Lipkowitz Kenny B., Boyd Donald B. (ed.). Reviews in Computational Chemistry. Volume 07

Wiley–VCH, Inc., 1996. – 414 p.
This volume of Reviews in Computational Chemistry includes an appendix with a lengthy compilation of books on the various topics in computational chemistry: similarity searching in databases of chemical structures, three-dimensional structure database searches, methods and applications of combined quantum mechanical and molecular mechanical potentials, an introduction to density functional theory, density functional methods in biomolecular modeling, and the a priori calculation of vibrational circular dichroism intensities.Similarity Searching in Databases of Chemical Structures
Geoffrey M. Downs and Peter WillettIntroduction
Chemical Information Systems
Representation and Substructure Searching of 2D Chemical Structures
Representation and Substructure Searching of 3D Chemical Structures
Limitations of Substructure Searching
Similarity Searching in Databases of 2D StructuresStructural Descriptors
Weighting Schemes
Similarity Coefficients
Examples of 2D Similarity-Searching Systems
Clustering Databases of 2D StructuresHierarchical Clustering
Nonhierarchical Clustering
Dissimilarity Approaches
Similarity Searching in Databases of 3D StructuresGlobal Measures for 3D Similarity Searching
Local Measures for Distance-Based 3D Similarity
Searching
Flexible Similarity Searching
Docking Procedures
Conclusions
Overview
Efficiency of Searching
Applications of Similarity Searching
Future DevelopmentsThree-Dimensional Structure Database Searches
Andreu' C. Good and Jonathan S. Mason3D Database Searching and the Drug Design Process
Advances in 3D Search Methodology
3D Database and Pharmacophore Query Construction
Structure Generation
Atom Typing on Compound Registration
Search- Time-Defined Atom Environment
Dealing with Conformational Flexibility
Explicit Conformation Storage
3D Screens Incorporating Conformational Flexibility
Torsional Fitting
Choice of Technique
Pharmacophore Generation and Validation
Molecular Graphics
Automating the Search for Pharmacophores
Molecular Similarity Calculations
Pharmacophore Validation
Pharmacophore Search Successes
Receptor-Constrained 3D Screening
Shape-Constrained 3D Database Searches
Vector-Constrained 3D Searches
De Novo Design
ConclusionsMethods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials
Jiali GaoIncorporation of Explicit Solvent Effects in Quantum Mechanical Calculations
Combined Quantum Mechanical and Molecular Mechanical Potentials
Boundary Conditions
Dividing Covalent Bonds across the QM and MM Regions
Solvent Polarization Effects
Simulation of Excited States and Solvatochromic Spectral Shifts
The QM Method
Implementations
A Critical Evaluation of the Combined Semiempirical AM1/MM Model
Bimolecular Hydrogen-Bonding Interactions
Free Energies of Solvation of Organic Compounds
Electronic Polarization
Conformational Equilibria in Aqueous and Organic Solutions
Relative Free Energies of Tautomeric Equilibria in Pyridone
Solvent Effects on Chemical Reactions
The Claisen Rearrangement of Allyl Vinyl Ether
Simulations of Nucleophilic Substitution Reactions
The Decarboxylation Reaction of 3-Carboxybenzisoxazole
Potential Surface for the Proton Transfer in [H₃N-H-NH₃]⁺
Solvatochromic Shifts of Acetone in Aqueous and Organic Solutions
Enzymatic Reaction and Chemisorption on Surfaces
ConclusionsAn Introduction to Density Functional Theory
Libero J. Bartolotti and Ken FlurchickSome Basic Calculus
Early Models
Formal Development of Density Functional Theory
Orbital-Density Formalism
Discussion and PracticeDensity Functional Methods in Biomolecular Modeling
Alain St-AmantDensity Functional Theory
The Kohn-Sham Approach
Exchange and Correlation Energy Functionals
Computational Strategies for Solving the Kohn-Sham Equations
Analytic Gradients and Hessians
Car-Parrinello Methods
Applications of Density Functional Theory in Biomolecular Modeling
Molecular Geometries and Vibrational frequencies
Modeling Reactions
Conformational Energies
Electrostatics
Water Dimer, Water Clusters, and Liquid Water
Glycine and Alanine Dipeptide Analogs
Nucleic Acid Base Pairs
Conclusions: The OutlookThe A Priori Calculation of Vibrational Circular Dichroism Intensities
Danya Yang and Arvi RaukHistorical Overview
Experimental Aspects
Theory in Brief
Computational Considerations
Origin Gauges
Electronic Wavefunctions and Calculation of Matrix Elements
Geometry and Force field
Basis Sets
Computer Programs
Applications
(S)-NHDT
Cyclopropanes
Oxiranes
Thiiranes
Aziridines
CYclobutanes
Lactones
Allenes
Alcohols
Larger Molecules
ConclusionsAppendix: Compendium of Software for Molecular Modeling
Donald B. BoydThe InternetSoftware For Personal Computers
General Purpose Molecular Modeling
Quantum Chemistry Calculations
Databases of Molecular Structures
Molecular Graphics
Quantitative Structure-Property Relationships and Statistics
Other Applications
Software for Minicomputers, Superminicomputers, Workstations, and Supercomputers
General Purpose Molecular Modeling
Quantum Chemistry Calculations
Databases of Molecular Structures
Molecular Graphics
Quantitative Structure-Property Relationships and Statistics
Other ApplicationsAuthor Index
Subject Index