Reviews in Computational Chemistry

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.