuge
1200 15 – Electrocentrifuge
177 10 0 Electrospinning

15.4 CONCLUSION

Centrifugal and electrical forces have been employed simultaneously for

nanofiber production, and the effect of adding the centrifugal force to the
electrical forces on the nanofiber diameter and production rate (which are
the most important factors for nanofiber production) has been investigated
in this study.
At first, the effect of increasing the rotational speed at a constant flow
rate on the fiber diameter was investigated, which causes an increase in the
diameter of the produced fibers upon increasing the rotational speed. As a
result of an increase in the impact intensity of the air surrounding the nozzle
with the exiting jet, the jet dries quickly.
A Comparative Study on Electrocentrifuge Spinning 339

In addition, the nanofiber production capability of the novel method

was investigated and compared with conventional electrospinning. Results
demonstrate a significant increase in the production rate of the electrocen-
trifuge method compared with electrospinning which is depended on the
concentration of the polymer solution and the applied voltage. Employing
the electrocentrifuge technique can overcome the low production rate of
electrospinning method. Therefore, this approach can be a satisfactory alter-
native to electrospinning.

KEYWORDS

•• tensile strength
•• nanofibers
•• electrospinning
•• polymers
•• electrocentrifuge

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33. Dosunmu, O., et al. Electrospinning of Polymer Nanofibres from Multiple Jets on a
Porous Tubular Surface. Nanotechnology 2006, 17(4), 1123–1127.
34. Arya, A. P. Introduction to Classical Mechanics; Allyn and Bacon: Boston, Massachu-
setts, 1990.
35. Badrossamay, M. R., et al. Nanofiber Assembly by Rotary Jet-spinning. Nano Lett.
2010, 10(6), 2257–2261.
36. Truesdell, C. Rational Mechanics; Academic Press: New York, 1983.
37. Synge, J. L. Principles of Mechanics; Read Books Ltd.: UK, 2013.
38. Gantmakher, F. R. Lectures in Analytical Mechanics; Mir Publishers: Russia, 1970.
39. Sandou, T.; Oya, A. Preparation of Carbon Nanotubes by Centrifugal Spinning of
Coreshell Polymer Particles. Carbon 2005, 43(9), 2015–2017.
CHAPTER 16

RESULTS OF TESTING OF
HELIODRYING APPARATUS WITH
POLYCARBONATE COVERING
K. T. ARCHVADZE1,2,*, T. I. MEGRELIDZE1,2, L. V. TABATADZE1,2,
and I. R. CHACHAVA1,2
1
Food Industry Department, Georgian Technical University, 77
Kostava 0175, Tbilisi, Georgia
2
Department of Technology, Sukhumi State University, Ana
Politkobskaia 9, 0186, Tbilisi, Georgia
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.....................................................................................................344
16.1 Introduction....................................................................................344
16.2 Experimental..................................................................................344
16.3 Results and Discussion..................................................................346
Keywords..................................................................................................351
References.................................................................................................351
344 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT
For drying of agricultural products, there are offered three heliodrying appa-
ratus—convective, large-scaled, and sheet with polycarbonate coverings,
developed and probated at Georgian Technical University. These apparatus
are used for getting of dried mushrooms and other agricultural products.
Driers can be used in private subsidiary, farm economies, and agricultural
companies. They do not need big capital investment, they are simple in
production, and keep qualitative characteristics of dried products.

16.1 INTRODUCTION
Use of solar energy in rational combination with other sources of energy in
many cases allows to economize significant amount of fuel-energetic resources.
Effect from the use of solar energy is specially felt during realization of most
power-consuming thermotechnological processes in helioapparatus. Nowa-
days, problems of searching new alternative sources of energy have become
especially actual. Today, the different forms of renewable energy resources
include hydropower, solar, wind, and animal and vegetative biomass.
In recent years, the extended assortment of products with new species of
nutritional concentrates more often included cultivated mushrooms. Provi-
sion of safety and quality of food products shall be one of the key directions
of the state policy of Georgia in the sphere of healthy nutrition. Edible mush-
rooms do not take last place in the food ration of human. Mushrooms are
used in fresh, frozen, conserved, and dried forms. Although included last in
listed productions, mushrooms are included in recipes of other food products
in form of aroma and/or enriching supplements. Besides, mushrooms are
used in products of nonfood and medical purposes. Mushrooms have high
nutritional value, and they are under solidly high demand at the markets of
European countries and in other countries worldwide. Edible mushrooms
most often are used as additional source of vegetable protein.

16.2 EXPERIMENTAL

16.2.1 MATERIALS

Sheet heliodrying apparatus, a large heliodrying apparatus, the convec-

tive heliodrying apparatus, dog rose, honey agarics, food products, and
рolycarbonate.
Results of Testing of Heliodrying Apparatus 345

16.2.2  OBJECTS OF STUDY

Heliodrying apparatus, polycarbonate, dog rose, and honey agarics.

Drying in heliodrying apparatus with polycarbonate (Fig. 16.1) covering
is recommended for effectively drying agricultural products.

FIGURE 16.1  Polycarbonate.

There are inventions of different complicated collectors of solar energy. We

offer three heliodrying apparatus with polycarbonate covering, constructed
and developed at Georgian Technical University—convective, large-scaled,
and sheet heliodrying apparatus, and also 11 variants of mentioned construc-
tions. Use of such heliodrying apparatus, according to the data of studies,
decreases time of drying, improves keeping of aroma, useful substances,
and taste, provides sterility of products, and also simplifies storage of dried
product (the product is not spoiled and is kept for longer time than usual). As
experiments have shown, use of noncomplicated heliodrying apparatus with
polycarbonate covering in small peasant farms, as well as in city habitants
allow to economize means and physical labor, and the method is ecologically
friendly (there is no heat and carbonic acid release in environment). Use of
high temperatures (in electric drying machine and oven) for preparation of
dried fruits often leads to destruction of vitamins. Drying of raw materials
by natural solar–air method usually takes a long time, but this does not affect
the quality of product and its vitamin composition. But drying in heliodrying
apparatus with polycarbonate coverings, according to the analysis of data of
dried products on vitamins, is the most optimal because vitamins composi-
tion is maintained at maximally high level, as well as consumption and taste
346 Applied Chemistry and Chemical Engineering: Volume 4

of products, and also in dried products ferments and microorganisms are

inactivating. We shall note that during the storage process, the products dried
in heliodrying apparatus (Fig. 16.2) were more resistant to effect of mold,
and they were stored for longer time than products dried by natural drying
in open air.

FIGURE 16.2  One of heliodrying apparatus: sheet heliodrying apparatus.

16.3  RESULTS AND DISCUSSION

16.3.1  DRYING OF MUSHROOMS “HONEY AGARICS”

16.3.1.1  NUTRITIONAL VALUE AND CHEMICAL COMPOSITION

“HONEY AGARICS”.

Table 16.1 shows contents of nutritional substances (calorie, proteins, fats,

carbohydrates, vitamins, and minerals) per 100 g of edible part. The ener-
getic balance of “honey agarics” is presented in Figure 16.3.
Results of Testing of Heliodrying Apparatus 347

TABLE 16.1  Nutritional Value and Chemical Composition “Honey Agarics.”

Nutritional value Vitamins
Calorie 22 kcal Vitamin PP 10.3 mg
Proteins 2.2 g Vitamin B1 (thiamine) 0.02 mg
Fats 1.2 g Vitamin B2 (riboflavin) 0.38 mg
Carbohydrates 0.5 g Vitamin C 11 mg
Dietary fibers 5.1 g Vitamin E (TE) 0.1 mg
Water 90 g Vitamin PP 10.7 mg
Unsaturated fatty acids 0.2 g
Mono and disaccharides 0.5 g
Ash 1 g
Saturated fatty acids 0.2 g

Macroelements Microelements
Calcium 5 mg Iron 0.8 mg
Magnesium 20 mg
Sodium 5 mg
Potassium 400 mg
Phosphor 45 mg

FIGURE 16.3  Energetic balance of “honey agarics.”

The results of experiments are given in Figures 16.4–16.6 and Tables

16.2–16.6.
348 Applied Chemistry and Chemical Engineering: Volume 4

1 Day of Drying
TABLE 16.2  Data Sheet Table for Drying of Product “Honey Agarics.”
Time (h) Relative Atmospheric Wind Tempera- Temperature Notes
humidity pressure velocity ture of air in of air in sun
of air (%) (kPa) (km/h) shadow (°C) (°C)
10.00 56 102.2 12 14 17
12.00 41 102.2 12 16 20
14.00 24 102.0 14 19 26
16.00 21 101.9 16 20 26
18.00 22 102.0 16 18 21
20.00 30 101.8 16 14 14

FIGURE 16.4  Changing of mass of raw materials “honey agarics” during the day: (I)
changing of the mass of raw material, dried by natural drying (n/d) in the open air and (II)
changing of the mass of raw material, dried in heliodrying (h/d).

2 Days of Drying
TABLE 16.3  Data Sheet Table for Drying of Product “Honey Agarics.”
Time Relative Atmospheric Wind Temperature Temperature Notes
(h) humidity pressure velocity of air in of air in sun
of air (%) (kPa) (km/h) shadow (°C) (°C)
10.00 48 101.7 12 18 20
12.00 38 101.6 10 20 24
14.00 34 102.4 8 22 28.5
16.00 32 102.2 8 23 26
18.00 28 102.1 8 20 21
20.00 34 101.4 8 17 17
Results of Testing of Heliodrying Apparatus 349

FIGURE 16.5  Changing of mass of raw materials “honey agarics” during the day: (I)
changing of the mass of raw material, dried by natural drying on the open air and (II) changing
of the mass of raw material, dried in heliodrying.

TABLE 16.4  Analysis of Experienced Data.

Name of product
Mushrooms “honey agarics”
h/d n/d
Initial mass (g) 580 540
Final mass (g) 150 160
Decrease of mass (%) 74.1 70.4
Duration of drying (h) 22 36

Duration of drying in heliodrying apparatus was 1.7 times shorter than

duration of drying in open air.

TABLE 16.5  Nutritional Value and Chemical Composition of Product “Dog Rose.”
Nutritional value Vitamins
Calorie 109 kcal Vitamin PP 0.6 mg
Proteins 1.6 g Beta-carotin 2.6 mg
Fats 0.7 g Vitamin A (RE) 434 mcg
Carbohydrates 22.4 g Vitamin B1 (thiamine) 0.05 mg
Dietary fibers 10.8 g Vitamin B2 (riboflavin) 0.13 mg
Organic acids 2.3 g Vitamin C 650 mg
Water 60 g Vitamin E (TE) 1.7 mg
Mono and disaccharides 19.4 g Vitamin PP 0.7 mg
Starch 3g
Ash 2.2 g
Saturated fatty acids 0.1 g
350 Applied Chemistry and Chemical Engineering: Volume 4

TABLE 16.5  (Continued)

Macroelements Microelements
Calcium 28 mg Iron 1.3 mg
Magnesium 8 mg Zinc 1.1 mg
Sodium 5 mg Copper 37,000 mcg
Potassium 23 mg Manganese 19 mg
Phosphor 8 mg Molybdenum 4330 mcg

FIGURE 16.6  Energetic balance of product “dog rose.”

TABLE 16.6  Analysis of Experienced Data.

Name of product
Dog rose
h/d n/d
Initial mass (g) 700 690
Final mass (g) 350 350
Decrease of mass (%) 50 49.3
Duration of drying (24 h) 5 20

16.3.2  DRYING OF DOG ROSE

Drying of dog rose by natural drying in shadow took 20 day–nights, and in

heliodrying apparatus with polycarbonate covering 5 day–nights. Therefore,
drying in the heliodrying apparatus took four times shorter period.
Laboratory analysis of vitamin C showed that 23% of mentioned vitamin
is destructed during natural drying and 15% was destructed during the use
of heliodrying apparatus.
Results of Testing of Heliodrying Apparatus 351

Solar drying of fruits and vegetables is one of the most acceptable and
cheap methods of their conservation, which makes possible the preserva-
tion of maximum amount of vitamins and minerals. The dried vegetables,
fruits, and mushrooms differ in the high content of sugar, organic acids,
mineral salts, and vitamins and, also, the fibers and carbohydrates riches
which not were destroyed in the drying process. They can keep the useful
substances for a long time and indemnify the deficiency of the vitamins.
As a result of the drying, we receive the stable food products, which do
not keep the conservants, dyestuffs, aromatizators, and other strange
substances. The dried fruits well substitute the refined sugar, actively
promote the radionuclides and slags help out from organism, and operate
as antioxidant.
For the effective drying, it is recommended to use the heliodrying appa-
ratus with polycarbonate covering, so far as it shortens the drying time,
better preserves aroma, useful matter, and taste of the product, and provides
sterility of the product; the dried products are easier to keep, also for longer
time. As experiments on drying of various kinds of agricultural products
show, drying rate increases—three to five times in comparison with tradi-
tional open-air drying. Products dried in the heliodrying device have better
consumer properties than products prepared by means of natural drying.

KEYWORDS

•• polycarbonate
•• heliodrying apparatus
•• drying
•• product
•• mushrooms

REFERENCES

1. Zuev, V. V.; Uspenskaia, M. V.; Olehnovich, A. O. Physics and Chemistry of Polymers;

Proc. in Russian. SPb.: ITMO, 2010; pp 45–85.
2. Magazine Fast canning; Publisher: OOO “News Express.” Special Issue. No. 06, 2011.
3. Kondrashova, E. A.; Konik, N. V.; Peshkova, T. A. Commodity Food Products. M.
“Alpha-book”; 2009, 338 p.
352 Applied Chemistry and Chemical Engineering: Volume 4

4. Antipov, S. T.; Cretov, I. T.; Ostrikov, A. N. Machinery and Equipment for Food Produc-
tion, a Textbook for High Schools (In two volumes); M: High School; Acad RAAS
Panfilov, V. A., Ed.; Russian Academy of Sciences: Moscow, 2007; 1379 p.
5. Semchikov, Y. D. Macromolecular Compounds (in Russian); Russian Academy of
Sciences: Moscow, 2003, 368 p.
6. Jenning, D. H. The Physiology of Fungal Nutrition; Cambridge University Press:
Cambridge, UK, 2007; 622 p.
7. Plaksin, Y. M; Malakhov, H. N.; Larin, B. A. Processes and Devices for Foodstuffs
Processing, 2nd Edition; Rev. and add. M.: Colossus: Tbilisi, Georgia, 2007; 760 p.
8. Chagin, O. V.; Kokin, N. R; Pastine, V. V. Equipment for Drying Foodstuffs; Ivan.
Chemical—Primary Process: Univ.: Ivanovo, 2007; 138 p.
9. Morozov, A. I. Large Mushroom Encyclopedia; M.: AST; Stalker: Donetsk, 2005; 479 p.
10. Kiseleva, T. F. Drying Technology. In Training and Methodology Complex; KemTIPP:
Kemerovo, 2007; 117 p.
CHAPTER 17

DEPENDENCE OF MORPHOLOGY
ON OPTICAL AND ELECTRICAL
PROPERTIES OF METAL OXIDE
NANOSTRUCTURES
PAULOSE THOMAS1 and AJITH JAMES JOSE2,*
1
Optoelectronic Lab, St. Berchmans College, Changanassery, Kerala,
India
Research Department of Chemistry, St. Berchmans College,
2

Changanassery, Kerala, India

Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.....................................................................................................354
17.1 Introduction....................................................................................354
17.2 Conclusions....................................................................................363
Keywords..................................................................................................363
References.................................................................................................363
354 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

Synthesis and study of nanomaterials are challenging area of mate-

rials research. Researchers have focused on developing diverse proper-
ties of nanoamaterials through different methods. There are large factors
affecting the changes of physics properties of nanomaterials as compared
with its bulk form. One of the important property controlling parameter is
its surface morphology. Nanoparticles possess variety of shapes and their
names are characterized by their different shapes. For examples nanowires,
nanorods, nanotubes, nanorings, nanospheres, nanoflakes, nanoflowers,
nanobelts, etc. These shapes or morphologies sometimes arise sponta-
neously as an effect of a templating or directing agent during synthesis.
Morphology of different nanostructures may vary significantly depending
on their material composition, crystal structure and manufacturing method.
Variation of different synthesis parameters such as temperature, pressure,
reagent concentration, treatment time and pH results in different morpholo-
gies. Controlling the morphology of nanoparticles is of key importance for
exploiting their properties for their use in several emerging technologies.
Also morphology variation is an effective way of controlling functionality
of nanomaterials because the variation of large number of surface atoms
with respect to their surface morphology that determine their physical and
chemical properties. In the present chapter, the tuning of optical and elec-
trical properties of metal oxide nanostructures explained on account of
various surface morphologies.

17.1 INTRODUCTION

Nanomaterial research is an application oriented study conducted in science

and engineering. It has been done on atomic or molecular level to build up
discrete number of assembled atomic/molecular units for wide variety of
applications. Nanotechnology and nanoscience are like two sides of a coin
and both are complement to each other. Basically, both concentrate on the
study and application of small matters. It can be employed in all science
fields, such as chemistry, physics, materials science, biology, and engi-
neering.1–5 For the last 50 years, huge developments have been created in
all areas of science,6–9 particularly in miniaturization of materials and appli-
ances with the effective use of nanoscience and nanotechnology. The size
reduction in electronic equipments, advanced medical diagnostic apparatus,
fast and precise communication systems, developments in industrial and
Dependence of Morphology on Optical and Electrical 355

agricultural field, etc. are the examples of miniaturization followed by the

developments of nanoscience and nanotechnology.
However, nanoscience need not be considered as a new science. In early
15th century, many physicist and chemists had studied properties of matter
down to the atomic and molecular level. The novelty of present status of
nanoscience lies on the exceptional properties of matter at the nanoscale
level and the methods used to build new materials, systems, and devices.
There are multiple factors that control the properties of nanomaterials. The
crystallite structure, reduced particle size dimensions, multiple morphology,
etc. are the prime important parameter for changing the property of nano-
materials from its bulk form.10 The present chapter explains the various
morphologies of nanomaterials and how they can be dependent on optical
and electrical property of metal oxide nanostructures.

17.1.1  SURFACE MORPHOLOGY OF NANOMATERIALS

Morphology of different nanostructures may vary significantly depending

on their material composition, crystal structure, and manufacturing method.
At the earlier stages of nanoresearch, the researchers suggested that particle
morphology is a strong dependent parameter for all physical and chemical
properties of nanomaterials. On account of this assumption, over the last
decades researchers in all over the world fabricated various morphological
nanostructures by numerous physical and chemical synthesis methods. The
nanotube, nanowires, nanorods, nanoflowers, nanoflakes, nanospheres,
nanocubes, etc. are the important attractive nanomorphologies. The surface-
to-volume ratio and quantum confinement effect of nanostructures vary
with respect to different morphologies.5–8 These shapes or morphologies
sometimes arise spontaneously as an effect of reactants or directing/capping
agents during synthesis. The morphologies of nanoparticles help serve their
various purposes such as long carbon nanotubes being used to bridge an elec-
trical junction, pores shaped nanostructures helps for construction of energy
storage devices such as supercapacitors, etc. Existing synthesis methods
allow the production of nanoparticles with a variety of shapes and sizes.
The nanolithographic method, chemical vapor deposition method, laser
ablation method, sputtering method, hydrothermal method, etc. are the most
important synthesis methods for fabricating verity of nanomorphologies.
Over these methods, hydrothermal method has got more attention in nanore-
search as its synthesis parameters such as temperature, pressure, reagent
concentration, treatment time, and pH results in different morphologies,
356 Applied Chemistry and Chemical Engineering: Volume 4

compositions, and better crystallinity of the products. Hence, hydrothermal

method is considered as an easy low-cost method for fabricating different
nanomorphologies. Sometimes a single synthesis method is not suitable for
fabricating the same morphology of different material. For example, hydro-
thermal method is much useful for fabricating ZnO nanotubes, whereas it
is inefficient for CdO nanotube synthesis. The surface effect, particle size,
and size-induced quantum confinement property are closely dependent on
morphology of nanostructures. Controlling the morphology of nanoparticles
is of key importance for exploiting their properties for their use in several
emerging technologies. Optical filters and biosensors are among the many
applications that use optical properties of metal or metal oxide nanopar-
ticles. Nanostructures aspect ratio is one of the important parameters for
morphological characterization. The aspect ratio is the average ratio of the
highest to the lowest dimension over a number of similar particles. Recent
studies indicated that the aspect ratio of nanoparticles varies with different
morphologies. Nanoparticles with high and low aspect ratio are classified
separately. High aspect ratio nanoparticles include nanotubes and nanow-
ires, with various shapes, such as helices, zigzags, belts, or perhaps nanow-
ires with diameter that varies with length. Small aspect ratio morphologies
include spherical, oval, cubic, prism, helical, or pillar. A nanomaterial has
high aspect ratio that indicates the high surface energy or high activity of
those nanoparticles.

17.1.2  DIMENSIONALITY AND CLASSIFICATION OF

NANOMATERIALS

The capability of nanostructure materials can produce improved properties

such as increased hardness, ductility, selective absorption showing more
efficient optical and electronic behavior, etc. There are several types of
nanostructured materials that are categorized according to their dimensions
such as zero-dimensional, one-dimensional, two-dimensional, and three-
dimensional nanostructures.11–16
The quantum dot is an example of zero-dimensional nanostructure.
One-dimensional nanostructures include whiskers, fibers, nanowires, and
nanorods. Two-dimensional nanostructures include thin films which have
thickness of the order of few nanometers. Three-dimensional nanoma-
terials or bulk nanomaterials are materials that are not confined to the
nanoscale in any dimension. Generally, nanomaterials are synthesized
either by top-down or bottom-up approaches12–15 In top-down approach, a
Dependence of Morphology on Optical and Electrical 357

bulk material is crushed into fine particles using the processes as mechan-
ical and chemical fabrication techniques such as laser ablation, ball mill,
sputtering, etc. Other examples of top-down approaches are: nanolithog-
raphy, plasma arc deposition, electron beam evaporation, etc. In ancient
days, the mankind used stone ball miller to grind rice in to powder form.
This is the better example for understanding a layman to top-down
approach in nanofabrication. Bottom-up fabrication is similar to building
a brick house. The desired nanomaterials are prepared by arranging atom
by atom or molecule by molecule. Researchers prefer bottom-up approach
to the other for nanoparticles synthesis. There are several reasons behind
which the bottom-up approach plays an important role in the fabrication
of nanostructures. In bottom-up approach, the prepared nanostructures
has better chemical composition, phase purity, perfect morphology, less
defect, etc. The examples of bottom-up processes are: chemical vapor
deposition, coprecipitation, electro deposition, sol–gel method, hydro-
thermal method, etc.

FIGURE 17.1  Classification of nanomaterials (a) 0D spheres and clusters, (b) 1D nanofibers,
wires, and rods, (c) 2D films or flakes, and (d) 3D nanomaterials.

Basically, two principal factors affect the property of nanomaterials

namely, increased relative surface or larger surface to volume ratio area
and quantum confinement effect.16–19 Nanomaterials have a larger surface to
volume ratio compared to same volume or mass of its corresponding bulk
material. For example, consider a sphere of radius “r.” Its surface area and
volume are 4πr2 and 4/3πr3, respectively. Its surface area to volume ratio
is equal to 3/r. Hence, as the radius of the sphere decreases its surface to
volume ratio increases. Accordingly, nanoparticles of the same material
but different size (nanoscale) may have different properties. This surface
to volume ratio and its effects on nanomaterials properties is a key feature
of nanoscience and nanotechnology. For these reasons, a nanomaterial’s
358 Applied Chemistry and Chemical Engineering: Volume 4

surface morphology is of great interest because various morphologies will

produce distinct surface to volume ratio and therefore different properties.
Size induced restriction to the free movement of charge carriers is an
example of quantum confinement. When the radius of the nanoparticles
is smaller than or equal to the size of its exciton Bohr radius, excitons are
pinched in to the discrete energy levels created in between the valance
and conduction band. As a result, its effective bang gap is increased as
compared to bulk. Hence, the band gap of nanomaterials gets widened
as the size of nanoparticle is reduced. This phenomenon is a quantum
confinement effect. In addition, quantum confinement leads to a collapse
of the continuous energy bands of a bulk material into discrete, atomic-like
energy levels.20–22 There are two types of quantum confinement effect: weak
confinement and strong confinement. The nanoparticles are said to be in
the weak confinement regime, if their radii are of the order of the exciton
Bohr radius. The strong confinement effect is mainly originated when the
nanoparticles radii is smaller than the exciton Bohr radius. If the size of the
nanoparticles is less than 10 nm, the quantum confinement effects dominate
and the electronic and optical properties becomes highly tunable. Based
on the confinement direction, quantum confined structure will be classified
into three categories as quantum well, quantum wire, and quantum dots. For
zero-dimensional nanomaterials, the electrons are confined in all the three
directions, that is, no electron is free to move or delocalize. Quantum wires
are formed when two dimensions of the system are confined. In quantum
well, charge carriers are confined to move in a plane and are free to move
in two dimensions.23,24

17.1.3  MORPHOLOGICAL CHARACTERIZATION OF

NANOSTRUCTURES

Electron microscopy is a good tool for studying the surface and morphology
of nanostructures. The maximum magnification of optical microscope is
1000× which is insufficient for the study of surface morphology of nanopar-
ticles. In an electron microscope, a magnification of about 10,000,000× can
be smoothly achieved with a better resolution. There are different types of
electron microscope used in nanoparticles research, that is, scanning elec-
tron microscopy (SEM), transmission electron microscopy (TEM), field
emission scanning electron microscopy (FE-SEM), focused ion beam—
scanning electron microscopy (FIB-SEM), scanning transmission electron
microscopy (STEM), and ultrahigh-resolution SEM (UHR-SEM).
Dependence of Morphology on Optical and Electrical 359

An electron microscope (SEM) can produces images of a sample by

scanning it with a focused beam of electrons. These high-energy electrons
interact with electrons in the sample and reveal information about external
morphology (texture), chemical composition, crystalline structure, and orien-
tation of materials of the sample. The electron beam is generally scanned
in a raster scan pattern, and the beam position combined with the detected
signal to produce a two-dimensional image that displays spatial variations in
the scanned objects. An accelerated electron in electron microscopy carries
significant amounts of kinetic energy which is dissipated as signals through
electron–sample interactions. Essential components of all electron micros-
copy instruments include the electron source, electron lenses, sample stage,
detectors, and display devices. For the surface analysis of thin films, mainly
atomic force microscopy (AFM) is used. AFM uses a cantilever with a very
sharp tip to scan over a sample surface. As the tip approaches the surface,
the close-range, attractive force between the surface and the tip cause the
cantilever to deflect toward the surface. A laser beam is used to detect canti-
lever deflections toward or away from the surface. The raised and lowered
features on the sample surface influence the deflection of the cantilever,
which is monitored by the position-sensitive photo diode (PSPD).
The main disadvantages of electron microscopes are that it is much
expensive to build and maintain. Microscopes designed to achieve high
resolutions must be housed in stable buildings with special services such
as magnetic field cancelling systems, ultrahigh vacuum for perfect working
condition, etc.

17.1.4  MORPHOLOGY-DEPENDENT OPTICAL AND ELECTRICAL

ANALYSES OF METAL OXIDE NANOSTRUCTURES

The synthesis and characterization of semiconductor metal oxide nano-

structure is a major research topic in materials research.25–29 Semiconductor
metal oxide nanomaterials have attracted wide attention due to their striking
optical and electrical properties, which make these materials potentially
suitable for applications in electronics, optics, and photonics. For examples,
high-sensitivity sensors, high-performance electronic devices, nonlinear
applications, storage devices, solar cell fabrications, fuel cells, optical
limiters, antibacterial activity, etc. A few metal oxides have been synthesized
in wide variety of morphologies such as nanowires, nanorods, nanotubes,
nanorings, nanosphere, nanoflakes, nanoflowers, and nanobelts. Synthesis
and investigation of these metal oxide nanostructures are beneficial not only
360 Applied Chemistry and Chemical Engineering: Volume 4

for the understanding of the fundamental phenomena in nanoscale but also

for development of new generation nanodevices with high performances.
Researchers are still continuing their research in metal oxide because of
many potential applications at nanometer scale of these materials. The struc-
tural characters of metal oxide nanostructures such as lattice symmetry, cell
parameters, surface morphology, etc. have been changed in nanometer size
range. Some of important semiconductor metal oxide nanostructures are
ZnO, CuO, TiO2, MnO2, CdO, Fe2O3, MgO, SnO2, etc.
It is well known that the crystalline phase, particle sizes, and surface
morphologies of nanomaterials have immense influence on their optical,
magnetic, and electrical properties. Accordingly, the controlled synthesis
of nanostructured materials with novel morphologies has recently received
much attention25,26 In the recent years, many researchers have focused on
synthesis of various metal oxide semiconductor nanomorphotypes26–29
However, cost-effective single-step production of various nanomorphot-
ypes with high yield and reproducibility are still remaining an important
problem. The electrical and optical properties of metal oxides have been
studied on account of their particle size, crystalline phase, chemical compo-
sition, synthesis route, etc. Unfortunately, very little work is available on the
study of dependency of structural, electrical, and optical property of metal
oxides upon their surface morphology. Here, we analyze the morphology-
dependent optical and electrical properties of metal oxide nanostructures on
surface morphology.
The optical analysis is essential for determining the electronic band
structure of a material. The electronic band structure would lighten to the
optoelectronic capability of nanostructures. The UV-visible spectrum helps
to find out the band edge energy of these nanomaterials. Though band gap is
a material property, variation in band gap of nanomaterials can be observed
due to change in particles size dimensions. Thomas et al. observed a clear
picture of change in band gap of CdO nanostructure owing to particle size
and surface morphology.65 They presented variation of band gap of nano-
material originated by the size induced and morphology assisted quantum
confinement effect on different morphologies of CdO nanostructures. The
photoluminescence analysis helps to understand the energy gap absorption
and subsequent photon emission of the materials. There are numerous studies
on the photoluminescence emission spectra of metal oxides and changes in
the band edge emission spectral behavior with excitation wavelength as well
as morphology. 34-38 The evolution of the excitation wavelength-dependent
PL emission line is observed in crystalline ZnO nanomaterials and suggested
that every PL peak corresponds to an individual excitation wavelength.44
Dependence of Morphology on Optical and Electrical 361

Ellingson et al. observed evolution of excitation energy-dependent efficiency

of charge carrier relaxation and photoluminescence in colloidal InP quantum
dots.39, 44 Micic et al. carried out a study on size-dependent PL spectroscopy
of InP quantum dots and suggest the emission and absorption features shift
to higher energy with decreasing quantum dots size.40-42, 45 Similarly in the
case of polymer nanocomposite materials, fine excitation energy-dependent
photoluminescence property is observed. For example, Hairong Zhang et al.
presented excitation-wavelength-dependent photoluminescence of a pyro-
mellitic diimide (PMDI) nanowires network and suggest that the lumines-
cence peaks of PMDI nanowires red-shifted as the excitation wavelength
gets increased.46 Ghoshal et al. presents the synthesis of CdO nanostructures
in hexagonal sheet and rods structures.30 Fabrication of CdO microspheres
through Ostwald ripening method was developed by Wang et al.31 Barakat
et al. illustrated the photoluminescence and optical characterization of CdO
nanorods.32 Jia et al. fabricated porous CdO nanostructures such as nanow-
ires, nanobelts, nanorods, and one-dimensional hierarchical structures.33
Nonlinear optics is one of the leading areas of optoelectronic research
in nanomaterial for its importance in optical switching, optical limiting,
photothermal cancer therapy, and sensor and eye protection applications.47,48
But very rare literatures are available for the nonlinear optical properties of
nanostructures compared with surface morphology. Chang et al. elucidates
the optical limiting property of CdO nanowires in ethanol and water suspen-
sions and concluded that the optical limiting property is due to nonlinear
scattering.49 Thomas and coworkers presented the morphology-dependent
nanosecond and ultrafast optical limiting properties of CdO nanostructures
in their recent literature.66,67 They suggest that the nonlinear optical behavior
is closely dependent on variation of surface energy of different nanomor-
phologies of CdO nanostructures and also shows the difference of surface
energy of nanostructure upon different morphologies of nanostructures
through BET surface area analysis.
Singh et al.50 reveal the comparative study of optical limiting properties as
a function of size in iron oxide nanoparticles and indicate that the prevailing
mechanism for the optical limiting in iron oxide nanoparticles is nonlinear
scattering. Many researchers have studied the optical limiting property of
nanostructures with various morphotypes. For example, Pan et al. presented
the nonlinear analysis of Pd, Cu, Ni, Pt, Ag, and Co nanowires.51 Chang et
al. and Venkatram et al. conducted the study on optical limiting property of
CdS nanowires and C60 TPY-Pb nanowires.52,53
Over the last decades, the dielectric and conductivity properties of metal
oxide semiconductor materials have caught additional attention because of
362 Applied Chemistry and Chemical Engineering: Volume 4

its colossal dielectric constant values obtained at nanosize range. Due to

the large surface to volume ratio and quantum confinement effect, dielectric
and conductivity behavior of nanomaterials have been found altered much
compared with its bulk materials. In the past decades, many researchers satis-
factorily examined electrical transport and dielectric behavior of semicon-
ductor metal oxide nanomaterials with different morphologies. For example,
Zhi-Min Liao et al. presented the surface state effect on electron transport in
individual ZnO nanowires and confirm that the surface states have greatly
affected the electronic transport in single ZnO nanowires.54 Zhimin Dang
and coworkers examined the dielectric properties and morphologies of
composites filled with whisker and nanosized ZnO.55 They claim that dielec-
tric constant and losses increases with increasing w-ZnO content in compos-
ites. Sagadevan Suresh conducted the dielectric relaxation behavior of CdS
nanoparticles and found that dielectric properties of CdS nanoparticles are
found to be significantly enhanced especially in the low-frequency range
due to confinement.56 Velayutham et al. presented the theoretical and experi-
mental approach on dielectric properties of ZnO nanoparticles and polyure-
thane/ZnO nanocomposites.57
Sayed and coworkers carried out a study on synthesis, characterization,
optical and dielectric properties of polyvinyl chloride/cadmium oxide nano-
composite films.58 They concluded that optical and dielectric properties were
reinforced by adding the CdO nanoparticles in PVC matrix. Mallikarjuna
and team reported the novel high dielectric constant nanocomposites of poly-
aniline dispersed with Fe2O3 nanoparticles and they suggested that conduc-
tivity and dielectric constant values are increased by increasing the amount
of Fe2O3 in the matrix.59 Srikrishna Ramya and Mahadevan conducted a
work on the effect of calcination on the electrical properties and quantum
confinement of Fe2O3 nanoparticles and reported that dielectric property is
strongly dependent to quantum confinement effect.60 Sahoo et al. studied
the characterization of α and γ -Fe2O3 nanopowder synthesized by emulsion
precipitation–calcination route and also examine the rheological behavior of
γ-Fe2O3.61 Reda tests out the electric and dielectric properties of Fe2O3/silica
nanocomposites and suggested that AC conductivity and dielectric loss of
both composites increased gradually with increasing annealing temperature
and particle size.62 Shinde and coworkers fabricated the hematite Fe2O3 thin
films and examine its application to photoelectron chemical solar cells.63
Ambika Prasad et al. studied the electrical and sensing properties of polyani-
line/iron oxide nanocomposites and reported that prepared nanocomposite
has potential application in sensing devices.64
Dependence of Morphology on Optical and Electrical 363

17.2 CONCLUSIONS

Out of these literatures, we robustly observed that nanostructures morphology

is a dependable parameter for change in optical and electrical properties of
metal oxide nanostructures. The real mechanism for these property varia-
tions are created by the change in morphology of nanostructures which
generates large variation in both surface to volume ratio and confinement
effect on nanostructures.

KEYWORDS

•• nanotechnology
•• nanomaterials
•• surface morphology

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CHAPTER 18

MECHANISM OF Ni(Fe)ARD ACTION

IN METHIONINE SALVAGE PATHWAY,
IN BIOSYNTHESIS OF ETHYLENE,
AND ROLE OF TYR-FRAGMENT AS
REGULATORY FACTOR
LUDMILA I. MATIENKO*, LARISA A. MOSOLOVA,
VLADIMIR I. BINYUKOV, ELENA M. MIL, and GENNADY E. ZAIKOV
Emanuel Institute of Biochemical Physics, Russian Academy of
Sciences, 4, Kosygin Str., Moscow 119334, Russia
Corresponding author. E-mail: [email protected]
*

CONTENTS

Abstract.....................................................................................................368
18.1 Introduction....................................................................................368
18.2 Materials and Methodology...........................................................370
18.3 Results and Discussion..................................................................370
18.4 Conclusion.....................................................................................384
Keywords..................................................................................................385
References.................................................................................................385
368 Applied Chemistry and Chemical Engineering: Volume 4

ABSTRACT

Role of Ni(Fe)-macrostructures due to H-bonds in mechanisms of Ni(Fe)

ARD action in methionine salvage pathway, in biosynthesis of ethylene,
is discussed. The AFM method was used for research of possibility of the
stable supramolecular nanostructures formation based on Ni(Fe)ARD model
system {NiII(acac)2 + MP + Tyr} (Tyr = L-Tyrosine)—with the assistance of
intermolecular H-bonds. Using UV-spectroscopy, we received the confirma-
tion of the of triple complexes {Ni(acac)2∙MP∙Tyr} formation.

18.1 INTRODUCTION

The methionine salvage pathway (MSP) (Scheme 18.1) plays a critical role in
regulating a number of important metabolites in prokaryotes and eukaryotes.
MSP is a ubiquitous pathway found in plants, animals, and bacteria. Methyl-
thioadenosine (MTA) is the first intermediate in this pathway and is formed
from S-adenosyl methionine (SAM) during polyamine synthesis in animals
and ethylene synthesis in plants (Scheme 18.2). Polyamine is required for
cell growth and proliferation, and ethylene is required for ripening of fruits
and vegetables. MTA is an inhibitor of both polyamine synthesis and reac-
tions of transmethylation. Inhibition of polyamine synthesis arrests DNA
replication, and elevated polyamine is associated with tumor formation.
Hence, the concentration of MTA in cells must be tightly regulated. The
MSP controls the concentration of MTA by returning it through a series of
reactions to methionine, thereby “salvaging” the thiomethyl group of SAM.
Acireductone dioxygenases (ARDs) Ni(Fe)-ARD are enzymes involved
in the methionine recycle pathway. Fe-ARD catalyze the penultimate step
in the pathway, the oxidative decomposition of substrate acireductone
(1,2-dihydoxy-3-keto-5-(thiomethyl)pent-1-ene) to formate and 2-keto-4-
(thiomethyl)butyrate (KMTB), the keto acid precursor of methionine. The
purpose of the off-pathway reaction catalyzed by Ni-ARD is unknown.
These represent the only known pair of naturally occurring metalloenzymes
with distinct chemical and physical properties determined solely by the iden-
tity of the metal ion in the active site.1
Both enzymes Ni(Fe)-ARD are members of the structural super family,
known as cupins, which also include Fe-acetyl acetone dioxygenase (Dke1)2,3
and cysteine dioxygenase. These family of cupins use a triad of histidine-
ligands (His), and also one or two oxygens from water and a carboxylate
oxygen (Glu), for binding with Fe (Ni)-center.2 Being the members of
Mechanism of Ni(Fe)ARD Action in Methionine Salvage 369

structural super family of cupins, the Ni(Fe)-ARDs present the unusual

case of catalysis, as differ in the mechanism of action in relation to general
substrates (1,2-dihydroxy-3-oxo-5 (methylthio)pent-1-ene (acireductone)
and dioxygen).
In recent years, the studies in the field of homogeneous catalytic
oxidation of hydrocarbons with molecular oxygen were developed in two
directions, namely, the free-radical chain oxidation catalyzed by transi-
tion metal complexes and the catalysis by metal complexes that mimic
enzymes.4,5 The findings on the mechanism of action of enzymes, and,
in particular, dioxygenases and their models, are very useful in the treat-
ment of the mechanism of catalysis by heteroligand Ni(Fe) complexes in
the processes of oxidation of hydrocarbons with molecular oxygen in our
works.4–6 Moreover, as one will see below, the investigation of the mecha-
nism of catalysis by metal complexes that modeled the enzymes actions
can give the necessary material for the study of the mechanism of action
of enzymes.
We have offered the new approach to research of mechanism of homog-
enous catalysis, and the mechanism of action of enzymes also.7,8 The first
time we have successfully used the method of atomic force microscopy
(AFM) to study the possibility of formation of supramolecular nanostruc-
tures, based on heteroligand nickel and iron complexes, which are selec-
tive catalysts on the one hand and also are models of dioxygenases on
the other hand, due to the intermolecular hydrogen bonds.7,8 Namely, the
complexes Ni2(acac)(OAc)3∙MP∙2H2O (“A”), FeIIIx(acac)y18C6m(H2O)n
(“B”), {Ni(acac)2∙L2∙PhOH} (“C”) are effective catalysts of selective ethyl
benzene oxidation to α-phenyl ethyl hydro peroxide and also are structure
and functional models of dioxygenases Ni(Fe)-ARD (A–C) and FeII-Dke1
(B). We assumed that the stability of the complexes A–B as the alkylar-
enes oxidation catalysts could be related to formation of the stable supra-
molecular structures due to the intermolecular hydrogen bonds. And specific
activities of Ni(Fe)-ARD toward common substrates (acireductone and
dioxygen) in synthesis and reproduction of methionine (and ethylene) as
one of the reasons—with self-organization into various macrostructures due
to intermolecular hydrogen bonds. These assumptions are supported by our
AFM research outlined in this chapter.
In this chapter, we discuss the possible role of Tyr-fragment in mech-
anism of Ni(ARD) dioxygenase actions, based on experience data that
we received at the first time with AFM and UV-spectroscopy on model
systems.
370 Applied Chemistry and Chemical Engineering: Volume 4

18.2  MATERIALS AND METHODOLOGY

AFM SOLVER P47/SMENA/ with Silicon Cantilevers NSG11S (NT MDT)

with curvature radius 10 nm, tip height: 10–15 µm, and cone angle ≤22° in
taping mode on resonant frequency 150 kHz was used.7,8
As substrate, a special chemically modified polished silicone surface was
used.
Waterproof modified silicone surface was exploit for the self-assembly-
driven growth due to H-bonding of complexes FeIIIx(acac)y18C6m(H2O)n,
NixL1y(L1ox)z(L2)n(H2O)m, {NiII(acac)2·L2·PhOH} (L2 = MP (N-metylpyrrol-
idone-2), HMPA, MSt), systems {NiII(acac)2 + MP + Tyr} and {NiII(acac)2}
+ Tyr} (Tyr = L-Tyrosine) with silicone surface. The saturated chloroform
(CHCl3) or water solutions of complexes was put on a surface, maintained
for some time, and then solvent was deleted from a surface by means of
special method—spin-coating process.
In the course of scanning of investigated samples, it has been found that
the structures are fixed on a surface strongly enough due to H-bonding. The
self-assembly-driven growth of the supramolecular structures on modified
silicone surface on the basis of researched complexes, due to H-bonds and
perhaps the other noncovalent interactions, was observed.
Method of UV-spectroscopy we used first to prove the possible
regulatory role of Tyr-fragment (the formation of triple complexes
Ni(acac)2∙MP∙Tyr).

18.3  RESULTS AND DISCUSSION

18.3.1  THE MECHANISM OF FORMATION OF HIGH EFFECTIVE

CATALYSTS, HETEROLIGAND NI (OR FE) COMPLEXES, IN THE
HYDROCARBON OXIDATIONS WITH DIOXYGEN: THE ROLE OF
H-BONDS

In our works, we have modeled efficient catalytic systems {ML1n + L2} (M

= Ni, Fe, L1 = acac−, L2 are crown ethers or quaternary ammonium salts,
different electron-donating modifying extraligands) for selective ethyl-
benzene oxidation to α-phenyl ethyl hydro peroxide, that was based on the
established (for Ni complexes) and hypothetical (for Fe complexes) mecha-
nisms of formation of catalytically active species and their operation.4,5 The
high activity of systems {ML1n + L2} is associated with the fact that during
the ethylbenzene oxidation, the active primary (MIIL12)x(L2)y complexes and
Mechanism of Ni(Fe)ARD Action in Methionine Salvage 371

heteroligand MIIxL1y(L1ox)z(L2)n(H2O)m complexes are formed to be involved

in the oxidation process.
We established mechanism of formation of high effective catalysts,
heteroligand complexes MIIxL1y(L1ox)z(L2)n(H2O)m. The axially coordi-
nated electron-donating ligand L2 controls the formation of primary active
complexes ML12 L2 and the subsequent reactions of β-diketonate ligands
in the outer coordination sphere of these complexes. The coordination of
an electron-donating extraligand L2 with an MIIL12 complex, favorable for
stabilization of the transient zwitter-ion L2[L1M(L1)+O2−], enhances the prob-
ability of regioselective O2 addition to the methine C–H bond of an acety-
lacetonate ligand activated by its coordination with metal ions. The outer-
sphere reaction of O2 incorporation into the chelate ring depends on the
nature of the metal and the modifying ligand L2.4,5 Thus, formation of nickel
complexes NiIIxL1y(L1ox)z(L2)n, as a result of the reaction of oxygenation of
ligand L1 = acac− in NiII(acac)2, follows a mechanism analogous to those
of NiII-containing ARD1 or Cu- and Fe-containing quercetin 2,3-dioxygen-
ases.9,10 Namely, incorporation of O2 into the chelate acac ring was accom-
panied by the proton transfer and the redistribution of bonds in the transition
complex leading to the scission of the cyclic system to form a chelate ligand
L1ox = OAc−, acetaldehyde, and CO (in the Criegee rearrangement).
In the effect of iron(II) acetylacetonate complexes FeIIxL1y(L1ox)z(L2)n, we
have found an analogy with the action of FeII-ARD1 or FeII-acetyl acetone
dioxygenase (Dke1).3 For iron complexes oxygen adds to C–C bond (rather
than inserts into the C=C bond as in the case of catalysis with nickel(II)
complexes) to afford intermediate, that is, an Fe complex with a chelate
ligand containing 1,2-dioxetane fragment. The process is completed with
the formation of the (OAc)− chelate ligand and methylglyoxal as the second
decomposition product of a modified acac ring (as it has been shown in 3).
High effectivity of catalytic complexes MIIxL1y(L1ox)z(L2)n, (M = Ni, Fe,
L1 = acac−, L1ox = OAc−, L2 = crown ethers or quaternary ammonium salts),
which are formed in the process of selective oxidation of ethylbenzene to
PEH at catalysis with primary complexes (MII,IIIL1n)x(L2)y seems to be associ-
ated with the formation of stable supramolecular structures due to intermo-
lecular H-bonds.
One of the most effective catalytic systems of the ethylbenzene oxidation
to the α-phenyl ethyl hydroperoxide are the triple systems.4–6 Namely, the
phenomenon of a substantial increase in the selectivity (S) and conversion
(C) of the ethylbenzene oxidation to the α-phenyl ethyl hydro peroxide upon
addition of PhOH together with ligands N-metylpyrrolidone-2 (MP), hexa-
methylphosphorotriamide (HMPA) or alkali metal stearate MSt (M = Li, Na)
372 Applied Chemistry and Chemical Engineering: Volume 4

to metal complex NiII(acac)2 was discovered in works Matienko and Moso-

lova.4–6 The role of intramolecular H-bonds was established by us in mecha-
nism of formation of triple catalytic complexes {Ni(II)(acac)2∙L2∙PhOH} (L2
= MP) in the process of ethylbenzene oxidation with molecular oxygen.5,6
The formation of triple complexes NiII(acac)2∙L2∙PhOH from the earliest
stages of oxidation was established with kinetic methods.4–6 We assumed
that the stability of complexes Ni(acac)2∙L2∙PhOH in the process of ethyl
benzene oxidation can be associated as one of reasons with the supramo-
lecular structures formation due to intermolecular H-bonds (phenol–carbox-
ylate) (see below) and, possible, the other noncovalent interactions:

{NiII(acac)2 + L2 + PhOH} → Ni(acac)2∙L2∙PhOH → {Ni(acac)2∙L2∙PhOH}n

In favor of formation of supramolecular macrostructures based on the triple

complexes {Ni(acac)2∙L2∙PhOH} (and Ni(acac)2∙MP∙Tyr (Tyr = Tyrosine-L))
in the real systems of homogeneous (and enzymatic catalysis (see below)),
show data of AFM and UV-spectroscopy.

18.3.2  ROLE OF SUPRAMOLECULAR NANOSTRUCTURES

FORMED DUE TO H-BONDING, IN MECHANISMS OF
CATALYSIS, MODELS OF NI(FE)ARD DIOXYGENASES: ROLE OF
TYR-FRAGMENT

Hydrogen bonds vary enormously in bond energy from ~15–40 kcal/mol

for the strongest interactions to less than 4 kcal/mol for the weakest. It is
proposed, largely based on calculations, that strong hydrogen bonds have
more covalent character, whereas electrostatics are more important for weak
hydrogen bonds, but the precise contribution of electrostatics to hydrogen
bonding is widely debated.11 Hydrogen bonds are important in noncovalent
aromatic interactions, where π-electrons play the role of the proton acceptor,
which are a very common phenomenon in chemistry and biology. They play
an important role in the structures of proteins and DNA, as well as in drug–
receptor binding and catalysis.12
Proton-coupled bicarboxylates top the list as the earliest and still the best
studied systems suspected of forming low-barrier hydrogen bonds (LBHBs)
in the vicinity of the active sites of enzymes.12 Proton-coupled bicarboxylates
appear in 16% of all protein X-ray structures. There are at least five X-ray
structures showing short (and therefore strong) hydrogen bonds between an
enzyme carboxylate and a reaction intermediate or transition state analogue
Mechanism of Ni(Fe)ARD Action in Methionine Salvage 373

bound at the enzyme active site. The authors12 consider these structures to be
the best de facto evidence of the existence of LBHBs stabilizing high-energy
reaction intermediates at enzyme active sites. Carboxylates figure promi-
nently in the LBHB enzymatic story in part because all negative charges on
proteins are carboxylates.
The porphyrin linkage through H-bonds is the binding type generally
observed in nature. One of the simplest artificial self-assembling supramo-
lecular porphyrin systems is the formation of a dimer based on carboxylic
acid functionality.13

18.3.2.1  THE POSSIBLE ROLE OF THE SELF-ASSEMBLING

SUPRAMOLECULAR MACROSTRUCTURES IN MECHANISM OF
ACTION OF ARDS NI(FE)-ARD INVOLVED IN THE METHIONINE
RECYCLE PATHWAY

Structural and functional differences between the two Ni-ARD and Fe-ARD
enzymes are determined by the type of metal ion bound in the active site of
the enzyme.14
Ni-ARD and Fe-ARD act on the same substrate, the acireductone,
1,2-dihydroxy-3-keto-5-methylthiopentene anion, but they yield different
products. Fe-ARD catalyzes a 1,2-oxygenolytic reaction, yielding formate
and 2-keto-4-methylthiobutyrate, a precursor of methionine (and ethylene),
and thereby part of the MSP, while Ni-ARD catalyzes a 1,3-oxygenolytic
reaction, yielding formate, carbon monoxide, and 3-methylthiopropionate,
an off-pathway transformation of the acireductone. At that the role of a reac-
tion catalyzed by the enzyme Ni-ARD, still not clear14,15 (see Schemes 18.1
and 18.2).
Pochapsky et al. showed that this dual chemistry can also occur in
mammals (MmARD) (before Ni(Fe)ARD activity was discovered by
Pochapsky et al. for bacteria and plants). It has been established, that the
Fe-bound protein, which shows about 10-fold higher activity than that of
Ni-protein, catalyzes on-pathway chemistry, whereas the Ni-ARD forms
exhibit off-pathway chemistry.15
Interestingly, that in the case of KoARD (Klebsiella oxytoca ARD,
bacterial enzyme ARD) unlike MmARD, Ni-bound form has higher activity
than Fe-KoARD.1 All forms remain monomeric regardless of bound metal
ion. While both Fe- and Ni-ARD from Klebsiella oxytoca are monomers,15
Fe-ARD from Oryza sativa L (OsARD) is a trimer, and Ni-bound OsARD is
a polymer consisting of several types of oligomers.15
374 Applied Chemistry and Chemical Engineering: Volume 4

SCHEME 18.1  Acireductone dioxygenases Ni-ARD and Fe-ARD14 are involved in the
methionine recycle pathway.

SCHEME 18.2  Acireductone dioxygenases Ni-ARD and Fe-ARD in methionine salvage

pathway, in biosynthesis of ethylene.15

We assumed that one of the reasons for the different activity of NiII(FeII)-
ARD in the functioning of enzymes in relation to the common substrates
Mechanism of Ni(Fe)ARD Action in Methionine Salvage 375

(acireductone and O2) can be the association of catalyst in various macro-

structure due to intermolecular H-bonds.
We assumed that the FeIIARD operation comprises the step of oxygen
activation.
(FeII + O2 → FeIII−O2−·) (by analogy with Dke1 action).3 Specific struc-
tural organization of iron complexes may facilitate the following regiose-
lective addition of activated oxygen to acireductone ligand and the reac-
tions leading to formation of methionine (and ethylene also). Association
of the catalyst in macrostructures with the assistance of the intermolecular
H-bonds may be one of reasons of reducing NiIIARD activity in mechanisms
of NiII(FeII)ARD.14
Earlier, we demonstrated a specific structural organization of functional
models of iron (nickel) enzymes NiII(FeII)ARD. We used an AFM method to
research the possibility of the formation of stable supramolecular nanostruc-
tures based on iron (nickel) heteroligand complexes due to intermolecular
H-bonds.7,8
So, in Figures 18.1 and 18.2, three-dimensional and two-dimensional
AFM image of the structures on the basis of iron complex with 18C6
FeIIIx(acac)y18C6m(H2O)n, formed at putting a uterine solution on a hydro-
phobic surface of modified silicone are presented. It is visible that the
generated structures are organized in certain way forming structures resem-
bling the shape of tubule microfiber cavity (Fig. 18.2c). The heights of
particles are about 3–4 nm. In control experiments, it was shown that for
similar complexes of nickel NiII(acac)2·18C6·(H2O)n (as well as complexes
Ni2(OAc)3(acac)·MP·2H2O) this structural organization is not observed. It
was established that these iron constructions are not formed in the absence
of the aqueous environment. Earlier we showed the participation of H2O
molecules in mechanism of FeIII,IIx(acac)y18C6m(H2O)n transformation by
analogy with Dke1 action, and also the increase in catalytic activity of
iron complexes (FeIIIx(acac)y18C6m(H2O)n, FeIIx(acac)y18C6m(H2O)n, and
FeIIxL1y(L1ox)z(18C6)n(H2O)m) in the ethyl benzene oxidation in the presence
of small amounts of water.16
After our works, it was found that the possibility of decomposition of
the β-diketone in iron complex by analogy with Fe-ARD action increases in
aquatic environment.17 That apparently is consistent with data, published by
us earlier in our initial work.16
Unlike catalysis with Fe-ARD, mechanism of catalysis by Ni-ARD
does not include O2 activation, and oxygenation of acireductone leads to
the formation of products not being precursors of methionine.1,14,15 In our
previous works, we have shown that formation of multidimensional forms
376 Applied Chemistry and Chemical Engineering: Volume 4

based on nickel complexes can be one of the ways of regulating the activity
of two enzymes.7
The association of complexes Ni2(AcO)3(acac)·MP·2H2O, which are
functional and structure models of Ni-ARD, to supramolecular nanostruc-
ture due to intermolecular H-bonds [H2O–MP, H2O–(OAc–)] [or (acac−)], is
demonstrated on the next Figure 18.3. All structures (Fig. 18.3) have various
heights from the minimal 3–4 nm to ~20–25 nm for maximal values (in the
form reminding three almost merged spheres)7

FIGURE 18.1  The AFM two-dimensional (a) and three-dimensional (b) images of
nanoparticles on the basis Fex(acac)y18C6m(H2O)n formed on the surface of modified silicone.

FIGURE 18.2  The AFM two-dimensional image (a) of nanoparticles on the basis Fex(acac)
y
18C6m(H2O)n formed on the hydrophobic surface of modified silicone, (b) the section of a
circular shape with fixed length and orientation is about 50–80 nm, and (c) the structure of
the cell microtubules.
Mechanism of Ni(Fe)ARD Action in Methionine Salvage 377

FIGURE 18.3  The AFM two-dimensional (a) and three-dimensional (b) images of
nanoparticles on the basis Ni2(AcO)3(acac)·L2·2H2O formed on the hydrophobic surface of
modified silicone.

In case of binary complexes {Ni(acac)2∙MP} (see below Fig. 18.9c), we

also observed formation of nanostructures due to H-bonds. But these nanopar-
ticles differ on form and are characterized with less height: h ~ 8 nm as
compared with nanostructures based on complexes Ni2(AcO)3(acac)·L2·2H2O
(Fig. 18.3).

18.3.2.2  POSSIBLE EFFECT OF TYR-FRAGMENT, BEING IN THE

SECOND COORDINATION SPHERE OF METAL COMPLEX

We assume that it may be necessary to take into account the role of the
second coordination sphere, including Tyr-fragment (see Fig. 18.4).14 We
first suggest the participation of Tyrosine moiety in mechanisms of action of
Ni(Fe)-ARD enzymes.
It is known that Tyr residues are located in different regions of protein
by virtue of the relatively large phenol amphiphilic side chain capable of (a)
interacting with water and participating in H-bond formation and (b) under-
going cation-π and nonpolar interactions.18 The versatile physicochemical
properties of Tyrosine allow it to play a central role in conformation and
molecular recognition.19
Tyrosine can participate in different enzymatic reactions. Recently, it has
been researched role of Tyrosine residue in mechanism of heme oxygenase
(HO) action. HO is responsible for the degradation of a histidine-ligated
ferric protoporphyrin IX (Por) to biliverdin, CO, and the free ferrous ion. The
role of reactions of Tyrosyl radical formation which occurs after oxidation of
378 Applied Chemistry and Chemical Engineering: Volume 4

Fe(III)(Por) to Fe(IV) = O(Por(·+)) in mechanism of human heme oxygenase

isoform-1 (hHO-1) and the structurally homologous protein from Coryne-
bacterium diphtheriae (cdHO) is described.20
It assumed that Tyr-fragment may be involved in substrate H-binding in
step of O2 activation by iron catalyst, and this can decrease the oxygenation
rate of substrate in the case of homoprotocatechuate 2,3-dioxygenase action.21
Tyr-fragment is discussed as important in methyl group transfer from
S-adenosylmethionine (AdoMet) to dopamine.22 The experimental findings
with the model of methyltransferase and structure survey imply that methyl
CH–O hydrogen bonding (with participation of Tyr-fragment) represents a
convergent evolutionary feature of AdoMet-dependent methyltransferases,
mediating a universal mechanism for methyl transfer.23
Tyrosine residue Tyr149 is found in the Met-turn for astacin endopepti-
dases and serralisines. Tyr149 giving a proton, forms a hydrogen bond with
zinc and becomes the fifth ligand. This switch plays a specific role, partici-
pating in the stabilization of the transition state during the binding of the
substrate to the enzyme.24
In the case of Ni-ARD, Tyr-fragment, involved in mechanism, can reduce
the Ni-ARD activity. The structure of the active center of Ni-ARD with Tyr
residue in second coordination sphere is shown in Figure 18.4.

FIGURE 18.4  The structure of NiIIARD with Tyr residue in the second coordination sphere.14
Mechanism of Ni(Fe)ARD Action in Methionine Salvage 379

Really, as mentioned above we have found5 that the inclusion of PhOH

in complex Ni(acac)2∙L2 (L2 = N-methylpirrolidone-2), which is the primary
model of NiIIARD, leads to the stabilization of formed triple complex
Ni(acac)2•L2•PhOH. In this case, as we have emphasized above, ligand
(acac)− is not oxygenated with molecular O2. Also the stability of triple
complexes Ni(acac)2•L2•PhOH seems to be due to the formation of supramo-
lecular macrostructures that are stable to oxidation with dioxygen. Forma-
tion of supramolecular macrostructures due to intermolecular (phenol–
carboxylate) H-bonds and, possible, the other noncovalent interactions25–27
based on the triple complexes Ni(acac)2∙L2∙PhOH, that we have established
with the AFM-method7,8,28 (in the case of L2 = MP, HMPA, NaSt, LiSt), is in
favor of this hypothesis (Fig. 18.5).

FIGURE 18.5  (a) The AFM three-dimensional image [5.0 × 5.0 (µm)] of the structures
(h ~ 80–100 nm) formed on a surface of modified silicone on the basis of triple complexes
NiII(acac)2∙MP∙PhOH, (b) AFM three-dimensional image [6.0 × 6.0 (µm)] of the structures
(h ~ 40 nm) formed on a surface of modified silicone on the basis of triple complexes
{NiII(acac)2∙HMPA∙PhOH}, (c) AFM three-dimensional image [30 × 30 (µm)] of the
structures (h ~ 300 nm) formed on a surface of modified silicone on the basis of triple
complexes NiII(acac)2∙NaSt∙PhOH, and (d) AFM three-dimensional image [4.5 × 4.5 (µm)]
of the structures (h ~ 10 nm) formed on a surface of modified silicone on the basis of triple
complexes NiII(acac)2∙LiSt∙PhOH.
380 Applied Chemistry and Chemical Engineering: Volume 4

Conclusive evidence in favor of the participation of tyrosine fragment

in stabilizing primary Ni- complexes as one of regulatory factors in mecha-
nism of action of Ni-ARD has been obtained by AFM. We observed first the
formation of nanostructures based on Ni-systems using L-Tyrosine (Tyr) as
an extraligand. The growth of self-assembly of supramolecular macrostruc-
tures due to intermolecular (phenol–carboxylate) H-bonds and, possible, the
other noncovalent interactions,25–27 based on the triple systems {Ni(acac)2 +
MP + Tyr}, we observed at the apartment of a uterine H2O solution of triple
system {Ni(acac)2 + MP + Tyr} on surfaces of modified silicon (Fig. 18.6).
Spontaneous organization process, that is, self-organization, of researched
triple complexes (Figs. 18.5 and 18.6) at the apartment of a uterine solu-
tion of complexes on surfaces of modified silicon are driven by the balance
between intermolecular and molecule-surface interactions, which may be
the consequence of hydrogen bonds and the other noncovalent interactions.29

FIGURE 18.6  The AFM three-dimensional image [2.0 × 2.0 (µm)] of the structures (h ~
25 nm) (a) and three-dimensional image [0.3 × 0.6 (µm)] of the structures (h ~ 50 nm) (b),
formed on a surface of modified silicone on the basis of triple systems {NiII(acac)2 + MP
+ Tyr}.

Histogram of volumes of the particles based on systems {NiII(acac)2 +

MP + Tyr}, and also the empirical and theoretical cumulative normal prob-
ability distribution of volumes, and the empirical and theoretical cumula-
tive log-normal distribution of volumes of the particles based on systems
{NiII(acac)2 + MP + Tyr}, formed on the surfaces of modified silicon, are
presented in Figure 18.7. As can be seen, distribution of volumes of the
particles in this case is well described by a log-normal law.
But as one can see in Figure 18.8, in case of binary systems {Ni(acac)2
+ Tyr}, we also observed formation of nanostructures due to H-bonds. But
these nanoparticles as well as particle based on {Ni(acac)2∙MP} complexes
Mechanism of Ni(Fe)ARD Action in Methionine Salvage 381

(Fig. 18.8c) differ in form and high from the nanostructures on the basis of
triple systems {Ni(acac)2 + MP + Tyr} (Fig. 18.6).

FIGURE 18.7  (a) Histogram of volumes of the particles based on systems {NiII(acac)2 +
MP + Tyr}, (b) the empirical and theoretical cumulative normal distribution of volumes of
the particles based on systems {NiII(acac)2 + MP + Tyr}, and (c) the empirical and theoretical
cumulative log-normal distribution of volumes of the particles based on systems {NiII(acac)2
+ MP + Tyr}.

Here, first the formation of complexes {Ni(acac)2∙MP Tyr} was confirmed

by electron absorption spectra (method of UV-spectroscopy).
As can be seen from Figure 18.9, when an aqueous solution of Tyr is
added to the Ni(acac)2 aqueous solution, a decrease in absorption intensity
of acetylacetonate ion (acac)− (λmax = 296 nm) and a small short-wavelength
shift of the absorption maximum (to λmax ~ 294 nm) (hypsochromic shift of
the absorption maximum) takes place. A similar change in the intensity of
the (acac)− absorption band is observed in the absorption spectra of Ni(acac)2
382 Applied Chemistry and Chemical Engineering: Volume 4

when it is coordinated with monodentate ligand MP, or crown-ether 18C6,

and in the case of the coordination of axial monodentate ligands with the
other metal acetylacetonates.5

FIGURE 18.8  (a), (b) The AFM three-dimensional image [4.5 × 4.5 (µm)] of the structures
[h ~ 10–15 (20) nm] based on binary systems {NiII(acac)2 + Tyr} formed on a surface of
modified silicone. (c) The AFM of three-dimensional image [4.0 × 4.0 (µm)] of nanoparticles
based on {Ni(acac)2∙MP} formed on the surface of modified silicone. Figure 18.8 shows our
original data published for the first time.

FIGURE 18.9  Electron absorption spectra of aqueous solutions: (1) Ni(acac)2, (2) Tyr, (3)
{Ni(acac)2 + Tyr}, and (4) {Ni(acac)2 + Tyr + MP} at 20°C.
Mechanism of Ni(Fe)ARD Action in Methionine Salvage 383

With the introduction of the third component MP, there was an additional
reduction of the absorption maximum, indicating MP coordination5 with
{Ni(acac)2∙Tyr} and triple complex {Ni(acac)2∙MP∙Tyr} formation.
At that, we observed the growth of max of absorption spectra of Tyr with
small bathochromic shift (from λmax ~ 274 nm to λmax ~ 280, 275 nm). It is
known, that phenol absorption band (λmax ~ 275 nm), associated with π–π*
transition, can undergo a bathochromic shift, for example, due to the outer
sphere interaction of π-system of PhOH with π-inner-ligand systems (at the
outer sphere complex OSC formation).30
The data shown in Figure 18.10 (sum of the spectra of Tyr and (acac)−
ligand with respect to the spectrum of a mixture {NiII(acac)2 + MP + Tyr}
(Fig. 18.10a), as well as the result of subtraction of Tyr spectrum from spec-
trum of mixture {NiII(acac)2 + MP + Tyr} (Fig. 18.10b) also favor the forma-
tion of triple complexes {Ni(acac)2∙MP∙Tyr}.

FIGURE 18.10  (a) Sum of the electron absorption spectra of aqueous solutions of Tyr
(spectrum 2, Fig. 18.9) and (acac)− ligand (spectrum 1, Fig. 18.9) with respect to the spectrum
of a mixture {NiII(acac)2 + MP + Tyr} (spectrum 4, Fig. 18.9). (b) The result of subtraction of
Tyr spectrum (2, Fig. 18.9) from spectrum of mixture {NiII(acac)2 + MP + Tyr} (4, Fig. 18.9).

It should be noted that the absorption at λ = 295 nm does not disap-

pear completely, as it takes place in the presence of CH3COOH acid by
displacing the acac− ligand to outer coordination sphere of the Ni complex
that be accompanied by appearance of (acac)− absorption band at λ = 275
nm.31 So received experimental data cannot be explained by coordination
of the carboxyl group of tyrosine with the nickel ion. So apparently, the
formation of triple complexes {Ni(acac)2∙MP∙Tyr} is due to coordination by
OH– group of tyrosine.
384 Applied Chemistry and Chemical Engineering: Volume 4

At the same time, it is necessary to mean that important function of

NiIIARD in cells is established now. Namely, carbon monoxide (CO) is
formed as a result of action of nickel-containing dioxygenase NiIIARD.
It was established that CO is a representative of the new class of neural
messengers, and seems to be a signal transducer such as nitrogen oxide,
NO.1,14,15

18.4 CONCLUSION

Usually in the quest for axial modifying ligands that control the activity and
selectivity of homogeneous metal complex catalysts, the attention of scien-
tists is focused on their steric and electronic properties. The interactions in
the outer coordination sphere, the role of hydrogen bonds and also the other
noncovalent interactions are less studied.
We have assumed that the high stability of heteroligand MIIxL1y(L1ox)z
(L )n(H2O)m (M = Ni, Fe, L1 = acac−, L1ox = OAc−, L2 = electron-donating
2

mono, or multidentate activating ligands) complexes as selective catalysts

of the ethylbenzene oxidation to PEH, formed during the ethylbenzene
oxidation in the presence of {ML1n + L2} systems as a result of oxygenation
of the primary complexes (MIIL12)x(L2)y, can be associated with the forma-
tion of the supramolecular structures due to the intermolecular H-bonds.
The supramolecular nanostructures on the basis of catalytic active iron
FeIIIx(acac)y18C6m(H2O)n and nickel complexes NiIIxL1y(L1ox)z(L2)n(H2O)m
(L1 = acac−, L1ox = OAc−, L2 = N-methylpirrolidone-2, x = 2, y = 1, z = 3,
n = 1, m = 2), Ni2(AcO)3(acac)·L2·2H2O; {Ni(acac)2∙L2∙PhOH} (L2 = MP,
HMPA, NaSt, LiSt), obtained with AFM method, indicate high probability
of supramolecular structures formation due to H-bonds in the real systems,
namely, in the processes of alkylarens oxidation.
Since the investigated complexes are structural and functional models of
NiII(FeII)ARD dioxygenases, the data could be useful in the interpretation of
the action of these enzymes.
Specific structural organization of iron complexes may facilitate the first
step in FeIIARD operation: O2 activation and following regioselective addi-
tion of activated oxygen to acireductone ligand (unlike mechanism of regi-
oselective addition of no activated O2 to acireductone ligand in the case of
NiIIARD action), and reactions leading to formation of methionine.
The formation of multidimensional forms (in the case of NiIIARD) may
be one way of controlling NiII(FeII)ARD activity.
Mechanism of Ni(Fe)ARD Action in Methionine Salvage 385

We assumed the participation of Tyr-fragment which is in the second

coordination sphere in mechanism of NiII(FeII)ARD operation, as one of
possible mechanisms of reduction in enzyme activity in NiII(FeII)ARD
enzymes operation, and we received experimental facts in favor this assump-
tion. So with AFM method, we observed first the formation of supramo-
lecular macrostructures based on triple systems {Ni(acac)2 + MP + Tyr}
that included L-Tyrosine as extraligand, formed on a surface of modified
silicone due to intermolecular (phenol–carboxylate) H-bonds and, possible,
the other noncovalent interactions. Earlier, self-assembly based on the triple
complexes Ni(acac)2∙L2∙PhOH, we observed with the AFM-method for L2 =
MP, HMPA, NaSt, LiSt).
In this chapter, using method of UV-spectroscopy, we received the
confirmation of the of triple complexes {Ni(acac)2∙MP∙Tyr} formation.

KEYWORDS

•• models of Ni(Fe)ARD dioxygenases

•• dioxygen
•• AFM method
•• nanostructures based on model triple systems
{NiII(acac)2 + MP + Tyr}
•• triple complexes {Ni(acac)2∙MP∙Tyr} with UV-spectroscopy

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Chem. Soc. 2011, 133, 17134–17137.
23. Horowitz, S.; Dirk, L. M. A.; Yesselman, J. D.; Nimtz, J. S.; Adhikari, U.; Mehl, R. A.;
Scheiner S.; Houtz, R. L.; Al-Hashimi, H. M.; Trievel, R. C. Conservation and Func-
tional Importance of Carbon–Oxygen Hydrogen Bonding in AdoMet-Dependent Meth-
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25. Dubey, M.; Koner, R. R.; Ray, M. Sodium and Potassium Ion Directed Self-assembled
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INDEX

A correlation plot of electrophilicity index

Acireductone (1,2-dihydoxy-3-keto-5- versus HOMO-LUMO gap, 172
(thiomethyl)pent-1-ene), 368 even-odd oscillation behavior of, 173
Adsorption isotherms, 251 results and discussion
Dubinin–Radushkevich(D–R) model, electronic properties and DFT-
252–253 based descriptors, 170–171
Langmuir and Freundlich models, lowest energy and low-lying struc-
parameters of, 252 tures of, 170
Adverse drug reactions (ADRs), 188 structure of copper-gold, 169–170
Alumina, 216–217 Biodegradable poly(ester amide)s, 4
Antifriction self-lubricating polymer Bioinformatics, 185
materials, 46 advantages, 194–195
creation of, 46 cancer and, 196–197
polyethylene oxide, 47 forensic DNA and, 195–197
Array comparative genomic hybridization application, 186
(ACGH), 188 ACGH, 188
Azodicarbonamide (ADC), 19 biological database, 190–191
decomposition of, 19–20 drug discovery, 193
design cube, 38, 39 genomics, biomedicine, and micro-
design table for response density and biology, 187–190
variables, 37 pathway databases, 192
prevention and treatment of dis-
foam formation, 27–28
eases, 192–193
3D plot of desirability, 38, 40
sequence databases, 191
PVC, 20
structure databases, 191–192
thermal characterization of
commercialization of, 193–194
Kissinger plot of, 32
future direction of, 198
onset temperature and, 31
purpose of studying, 185
TG curves, 30–31
TGA results, 32 C
B Centrifuge spinning setup, 334
Charged-couple devices (CDD), 184
Bimetallic nanoalloy clusters, 166, 167
Chemical blowing agents (CBA)
calculated bond lengths (Å)
ADC
Au2, Cu2, and Cu Au species for,
decomposition of, 19–20
173
PVC, 20
computational details, 168–169 Chemical process modeling
computed DFT-based descriptors, 172 futuristic vision of, 158
copper-gold structure of, 169–170 science of scale-up, 159
390 Applied Chemistry and Chemical Engineering: Volume 4

Chimeric antigen receptors (CAR), 189 nitrogen adsorption and desorption

Conceptual Density Functional Theory isotherms
(CDFT), 167 alumina, 225
HAP, 226
D silica, 225
Density functional theory (DFT), 166 results and discussion, 219
Differential scanning calorimeter, 61 adsorbents, composition by XRF,
Differential scanning calorimeter (DSC), 220
81, 264 adsorption equilibrium, 246–254
open and hermetically sealed cells in, adsorption kinetics, 254–260
281 adsorbents, surface characteristics
curves for, 282–283 of, 224–226
extent of reactions, heating rate, FTIR spectrum, 220–223
285 silica, alumina, and HAP
hypothetical, 286 characterization of, 219
Tm and enthalpy changes, 287 sorption isotherm method, 235
Diffusion models Dubinin–Radushkevich (D–R),
Mathews and Webber model, 241 237–238
micropore Freundlich model, 236–237
DNA adsorption to silica, kinetic Langmuir model, 236
model, 243–244 surfaces used in, 205
Weber–Morris Model, 241–242 XRD
DNA adsorption alumina, 222
adsorbents, 206 HAP, 223
alumina, 216–217 peaks of HAP, 224
HAP, 217–218 peaks of α-Alumina, 222
silica, 206–216 silica gel, 221
composites, 204 Dog rose drying, 350–351
equilibrium and kinetics of analysis of experienced data, 350
absorbents on, 234 energetic balance of product, 350
FTIR spectrum nutritional value and chemical composi-
alumina, 221 tion of product, 349–350
HAP, 223 DSC analysis
main infrared bands, silica gel, 220 open and hermetically sealed cells in,
silica gel, 221 281
isotherm, 235 curves for, 282–283
kinetics extent of reactions, 284
diffusion models, 240–244 extent of reactions, effect of heat-
reaction models, 239–240 ing rate on, 285
sorption rate, 238–239 hypothetical, 286
materials, 218, 244–245 Tm and enthalpy changes, 287
methods Dubinin–Radushkevich (D–R)
adsorption experiment, 245 DNA adsorption
adsorption kinetics, 246 sorption isotherm method, 237–238
buffer solutions, 246
Index 391

E vision and modeling, 147–148

Electrocentrifuge setup, 334 vision, challenge, and deep scientific
Environmental engineering science, 309 introspection, 145
vision and challenges, 319 visionary scientific endeavor in field of
Epoxidized natural rubbers (ENR), 57 design of riser in, 150–153
Epoxy resins, cross-linking, 95 Fluidized catalytic cracking unit (FCCU),
Epoxy–isocyanate mixtures 138
experimental Flynn–Wall–Ozawa (FWO), 274
composition of, 96 Fossil-fuel resources depletion, 159
cross-linking of, 96 Freundlich model
IR-spectroscopic investigations, 96 DNA adsorption
materials, 95 sorption isotherm method, 236–237
results and discussion Friedman method, 275
decrease in temperature, 101 FTIR spectroscopy, 61
dependence of gel-fraction content,
G
97
film hardness upon temperature Gel permeation chromatography (GPC),
and, 97 59–60
HAO, 97–99 Genetic algorithm (GA), 138
hardness of, 100 application areas, 147, 158
intensity of absorption band, bioinspired optimization, 144
102–104 challenges, futuristic vision, and
structural changes in, 102 avenues of research pursuit, 155–156
Epoxy-urethane, isocyanate with, 94 scientific vision and deep scientific
understanding behind application of,
F 144
Fe-acetyl acetone dioxygenase (Dke1), Glass transition temperature, 83
368 PEO/PnBMA blends
Fluid catalytic cracking (FCC), 138 changes in heat capacity of PEO
difficulties in, 84
computational time, 156 DSC traces of, 84
science of optimization, 156 Global water crisis
fundamentals, 143 arsenic groundwater contamination
modeling, simulation, optimization, and global water shortage, 314,
control of, 159–160 318–319
petroleum refinery in and application of technology initiative
evolutionary MOO, 149 developed and developing coun-
riser design in, 148 tries in, 318
scientific acuity and deep scientific Gold nanoclusters, 167
understanding, 160
H
scientific doctrine and vision behind
design of, 145 Heliodrying apparatus with polycarbonate
covering test
validation of science and engineering,
experimental
157
materials, 344
392 Applied Chemistry and Chemical Engineering: Volume 4

objects of study, 345–346 partial and integrated mass losses for,

results and discussion 276
drying, 346–351 thermogravimetric curves for DNA, 276
Highest occupied-lowest unoccupied water content of DNA, variation of, 277
molecular orbital (HOMO-LUMO), Kissinger–Akahira–Sunose (KAS), 275
166, 168
Honey agarics, mushrooms drying. See L
also Heliodrying apparatus with poly-
Langmuir model
carbonate covering test
DNA adsorption
analysis of experienced data, 349
sorption isotherm method, 236
changing of mass of raw materials, 349
data sheet table, 348 M
energetic balance of, 347
Membrane separation processes
nutritional value and chemical composi-
barriers, difficulties, and, 320
tion, 346–347
current trends and future challenges,
Human civilization, 156–157
Hydroxy–acrylic oligomer (HAO), 95 317
Hydroxylapatite (HAP) DNA adsorption, doctrine of, 316–317
217–218 scientific vision, scientific cognizance,
315
I vision
Information system (IS), 182, 185 application, 315–316
Fuzzy Arden Syntax, 183 science, 317–318
OWL reasoner Pronto, 183 visionary scientific endeavor in field of,
roles of, 183 312–313
Information technology (IT), 183 world of visionary frontiers and prog-
CDD, 184 ress of, 319–320
role toward software, 184 Metal oxide nanostructures, optical and
electrical properties, 354–355
used for, 184
Intraparticle diffusion, 259 analyses, 359–362
absorbents characterization, 358–359
diffusivity of DNA, 260 classification, 356–358
dimensionality, 356–358
K surface morphology, 355–356
2-Keto-4-(thiomethyl) butyrate (KMTB), Methionine salvage pathway (MSP), 368
368 Methylthioadenosine (MTA), 368
Kissinger analysis, 287 Multiobjective optimization (MOO)
science, 139
activation energies, DTG peaks by, 288,
application areas in field, 146
289–291
definition of, 142–143
plots
evolutionary and, 149
for DNA, 288
linearity of, 290 future recommendations of study,
peaks detected in DTG, 289 141–142
Kissinger method, 275 future trends and future flow of
DTG curves for DNA, 277 thoughts in, 160
Index 393

need and rationale of study, 140–141 H bonds, 372–384

scientific doctrine and scientific cogni- mechanism, 370–372
zance behind, 142 Novel separation processes
scientific principles, 143–144 future of science and engineering, 321
scientific research pursuit in field of,
153–155 P
scope of study, 140 PEO/NR-g-PMMA blends
vision and aim of, 139–140 binary polymer blending, 57
vision and difficulties, 148–149 characteristic of, 59, 80
world of immense challenges, 146–147 compatibility and melting behavior
change of heat capacity of, 67
N DSC thermograms of, 66
Nanofibers glass transition, 65–68
creation techniques, experimental study melting endotherms of, 68
electro centrifuge method and melting temperatures of, 69
setup, 333–334 quantities ΔCp of, 66
flow rate theory, 335 crystallinity of, 69–70
production rates, 336–338 ENR, 57
rotational speed, effect of, 335–336 experimental part
Nanomaterials, 166 characterization, 59–61
bimetallic nanoclusters, 167 materials and sample preparation,
DFT, 167–168 58–59, 81–82
gold, 167 material characterization, 81–82
noble metal clusters, 167 melting behavior of
Natural rubber (NR), 56 apparent melting temperatures of
Natural rubber-graft-poly(methyl methac- PEO in, 86
rylate) (NR-g-PMMA) DSC traces for melting endotherms
binary polymer blending, 57 of PEO in, 85
ENR, 57 miscibility of, 79
experimental normalized mass loss fraction of, 83
characterization, 59–61 results and discussions
materials and sample preparation, crystallinity of PEO, 86–87
58–59 FTIR spectroscopy, 87–89
FTIR spectroscopy, 57 miscibility of, 83–86
PEO, 57 percent mass retained curves, 82
Natural rubber-graft-poly(methyl methac- thermal stability of neat polymers
rylate) (NR-g-PMMA) and, 82–83
results and discussion Petroleum refining
1H NMR spectra of, 62 future, energy sustainability, and,
characterization of, 61–62 145–146
Ni(Fe)ARD action in methionine salvage Physical blowing agents (PBA), 19
pathway mechanism, 368 Poly(ethylene oxide) (PEO), 56, 78
approach, 369 normalized mass loss fraction of, 83
materials and methodology, 370 Poly(methyl methacrylate) (PMMA), 56
results and discussion Poly(n-butyl methacrylate) (PnBMA), 78
394 Applied Chemistry and Chemical Engineering: Volume 4

Poly(vinyl chloride) (PVC), 20 unsaturated polyesters, 5

materials, 22 Polyurethane materials, 94
mechanical behavior of Pressed polyphenylene oxide (PPO)
samples PVC and PVC film, 29 experimental part, 47
stress-strain curves for films, 28 results and discussion, 47
preparation of, 22 crossed structures, formation of,
results and discussion 49–50
characterization of, 25–30 effect of temperature on products,
design of experiment, 37–40 48
thermal characterization of azodi- influence of friction duration, 50,
carbonamide, 30–32 51
thermal characterization of films, tribodestruction and thermal destruction
33–34 of purified, difference in, 51–52
thermal stability of composites, Pseudo-first- and second-order models
34–36 adsorption of DNA to alumina
thermal degradation and stabilization, pH 2 solution, 256
20–21 pH 5 solution, 256
dehydrochlorination, 20–21 pH 8 solution, 257
organic and inorganic compounds, adsorption of DNA to HAP
21 pH 2 solution, 257
thermal gravimetric analysis, 24 pH 5 solution, 258
thermal stability, 24–25 pH 8 solution, 258
Polyamine, 368 adsorption of DNA to silica
Polycarbonate, 345 pH 2 solution, 254
Polymer foams. See Poly(vinyl chloride) pH 5 solution, 255
(PVC), 18 pH 8 solution, 255
Polymers reaction model parameters of Calf
AABB-type poly(ester amide)s, 5 Thymus DNA
biomedical designation of, 4 on alumina, 259
mechanical properties, 13–14 on HAP, 259
synthesis of, 5 on silica, 259
di-p-nitrophenyl ether of fumaric
acid, 6 R
di-p-toluene sulfonic acid salts of Reaction models
bis(α-amino acid) α,ω-alkylene pseudo-first-order equation, 239
diesters, 6 pseudo-second-order equation, 239–240
thermal characteristics of
homopoly(ester amide)s, 10 S
thermal properties, 9–13 S-Adenosyl methionine (SAM), 368
thermogram Scanning electron microscopy (SEM), 24
8-Leu-12 of, 12 micrographs of PVC plastisol film, 26
FA-L-Leu-12 + phthalic anh (after Science vision, 320–321
3-month delay) of, 13 Science and technology
FA-L-Leu-12 + phthalic anh of, 12 future directions, 321–322
FA-L-Leu-12, 11 Scientific cognizance, 158–159
Index 395

Sheet heliodrying apparatus, 346 SSIR codification for 24 test set

Silica, 206 molecules, 128
aerogels, 210 SSIR codification, 118–120
aerogel properties and features with test for validation, 12–129
applications, 211 training and cross-validation,
chemical parameters, significance 122–123, 125–126
of, 213 cross-validation, 114
drying of gels, 213–216 framework, 110–111
gel and gelation, 213 molecular description, 111
pure substance, P-T plane phase quantifying rule significance, 112–113
diagram of, 215 rules, 111–112
silicon alkoxides, hydrolysis and TIBO
condensation for, 212 positions of 27 active, 125
sol-gel process, 211–213 ROC curve for BL2O cross-valida-
supercritical fluids, properties of, tion procedure of, 127
216 ROC curve for external test set,
DNA adsorptions, conceptual figures 129
of, 207 ROC curve for training of, 125
DNA to silanol groups, proposed Symmetrized fragment orbitals (SFOs),
binding of, 208 168
microchip packed with, 210
oxide forms of iron, 209 T
Single-walled carbon nanotubes (SWNT), T cells with antitumor antigen receptors
204 (TCR), 189
Solid polymer electrolytes (SPEs), 78 Tetrahydroimidazo[4,5,1-jk][1,4]benzodi-
Superposing Significant Interaction Rules azepinone (TIBO), 115
method (SSIR), 110 Thermogravimetric analysis (TGA), 60,
(Q)SAR SSIR model, 113 78, 81, 273–274
application example activation energies for individual
advantages and drawbacks and conversion ranges, 278
future prospects, 130–132 Friedman method, 275, 279–281
exploration results, 124 FWO method
inverse SAR, 129–130 plots, 278
molecular set, 115, 121 KAS method, 278–279
negative logarithm of p-values, Kissinger method, 275–278
distribution of, 122 Thermal behavior of sodium salt of calf
owner’s dictionary, 116–117 thymus DNA, 264
positions of 27 active TIBOs, 125 Abdurakhman and coworkers, 267–268
ROC curve for BL2O cross-valida- DNA structure, 264–265
tion procedure of TIBO, 127 DRIFT spectroscopy analysis, 272
ROC curve for TIBO external test
Falk and coworkers, 266–267
set, 129
FTIR analysis, 272
ROC curve for training of, 125
Hoyer and coworkers, 268
intumescent behavior, 269
Lavalle and coworkers, 268
396 Applied Chemistry and Chemical Engineering: Volume 4

Lee and coworkers, 267 variation of normalized intensities,

Marlowe and colleagues, 268 298–299
materials, 271 structural changes during melting of,
methods 265
DSC analyses, 271–272 thermal degradation, 270
scanning electron microscopy, 272 Whitson and coworkers, 268
thermal gravimetric analysis, 271 Thermal gravimetric analysis, 273–274
pUC19 and pGY1 plasmids FWO method, 274
thermal degradation of, 269 KAS method, 275
results and discussion
DRIFT spectroscopy, 298–300 U
DSC analysis in open and hermeti- Unsaturated polyesters, 5
cally sealed cells, 281–287 Water technology
morphological changes, 291–293 initiatives and technological vision in
scanning electron micrographs of, the field of, 315
292
thermal characterization of, 273– X
291 transmission FTIR, 293–298
X-ray diffraction diagram (XRD), 221