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100
Progress in the Chemistry
of Organic Natural Products
Authors:
U. Wagner, Ch. Kratky
H. Budzikiewicz
W.F. Reynolds, E.P. Mazzola
P. Joseph-Nathan, B. Gordillo-Román
R.W. Soukup, K. Soukup
Prof. A. Douglas Kinghorn, College of Pharmacy,
Ohio State University, Columbus, OH, USA
em. Univ.-Prof. Dr. H. Falk, Institut für Organische Chemie,
Johannes-Kepler-Universität, Linz, Austria
Prof. Dr. J. Kobayashi, Graduate School of Pharmaceutical Sciences,
Hokkaido University, Sapporo, Japan
ISSN 2191-7043 ISSN 2192-4309 (electronic)
ISBN 978-3-319-05274-8 ISBN 978-3-319-05275-5 (eBook)
DOI 10.1007/978-3-319-05275-5
Springer Cham Heidelberg New York Dordrecht London
Library of Congress Control Number: 2014954988
© Springer International Publishing Switzerland 2015
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Foreword
To reach Volume 100 of a scientific book series is certainly an occasion to celebrate.
We thought that this might be best achieved in two ways: on the one hand to
assemble timely overviews of present-day methodology for the structural analy-
sis of organic natural products, and on the other hand to discuss the historical
aspects of the over 400 past contributions to the series founded in 1938 by László
Zechmeister.
The first aspect is covered by contributions from pioneers and experts of the
various analytical methods used widely in natural products characterization. Thus,
the field is introduced by “Structure Elucidation of Natural Compounds by X-ray
Crystallography” written by Ulrike Wagner and Christoph Kratky of the University
of Graz (Austria)—interestingly enough, the father of the latter author was an
author in Volume 1 of our book series. This contribution is followed by “Mass
Spectrometry in Natural Product Structure Elucidation” by Herbert Budzikiewicz
of the University of Cologne (Germany), “Nuclear Magnetic Resonance in the
Structural Elucidation of Natural Products” by William F. Reynolds of the
University of Toronto (Canada) and Eugene P. Mazzola of the University of
Maryland (USA), and finally by “Vibrational Circular Dichroism Absolute
Configuration Determination of Natural Products” by Pedro Joseph-Nathan and
the late Bárbara Gordillo-Roman from the Instituto Politécnico Nacional, Mexico
City (Mexico).
The second aspect is covered by the contribution “The Series “Progress in the
Chemistry of Organic Natural Products”: 75 Years of Service in the Development of
Natural Product Chemistry” by Rudolf Werner Soukup and Klara Soukup of the
Vienna University of Technology and St. Anna Kinderspital (Austria), and short
descriptions of each of the past contributions of Volumes 1–99 are provided.
Past hallmarks of this book series have been the broad range of the subject matter
covered and the internationally acclaimed chapter authors who have represented all
six continents. Many thousands of natural products are presently known from
v
vi Foreword
marine and terrestrial organisms, and their number and potential uses grow annually.
In future years, the present Series Editors of “Progress in the Chemistry of Organic
Natural Products” intend to build on the considerable momentum that has already
been established by our illustrious editorial predecessors.
Columbus, OH A.D. Kinghorn
Linz, Austria H. Falk
Sapporo, Japan J. Kobayashi
Contents
Structure Elucidation of Natural Compounds
by X-Ray Crystallography ............................................................................. 1
Ulrike Wagner and Christoph Kratky
Mass Spectrometry in Natural Product Structure Elucidation .................. 77
Herbert Budzikiewicz
Nuclear Magnetic Resonance in the Structural Elucidation
of Natural Products......................................................................................... 223
William F. Reynolds and Eugene P. Mazzola
Vibrational Circular Dichroism Absolute Configuration
Determination of Natural Products ............................................................... 311
Pedro Joseph-Nathan and Bárbara Gordillo-Román
The Series “Progress in the Chemistry of Organic
Natural Products”: 75 Years of Service in the Development
of Natural Product Chemistry ....................................................................... 453
Rudolf Werner Soukup and Klara Soukup
Listed in PubMed
vii
Contributors
Christoph Kratky Institut für molekulare Biowissenschaften, Karl Franzens
Universität Graz, Graz, Austria
[email protected]Ulrike Wagner Institut für molekulare Biowissenschaften, Karl Franzens Universität
Graz, Graz, Austria
[email protected]Herbert Budzikiewicz Institut für Organische Chemie, Universität zu Köln, Köln,
Germany
[email protected]Eugene P. Mazzola University of Maryland-FDA Joint Institute, College Park,
MD, USA
[email protected]William F. Reynolds Department of Chemistry, University of Toronto, Toronto,
ON, Canada
[email protected]Pedro Joseph-Nathan Departamento de Química, Centro de Investigación y de
Estudios Avanzados del Instituto Politécnico Nacional, México, DF, Mexico
[email protected]Bárbara Gordillo-Román Departamento de Química, Centro de Investigación y
de Estudios Avanzados del Instituto Politécnico Nacional, México, DF, Mexico
Klara Soukup St. Anna Children’s Cancer Research Institute, Vienna, Austria
Rudolf Werner Soukup Institute of Chemical Technologies and Analytics, Vienna
University of Technology, Vienna, Austria
[email protected] ix
About the Authors
Christoph Kratky was born in Graz (Austria),
where he attended elementary and high school.
After one year of military service, he studied chem-
istry at ETH (Swiss Federal Institute of Technology)
in Zürich, followed by a Ph.D. thesis at ETH Zürich
under the supervision of Prof. J. D. Dunitz. In
1976, he obtained a Max-Kade Fellowship for a
postdoctoral in the laboratory of Martin Karplus at
the Department of Chemistry, Harvard University.
In 1977 he accepted the position of a University
Assistant at the Institute of Physical Chemistry,
University of Graz. There, he obtained his habilita-
tion in physical chemistry in 1978. Following an
eight-month sabbatical in Ada Yonath’s research
group in Structural Molecular Biology of the Max-Planck Institute in Hamburg, he
became a full professor of physical chemistry at University of Graz in 1995. From
2005 to 2013, Kratky has been the President of the Austrian Science Foundation
FWF, and in 2001 he became a member of the Austrian Academy of Sciences. His
research interests include the structure and function of enzymes with a B12 cofactor
and enzymes for industrial biocatalysis, structural genomics of lipid metabolism, and
the methodology of protein crystallography.
xi
xii About the Authors
Ulrike Wagner was born in Mödling, Austria in
1960. After studying chemistry at the Karl Franzens
University in Graz, Austria, she completed her Ph.D.
thesis in 1997 in the group of Prof. Dr. Christoph
Kratky and in collaboration with Prof.
Dr. Heinz Falk of the University of Linz, Austria, on
structural characterization of pyrrole systems. After
two years postdoctoral study at the Weizmann
Institute of Science in Rehovot, Israel in the group
of Prof. Joel Sussman, working on the structure of
superoxide dismutases, and another 16 months at the
Sandoz Research Institute in Vienna, Austria in the
group of Dr. Manfred Auer, she returned to Graz and
performed her habilitation work on the structure
determination of enzymes. In 1999, she spent five months at the European
Synchrotron Facility (ESRF) in Grenoble, France in the group of Dr. Michael Wulff
working on time-resolved crystallography. Her research interests are focused on the
structure and function of enzymes for biocatalysis, time-resolved crystallography,
and the methodology of protein crystallography.
Herbert Budzikiewicz was born Feb 20, 1933, in
Vienna (Austria). He received his Dr. Phil. degree in
chemistry in 1959 from the University of Vienna. In
1961–1965 he was head of the mass spectrometry
facilities of the Department of Chemistry at Stanford
University (CA, USA). In collaboration with the
research group of Prof. C. Djerassi he investigated the
fragmentation processes mainly of natural products
(alkaloids, steroids, terpenoids) using the results for
structure elucidation. In the years 1965–1969 he spent
at the University of Braunschweig (Germany) where
he received the venia legendi for organic chemistry. In
1970 he became professor ordinarius at the Institute
of Organic Chemistry of the University at Köln
(Germany). He was several times dean of the Faculty of Sciences. Since 1998 he has
been emeritus.
The fields of research of Herbert Budzikiewicz are mass spectrometry and natu-
ral products chemistry where he specialized in bacterial metabolites. He is the
author of over 500 research publications and he authored and coauthored several
books on mass spectrometry. In 2008 he received the Honor Medal of the German
Mass Spectrometry Society.
About the Authors xiii
Eugene P. Mazzola was born on Feb 2, 1942 in
Montclair, New Jersey. He obtained an A.B.
degree in 1964 from Franklin and Marshall
College in Lancaster, PA and a Ph.D. degree in
1971 in Organic Chemistry from the University
of Pittsburgh. From 1970 to 1972, he was a post-
doctoral fellow with Professor Harold Goldwhite
at the California State University, Los Angeles,
applying NMR spectroscopy to dynamic sys-
tems in organophosphorus compounds. He
joined the Bureau of Foods of the U.S. Food and
Drug Administration in Washington, DC in 1972 and took charge of the Bureau’s
NMR Facility in 1974, a position that he currently holds.
His research has focused primarily on the structural elucidation of natural product
food contaminants and food colorant manufacturing impurities. He has taught NMR
short courses at the Iowa State University, the Ohio State University, the University
of Pittsburgh, and the Virginia Polytechnic Institute and State University, at the 1986
U.S./Brazil NMR Workshop, and at the 2007 American Society of Pharmacognosy
Annual Meeting. He has served on the Editorial Advisory Board of Magnetic
Resonance in Chemistry since 1996 and the Organizing Committee of the Small
Molecule NMR Conference since 1999. He is Adjunct Professor of Chemistry at the
University of Maryland and the Virginia Polytechnic Institute and State University
and coauthor of the NMR text, “Nuclear Magnetic Resonance Spectroscopy: An
Introduction to Theory, Applications, and Experimental Methods.”
William F. Reynolds was born Oct 30, 1937 in
Bissett, a small mining town in northern
Manitoba, Canada. In 1959, he obtained a B.Sc.
(Honors Chemistry) degree from the University
of Manitoba. In 1963, he obtained a Ph.D. degree
in Physical Chemistry from the same institution,
specializing in NMR spectroscopy under the
supervision of the late Professor Ted Schaefer.
From 1963 to 1965, he was the Sir William
Ramsey Fellow for Canada at University College
London with Sir Ronald Nyholm, applying NMR
spectroscopy to problems in Inorganic Chemistry.
In 1965, he joined the Department of Chemistry at the University of Toronto, initially
as an Assistant Professor, but subsequently as Associate Professor and later Full
Professor. In 1997, he became a Lifetime Emeritus Professor, remaining active in
research.
xiv About the Authors
His initial research at Toronto mainly focused on investigations of transmission
of electronic effects in aromatic molecules by measurements of substituent-induced
chemical shifts and long-range coupling constants. However, since 1983, his major
interest has been investigations of natural products, particularly using 2D NMR
spectroscopy. Of his over 300 scientific publications, more than 200 have been in
the natural product field, carried out in collaboration with scientists and students
from Mexico, Jamaica, Trinidad, Barbados, and Guyana. He has also taught two
short courses in NMR at American Society of Pharmacognosy meetings and eight
others at various locations in Mexico and the West Indies. From 1993 to 2005 he
was an Editor of Magnetic Resonance in Chemistry with particular responsibility
for organic structure elucidation manuscripts. In 1998, he received the Gerhard
Herzberg Award from the Spectroscopy Society of Canada and, in the same year,
was made the first Canadian member of La Academia Mexicana de Ciancias, the
latter award in recognition of his contributions to Mexican Chemistry.
Pedro Joseph-Nathan was born in Mexico City,
Mexico on Sept 17, 1941. He undertook Chemistry
and Chemical Engineering undergraduate studies
simultaneously, obtaining degrees in 1963 and
1964, respectively, from UNAM in Mexico City
where he continued graduate work to obtain his
Doctor in Chemical Sciences degree in 1966. He
became a faculty member at the Department of
Chemistry, CINVESTAV-IPN in Mexico City in
1966, was promoted to Professor of Chemistry in
1972, and has been Emeritus since 1996. He has
traveled extensively through Latin America, for
meetings, scientific collaboration, and related activ-
ities, where he is corresponding or honorary mem-
ber of scientific societies and academies in Argentina, Bolivia, Chile, Colombia,
Peru, Puerto Rico, and Venezuela. He also holds Honorary Professor titles from the
Universidad Nacional Mayor de San Marcos in Peru and from the Universidad
Nacional de Jujuy in Argentina and has doctorates Honoris causa from the
Universidad Nacional de Tucuman in Argentina, the Universidad Michoacana de
San Nicolas de Hidalgo in Mexico, and the Universidad de Magallanes in Chile.
His preferred amusement is the natural products field of Ibero-American species
including structural elucidation, chemical transformations, and some physical
methods for chemical analysis like nuclear magnetic resonance, single crystal X-ray
diffraction, and more recently vibrational circular dichroism. He has coauthored
over 450 research publications and has received many scientific awards, including
the 1991 National Award of Sciences and Arts from the Government of Mexico.
About the Authors xv
Bárbara Gordillo-Román was born in Mexico
City, Mexico on Dec 4, 1958. She undertook
Chemistry undergraduate studies obtaining her
degree from Universidad Autonoma de Puebla,
Mexico in 1983, and continued graduate work at
CINVESTAV-IPN in Mexico City to obtain a
Master’s degree in 1985 and a Doctor in
Sciences degree in 1988. After postdoctoral
training at the Department of Chemistry,
University of North Carolina in Chapel Hill,
NC, USA from 1988 to 1990, she became a fac-
ulty member at the Department of Chemistry,
CINVESTAV-IPN in Mexico City in 1990 and
was promoted to Professor of Chemistry in 1995
from where she was on sabbatical leave at the Department of Chemistry,
Northwestern University, Evanston, IL, USA in 2001–2002. During her scientific
career she accumulated some 50 research articles until she delivered her final state-
ment to the Creator in the city of Puebla, Mexico on August 7, 2013.
xvi About the Authors
Klara Soukup earned a Bachelor’s degree in
Food and Biotechnology in 2010 and received
her Master’s degree from the University of
Natural Resources and Life Sciences Vienna in
Biotechnology in 2013. She conducted her
Master’s Thesis at St. Anna Children’s Cancer
Research Institute Vienna, where she is currently
working on her Ph.D. thesis in the Tumor
Immunology Department. Her research is
focused on preclinical development of dendritic
cell-based tumor immunotherapies. During her
studies, she spent five months at University
College Cork, Ireland and completed several
internships at pharmaceutical companies.
Rudolf Werner Soukup is Privatdozent of
Chemical History at the Vienna University of
Technology. His current fields of research include
alchemy and early chemistry, especially the
chemical technology of the sixteenth century,
chemical research in the Hapsburg monarchy
since the beginning of the eighteenth century, and
on Robert Bunsen’s library in Althofen
(Carinthia). He studied chemistry at the
Technische Hochschule in Vienna and philoso-
phy at the University of Vienna. During his aca-
demic career, he has published papers on
chemical kinetics, solvent properties, didactics,
and chemical history. R. Werner Soukup is the author or editor of the following
books: Alchemistisches Gold—Paracelsistische Pharmaca (Vienna 1997, together
with Helmut Meyer); Die wissenschaftliche Welt von gestern (Vienna 2004),
Chemie in Österreich (Vienna 2007); and Pioniere der Sexualhormonforschung
(Vienna 2010, together with Christian Noe).
Structure Elucidation of Natural Compounds
by X-Ray Crystallography
Ulrike Wagner and Christoph Kratky
1 Contents
1 Introduction......................................................................................................................... 2
2 History................................................................................................................................. 2
3 Theoretical Background...................................................................................................... 4
3.1 Heuristic Introduction................................................................................................ 4
3.2 Scattering Theory....................................................................................................... 6
3.3 Symmetry in Crystals................................................................................................. 10
3.4 Crystallographic Resolution....................................................................................... 11
3.5 Anomalous Dispersion............................................................................................... 13
3.6 The Patterson Function.............................................................................................. 14
4 Crystal Structure Analysis.................................................................................................. 15
4.1 Crystallization............................................................................................................ 15
4.2 Data Collection.......................................................................................................... 23
4.3 Data Reduction........................................................................................................... 29
4.4 Solving the Structure: The Phase Problem................................................................ 33
4.5 Model Building and Refinement................................................................................ 43
4.6 Structure Validation.................................................................................................... 47
5 Results................................................................................................................................. 48
5.1 Cambridge Structural Database................................................................................. 49
5.2 Crystallographic Open Database................................................................................ 49
5.3 Protein Data Bank...................................................................................................... 49
5.4 Other Databases......................................................................................................... 54
6 Special Techniques.............................................................................................................. 54
6.1 Time-Resolved Crystallography................................................................................ 54
6.2 Neutron Crystallography............................................................................................ 56
6.3 Electron Crystallography........................................................................................... 60
7 Outlook............................................................................................................................... 60
References................................................................................................................................. 62
U. Wagner • Ch. Kratky (*)
Institut für molekulare Biowissenschaften, Karl Franzens Universität Graz,
Humboldtstrasse 50, 8010 Graz, Austria
e-mail:
[email protected];
[email protected]A.D. Kinghorn, H. Falk, J. Kobayashi (eds.), Progress in the Chemistry 1
of Organic Natural Products, Vol. 100, DOI 10.1007/978-3-319-05275-5_1,
© Springer International Publishing Switzerland 2015
