Lipkowitz Kenny B., Larter R., Gundari Thomas R. (ed.). Reviews in Computational Chemistry. Volume 21

John Wiley & Sons, Inc., 2005. – 445 p.
This volume of Reviews in Computational Chemistry includes an appendix with a lengthy compilation of books on the various topics in computational chemistry: ab initio quantum simulation in solid state chemistry, molecular quantum similarity, enumerating molecules, variable selection, biomolecular applications of poisson–boltzmann methods, and data sources and computational approaches for generating models of gene regulatory networks.Ab Initio Quantum Simulation in Solid State Chemistry
Roberto Dovesi, Bartolomeo Civalleri, Roberto Orlando, Carla Roetti, and Victor R. SaundersTranslation Invariance Properties in a Crystal
The Direct Lattice
The Reciprocal Lattice
Bloch Theorem and Periodic Boundary Conditions
One-Electron Electrostatic Hamiltonian
Discussion of Band Structure Through a Few Simple Examples
A Monoatomic Linear Chain
A Two-Dimensional Periodic Example: Graphite
Three-Dimensional Periodic Examples
From the Band Structure to the Total Energy
Use of Symmetry in Reciprocal Space
Total Energy, Energy Differences, and Derivatives
Cohesive Energy
Polymorphism
Magnetic Phases
Positional Isomorphous Phases
Energy Derivatives
Modeling Surfaces and Interfaces
The Slab Model
Specifying the Surface Plane–Miller Indices
Choosing the Surface Termination
Surface Formation Energy and Stability
Surface Relaxation and Reconstruction
Vicinal Surfaces–Modeling Steps and Kinks
Adsorption on Surfaces
Interfaces
Modeling Defective Systems
Defects in Solids
How to Model a Defect
The Supercell Approach
Defect Formation Energy
ExamplesAppendix 1: Available Periodic Programs
Appendix 2: Performance of the Periodic Program Crystal
Appendix 3: AcronymsMolecular Quantum Similarity: Theory and Applications
Patrick Bultinck, Xavier Gironeґs, and Ramon Carboґ-DorcaBasic Elements of Molecular Similarity
The Electron Density as Molecular Descriptor
Molecular Quantum Similarity
Extension to Other Operators
Stochastic Manipulations and Graphical Representations of the Similarity Matrix
Electron Densities for Molecular Quantum Similarity
The Alignment Issue in Molecular Quantum Similarity
Statement of the Problem
Quantum Similarity Maximization–MaxiSim and QSSA
Structural Alignment Comparison of Alignment Techniques
Quantum Similarity Indices
Quantum Atoms-in-Molecules Similarity
The Hirshfeld Approach
AIM-Based Methods
Atom-Centered Basis Function Approach
Physical Connotations of (Self) Similarity Measures
Chirality and the Holographic Electron Density Theorem
Mathematical Aspects of Quantum Similarity
The Cramer Steroid Set – A Worked Out Example of MQS
ConclusionsEnumerating Molecules
Jean-Loup Faulon, Donald P. Visco, Jr., and Diana RoeEnumerating Molecules: Why
Enumerating Molecules: How
From Graph Theory to Chemistry
Counting Structures: How Many Isomers Has Decane?
Enumerating Structures: Are There any Isomers of Decane Having Seven Methyl Groups?
Enumerating Labeled and Unlabeled Graphs
Enumerating Molecules
Sampling Structures: What is the Decane Isomer With the Highest Boiling Point?
Sampling Labeled and Unlabeled Graphs
Sampling Molecules
Enumerating Molecules: What are the Uses?
Chemical Information
Structure Elucidation
Combinatorial Library Design
Molecular Design with Inverse-QSAR
Conclusion and Future DirectionsVariable Selection–Spoilt for Choice?
David J. Livingstone and David W. SaltThe Problem
Dimension Reduction
Variable Elimination
Why We Eliminate Variables
More Variables Than Objects
Multicolinearity
Identification of Multicolinearity
Which Variables Do We Eliminate?
Unsupervised Elimination
Supervised Elimination
Variable Selection
Ordinary Least Squares
Ridge Regression
Principal Component Regression, Partial Least Squares, and Continuum Regression
Best Variable Subset Selection
Forward Inclusion
Backward Elimination
Stepwise Regression
All Subset Regression
Other Stopping Rules
Case Study
Stepwise Regression
Best Subset Regression
Supervised and Unsupervised Variable Selection
Published Variable Selection Methods
ConclusionsAppendixBiomolecular Applications of Poisson–Boltzmann Methods
Nathan A. BakerIntroduction to Biomolecular Electrostatics
Simplifying the System: Implicit Solvent Methods
Polar Interactions
Nonpolar Interactions
Poisson–Boltzmann Theory: A Brief Overview
Solving the Poisson–Boltzmann Equation
Discretization Methods
Multilevel Solvers
Parallel Methods
Software for Computational Electrostatics
Applying Poisson–Boltzmann Methods
Solvation Free Energies
Conformational Free Energies
Binding Free Energies
Titration Calculations
Other Applications
ConclusionsData Sources and Computational Approaches for Generating Models of Gene Regulatory Networks
Baltazar D. Aguda, Georghe Craciun, and Rengul Cetin-AtalayFormal Representation of GRNs
An Example of a GRN: The Lac Operon
Hierarchies of GRN Models: From Probabilistic Graphs to Deterministic Models
A Guide to Databases and Knowledgebases on the Internet
Pathway Databases and Platforms
Ontologies for GRN Modeling
Current Gene, Interaction, and Pathway Ontologies
Whole-Cell Modeling Platforms
Ontology for Modeling Multiscale and Incomplete Networks
An Ontology for Cellular Processes
The PATIKA Pathway Ontology
Extracting Models from Pathways Databases
Pathway and Dynamic Analysis Tools for GRNs
Global Network Properties
Recurring Network Motifs
Identifying Pathway Channels in Networks: Extreme Pathway Analysis
Network Stability Analysis
Predicting Dynamics and Bistability from Network Structure Alone
Concluding RemarksAuthor Index
Subject Index