Practical aspects of computational chemistry i an overview of the last two decades and current trends

Practical Aspects of Computational Chemistry I



Jerzy Leszczynski • Manoj K. Shukla
Editors

Practical Aspects
of Computational
Chemistry I
An Overview of the Last Two Decades
and Current Trends

123


Editors
Prof. Jerzy Leszczynski
Department of Chemistry
Jackson State University
P.O. Box 17910
1400 Lynch Street
Jackson, MS 39217
USA


Prof. Manoj K. Shukla
Department of Chemistry
Jackson State University
P.O. Box 17910

1400 Lynch Street
Jackson, MS 39217
USA
Present affiliation:
Environmental Laboratory
US Army Engineer Research
and Development Center
3909 Halls Ferry Road
Vicksburg, MS 39180
USA


ISBN 978-94-007-0918-8
e-ISBN 978-94-007-0919-5
DOI 10.1007/978-94-007-0919-5
Springer Dordrecht Heidelberg London New York
Library of Congress Control Number: 2011940796
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Preface

It is a rare event that the impressive group of leading experts is willing to share their
views and reflections on development of their research areas in the last few decades.

The editors of this book have been very fortunate to attract such contributions, and as
an effect two volumes of “Practical Aspects of Computational Chemistry: Overview
of the Last Two Decades and Current Trends” are being published. Astonishingly,
we found that this task was not so difficult since the pool of authors was derived from
a large gathering of speakers who during the last 20 years have participated in the
series of meetings “Conferences on Current Trends in Computational Chemistry”
(CCTCC) organized by us in Jackson, Mississippi. We asked this group to prepare
for the 20th CCTCC that was hold in October 2011 the reviews of the last 20 years
of the progress in their research disciplines. Their response to our request was
overwhelming. This initiative was conveyed to Springer who in collaboration with
the European Academy of Sciences (EAS) invited as to edit such a book.
The current volume presents the compilation of splendid contributions distributed over 21 chapters. The very first chapter contributed by Istvan Hargittai
presents the historical account of development of structural chemistry. It also
depicts some historical memories of scientists presented in the form of their
pictures. This historical description covers a vast period of time. Intruder states pose
serious problem in the multireference formulation based on Rayleigh-Schrodinger
expansion. Ivan Hubac and Stephen Wilson discuss the current development and
future prospects of Many-Body Brillouin-Wigner theories to avoid the problem of
intruder states in the next chapter. The third chapter written by Vladimir Ivanov
and collaborators reveals the development of multireference state-specific coupled
cluster theory. The next chapter from Maria Barysz discusses the development
and application of relativistic effects in chemical problems while the fifth chapter
contributed by Manthos Papadopoulos and coworkers describes electronic, vibrational and relativistic contributions to the linear and nonlinear optical properties of
molecules.
James Chelikowsky and collaborators discuss use of Chebyshen-filtered subspace iteration and windowing methods to solve the Kohn-Sham problem in the
sixth chapter. Next chapter contributed by Karlheinz Schwarz and Peter Blaha
v


vi

Preface

provides a detailed account of applications of WIEN2K program to determination
of electronic structure of solids and surfaces. The recent development of model core
potentials during the first decade of the current century is discussed by Tao Zeng
and Mariusz Klobukowski in the Chap. 8. Next two chapters discuss Monte Carlo
method. Chapter 9 written by William Lester and coworkers describes practicality
of Monte Carlo method to study electronic structure of molecules and Chap. 10
describes the relativistic quantum Monte Carlo method and is written by Takahito
Nakajima and Yutaka Nakatsuka.
There are two chapters presenting discussion on the various important aspects
of nanoscience. Chapter 11 is written by Kwang Kim and coworkers and presents
description of computer aided nanomaterial design techniques applying to nanooptics, molecular electronics, spintronics and DNA sequencing. Jorge Seminario and
coworkers describe application of computational methods to design nanodevices
and other nanosystems in the Chap. 12. The problem of DNA photodimerization has
always been very attractive to research communities. Martin McCullagh and George
Schatz discuss the application of ground state dynamics to model the thyminethymine photodimerization reaction in the Chap. 13. In the next chapter A. Luzanov
and O. Zhikol review the excited state structural analysis using the time dependent
Density Functional Theory approach.
The next four chapters deal with molecular interactions. In the Chap. 15 Joanna
Sadlej and coworkers reveal the application of VCD chirality transfer to study
the intermolecular interactions. Peter Politzer and Jane Murray review different
aspects of non-hydrogen bonding intramolecular interactions in the Chap. 16.
The next chapter by Slawomir Grabowski describes characterization of X-H : : :  
and X-H : : : ¢ interactions. Chapter 18 deals with role of cation- ,  –  and
hydrogen bonding interaction towards modeling of finite molecular assemblies and
is written by A.S. Mahadevi and G.N. Sastry. In the Chap. 19, Oleg Shishkin
and Svitlana Shishkina discuss the conformational analysis of cyclohexene, its
derivatives and heterocyclic analogues. The stabilization of bivalent metal cations

in zeolite catalysts is reviewed by G. Zhidomirov in the Chap. 20. The last chapter
of the current volume written by Andrea Michalkova and Jerzy Leszczynski deals
with the interaction of nucleic acid bases with minerals that could shed a light on
the understanding of origin of life.
With great pleasure, we take this opportunity to thank all authors for devoting
their time and hard work enabling us to complete the current volume “Practical
Aspects of Computational Chemistry I: Overview of the Last Two Decades and
Current Trends”. We are grateful to excellent support from the President of the EAS
as well as Editors at the Springer. Many thanks go to our families and friends without
whom the realization of the book would be not possible.
Jackson, Mississippi, USA

Jerzy Leszczynski
Manoj K. Shukla


Contents

1

2

3

Models—Experiment—Computation: A History of Ideas
in Structural Chemistry.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . .
Istvan Hargittai

1

Many-Body Brillouin-Wigner Theories: Development
and Prospects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . .
Ivan Hubaˇc and Stephen Wilson

33

Multireference State–Specific Coupled Cluster Theory
with a Complete Active Space Reference . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . .
Vladimir V. Ivanov, Dmitry I. Lyakh, Tatyana A. Klimenko,
and Ludwik Adamowicz

69

4

Relativistic Effects in Chemistry and a Two-Component Theory .. . . . 103
Maria Barysz

5

On the Electronic, Vibrational and Relativistic
Contributions to the Linear and Nonlinear Optical
Properties of Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 129
Aggelos Avramopoulos, Heribert Reis,
and Manthos G. Papadopoulos

6

Using Chebyshev-Filtered Subspace Iteration and
Windowing Methods to Solve the Kohn-Sham Problem . . . . . . . . . . . . . . . 167

Grady Schofield, James R. Chelikowsky, and Yousef Saad

7

Electronic Structure of Solids and Surfaces with WIEN2k . . . . . . . . . . . . 191
Karlheinz Schwarz and Peter Blaha

8

Model Core Potentials in the First Decade of the XXI Century .. . . . . . 209
Tao Zeng and Mariusz Klobukowski

vii


viii

9

Contents

Practical Aspects of Quantum Monte Carlo
for the Electronic Structure of Molecules . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 255
Dmitry Yu. Zubarev, Brian M. Austin,
and William A. Lester Jr.

10 Relativistic Quantum Monte Carlo Method . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 293
Takahito Nakajima and Yutaka Nakatsuka
11 Computer Aided Nanomaterials Design – Self-assembly,
Nanooptics, Molecular Electronics/Spintronics,

and Fast DNA Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 319
Yeonchoo Cho, Seung Kyu Min, Ju Young Lee,
Woo Youn Kim, and Kwang S. Kim
12 Computational Molecular Engineering for Nanodevices
and Nanosystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 347
Norma L. Rangel, Paola A. Leon-Plata,
and Jorge M. Seminario
13 Theoretical Studies of Thymine–Thymine
Photodimerization: Using Ground State Dynamics
to Model Photoreaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 385
Martin McCullagh and George C. Schatz
14 Excited State Structural Analysis: TDDFT and Related Models . . . . . 415
A.V. Luzanov and O.A. Zhikol
15 VCD Chirality Transfer: A New Insight
into the Intermolecular Interactions . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 451
Jan Cz. Dobrowolski, Joanna E. Rode, and Joanna Sadlej
16 Non-hydrogen-Bonding Intramolecular Interactions:
Important but Often Overlooked . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 479
Peter Politzer and Jane S. Murray
17 X –H   and X –H ¢ Interactions – Hydrogen Bonds
with Multicenter Proton Acceptors . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 497
Sławomir J. Grabowski
18 Computational Approaches Towards Modeling Finite
Molecular Assemblies: Role of Cation- ,   – 
and Hydrogen Bonding Interactions . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 517
A. Subha Mahadevi and G. Narahari Sastry
19 Unusual Properties of Usual Molecules. Conformational
Analysis of Cyclohexene, Its Derivatives and Heterocyclic
Analogues .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 557
Oleg V. Shishkin and Svitlana V. Shishkina

Contents

ix

20 Molecular Models of the Stabilization of Bivalent Metal
Cations in Zeolite Catalysts . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 579
G.M. Zhidomirov, A.A. Shubin, A.V. Larin, S.E. Malykhin,
and A.A. Rybakov
21 Towards Involvement of Interactions of Nucleic Acid
Bases with Minerals in the Origin of Life: Quantum
Chemical Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 645
Andrea Michalkova and Jerzy Leszczynski
Index . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 673



Contributors

Ludwik Adamowicz University of Arizona, Tucson, AZ, USA,

Brian M. Austin Kenneth S. Pitzer Center for Theoretical Chemistry, Department
of Chemistry, University of California, Berkeley, CA 94720-1460, USA
National Energy Research Scientific Computing, Lawrence Berkeley National
Laboratory, Berkeley, CA 94720, USA,
Aggelos Avramopoulos Institute of Organic and Pharmaceutical Chemistry,
National Hellenic Research Foundation, 48 Vas. Constantinou Ave, Athens 116 35,
Greece,
Maria Barysz Institute of Chemistry, N. Copernicus University, Gagarina 7, Toru´n

87 100, Poland,
Peter Blaha Institute of Materials Chemistry, Vienna University of Technology,
Getreidemarkt 9/165-TC, A-1060 Vienna, Austria,
James R. Chelikowsky Institute for Computational Engineering and Sciences,
University of Texas, Austin, TX, 78712, USA
Departments of Physics and Chemical Engineering, University of Texas, Austin, TX
78712, USA,
Yeonchoo Cho Center for Superfunctional Materials, Department of Chemistry
and Department of Physics, Pohang University of Science and Technology, Hyojadong, Namgu, Pohang 790-784, South Korea
Jan Cz. Dobrowolski National Medicines Institute, 30/34 Chełmska Street,
00-725 Warsaw, Poland
Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland

xi


xii

Contributors

Sławomir J. Grabowski Kimika Fakultatea, Euskal Herriko Unibertsitatea and
Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi,
Spain
Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain,

Istvan Hargittai Materials Structure and Modeling of the Hungarian Academy of
Sciences at Budapest, University of Technology and Economics, POBox 91, 1521
Budapest, Hungary,
Ivan Hubaˇc Department of Nuclear Physics and Biophysics, Division of Chemical
Physics, Faculty of Mathematics, Physics and Informatics, Comenius University,

Bratislava, 84248, Slovakia
Institute of Physics, Silesian University, P.O. Box 74601, Opava, Czech Republic,

Vladimir V. Ivanov V. N. Karazin Kharkiv National University, Kharkiv, Ukraine,

Kwang S. Kim Center for Superfunctional Materials, Department of Chemistry
and Department of Physics, Pohang University of Science and Technology, Hyojadong, Namgu, Pohang 790-784, South Korea,
Woo Youn Kim Department of Chemistry, KAIST, Daejeon 305-701, South Korea
Tatyana A. Klimenko V. N. Karazin Kharkiv National University, Kharkiv,
Ukraine,
Mariusz Klobukowski Department of Chemistry, University of Alberta, Edmonton, AL, Canada T6G 2G2,
A.V. Larin Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1-3, Moscow GSP-2, 119992, Russia,
Ju Young Lee Center for Superfunctional Materials, Department of Chemistry and
Department of Physics, Pohang University of Science and Technology, Hyojadong,
Namgu, Pohang 790-784, Korea
Paola A. Leon-Plata Department of Chemical Engineering, Texas A&M University, College Station, TX, USA,
William A. Lester Jr. Chemical Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, CA 94720, USA
Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry,
University of California, Berkeley, CA 94720-1460, USA,
Jerzy Leszczynski Interdisciplinary Nanotoxicity Center, Jackson State University, Jackson, MS 39217, USA,


Contributors

xiii

A.V. Luzanov STC “Institute for Single Crystals” of National Academy of Sciences of Ukraine, 60 Lenin ave, Kharkiv 61001, Ukraine,

Dmitry I. Lyakh V. N. Karazin Kharkiv National University, Kharkiv, Ukraine,

A. Subha Mahadevi Molecular Modeling Group, Indian Institute of Chemical
Technology, Tarnaka, Hyderabad, 500607, India
S.E. Malykhin Boreskov Institute of Catalysis, Siberian Branch of the Russian
Academy of Sciences, Pr. Akad. Lavrentieva 5, Novosibirsk 630090, Russia,

Martin McCullagh Department of Chemistry, Northwestern University, Evanston,
IL 60208-3113, United States
Andrea Michalkova Interdisciplinary Nanotoxicity Center, Jackson State University, Jackson, MS, 39217, USA
Seung Kyu Min Center for Superfunctional Materials, Department of Chemistry
and Department of Physics, Pohang University of Science and Technology, Hyojadong, Namgu, Pohang 790-784, South Korea
Jane S. Murray CleveTheoComp, 1951 W. 26th Street, Cleveland, OH 44113,
USA
Takahito Nakajima Computational Molecular Science Research Team, Advanced
Institute for Computational Science, RIKEN, 7-1-26, Minatojima-minami, Cyuo,
Kobe, Hyogo 650-0047, Japan,
Yutaka Nakatsuka Computational Molecular Science Research Team, Advanced
Institute for Computational Science, RIKEN, 7-1-26, Minatojima-minami, Cyuo,
Kobe, Hyogo 650-0047, Japan,
Manthos G. Papadopoulos Institute of Organic and Pharmaceutical Chemistry,
National Hellenic Research Foundation, 48 Vas. Constantinou Ave, Athens 116 35,
Greece,
Peter Politzer CleveTheoComp, 1951 W. 26th Street, Cleveland, OH 44113, USA,

Norma L. Rangel Department of Chemical Engineering, Texas A&M University,
College Station, TX, USA
Materials Science and Engineering, Texas A&M University, College Station, TX,
USA,
Heribert Reis Institute of Organic and Pharmaceutical Chemistry, National
Hellenic Research Foundation, 48 Vas. Constantinou Ave, Athens 116 35, Greece,

xiv

Contributors

Joanna E. Rode Industrial Chemistry Research Institute, 8 Rydygiera Street,
01-793 Warsaw, Poland
A.A. Rybakov Chemistry Department, Lomonosov Moscow State University,
Leninskiye Gory 1-3, Moscow GSP-2, 119992, Russia,
Yousef Saad Department of Computer Science and Engineering, University of
Minnesota, Minneapolis, MN, 55455, USA,
Joanna Sadlej National Medicines Institute, 30/34 Chełmska Street, 00-725
Warsaw, Poland
Faculty of Chemistry, University of Warsaw, 1 Pasteura Street, 02-093 Warsaw,
Poland,
G. Narahari Sastry Molecular Modeling Group, Indian Institute of Chemical
Technology, Tarnaka, Hyderabad, 500607, India,
George C. Schatz Department of Chemistry, Northwestern University, Evanston,
IL, 60208-3113, United States,
Grady Schofield Institute for Computational Engineering and Sciences, University
of Texas, Austin, TX, 78712, USA,
Karlheinz Schwarz Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria,

Jorge M. Seminario Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
Materials Science and Engineering, Texas A&M University, College Station, TX,
USA
Department of Electrical and Computer Engineering, Texas A&M University,
College Station, TX, USA,

Oleg V. Shishkin Division of Functional Materials Chemistry, SSI “Institute for
Single Crystals”, National Academy of Science of Ukraine, 60 Lenina ave, Kharkiv
61001, Ukraine,
Svitlana V. Shishkina Division of Functional Materials Chemistry, SSI “Institute
for Single Crystals”, National Academy of Science of Ukraine, 60 Lenina ave,
Kharkiv 61001, Ukraine
A.A. Shubin Boreskov Institute of Catalysis, Siberian Branch of the Russian
Academy of Sciences, Pr. Akad. Lavrentieva 5, Novosibirsk 630090, Russia,

Stephen Wilson Theoretical Chemistry Group, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK


Contributors

xv

Division of Chemical Physics, Faculty of Mathematics, Physics and Informatics
Comenius University, Bratislava 84248, Slovakia,
Tao Zeng Department of Chemistry, University of Alberta, Edmonton, AL, Canada
T6G 2G2
G.M. Zhidomirov Boreskov Institute of Catalysis, Siberian Branch of the Russian
Academy of Sciences, Pr. Akad. Lavrentieva 5, Novosibirsk 630090, Russia
Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory
1-3, Moscow GSP-2, 119992, Russia,
O.A. Zhikol STC “Institute for Single Crystals” of National Academy of Sciences
of Ukraine, 60 Lenin ave, Kharkiv 61001, Ukraine,
Dmitry Yu. Zubarev Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA,

Chapter 1

Models—Experiment—Computation: A History
of Ideas in Structural Chemistry
Istvan Hargittai

Abstract Ideas about chemical structures have developed over hundreds of years,
but the pace has greatly accelerated during the twentieth century. The mechanical
interactions among building blocks of structures were taken into account in the
computational models by Frank Westheimer and by Terrel Hill, and Lou Allinger’s
programs made them especially popular. G. N. Lewis provided models of bonding
in molecules that served as starting points for later models, among them for
Ron Gillespie’s immensely popular VSEPR model. Accounting for non-bonded
interactions has conveniently augmented the considerations for bond configurations.
The emergence of X-ray crystallography almost 100 years ago, followed by
other diffraction techniques and a plethora of spectroscopic techniques provided
tremendous headway for experimental information of ever increasing precision.
The next step was attaining comparable accuracy that helped the meaningful
comparison and ultimately the combination of structural information from the most
diverse experimental and computational sources. Linus Pauling’s valence bond
theory and Friedrich Hund’s and Robert Mulliken’s molecular orbital approach had
their preeminence at different times, the latter finally prevailing due to its better
suitability for computation. Not only did John Pople build a whole systematics of
computations; he understood that if computation was to become a tool on a par
with experiment, error estimation had to be handled in a compatible way. Today,
qualitative models, experiments, and computations all have their own niches in the
realm of structure research, all contributing to our goal of uncovering “coherence
and regularities”—in the words of Michael Polanyi and Eugene Wigner—for our
understanding and utilization of the molecular world.

I. Hargittai ( )
Materials Structure and Modeling of the Hungarian Academy of Sciences at Budapest,
University of Technology and Economics, POBox 91, 1521 Budapest, Hungary
e-mail:
J. Leszczynski and M.K. Shukla (eds.), Practical Aspects of Computational Chemistry I:
An Overview of the Last Two Decades and Current Trends,
DOI 10.1007/978-94-007-0919-5 1, © Springer ScienceCBusiness Media B.V. 2012

1


2

I. Hargittai

Keywords Structural chemistry • Molecular mechanics • Gilbert N. Lewis •
Non-bonded interactions • Molecular structure • Molecular biology • Theory
of resonance • Alpha-helix • Geometrical parameters • John Pople • Eugene
P. Wigner

1.1 Introduction
Philosophically, Democritos’s maxim that “Nothing exists except atoms and empty
space; everything else is opinion” has been around for millennia [1]. Modern
atomistic approach dates only back a few hundred years. Johannes Kepler is credited
with being the first to build a model in which he packed equal spheres representing
in modern terms water molecules. He published his treatise in Latin in 1611,
De nive sexangula (The Six-cornered Snowflake) [2]. He tried to figure out why
the snowflakes have hexagonal shapes and in this connection discussed the structure
of the honeycomb. His drawings of closely packed spheres were forward-pointing

(Fig. 1.1a). It preceded another model of close packing of spheres which Dalton
produced almost two hundred years later, in 1805 with which he illustrated his
studies of the absorption of gases (Fig. 1.1b) [3].
There may be different considerations of what the beginning of modern
chemistry was. To me, it was the recognition that the building blocks—atoms—of
the same or different elements link up for different substances. Somehow—and
for a long time it was not clear how—in such a linkage the atoms must undergo

Fig. 1.1 (a) Packing of water “molecules” according to Johannes Kepler in 1611 (Ref. [2]);
(b) Packing of gaseous “molecules” in absorption according to John Dalton’s packing in 1805
(Ref. [3])


1 Models—Experiment—Computation: A History of Ideas in Structural Chemistry

3

some change which could only be consistent with throwing out the dogma of the
indivisibility of the atom. By advancing this concept chemistry anticipated—even if
only tacitly—the three major discoveries at the end of the nineteenth century. They
included the discoveries of radioactivity, the electron, and X-rays. This is also why
it is proper to say that the science of the twentieth century had begun at the end of
the previous century. These experimental discoveries created also the possibilities
of testing the various models that have been advanced to describe the structure of
matter.
Kepler used modeling not only in his studies of snowflakes but in his investigation of celestial conditions. Curiously though, his three-dimensional planetary
model appears to be closer to modern models in structural chemistry than to
astronomy. Albert Einstein referred to the significance of modeling in scientific
research on the occasion of the 300th anniversary of Kepler’s death in 1930 in
his article published in Frankfurter Zeitung: “It seems that the human mind has

first to construct forms independently before we can find them in things. Kepler’s
marvelous achievement is a particularly fine example of the truth that knowledge
cannot spring from experience alone but only from the comparison of the inventions
of the intellect with observed facts” [4]. In much of the success of structural
chemistry models have played a ubiquitous role.

1.2 Frank Westheimer and the Origin of Molecular Mechanics
At one point in the history of structural chemistry molecular mechanics calculations
dominated the computational work for relatively large molecules. The origins of
these calculations were intimately connected to another modeling approach that one
of its initiators vividly described. Frank Westheimer (Fig. 1.2a) had participated in
the American defense efforts during WWII and when the war had ended, he returned
to the University of Chicago to resume his teaching and research. He had to start
anew and had time to think about basic problems. This is how half a century later
he remembered the birth of molecular mechanics [5]:
I thought through the idea of calculating the energy of steric effects from first principles
and classical physics, relying on known values of force constants for bond stretching and
bending, and known values of van der Waals constants for interatomic repulsion. I applied
this idea to the calculation of the energy of activation for the racemization of optically
active biphenyls. Minimizing the energy of a model for the transition state leads to a set of
n equations in n unknowns, one for each stretch or bend of a bond in the molecule. It seemed
to me that, to solve these equations, one needed to solve a huge n n determinant.
Fortunately for me, Joe Mayer came to the University of Chicago at the end of WWII.
Joe was an outstanding physical chemist; he and his wife Maria [Goeppert Mayer] wrote the
outstanding text in statistical mechanics. During the war, he had been working at Aberdeen,
Maryland, using the world’s first digital computer to calculate artillery trajectories. Perhaps
Joe could have access to that computer, and could show me how to solve my determinant
on it. So I went to him and asked him to help me. He didn’t know about optically active
biphenyls, so I made some molecular models and explained the stereochemistry to him, and

4

I. Hargittai

Fig. 1.2 (a) Frank Westheimer in the laboratory (Photograph by MINOT, courtesy of the late
Frank Westheimer); (b) Norman (Lou) Allinger (Photograph and © by I. Hargittai)

showed him my mathematical development, up to the determinant. Then, in something like
half an hour, he found a mathematical trick that we used to solve my equations without
needing the determinant. That’s how the solution of real problems in molecular mechanics
got started. It has become big business since. Furthermore, it turns out that my instinct for
computerizing was correct, since that is the way in which the field has since been developed.
The history of molecular mechanics must include—in fact perhaps begins with—a
publication by Terrell Hill that presented the same general method I had invented for
expressing the energy of molecules in terms of bond stretching, bond bending, and van der
Waals interactions, and then minimizing that energy. Hill published the method, but with no
application, no “reduction to practice” [6]. I hadn’t known that we had a competitor, or that
one could publish a bare research idea. After Hill published, I immediately wrote up the
work that Mayer and I had already done, theory and successful application to determining
the activation energy for the racemization of an optically active biphenyl, and submitted it
for publication [7].

Eventually, Norman (“Lou”) Allinger’s (Fig. 1.2b) programs made molecular
mechanics accessible for many chemists and he kept expanding the scope of these
calculations toward further classes of compounds [8].


1 Models—Experiment—Computation: A History of Ideas in Structural Chemistry

5

1.3 Gilbert N. Lewis’s Models of Atoms and Bonding
As for modeling and advancement in the description of chemical bonding prior to
quantum chemistry, the importance of Gilbert N. Lewis’s (Fig. 1.3a) contributions
could hardly be overestimated. They were trend-setters in the first half of twentieth
century chemistry and his missing Nobel Prize has been rightly lamented about a
great deal.
The quantum chemical description of the covalent bond was given by Walter
Heitler and Fritz W. London, but their rigorous treatment severely limited their
approach to be utilized directly in chemistry. Heitler himself appreciated Lewis’s
forward-pointing contribution when he referred to it in his 1945 book Wave
Mechanics: “Long before wave mechanics was known Lewis put forward a semiempirical theory according to which the covalent bond between atoms was effected
by the formation of pairs of electrons shared by each pair of atoms. We see now that
wave mechanics affords a full justification of this picture, and, moreover, gives a
precise meaning to these electron pairs: they are pairs of electrons with antiparallel
spins” [9]. Figure 1.3b illustrates Lewis’s cubical atoms and some molecules built
from such atoms with his original sketches at the bottom [10].
Another testimony for the advanced nature of Lewis’s theory was given by
Robert S. Mulliken in his Nobel lecture. He described the relation of Lewis’s theory
to molecular orbital (MO) theory using chemical orbitals. Mulliken emphasized
that “Lewis resolved the long-standing conflict between, on the one hand, ionic
and charge-transfer theories of chemical bonding and, on the other hand, the kind
of bonding which is in evidence in bonds between equal atoms : : : ” [11]. Further,
in the same lecture, Mulliken writes, “for individual atoms, Lewis’ electron shells
were three-dimensional, in contrast to Bohr’s planar electron orbits, in this respect
being closer to the present quantum mechanics than the Bohr theory.” Nonetheless,
of course, Lewis’s theory was “empirical, schematic, and purely qualitative,” as
Mulliken pointed this out as well. Mulliken appreciated Lewis’s contribution so
much that he mentioned as a merit of the MO theory that it best approximates

Lewis’s theory. He writes, “ : : : These localized MO’s I like to call chemical MO’s
(or just chemical orbitals because of the fact that some of the orbitals used are now
really AO’s [atomic orbitals]). In simple molecules, electrons in chemical MO’s
usually represent the closest possible quantum-mechanical counterpart to Lewis’
beautiful pre-quantum valence theory : : : ”

1.4 VSEPRing an Efficient Model
The name of the model, VSEPR stands for Valence Shell Electron Pair Repulsion
and usually pronounced as “vesper,” almost like “whisper,” and I have used it
as a verb [12] to imply that its principal creator, Ron Gillespie often appeared


6

I. Hargittai

Fig. 1.3 (a) Young Gilbert N. Lewis (Courtesy of the Lawrence Berkeley National Laboratory);
(b) G. N. Lewis’s cubical atoms and some molecules built from such atoms, first proposed in 1916;
his original sketches are at the lower part of the Figure (Ref. [10])


1 Models—Experiment—Computation: A History of Ideas in Structural Chemistry

7

embarrassed by its great success on the background of its rudimentary nature,
and would have liked to lend it “respectability” by linking it directly to quantum
mechanical considerations.
The origin of the model goes back to N. V. Sidgwick and H. M. Powell who
correlated the number of electron pairs in the valence shell of the central atom and

its bond configuration in a molecule [13]. Then Ronald J. Gillespie and Ronald S.
Nyholm introduced allowances for the differences between the effects of bonding
pairs and lone pairs, and applied the model to large classes of inorganic compounds
[14]. With coining the VSEPR name the model was ready in its initial formulation.
It has since gone through improvements mainly by introducing additional sub-rules
and defining its scope of validity. A plethora of examples of VSEPR geometries and
geometrical variations through the compounds of main group elements have been
presented [15].
The attempts to provide a quantum-mechanical foundation for the VSEPR model
have occurred in two directions. One has been to understand better the reason why
the model works so well in large classes of compounds, and its basic tenets have
been interpreted by the Pauli exclusion principle. Another direction has been to
encourage comparisons between sophisticated computations and the application of
the model. It could have been expected that calculations of the total electron density
distribution should mimic the relative space requirements of the various electron
pairs. This was though not too successful—apparently due to the core electron
densities suppressing the minute variations in the valence shell. Closer scrutiny,
however, revealed that the spatial distributions of the various electron pairs—
modeled by electron densities assigned to molecular orbitals—indeed showed
distinguishing features in accordance with the expectations of the VSEPR model.
A set of examples are shown in Fig. 1.4 [16]. Here, close to the sulfur core, the lone
pair of electrons has the largest space requirement; next to it is that of the SO double
bond; the SH bonding pair follows; and the smallest space requirement in this series
characterizes that of the bonding pair linking the very electronegative fluorine to
sulfur.
There have been other approaches to enhance the relative contributions of the
valence shell electron density distributions. Thus, visualizing the second derivative
of the electron density distribution led to success and the emerging patterns
paralleled some important features predicted by the VSEPR model [17].
Some structures, however, have resisted persistently an unambiguous classification of their geometries. The XeF6 structure was originally considered a success

story for the VSEPR model when—contrary to the then available experimental
evidence—Gillespie predicted a distorted octahedral arrangement of the six fluorines about the central xenon atom. Recent computational work, however, has
suggested that the disturbing lone pair is so much beneath the xenon valence shell
that it is hardly expected to distort the regular octahedral arrangement of the ligands.
Thus the best that could be said about this molecular shape is that we still don’t know
it but today we don’t know it on a much more sophisticated basis than before [18].


8

I. Hargittai

Fig. 1.4 Localized molecular orbitals represented by contour lines denoting electron densities of
0.02, 0.04, 0.06, etc. electron/bohr3 from theoretical calculations for the S–H, S–F, and SDO bonds
and the lone pair on sulfur; the pluses indicate the positions of the atomic nuclei (After Ref. [16])

1.5 Non-bonded Interactions
A model usually singles out one or a few effects that it takes into consideration and
ignores the rest. Hence a reliable application of any model requires the delineation
of its applicability. Since the VSEPR model considers the interactions of the electron
pairs—even better to say, electron domains as the bonds may correspond to multiple
bonds—ligand–ligand interactions are ignored. Accordingly, the applicability of the
VSEPR model is enhanced with increasing central atom size with respect to ligand
sizes. Conversely, increasing ligand sizes with respect to the size of the central atom
diminishes the applicability of the VSEPR model.
In some molecular geometries of fairly large series of compounds, the distances
between atoms separated by another atom between them remain remarkably
constant, which points to the importance of non-bonded interactions. Thus, for
example, the O : : : O nonbonded distances in XSO2 Y sulfones have been found to
˚ while the lengths of the SDO bonds vary up to 0.05 A

˚
hardly deviate from 2.48 A
and the bond angles ODSDO up to 5ı , depending on the nature of the ligands X
and Y. This is depicted in Fig. 1.5 [19].
These geometrical variations and constancies could be visualized as if the two
oxygen ligands were firmly attached to two of the four vertices of the tetrahedron