Reviews in Computational Chemistry, Volume 17

Computational chemistry is increasingly used in most areas of molecular science including organic, inorganic, medicinal, biological, physical, and analytical chemistry. Researchers in these fields who do molecular modelling need to understand and stay current with recent developments. This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Two chapters focus on molecular docking, one of which relates to drug discovery and cheminformatics and the other to proteomics. In addition, this volume contains tutorials on spin-orbit coupling and cellular automata modeling, as well as an extensive bibliography of computational chemistry books.

FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."—JOURNAL OF MOLECULAR GRAPHICS AND MODELLING

"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."—JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In fast allen Bereichen der Wissenschaft der Moleküle - von der organischen über die anorganische, medizinische, physikalische und biologische bis zur analytischen Chemie - spielen moderne Rechenmethoden eine immer wichtigere Rolle. An Einsteiger und erfahrene Fachleute gleichermaßen wendet sich diese erfolgreiche und praxiserprobte Reihe, die Algorithmen aus der Quantenchemie, der Molekülmechanik und -dynamik sowie der QSAR erfasst. Die Methoden werden mit theoretischem Hintergrund, Hinweisen zur richtigen Anwendung, Warnungen vor häufigen Fehlern und einer umfangreichen Bibliographie besprochen. 1. Small Molecule Docking and Scoring (Ingo Muegge and Matthias Rarey).

Introduction.

Algorithms for Molecular Docking.

Appendix. Books Published on the Topics of Computational Chemistry (Kenny B. Lipkowitz and Donald B. Boyd).

Introduction.

Computers in Chemistry.

Chemical Information.

Computational Chemistry.

Artificial Intelligence and Chemometrics.

Crystallography, Spectroscopy, and Thermochemistry.

Quantum Chemistry.

Fundamentals of Quantum Theory.

Applied Quantum Chemistry.

Crystals, Polymers, and Materials.

Selected Series and Proceedings from Long-Running Conferences.

Molecular Modeling.

Molecular Simulation.

Molecular Design and Quantitative Structure-Activity Relationships.

Graph Theory in Chemistry.

Trends.

Concluding Remarks.

References.

Author Index.

Subject Index.

The Docking Problem.

Placing Fragments and Rigid Molecules.

Flexible Ligand Docking.

Handling Protein Flexibility.

Docking of Combinatorial Libraries.

Scoring.

Shape and Chemical Complementary Scores.

Force Field Scoring.

Empirical Scoring Functions.

Knowledge-Based Scoring Functions.

Comparing Scoring Functions in Docking Experiments: Consensus Scoring.

From Molecular Docking to Virtual Screening.

Protein Data Preparation.

Ligand Database Preparation.

Docking Calculation.

Postprocessing.

Applications.

Docking as a Virtual Screening Tool.

Docking as a Ligand Design Tool.

Concluding Remarks.

Acknowledgments.

References.

2. Protein-Protein Docking (Lutz P. Ehrlich and Rebecca C. Wade).

Introduction.

Why This Topic?

Protein-Protein Binding Data.

Challenges for Computational Docking Studies.

Computational Approaches to the Docking Problem.

Docking = Sampling + Scoring.

Rigid-Body Docking.

Flexible Docking.

Example.

Estimating the Extent of Conformational Change upon Binding.

Rigid-Body Docking.

Flexible Docking with Side-Chain Flexibility.

Flexible Docking with Full Flexibility.

Future Directions.

Conclusions.

References.

3. Spin-Orbit Coupling in Molecules (Christel M. Marian).

What It Is All About.

The Fourth Electronic Degree of Freedom.

The Stern-Gerlach Experiment.

Zeeman Spectroscopy.

Spin Is a Quantum Effect.

Angular Momenta.

Orbital Angular Momentum.

General Angular Momenta.

Spin Angular Momentum.

Spin-Orbit Hamiltonians.

Full One- and Two-Electron Spin-Orbit Operators.

Valence-Only Spin-Orbit Hamiltonians.

Effective One-Electron Spin-Orbit Hamiltonians.

Symmetry.

Transformation Properties of the Wave Function.

Transformation Properties of the Hamiltonian.

Matrix Elements.

Examples.

Summary.

Computational Aspects.

General Considerations.

Evaluation of Spin-Orbit Integrals.

Perturbational Approaches to Spin-Orbit Coupling.

Variational Procedures.

Comparison of Fine-Structure Splittings with Experiment.

First-Order Spin-Orbit Splitting.

Second-Order Spin-Orbit Splitting.

Spin-Forbidden Transitions.

Radiative Transitions.

Nonradiative Transitions.

Summary and Outlook.

Acknowledgments.

References.

4. Cellular Automata Models of Aqueous Solution Systems (Lemont B. Kier, Chao-Kun Cheng, and Paul G. Seybold).

Introduction.

Cellular Automata.

Historical Background.

The General Structure.

Cell Movement.

Movement (Transition) Rules.

Collection of Data.

Aqueous Solution Systems.

Water as a System.

The Molecular Model.

Significance of the Rules.

Studies of Water and Solution Phenomena.

A Cellular Automata Model of Water.

The Hydrophobic Effect.

Solute Dissolution.

Aqueous Diffusion.

Immiscible Liquids and Partitioning.

Micelle Formation.

Membrane Permeability.

Acid Dissociation.

Percolation.

Solution Kinetic Models.

First-Order Kinetics.

Kinetic and Thermodynamic Reaction Control.

Excited-State Kinetics.

Second-Order Kinetics.

Enzyme Reactions.

An Anticipatory Model.

Chromatographic Separation.

Conclusions.

Appendix.

References. "...true to the spirit of most of the collection, covering a diversity of aspects in computational chemistry...particularly valuable to those involved in computer-aided drug design." (Journal of Medicinal Chemistry, Vol. 45, No. 10)

Kenny B. Lipkowitz, PhD, is a retired Professor of Chemistry from North Dakota State University.

Donald B. Boyd was apponted Research Professor of Chemistry at Indiana University - Purdue University Indianapolis in 1994. He has published over 100 refereed journal papers and book chapters.

This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Two chapters focus on molecular docking, one of which relates to drug discovery and cheminformatics and the other to proteomics. In addition, this volume contains tutorials on spin-orbit coupling and cellular automata modeling, as well as an extensive bibliography of computational chemistry books.

FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."-JOURNAL OF MOLECULAR GRAPHICS AND MODELLING

"One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."-JOURNAL OF THE AMERICAN CHEMICAL SOCIETY