Fundamental Chemistry with MATLAB
A guide to using MATLAB scripts, models, and algorithms to explore the fundamentals and
applications of key topics in chemistry
Key Features
Provides practical examples of using the MATLAB platform to explore
contemporary problems in chemistry.
Outlines the use of MATLAB Simulink to produce block diagrams for dynamic
systems, such as in chemical reaction kinetics
Heavily illustrated with supportive block-diagrams and both 2D and 3D MATLAB
plots throughout
MATLAB offers huge capabilities for data processing, graphical presentation and
modelling, making it an important tool for chemists in navigating their increasingly data-
driven field. Fundamental Chemistry with MATLAB highlights how this functionality can
be used to explore the fundamentals and applications of key topics in chemistry.
After an introduction to MATLAB, the book goes on to provide examples of its application
in both fundamental and developing areas of chemistry, from atomic orbitals, chemical
kinetics and gaseous reactions, to clean coal combustion and ocean equilibria amongst
others. Complimentary scripts and datasets are provided to support experimentation and
learning, with scripts thoroughly outlined enabling the reader to modify them to fit their
particular needs.
Drawing on the experience of its expert authors, Fundamental Chemistry with MATLAB is a
practical guide for all those in chemistry who are interested in harnessing the scripts,
models, and algorithms of the MATLAB platform to further enhance their use,
understanding and visualization of data.
About the Authors
Daniele Mazza was Professor of Chemistry and Materials Science at the Politecnico di
Torino. His main research fields were the electrical and crystallochemical properties of ionic
conductors and ceramic superconductors.
He is author or co-author of more than 80 publications in international journals about solid
state chemistry, crystal structure determination, X-ray diffraction and modelization of ionic
movement in crystalline lattices. In addition, he is author of three books in chemistry. His
current research interests focus on environmental and climatic issues, in particular ocean
chemistry and CO2 equilibria in seawater.
Enrico Canuto has taught Automatic Control for more than 40 years at Politecnico di
Torino, Turin, Italy. He developed and applied the Embedded Model Control methodology
for the design and implementation of digital control systems. He contributed to data
reduction of the European astrometric mission Hipparcos, concluding with the publication
of the Hipparcos star Catalogue of 120,000 stars. He was active in the design of spacecraft
control systems, contributing to the European GOCE mission, to other forthcoming
missions, and to instruments for space qualification like the Nanobalance thrust-stand. In the
last ten years he has collaborated with the Center for Gravity Experiments, Huazhong
University of Science and Technology, Wuhan, and the Tianqin Centre, Sun-Yat-
Sen University, Zhuhai, China, in the field of scientific space missions. He has authored one
book and published over 150 papers.
Introduction
Matlab language and environment
Most developers today use the so called ‘ third-generation languages’ such as C, C++,
Python, and Java. A third-generation language, a general purpose language in nature, gives
the developer the kind of precise control needed to write exceptionally fast applications that
can perform a wide array of tasks. Fourth-generation languages, like Matlab (short for
Matrix Laboratory), on the contrary, are designed with a specific purpose in mind, which in
the case of Matlab, is scientific and technical computing. In this sense, it has been designed
for empowering the user to work with heterogeneous collections of data, rather than
individual variables, making it easier for the user to focus on the task, instead on the
language.
As programming languages progress through generations, they become more intelligible and
closer to human abstraction and language. Matlab took advantage since the early
developments of the abstraction levels inherent in the mathematical language and
operations, thus offering the user a mathematical environment suitable to any hardware and
operating system platform. Subsequent developments added graphical environments like
that of Simulink devoted to dynamic systems and their automatic control (to be employed in
Chapters 3 and 4), Graphical user interfaces (GUI), document editing, and a rich set of
toolboxes covering a wide spectrum of scientific and technical computing and real-time
applications in measurements and control.
The chemistry computations proposed in the book will just employ the Matlab core, without
any reference to Matlab toolboxes. To this end, we will exploits functions of the following
areas addressed by the core: Algebra, Linear algebra (many equations dealing with many
unknowns), Calculus, Differential equations, Optimization, Linear regression, Statistics,
Curve fitting, Graphing.
Code listing in this book is specifically designed to work on Matlab platform, however with
a little efforts most of the simple scripts can be exported to Octave, a very similar but free
platform. Indeed if you are looking for an open-source environment close to Matlab in terms
of compatibility and computational ability, then Octave is the best alternative. It runs on
any operating system without any modifications. Scilab is another open-source option for
numerical computing which runs across all the major platforms. Like Octave it is very
similar to Matlab in its implementation, although exact compatibility is not a goal of the
project developers. It has the advantage of possessing a graphical interface similar to
Simulink, named Xcos .
The Matlab scripts
Any computational exercise will be accompanied by a Matlab script, name like InitChem.m,
where <.m> is the extension of Matlab scripts, collecting data from external files,
performing computations and providing results either in a tabular form in the Command
Window or graphical plots in appropriate windows. No specific introduction to Matlab is
provided, except to Simulink in the Appendix D (Chapter 14), but the book scripts and the
key Matlab functions will be explained in some detail. The web version of the book will
show the default colors which distinguish four kinds of sentences and variables in the script:
1) Black is reserved to statements to be executed.
2) Green is reserved to comments which are introduced by the % character.
3) Bold green is reserved to comments introduced by the %% characters. They split the
script into sections which can run separately or step by step. Such comments have been
exploited to split the script into sections with different functionalities, for instance,
initialization, user data statements, data collection from external excel sheets, main
computation, result printout, 2D and 3D graphical plots.
Fairly all of the scripts designed to produce the book graphical plots, are reported in the
book itself. The complete library of scripts (main scripts and functions) of extension <.m>,
excel files of extension <.xlsx> and Simulink block diagrams (models) of extension <.slx>
can be found in the companion website [8] . Care has been taken to ensure the script
execution without warnings and errors, at least as they are reported in the book and in the
editor’s website. Of course, any bug can be reported to the authors via their e-mail
addresses.
Simulink models of extension <.slx> could not be included in the book (see the Appendix
D, Chapter 14), but the image of several block-diagrams has been added to Chapters 3 and
4.
Matlab scripts and Simulink models have been developed with an academic license of
Matlab/Simulink. No Matlab Toolbox has been employed.
The book topics
Fundamental or general chemistry is a huge field, therefore the ten chapters of this book will
focus on topics which are only partial sections of this field. The curious reader will be able
to spot similarities in adjacent fields of chemistry, not covered yet (but may be a future
treatise), and to adapt codes to this aim. Clues to this are be given below, in the summary of
chapter’s topics. Numerical data elaboration for advanced techniques in chemistry (e.g. X-
ray diffraction, NMR analysis, molecular dynamics or lattice energetics) are not covered in
this context; the relevant programs are to be found in specific web sites or textbooks, being
mainly addressed to expertises in the respective sectors.
Book chapters can be arranged into four groups, plus six appendixes of help to specific
topics and chapters.
Group one: atomic orbitals
Plotting atomic orbitals with Matlab (Chapter 1). The mathematical description of the
ondulatory behavior of electrons in atoms is shortly reviewed. On this basis, electron wave
functions are described and plotted in a simplified manner using Matlab surf and fsurf
functions. Some elements of wave functions theory and the Schroedinger equation is
recalled in the Appendix F (Chapter 16). Molecular orbitals are not covered yet but could be
in a next edition.
Group two: stoichiometry and kinetics
Balancing chemical reactions with Matlab (Chapter 2). The algebra underlying to the
balancing of chemical reactions is highlighted. In such a way, a generic and straightforward
solution is devised for simple acid-base or complex redox reactions. This could help solve
troublesome issues, being the correct mass balance of utmost relevance in general and
educational chemistry. The foundations of the algebraic algorithm employed are reviewed in
the Appendix A (Chapter 11). Only some examples of reactions are given, while the reader
will exploit other as well among the many possible.
Chemical kinetics aided by Matlab/Simulink (Chapter 3). The study of the rate of a chemical
reaction both in textbooks and in advanced applications requires to deal with differential
equations. Their solution, even for simple applications, is here easily enabled by Matlab
ODE (Ordinary Differential Equations) solver and by Matlab/Simulink block-diagrams. The
treatment agrees with the methods of system and control engineering. The foundations are
recalled in the Appendix B (Chapter 12). The two case-studies, NO oxidation and ozone
decomposition, can be extended to many other known reactions
More complex kinetics aided by Matlab/Simulink (Chapter 4). As an example for those
interested in more complex kinetics, like the famous oscillating reactions, here a complete
description is to be found, with stunning graphics and plotting, enabled by Matlab. As
already mentioned, this topic may be of interest of researchers in system theory and control
engineering.
Group three: gases and vapors
Gaseous reactions and equilibria aided by Matlab (Chapter 5). In dealing with
thermodynamics of even simple equilibrium reactions in a varying temperature/pressure
environment requires a precise approach. Matlab functions enable to read excel files with
the parameters needed to calculate entropy, enthalpy and free energy and therefrom the
equilibrium parameters for some reactions. By exploiting the indicated thermodynamic
database other reactions will be tackled, among the many of interest in environmental
issues.
Physical properties of gases and vapors aided by Matlab (Chapter 6). Electric interaction
between molecules are responsible for the phase transformation of gases to liquids. A
number of equations can be used for describing the behavior of real gases, in a wide range
of temperatures and pressures, which are graphically displayed by Matlab scripts. A gas of
choice can be used, as long as its van der Waals parameters are known.
Group four: aqueous solutions
Exploring acid-base equilibria in water with Matlab (Chapter 7), In general chemistry this
is a relevant topic. Many Matlab functions, among them fzero, enables in a few program
lines to solve even complex equilibria of this kind. Examples range from monoprotic acids
to titratrion of polyprotic acids. Though a few working examples are given, the reader will
be able to insert other acid/base equilibria in solution, even admixtures of acids and bases.
Colligative properties of solutions aided by Matlab (Chapter 8). These properties only
depend on the solute molar concentration and temperature, being independent of the nature
of the solute particles. As an example, aqueous solution of NaCl is chosen and discussed,
but the conclusion can be extended to all other solutions of this type, including other binary,
ternary or complex salts.
Exploring seawater chemical equilibria with Matlab (Chapter 9). Seawater is not a simple
reservoir of different dissolved salts, like sodium chloride, but is capable of reacting with
different substances like the atmosphere’s carbon dioxide, by modifying its concentration
and buffering the anthropogenic increase. This is one of to-day most debated topics. The
only quantitative way to tackle the issue is by proper solution of chemical equilibrium
equations. All this is discussed, explained and calculated by the simple use of Matlab
scripts. As with other scripts of this book, the reader can vary the relevant parameters, and
discover what happens. The variety of simulations is really amazing, but only some of them
are discussed
Prevalence diagrams for some common elements aided by Matlab (Chapter 10), Any
element in aqueous solution is capable of transforming into different chemical forms,
according to pH and E H , the redox potential of the same solution. In this way, we
obtain pH / E H diagrams, known as prevalence (or Pourbaix) diagrams (M. Pourbaix,
1904-1998). Matlab graphical capabilities enable an easy representation of these diagrams
for some common elements, like Fe , S and Mn . The methods can be applied as well
to other elements, by providing the pertinent electrochemical potentials.
Appendices
Appendix A (Chapter 11): Introduction to linear algebra
Appendix B (Chapter 12): Introduction to dynamic systems
Appendix C (Chapter 13): Introduction to linear regression
Appendix D (Chapter 14): Introduction to Matlab Simulink
Appendix E (Chapter 15): Table of sea water coefficients
Appendix F (Chapter 16): Introduction to the Schroedinger equation
Authorship and acknowledgments
The book was conceived by the first author, as an offspring of his several decade experience
as a teacher of fundamental chemistry at Politecnico di Torino, Turin, Italy, and recently as
author of two books on current hot topics in environment chemistry, The second author was
firstly involved to improve the stoichiometric balance of Chapter 2, taking advantage of the
nullspace algorithm. Despite his scholar-level chemistry knowledge, he became passionate
of the first author’s conception, topics and algorithms, leading him to a full immersion in the
draft revision, enrichment and completion. He brought two-year experience in the
conception and writing of the eight hundred pages of the book as well as a lomg-time
experience in the field of dynamic system simulation and control aided by Matlab/Simulink
environment.
A first draft of the book was written with the Word text editor of Microsoft Office, but soon
the authors realized that their collaboration could greatly benefit from a free text editor like
Writer of the LibreOffice suite. The only Microsoft Office residuals are the excel tables,
which accompany, as data sources, the abundant suite of Matlab scripts presented by the
book.
Last but not least, the work of both authors could not have been matured without the
patience and support of their respective wives, Maria Teresa and Maria Angela.
