Lipkowitz Kenny B., Boyd Donald B. (ed.). Reviews in Computational Chemistry. Volume 10

VCH–Publishers, Inc., 1997. – 334 p.
This volume of Reviews in Computational Chemistry includes an appendix with a lengthy compilation of books on the various topics in computational chemistry: genetic algorithms and their use in chemistry, does combinatorial chemistry obviate computer-aided drug design?, visualizing molecular phase space: nonstatistical effects in reaction dynamics, computational studies in nonlinear dynamics, and the development of computational chemistry in the united kingdom.Genetic Algorithms and Their Use in Chemistry
Richard JudsonNatural Evolution as an Optimization Process
The Genetic Algorithm as a Metaphor
Overview
Genetic Algorithms Tutorial
The Simple Genetic Algorithm
Analysis of the Simple Genetic Algorithm
The Schema Theorem
Convergence
Known Problems
Estimating Parameter Values
Variations on the Simple Genetic Algorithm
Is It Real or Is It a Genetic Algorithm?
Examples of Chemical Applications (With Emphasis on the Genetic Algorithm Method)
Conformational Searching: Molecular Clusters
Conformational Searching: Small Molecules
Conformational Searching: Proteins
Conformational Searching: Docking
Conformational Searching: DNA/RNA
Protein NMR Data Analysis
Protein X-ray Data Analysis
Molecular Similarity
QSAR
Design of Molecules
DNA and Protein Sequence Applications
Data Clustering
Spectral Curve Fitting
General Model Fitting
Potential Energy Functions
Summary and Comparison with Other Global
Optimization Methods
Brief Overview of Other Global Search Methods
Summary of Comparison Between Genetic Algorithm and Other Methods
Appendix
1. Literature Sources
Appendix
2. Public Domain Genetic Algorithm CodesDoes Combinatorial Chemistry Obviate Computer-Aided Drug Design?
Eric J. Martin, David C. Spellmeyer, Roger E. Critchlow Jr., and Jeffrey M. BlaneyFragments vs. Whole Molecules
Similarity and "Property Space"
Properties
Experimental Design
Selecting Substituent Sets
Template Diversity
Second-Generation Libraries
Structure-Based Library Design
Calibration of Diversity Score
Evaluating Efficiency of Experimental Design
Comparison to Clustering Corporate Archives
Diversity Space
Comparing Diversity Among Libraries
Synthesis and Testing of Mixtures
ConclusionsVisualizing Molecular Phase Space: Nonstatistical Effects in Reaction Dynamics
Robert Q. TopperMolecular Dynamics in Phase SpaceWhat We Hope to Gain: Semiclassical Insight
Reaction Rates from Dynamics Simulations
Initial Conditions
Rate Constants
Chemical Kinetics, Chaos, and Molecular Motions
A Brief Review of Absolute Rate Theory
Overview of Nonlinear Dynamics and Chaos Theory
Visualizing Uncoupled Isomerization Dynamics in Phase Space
Technical Overview of Nonlinear Dynamics
Some Essential Theorems
Visualizing Phase Space on Poincare Maps: Practical Aspects
Interpreting Poincare Maps
Linear Stability Analysis of Periodic Orbits
Numerical Reconstruction of the Separatrix
Visualizing Coupled Isomerization Dynamics in Phase Space
Isomerization in Two Coupled Degrees of Freedom
Reactive Islands Kinetic Theory
Isomerization in Many Coupled Degrees of Freedom
The Poincare Integral Invariants
A Note on Arnold Diffusion
Summary and ConclusionsComputational Studies in Nonlinear Dynamics
Raima Larter and Kenneth ShowalterIntroduction: Nonlinear Dynamics and Universal Behavior
Homogeneous Systems
Multiple Steady States
Autocatalysis as a Source of Bistability
The Iodate-Arsenite Reaction
Bistability as a Universal Phenomenon
Normal Forms
Bifurcations and Stability Analysis
Generalization to Multiple Variable Systems
Oscillations
Numerical Methods for the Solution of Ordinary Differential Equations
Continuation Method for Steady State Computations
Nonhomogeneous Systems
Turing Patterns: Nonhomogeneous, Steady State Patterns from Reaction-Diffusion Processes
Chemical Waves: Propagating Reaction-Diffusion Fronts
Quadratic Autocatalysis Fronts
Cubic Autocatalysis Fronts
Lateral Instabilities: Two- and Three-Dimensional Patterns
Numerical Methods for Solution of Partial Differential Equations
Cellular Automata and Other Coupled Lattice Methods
Geometric Representations of Nonlinear Dynamics
Phase Space, Poincare Sections, and Poincare Maps
Chaos
Attractors
Sensitive Dependence on Initial Conditions: The Lyapunov Exponent
Routes to Chaos
Numerical Analysis of Experimental Data
Reconstruction of Phase Portraits
Calculation of the Correlation Dimension
Lyapunov Exponents
ConcluonsThe Development of Computational Chemistry in the United Kingdom
Stephen J. Smith and Brian T. SutcliffeBeginnings
Manchester
Cambridge
Emerging from the 1950s
The 1960s
The Atlas Computer Laboratory
The Flowers Report
Emerging from the 1960s
The 1970s
The Meeting House Developments
The Chemical Database Developments
The Growth of Networking
Daresbury and Collaborative Research Projects
CCPl and the Advent of Vector Processing
Quantum Chemistry Outside CCPl
Into the 1980s
Computer Developments
Computational Chemistry Developments
EpilogueAuthor Index
Subject Index