Lipkowitz Kenny B., Boyd Donald B. (ed.). Reviews in Computational Chemistry. Volume 17

John Wiley & Sons, Inc., 2001. – 357 p.
This volume of Reviews in Computational Chemistry includes an appendix with a lengthy compilation of books on the various topics in computational chemistry: small molecule docking and scoring, protein–protein docking, spin–orbit coupling in molecules and cellular automata models of aqueous solution systems.Small Molecule Docking and Scoring
Ingo Muegge and Matthias RareyAlgorithms for Molecular Docking
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 RemarksProtein–Protein Docking
Lutz P. Ehrlich and Rebecca C. WadeWhy This Topic?
Protein–Protein Binding Data
Challenges for Computational Docking Studies
Computational Approaches to the Docking Problem
Docking ј Sampling ю 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
ConclusionsSpin–Orbit Coupling in Molecules
Christel M. MarianWhat 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
ExamplesComputational 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 OutlookCellular Automata Models of Aqueous Solution Systems
Lemont B. Kier, Chao-Kun Cheng, and Paul G. SeyboldCellular 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
AppendixAppendix. Books Published on the Topics of Computational Chemistry
Kenny B. Lipkowitz and Donald B. BoydComputers 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 RemarksAuthor Index
Subject Index