Lipkowitz Kenny B., Boyd Donald B. (ed.). Reviews in Computational Chemistry. Volume 18

John Wiley & Sons, Inc., 2002. – 210 p.
This volume of Reviews in Computational Chemistry includes an appendix with a lengthy compilation of books on the various topics in computational chemistry: clustering methods and their uses in computational chemistry, the use of scoring functions in drug discovery applications, potentials and algorithms for incorporating polarizability in computer simulations, developments in the theoretical description of charge-transfer reactions in condensed phases and examination of the employment environment for computational chemistry.Clustering Methods and Their Uses in Computational Chemistry
Geoff M. Downs and John M. BarnardClustering Algorithms
Hierarchical Methods
Nonhierarchical Methods
Progress in Clustering Methodology
Algorithm Developments
Comparative Studies on Chemical Data Sets
How Many Clusters?
Chemical Applications
ConclusionsThe Use of Scoring Functions in Drug Discovery Applications
Hans-Joachim Bo¨hm and Martin StahlThe Process of Virtual Screening
Major Contributions to Protein–Ligand Interactions
Description of Scoring Functions for Receptor–Ligand Interactions
Force Field-Based Methods
Empirical Scoring Functions
Knowledge-Based Methods
Critical Assessment of Current Scoring Functions
Influence of the Training Data
Molecular Size
Other Penalty Terms
Specific Attractive Interactions
Water Structure and Protonation State
Performance in Structure Prediction
Rank Ordering Sets of Related Ligands
Application of Scoring Functions in Virtual Screening
Seeding Experiments
Hydrogen Bonding versus Hydrophobic Interactions
Finding Weak Inhibitors
Consensus Scoring
Successful Identification of Novel Leads through Virtual Screening
OutlookPotentials and Algorithms for Incorporating Polarizability in Computer Simulations
Steven W. Rick and Steven J. StuartNonpolarizable Models
Polarizable Point Dipoles
Shell Models
Electronegativity Equalization Models
Semiempirical Models
Applications
Water
Proteins and Nucleic Acids
Comparison of the Polarization Models
Mechanical Polarization
Computational Efficiency
Hyperpolarizability
Charge-Transfer Effects
The Electrostatic Potential
Summary and ConclusionsNew Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases
Dmitry V. Matyushov and Gregory A. VothParadigm of Free Energy Surfaces
Formulation
Two-State Model
Heterogeneous Discharge
Beyond the Parabolas
Bilinear Coupling Model
Electron Transfer in Polarizable Donor–Acceptor Complexes
Nonlinear Solvation Effects
Electron-Delocalization Effects
Nonlinear Solvation versus Intramolecular Effects
Optical Band Shape
Optical Franck–Condon Factors
Absorption Intensity and Radiative Rates
Electron-Transfer Matrix Element
Electronically Delocalized Chromophores
Polarizable Chromophores
Hybrid ModelLinear Free Energy Relationships Using Quantum Mechanical Descriptors
George R. Famini and Leland Y. WilsonLFER Methodology
Background
Computational Methods
Linear Free Energy Relationships
Descriptors
Classifications
Quantum Mechanical Descriptors
Quantum Mechanical Calculations
Statistical Procedures
Multiple Regression Analysis
Examples of LFER Equations
Model-Based Methods
Nonmodel-Based Methods
ConclusionsThe Development of Computational Chemistry in Germany
Sigrid D. PeyerimhoffComputer Development
The ZUSE Computers
The G1, G2, and G3 of Billing in Go¨ ttingen
Computer Development at Universities
The Analog Computer in Chemistry
Quantum Chemistry, A New Start
Theoretical Chemistry 1960–1970
The Deutsche Rechenzentrum at Darmstadt
Formation of Theoretical Chemistry Groups
Deutsche Forschungsgemeinschaft–Schwerpunktprogramm Theoretische Chemie
Theoretical Chemistry Symposia
Scientific Developments
Computational Chemistry 1970–1980
European Efforts
Computer-Aided Synthesis
Progress in Quantum Chemical Methods
Beyond 1980Appendix. Examination of the Employment Environment for Computational Chemistry
Donald B. Boyd and Kenny B. LipkowitzHiring Trends
Skills in Demand
The Broader Context
Salaries
ConclusionsAuthor Index
Subject Index