Reviews in Computational Chemistry

xii Preface

topics like quantum mechanics to narrow ones like graph theory. The categories should aid finding books in specific areas. But it is worth remembering that all the books tabulated in the appendix, whether on molecular modeling, chemometrics, simulations, and so on, represent facets of computational chemistry. As defined in the first volume of our series,* computational chemistry consists of those aspects of chemical research that are expedited or rendered practical by computers. Analysis of the number of computational chemistry books published each year revealed an interesting phenomenon. The numbers have been increasing and occurring in waves four to five years apart.

As always, we try to be heedful of the needs of our readers and authors. Every effort is made to produce volumes that will have sustained usefulness in learning, teaching, and research. We appreciate the fact that the community of computational chemists has found that these volumes fulfill a need. In the most recent data on impact factors from the Institute of Scientific Information (Philadelphia, Pennsylvania), Reviews in Computational Chemistry is ranked fourth among serials (journals and books) in the field of computational chemistry. (In first place is the Journal of Molecular Graphics and Modelling, followed by the Journal of Computational Chemistry and Theoretical Chemistry Accounts. In fifth and sixth places are the Journal of Computer-Aided Molecular Design and the Journal of Chemical Information and Computer Science, respectively.)

We invite our readers to visit the Reviews in Computational Chemistry website at http://chem.iupui.edu/rcc/rcc.html. It includes the author and subject indexes, color graphics, errata, and other materials supplementing the chapters.

We thank the authors in this volume for their excellent chapters. Mrs. Joanne Hequembourg Boyd provided valued editorial assistance.

Kenny B. Lipkowitz and Donald B. Boyd

Indianapolis

February 2001

*K. B. Lipkowitz and D. B. Boyd, Eds., Reviews in Computational Chemistry, VCH Publishers, New York, 1990, Vol. 1, pp. vii–xii. Preface.

Contents

1. Small Molecule Docking and Scoring	1
Ingo Muegge and Matthias Rarey
Introduction	1
Algorithms for Molecular Docking	4
The Docking Problem	5
Placing Fragments and Rigid Molecules	6
Flexible Ligand Docking	10
Handling Protein Flexibility	20
Docking of Combinatorial Libraries	21
Scoring	23
Shape and Chemical Complementary Scores	25
Force Field Scoring	26
Empirical Scoring Functions	28
Knowledge-Based Scoring Functions	30
Comparing Scoring Functions in Docking
Experiments: Consensus Scoring	33
From Molecular Docking to Virtual Screening	35
Protein Data Preparation	36
Ligand Database Preparation	36
Docking Calculation	36
Postprocessing	37
Applications	37
Docking as a Virtual Screening Tool	37
Docking as a Ligand Design Tool	40
Concluding Remarks	44
Acknowledgments	46
References	46
2. Protein–Protein Docking	61
Lutz P. Ehrlich and Rebecca C. Wade
Introduction	61
Why This Topic?	62
Protein–Protein Binding Data	62

xiii

xiv	Contents
	Challenges for Computational Docking Studies	67
	Computational Approaches to the Docking Problem	69
	Docking ¼ Sampling þ Scoring	70
	Rigid-Body Docking	73
	Flexible Docking	79
	Example	82
	Estimating the Extent of Conformational Change
	upon Binding	83
	Rigid-Body Docking	83
	Flexible Docking with Side-Chain Flexibility	86
	Flexible Docking with Full Flexibility	88
	Future Directions	90
	Conclusions	91
	References	92
3. Spin–Orbit Coupling in Molecules		99
	Christel M. Marian
	What It Is All About	99
	The Fourth Electronic Degree of Freedom	101
	The Stern–Gerlach Experiment	101
	Zeeman Spectroscopy	103
	Spin Is a Quantum Effect	108
	Angular Momenta	109
	Orbital Angular Momentum	109
	General Angular Momenta	114
	Spin Angular Momentum	121
	Spin–Orbit Hamiltonians	124
	Full Oneand Two-Electron Spin–Orbit
	Operators	125
	Valence-Only Spin–Orbit Hamiltonians	127
	Effective One-Electron Spin–Orbit Hamiltonians	132
	Symmetry	136
	Transformation Properties of the Wave Function	137
	Transformation Properties of the Hamiltonian	143
	Matrix Elements	148
	Examples	154
	Summary	158
	Computational Aspects	159
	General Considerations	159
	Evaluation of Spin–Orbit Integrals	161
	Perturbational Approaches to Spin–Orbit Coupling	163
	Variational Procedures	166
	Comparison of Fine-Structure Splittings with Experiment	170

Contents	xv
First-Order Spin–Orbit Splitting	171
Second-Order Spin–Orbit Splitting	175
Spin-Forbidden Transitions	177
Radiative Transitions	179
Nonradiative Transitions	187
Summary and Outlook	193
Acknowledgments	195
References	195
4. Cellular Automata Models of Aqueous Solution Systems	205
Lemont B. Kier, Chao-Kun Cheng, and Paul G. Seybold
Introduction	205
Cellular Automata	208
Historical Background	208
The General Structure	209
Cell Movement	212
Movement (Transition) Rules	215
Collection of Data	219
Aqueous Solution Systems	221
Water as a System	221
The Molecular Model	221
Significance of the Rules	223
Studies of Water and Solution Phenomena	224
A Cellular Automata Model of Water	224
The Hydrophobic Effect	224
Solute Dissolution	226
Aqueous Diffusion	228
Immiscible Liquids and Partitioning	229
Micelle Formation	231
Membrane Permeability	232
Acid Dissociation	234
Percolation	235
Solution Kinetic Models	237
First-Order Kinetics	237
Kinetic and Thermodynamic Reaction Control	240
Excited-State Kinetics	240
Second-Order Kinetics	242
Enzyme Reactions	245
An Anticipatory Model	246
Chromatographic Separation	247
Conclusions	248
Appendix	249
References	250

xvi	Contents
Appendix. Books Published on the Topics of
	Computational Chemistry	255
	Kenny B. Lipkowitz and Donald B. Boyd
	Introduction	255
	Computers in Chemistry	261
	Chemical Information	271
	Computational Chemistry	280
	Artificial Intelligence and Chemometrics	287
	Crystallography, Spectroscopy, and Thermochemistry	289
	Quantum Chemistry	293
	Fundamentals of Quantum Theory	293
	Applied Quantum Chemistry	304
	Crystals, Polymers, and Materials	319
	Selected Series and Proceedings from Long-Running
	Conferences	322
	Molecular Modeling	331
	Molecular Simulation	335
	Molecular Design and Quantitative Structure-Activity
	Relationships	345
	Graph Theory in Chemistry	352
	Trends	353
	Concluding Remarks	356
	References	357
Author Index		359
Subject Index		389

Contributors

Donald B. Boyd, Department of Chemistry, Indiana University–Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202-3274, U.S.A. (Electronic mail: [e-mail])

Chao-Kun Cheng, Department of Mathematics, Virginia Commonwealth University, Richmond, Virginia 23298, U.S.A. (Electronic mail: [e-mail])

Lutz P. Ehrlich, LION Bioscience AG, Waldhofer Strasse 98, D-69123 Heidelberg, Germany (Electronic mail: [e-mail])

Lemont B. Kier, Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, 23298, U.S.A. (Electronic mail: [e-mail])

Kenny B. Lipkowitz, Department of Chemistry, Indiana University–Purdue University at Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202-3274, U.S.A. (Electronic mail: [e-mail])

Christel M. Marian, German National Research Center for Information Technology (GMD), Scientific Computing and Algorithms Institute (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany (Electronic mail: [e-mail] and [e-mail])

Ingo Mu¨ gge, Bayer Research Center, 400 Morgan Lane, West Haven, Connecticut 06516, U.S.A. (Electronic mail: [e-mail])

Matthias Rarey, German National Research Center for Information Technology (GMD), Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany (Electronic mail: [e-mail])

xvii

xviii Contributors

Paul Seybold, Chemistry Department, Wright State University, Dayton, Ohio 45435, U.S.A. (Electronic mail: [e-mail])

Rebecca C. Wade, European Media Laboratory, Villa Bosch, SchlossWolfsbrunnenweg 33, D-69118 Heidelberg, Germany (Electronic mail: [e-mail])

Contributors to Previous Volumes*

Volume 1

David Feller and Ernest R. Davidson, Basis Sets for Ab Initio Molecular Orbital Calculations and Intermolecular Interactions.

James J. P. Stewart,y Semiempirical Molecular Orbital Methods.

Clifford E. Dykstra,z Joseph D. Augspurger, Bernard Kirtman, and David J. Malik, Properties of Molecules by Direct Calculation.

Ernest L. Plummer, The Application of Quantitative Design Strategies in Pesticide Design.

Peter C. Jurs, Chemometrics and Multivariate Analysis in Analytical Chemistry.

Yvonne C. Martin, Mark G. Bures, and Peter Willett, Searching Databases of Three-Dimensional Structures.

Paul G. Mezey, Molecular Surfaces.

Terry P. Lybrand,} Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods.

*When no author of a chapter can be reached at the addresses shown in the original volume, the current affiliation of the senior or corresponding author is given here as a convenience to our readers.

yCurrent address: 15210 Paddington Circle, Colorado Springs, Colorado 80921-2512 (Electronic mail: [e-mail]).

zCurrent address: Department of Chemistry, Indiana University–Purdue University at Indianapolis, Indianapolis, Indiana 46202 (Electronic mail: [e-mail]).

}Current address: University of Washington, Seattle, Washington 98195 (Electronic mail: [e-mail]).

xix

xx Contributors to Previous Volumes

Donald B. Boyd, Aspects of Molecular Modeling.

Donald B. Boyd, Successes of Computer-Assisted Molecular Design.

Ernest R. Davidson, Perspectives on Ab Initio Calculations.

Volume 2

Andrew R. Leach,* A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules.

John M. Troyer and Fred E. Cohen, Simplified Models for Understanding and Predicting Protein Structure.

J. Phillip Bowen and Norman L. Allinger, Molecular Mechanics: The Art and Science of Parameterization.

Uri Dinur and Arnold T. Hagler, New Approaches to Empirical Force Fields.

Steve Scheiner,y Calculating the Properties of Hydrogen Bonds by Ab Initio Methods.

Donald E. Williams, Net Atomic Charge and Multipole Models for the Ab Initio Molecular Electric Potential.

Peter Politzer and Jane S. Murray, Molecular Electrostatic Potentials and Chemical Reactivity.

Michael C. Zerner, Semiempirical Molecular Orbital Methods.

Lowell H. Hall and Lemont B. Kier, The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure–Property Modeling.

I. B. Bersukerz and A. S. Dimoglo, The Electron–Topological Approach to the QSAR Problem.

Donald B. Boyd, The Computational Chemistry Literature.

*Current address: GlaxoSmithKline, Greenford, Middlesex, UB6 0HE, United Kingdom (Electronic mail: [e-mail]).

yCurrent address: Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322 (Electronic mail: [e-mail]).

zCurrent address: College of Pharmacy, The University of Texas, Austin, Texas 78712 (Electronic mail: [e-mail]).

Contributors to Previous Volumes

xxi

Volume 3

Tamar Schlick, Optimization Methods in Computational Chemistry.

Harold A. Scheraga, Predicting Three-Dimensional Structures of

Oligopeptides.

Andrew E. Torda and Wilfred F. van Gunsteren, Molecular Modeling Using NMR Data.

David F. V. Lewis, Computer-Assisted Methods in the Evaluation of Chemical Toxicity.

Volume 4

Jerzy Cioslowski, Ab Initio Calculations on Large Molecules: Methodology and Applications.

Michael L. McKee and Michael Page, Computing Reaction Pathways on Molecular Potential Energy Surfaces.

Robert M. Whitnell and Kent R. Wilson, Computational Molecular Dynamics of Chemical Reactions in Solution.

Roger L. DeKock, Jeffry D. Madura, Frank Rioux, and Joseph Casanova,

Computational Chemistry in the Undergraduate Curriculum.

Volume 5

John D. Bolcer and Robert B. Hermann, The Development of Computational Chemistry in the United States.

Rodney J. Bartlett and John F. Stanton, Applications of Post-Hartree–Fock Methods: A Tutorial.

Steven M. Bachrach,* Population Analysis and Electron Densities from Quantum Mechanics.

*Current address: Department of Chemistry, Trinity University, San Antonio, Texas 78212 (Electronic mail: [e-mail]).