Note: Cover -- Title Page -- Copyright -- Contents -- List of Contributors -- Preface -- Contributors to Previous Volumes -- Chapter 1 Chemical Bonding at High Pressure -- High-Pressure Science -- Motivation -- Pressure in Industrial Processes -- High-Pressure Experiments -- Pressure Effects in Materials -- Close Packing and Metallicity-or Not -- Hydrogen and Hydrogen-Rich Compounds -- Molecular Crystals -- Closed-Shell Reactivity -- Unusual Chemistry -- New Electronic States -- Electronic Structure Calculations on Materials Under Pressure -- Density and Wave Function--Based Approaches -- Basis Sets and Pseudopotentials -- Identifying High-Pressure Crystal Structures -- Stability of High-Pressure Phases -- Properties of Materials Under Pressure -- Mechanical Properties -- Electronic Properties -- Spectroscopic Properties -- Conclusions -- Acknowledgments -- References -- Chapter 2 Molecular Dynamics Simulations of Shock Loading of Materials: A Review and Tutorial -- Introduction -- Shock Loading of Solids 101 -- Chapter Organization -- Molecular Simulations of Shockwaves in Solids -- Molecular Dynamics and Coarse Grain Dynamics -- Direct Shock Simulations -- Indirect Shock Simulations: Achieving Longer Timescales -- Shock-Induced Plasticity and Failure -- Plastic Deformation -- Preexisting Defects: Voids and Vacancies -- Preexisting Defects: Polycrystalline Materials -- Granular Materials -- Dynamical Failure -- Critical Phenomena in Spallation and Cluster Formation -- Ejecta Formation and the Richtmyer-Meshkov Instability -- Shock-Induced Phase Transformation and Materials Synthesis -- Phase Transformations -- Shock-Induced and Shock-Assisted Chemical Reactions -- Reactive Composites -- Energetic Materials and Detonation -- Model Explosives: Shock to Detonation -- Reactive MD Simulations of Explosives -- Electronic Structure-Based Modeling. , Coarse-Grained Descriptions of Shock-Induced Chemistry -- Summary and Outlook -- Acknowledgments -- Appendix -- References -- Chapter 3 Basis Sets in Quantum Chemistry -- Introduction -- The Basis Set Approximation -- Basis Set Desiderata -- Types of Basis Functions -- Slater and Gaussian Type Functions -- Plane-Wave Functions -- Real-Space Functions -- Other Functions -- Structure and Classification of Gaussian Type Basis Sets -- Contracted Basis Functions -- Optimization of Basis Set Parameters -- Basis Set Augmentation -- Diffuse Functions -- Tight Functions -- Fitting Functions -- Nonatom-Centered Basis Sets -- Examples of Basis Sets -- Segmented Contracted Basis Sets -- General Contracted Basis Sets -- Property Basis Sets -- Electric Properties -- Magnetic Properties -- Mixed Properties -- Relativistic Basis Sets -- Pseudopotentials -- Basis Set Convergence -- Convergence of Electronic Structure Methods with Gaussian Type Basis Sets -- Composite Extrapolation Methods -- Basis Set Incompleteness and Superposition Errors -- Aspects of Choosing A Suitable Basis Set -- Availability of Basis Sets -- Acknowledgment -- References -- Chapter 4 The Quantum Chemistry of Open-Shell Species -- Introduction and Overview -- Quantum Chemistry Methods for Open- and Closed-Shell Species -- Some Aspects of Electronic Structure of Open-Shell Species -- Spin Contamination of Approximate Open-Shell Wave Functions -- Jahn-Teller Effect -- Vibronic Interactions and Pseudo-Jahn-Teller Effect -- High-Spin Open-Shell States -- Open-Shell States with Multiconfigurational Character -- EOM-IP and EOM-EA Methods for Open-Shell Systems -- Examples -- Diradicals, Triradicals, and Beyond -- Excited States of Open-Shell Species -- Metastable Radicals -- Bonding in Open-Shell Species -- Dyson Orbitals -- Density-Based Wave Function Analysis. , Insight into Bonding from Physical Observables -- Properties and Spectroscopy -- Vibrational Spectroscopy -- Electronic and Photoelectron Spectroscopy -- Electronic Transitions -- Outlook -- Acknowledgments -- Appendix: List of Acronyms -- References -- Chapter 5 Machine Learning, Quantum Chemistry, and Chemical Space -- Introduction -- Paradigm -- Kernel Ridge Regression -- Representation -- Data -- Kernel -- Electrons -- -Machine Learning -- Atoms in Molecules -- Crystals -- Conclusions and Outlook -- Acknowledgments -- References -- Chapter 6 The Master Equation Approach to Problems in Chemical and Biological Physics -- Introduction -- The General Form of A Master Equation and its Solution -- Microscopic Reversibility, Detailed Balance, and Their Consequences -- The Kinetic Monte Carlo (KMC) Method -- Quantum Master Equations -- The Reduced Density Matrix as a Description of a Molecule Interacting with Its Surroundings -- Diagonal and Off-Diagonal Elements of the Density Matrix and Significance of Dephasing -- Relaxation -- Kinetic Monte Carlo for Quantum Master Equations -- Physical Significance of The Quantum Kinetic Monte Carlo Scheme -- Concluding Remarks -- Acknowledgments -- References -- Chapter 7 Continuous Symmetry Measures: A New Tool in Quantum Chemistry -- Introduction -- Symmetry as a Fundamental Concept in Quantum Chemistry -- Symmetry, Pseudosymmetry, and Quasisymmetry -- Continuous Symmetry Measures -- General Definition of CSMs -- CSMs in Molecular Quantum Chemistry -- CSM for the Nuclear Framework -- CSMs for Matrices and Operators -- CSM for Functions: Electron Density, Wave Functions, and Molecular Orbitals -- CSMs for Irreducible Representations of a Group -- Pseudosymmetry Analysis of Molecular Orbitals -- Applications -- The Nature of the Chemical Bond from the Point of View of CSMs. , CSM Analysis of the Electronic Structure of Conjugated Hydrocarbons and Related Compounds -- Pseudosymmetry Analysis of the d-Block Molecular Orbitals of "Octahedral" ML6 Transition Metal Compounds -- Symmetry, Pseudosymmetry and Walsh Diagrams for ML4 Compounds along the Planarization Path -- Conclusions -- Acknowledgment -- References -- Index -- Supplemental Images -- EULA.

Note: Reviews in Computational Chemistry Volume 11 -- Contents -- Recent Advances in Ligand Design Methods -- Introduction -- Classes of Ligand Design Methods -- Other Factors to Consider When Evaluating a Ligand Design Method -- Organization of This Chapter -- Overview of Classes of De Novo Design Methods -- Category 1. Fragment Location (Fragment Placement) Methods -- Category 2. Site Point Connection Methods -- Category 3. Fragment Connection Methods -- Category 4. Sequential Buildup Methods -- Category 5. Whole Molecule Methods -- Category 6. Random Connection/Disconnection Methods -- Details of Specific De Novo Ligand Design Methods -- Fragment Location Methods -- Site Point Connection Methods -- Fragment Connection Methods -- Sequential Buildup Methods -- Whole Molecule Methods -- Random Connection Methods -- General Discussion of Ligand Design Approaches -- Take-Home Lessons -- Issues To Be Addressed in Ligand Design Software -- Acknowledgments and Mea Culpas -- References -- Current Issues in De Novo Molecular Design -- Introduction -- Overview of De Novo Design Methods -- Outline of Chapter -- How Are the Design Constraints Derived? -- Molecular Interactions -- Characterizing a Receptor -- When No Receptor Structure Is Available -- Scalar Constraints -- Accuracy and Appropriateness of Constraints -- What Chemical Diversity Is Available? -- Fragment Library Issues -- Building Strategies -- How Is Molecular Flexibility Handled? -- Ligand Flexibility -- Receptor Flexibility -- Future Directions for Flexibility -- How Useful Are Current Scoring Functions? -- Why Are Scoring Functions Needed? -- What Is Available? -- Critique of Current Scoring Methods Used in De Novo Design -- Future Directions for Scoring Methods -- How Are Large Numbers of Generated Structures Handled? -- Currently Available Tools and Protocols -- Discussion. , How Are the Best Designs Verified? -- Molecular Dynamics -- Molecular Docking -- Free Energy Calculations -- What About the Interface? -- Interface with the User -- Interface to Other Design Tools -- When Are De Novo Design Techniques Applicable? -- Published Test Cases -- Validated Examples -- Discussion -- Practical Advice on the Application of De Novo Design Methods -- Conclusions -- Acknowledgments -- References -- Theoretical and Practical Aspects of Three-Dimensional Quantitative Structure-Activity Relationships -- An Introduction to the QSAR Problem -- Chemical Space and the Linear Free Energy Formalism -- Hansch Analysis and Classical QSAR -- Three-Dimensional QSAR: An Overview -- Assumptions in 3D-QSAR -- Current 3D-QSAR Methods -- CoMFA Application Notes -- Training Set Composition -- Alignment Rules -- Electrostadc Descriptors and Choice of Partial Atomic Charges -- CoMFA Region Description -- CoMFA Standard Fields -- Additional CoMFA Fields -- PCA/PLS: A Brief Overview -- Cross-Validation Techniques -- Frequently Used Statistical Indices in 3D-QSAR -- Interpretation of CoMFA Results -- Model Predictivity -- Explanatory Power -- Model Simplicity -- Variable Selection -- Lateral Validation -- Basic Qualities of a Good QSAR Model -- Final Remarks -- Acknowledgments -- Appendix -- References -- Approaches to Three-Dimensional Quantitative Structure-Activity Relationships -- What Is 3D-QSAR? -- 3D -- Quantitative . . . Relationship -- Structures -- Activity -- General Aspects of 3D-QSAR Methods -- Tools for Selecting a Proper Molecular Alignment -- Tools for Deriving a Quantitative 3D-QSAR Model -- 3D-QSAR Methods That Use Only Ligand Structures and Bioactivity -- Receptor Binding Site Models -- Molecular Shape Analysis (MSA) -- Minimal Topological Difference (MTD) -- REMOTEDISC Distance Geometry Method. , Comparative Molecular Field Analysis (CoMFA) -- Hypothetical Active Site Lattice (HASL) -- 3D-QSAR Based on Molecular Similarity and Distances -- Comparative Molecular Similarity Indices Analysis (CoMSIA) -- 3D-QSARs Derived by Tensor Analysis -- Compass -- Genetically Evolved Receptor Models (GERM) -- Autocorrelation of 3D Molecular Properties -- Receptor Surface Models (RSM) -- Comparative Molecular Moment Analysis (CoMMA) -- 3D-QSAR Methods That Require 3D Structures of the Ligand-Macromolecule Complexes -- CoMFA and CoMFA-like Approaches -- Correlations with Calculated Interaction Energies -- Empirical Correlations with the Types of Interaction Present -- Concluding Remarks -- Overview of the Methods -- Role of 3D-QSAR in 3D Database Searching, Combinatorial Library Design, and Computer De Novo Design -- References -- Computational Approaches to Lipophilicity: Methods and Applications -- Introduction -- Setting the Scene and Defining Lipophilicity -- Scope and Layout of the Chapter -- Intermolecular Forces Encoded in Lipophilicity -- Recognition Forces in Pharmacological and Biological Processes -- Factorization of Molecular Lipophilicity -- Polar and Nonpolar Interactions Encoded in Lipophilicity -- Intramolecular Interactions Encoded in Lipophilicity -- Electronic Conjugations -- Interactions Involving Polar Croups -- Steric/Hydrophobic Effects -- Structural Factors Influencing Intramolecular Interactions -- Positional Isomerism and Stereoisomerism -- Ionization -- Molecular Size and Chameleonic Behavior -- One-Dimensional" Approaches for Calculating Partition Coefficients -- The Substituent Constants of Hansch and Fujita -- One-Dimensional" Lipophilicity Scale for Amino Acid Side Chains -- Two-Dimensional" Approaches for Calculating Partition Coefficients -- Methods Based on Fragmental Constants and Correction Factors. , Methods Based on Fragmental Constants Only -- Methods Based on Global Two-Dimensional Structural Properties -- Three-Dimensional" Approaches for Calculating Partition Coefficients -- Methods Based on Theoretical Parameters -- Methods Based on Molecular Fields -- Four-Dimensional" Approaches for Calculating Lipophilicity -- Methods Based on an Ensemble of Conformers -- Methods Based on Direct Computation -- Comparison of the Accuracy of Some Methods -- Examples of Applications in Drug Design -- Computed log P as a Tool to Unravel lntrarnolecular Interactions -- Computed log P Values in Two-Dimensional Quantitative Structure-Activity Relationships -- Computed Lipophilicity Fields: An Enhancement of Three-Dimensional Quantitative Structure-Activity Relationships -- Computational Aspects -- Two-Dimensional" Approaches -- Three-Dimensional" Approaches -- Four-Dimensional" Approaches -- Concluding Remarks -- Acknowledgments -- References -- Treatment of Counterions in Computer Simulations of DNA -- Introduction -- Background -- Structure of DNA -- Counterions in DNA: Counterion Condensation and Manning Theory -- Methodology -- Computer Simulations: An Overview -- System Description -- Placement of Ions -- Placement of Water Molecules -- Force Fields -- Energy -- Simulation Protocols -- Ensembles -- System Environment -- Periodic Boxes and Cutoff Distances -- Time Scale -- Nonbonded Interactions -- Switching Functions -- Shifting Functions -- Ewald Summation -- Restraints and Constraints -- Validation and Analysis -- Atomistic Computer Simulations: Examples -- Monte Carlo Approaches -- Molecular Dynamics Approaches -- Conclusions -- Acknowledgments -- References -- Appendix. Compendium of Software and Internet Tools for Computational Chemistry -- Introduction -- The Internet and Electronic Mail -- The World Wide Web -- Transferring Files. , Electronic Bulletin Boards -- References -- Author Index -- Subject Index.

Note: Intro -- Revievvs in Computational Chemistry 10 -- Contents -- Genetic Algorithms and Their Use in Chemistry -- Introduction -- Natural 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 Codes -- Acknowledgments -- References -- Does Combinatorial Chemistry Obviate Computer- Aided Drug Design? -- Introduction -- Fragments vs. Whole Molecules -- Similarity and "Property Space" -- Properties -- Experimental Design -- Selecting Substituent Sets -- Template Diversity -- SecondGeneration 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 -- Conclusions -- References -- Visualizing Molecular Phase Space: Nonstatistical Effects in Reaction Dynamics -- Molecular Dynamics in Phase Space -- Introduction -- What 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 PoincarC Maps: Practical Aspects -- Interpreting Poincari Maps -- Linear Stability Analysis of Periodic Orbits -- Numerical Reconstruction of the Separatrix -- Visualizing Coupled lsomerization 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 Conclusions -- Acknowledgments -- References -- Computational Studies in Nonlinear Dynamics -- Introduction: 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-Diflusion 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 -- Lyapwnov Exponents -- Conclusions -- Acknowledgments -- References -- The Development of Computational Chemistry in the United Kingdom -- Introduction -- Beginnings -- 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 -- Epilogue -- Acknowledgments -- References -- Author Index -- Subject Index.

Note: Intro -- Reviews in Computational Chemistry Volume 16 -- Contents -- Computer-Aided Molecular Diversity Analysis and Combinatorial Library Design -- Introduction -- Molecular Recognition: Similarity and Diversity -- Describing Diversity Space -- Types of Descriptor -- Choosing Appropriate Descriptors -- Validation of Descriptors -- Applications -- Diversity Analysis -- Combinatorial Library Design -- Diversity Is Not the Be-All and End-All! -- Current Issues and Future Directions -- Diversity Descriptors -- Library Design -- Speed Requirement -- "Quick and Dirty" QSAR -- Integration with Other Modeling Tools -- Persuading the Customers -- Conclusions -- Acknowledgments -- References -- Artificial Neural Networks and Their Use in Chemistry -- Introduction -- Overview and Goals -- What Are Artificial Neural Networks? -- Analogy with the Brain -- Artificial Neural Networks -- Summary of Neural Network Operation -- Brief History of Neural Networks -- What Can Neural Networks Be Used for and When Should You Use Them? -- Classification -- Modeling -- Mapping and Associations -- General Comments on ANNs, Statistics, and Artificial Intelligence -- Processing Elements -- Summation Functions -- Transfer Functions -- Output Functions -- Error Functions -- Learning Rules -- Collections of Processing Elements -- Different Types of Artificial Neural Network -- Adaptive Resonance Theory (ART) Networks -- Backpropagation (BP) and Related Networks -- Biassociative Memory (BAM) Networks -- Counterpropagation Networks -- Generalized Regression Networks (GRN) -- Hopfield Networks -- Kohonen Self-organizing Map (SOM) Networks -- Perceptron Networks -- Radial Basis Function (RBF) Networks -- Recirculation Networks -- Miscellaneous Networks -- Practical Considerations in Solving Problems with Neural Networks -- What Type of Network? -- Data Preprocessing. , Variable Selection, Reduction, and Orthogonalization -- Training and Testing Sets -- Training the Network -- Learning Versus Generalization -- Performance Metrics -- Classification Problems -- Nonclassification, Supervised Learning Problems -- Miscellaneous Remarks -- Analysis of Neural Networks -- Concluding Remarks -- Appendix: Neural Network Software -- References -- Use of Force Fields in Materials Modeling -- Introduction -- The Force Field Approach to Describing Structures of Materials -- What Are Force Fields? -- Ion Pair and Shell Model Potentials -- Molecular Mechanics Force Fields -- Comparison of Ion Pair and Molecular Mechanics Force Fields -- Force Field Parameterization -- Ab Initio Based Force Fields -- Empirical Force Fields -- Transferability -- Rule-Based Force Fields -- Application of Force Fields in Materials Science -- Metal Oxides and Ceramics -- Superconductors -- Zeolites and Related Microporous Materials -- Glasses -- Polymers -- Conclusions -- Acknowledgments -- References -- Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities -- Introduction -- Theory -- Methodology Overview -- Computational Details -- Molecular Mechanics Force Fields -- Treatment of Long-Range Forces -- Polarization -- Bond Length Constraints -- Treatment of Boundaries -- Solvent Models -- Convergence of Free Energy Results -- Free Energy Perturbation Calculations for Small Molecules -- Tautomerization -- Ionization -- Log P -- Covalent Hydration -- Solvation -- Free Energy Perturbation Calculations for Macromolecules -- Nonprotein-Ligand Complexes -- Protease Inhibitors -- Lyases -- Oxidases and Reductases -- Allosteric Binding Site Ligands -- DNA Binding Proteins -- Miscellaneous Studies -- Guide to Structure-Based Ligand Optimization -- Computer Model -- Characterization of the Binding Site -- Lead Generation. , Optimization of Lead Compounds -- Optimization of Ligands to HIV-1 Protease: Using the FEP Method -- Design Considerations -- X-Ray Structures of HIV-1 Protease Complexes -- Force Field Parameters -- Computational Details for Solvent -- Computational Details for Complex -- Computer Model Validation -- Validation of FEP Methodology -- Convergence and Error Analysis -- Binding Affinity Predictions -- Summary -- Conclusions -- Advantages of Free Energy Calculations -- Limitations of Free Energy Calculations -- Brief Guide for Free Energy Calculations and Their Use in Ligand Optimization -- Acknowledgments -- References -- Author Index -- Subject Index.

Note: Intro -- Reviews in Computational Chemistry Volume 15 -- Contents -- Kohn-Sham Density Functional Theory: Predicting and Understanding Chemistry -- Introduction -- Scope -- Historical Overview -- Outline -- The Kohn-Sham Molecular Orbital Model -- MO-Theoretical Analysis of Chemical Bonding: Beyond a Qualitative MO Theory -- Introduction -- Electrostatic Interaction and Steric Repulsion -- Attractive Orbital Interactions -- Interplay of Steric Repulsion and Orbital Interaction -- The Electron Pair Bond and Pauli Repulsion -- Introduction -- The Potential Energy Surfaces of CN and CP Dimers -- Bonding in CN and CP Dimers: Qualitative Considerations -- Bonding in CN and CP Dimers: Quantitative Analysis -- Summary -- The Three-Electron Bond and One-Electron Bonding -- Introduction -- The Fragment Approach to the Three-Electron Bond -- Summary -- The Role of Steric Repulsion in Bonding Models -- Introduction -- Structure and Inversion Barrier in AH.3 Radicals -- Interhydrogen Steric Repulsion Versus A-H Electronic Interaction in AH -- 3 Radicals -- Summary -- Strongly Polar Electron Pair Bonding -- Introduction -- The Polar C-Li Electron Pair Bond in Monomeric CH3Li -- The Polar C-Li Electron Pair Bond in Tetrameric CH3Li -- Analysis of the Charge Distributions in CH3Li Oligomers -- Summary -- Conclusions and Outlook -- Acknowledgments -- References -- A Computational Strategy for Organic Photochemistry -- Introduction -- Modeling Photochemical Reactions -- Aims and Objectives -- Characterization of Conical Intersections -- "Noncrossing Rule" and Conical Intersections -- Conical Intersection Structure -- An Example: The S,/So Conical Intersection of Benzene -- Practical Computation of Photochemical Reaction Paths -- Quantum Chemical Methods and Software for Excited State Energy and Gradient Computations -- Conical Intersection Optimization. , Locating Decay Paths from a Conical Intersection -- Semiclassical Trajectories -- Mechanistic Organic Photochemistry: Some Case Studies -- Three-Electron Conical Intersections of Conjugated Hydrocarbons -- Conical Intersections of n--7t" Excited States -- The S1/S0 Conical Intersection of Protonated Schiff Bases -- Competitive Ground State Relaxation Paths from Conical Intersection -- Competitive Excited State Photoisomerization Paths -- Conclusions -- Acknowledgments -- References -- Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds -- Introduction -- Enthalpies of Formation -- Overview of Theoretical Methods -- Test Sets for Assessments of Predictive Methods -- Quantum Chemical Methods -- Ab Initio Molecular Orbital Methods -- Extrapolation Methods -- Density Functional Methods -- Semiempirical Molecular Orbital Methods -- Illustrative Examles of Quantum Chemical Methods -- Empirical Methods -- Bond Energy Approach -- Benson's Method -- Correcting from the Condensed Phase to the Gas Phase -- Concluding Remarks -- Acknowledgments -- References -- The Development of Computational Chemistry in Canada -- Introduction -- In the Beginning There Was Quantum Chemistry and Spectroscopy -- Expo 67 and Fullerenes -- Canadian Association of Theoretical Chemists -- Demographic Facts -- Toward a Steady-State Population -- Family Trees and Trends -- Departmental Histories -- University of Montreal (1954) -- University of British Columbia (1957) -- University of Alberta (1959) -- University of Ottawa (1959) -- University of Saskatchewan (1959) -- Laval University (1961) -- University of Toronto (1961) -- University of Waterloo (1961) -- McGill University (1962) -- Queen's University (1962) -- University of New Brunswick (1962) -- McMaster University (1963) -- University of Calgary (1964) -- University of Western Ontario (1965). , York University (1965) -- Simon Fraser University (1966) -- University of Manitoba (1966) -- Carleton University (1970) -- Dalhousie University (1970) -- University of Guelph (1970) -- University of Sherbrooke (1970) -- Computational Chemistry in Canadian Industry -- Hypercube, Inc. -- Ayerst Laboratories -- Merck Frosst Canada Inc. -- Xerox Research Centre of Canada -- ORTECH, Inc. -- BioChem Therapeutic -- Advanced Chemistry Development, Inc. -- SynPhar Labs, Inc. -- Bio-Mega -- Astra -- Other Examples -- History of Theoretical Chemistry at the National Research Council of Canada -- High-Performance Computing in Canada -- Major Conferences -- Fifth International Congress on Quantum Chemistry -- Second World Congress of Theoretical Organic Chemists -- Canadian Computational Chemistry Conference -- Spreading Their Wings -- Acknowledgments -- References -- Author Index -- Subject Index.

Note: Intro -- Reviews in Computational Chemistry 9 -- Contents -- Peptide Mimetic Design with the Aid of Computational Chemistry -- Introduction -- Peptide Mimetic Design Considerations -- Case Studies in Peptide Mimetic Design -- Human Leukocyte Elastase -- The Renin-Angiotensin System -- Renin -- Angiotensin-Converting Enzyme -- Angiotensin II -- Combined Angiotensin-Converting Enzyme and Neutral Endopeptidase -- Human Immunodeficiency Virus Protease -- CD4 -- Thermolysin -- Collagenase -- a-Amylase -- Fibrinogen -- Thrombin -- Endothelin-1 -- Somatostatin -- Growth Hormone -- Oxytocin -- Neurotensin -- Enkephalin -- Dopamine Receptor Modulating Peptide -- Thyrotropin-Releasing Hormone -- Substance P -- R-Loop of Interleukin la -- Bradykinin -- Complementarity-Determining Regions -- Gramicidin-S -- Hypertrehalosemic Hormone -- Erabutoxin B -- Jaspamide -- Taste Molecules -- Other Mimetics -- Summary of Computational Chemistry Techniques Applied to Peptide Mimetic Design -- Nomenclature -- Acknowledgment -- References -- Free Energy by Molecular Simulation -- Introduction -- Classical Statistical Thermodynamical Background -- Computer Simulation Methods -- Hamiltonian -- Monte Carlo Simulations -- Molecular Dynamics Simulations -- Thermodynamic Perturbation -- Thermodynamic Integration -- Thermodynamic Cycles -- Potentials of Mean Force -- Free Energy Evaluations in Practice -- Hamiltonian Coupling -- Creation and Annihilation of Atoms -- Constraints -- Conformational Isomeric States -- Long-Range Interactions -- Boundary Conditions -- Error Analysis -- Sensitivity of Calculated Free Energies to Force Field Parameters -- Electronic Polarization -- Atomic Replacement Calculations -- Recommendations -- Free Energy Methodology -- Choice of Pathway -- Standard Protocol -- Analysis of Results -- Conclusion -- Acknowledgment -- References. , The Application of Molecular Modeling Techniques to the Determination of Oligosaccharide Solution Conformations -- Introduction -- Carbohydrate Conformational Analysis: The Motivation and the Challenge -- Electronic Effects and Carbohydrate Conformation -- Carbohydrate Force Fields: An Overview -- Hard Sphere Exo-Anomeric (HSEA) and Monte Carlo Methods -- MM2/MM3 -- Macromolecular Force Fields and Molecular Dynamics Simulations -- Role of Water-Sugar Interactions -- Conclusions -- References -- Molecular Mechanics Calculated Con formational Energies of Organic Molecules: A Comparison of Force Fields -- Introduction -- The Principles of Molecular Mechanics -- Forms of Potential Energy Functions -- Bond Stretching/Compression Functions -- Bond Angle Bending Functions -- Torsional Functions -- Van der Waals Functions -- Electrostatic Functions -- Cross-Terms -- Conjugated Systems -- Parameterization -- Comparisons of Calculated Conformational Energies -- Reproducibility of Conformational Energies -- Summary and Conclusions -- Acknowledgments -- References -- Molecular Shape Descriptors -- Introduction -- Hierarchical Levels of Molecular Shape and Shape Descriptors -- Some Notions Regarding Molecular Shape and Scaling -- Classification of Molecular Models and Shape Descriptors -- Characterizing the Nuclear Geometry -- Measures of Molecular Size and Anisometry -- Configurational Averages of Zero-Dimensional Descriptors -- One-Dimensional Descriptors: Atomic Radial Distribution Functions -- Two-Dimensional Descriptors: Distance Maps and Related Descriptions -- Characterizing Molecular Shape by Geometry and Connectivity -- Simple Descritors That Use Geometry and Connectivity -- Detailed Shape Description of Macromolecular Folding -- Shape Descriptors of Macromolecular Topology. , Characterizing the Three-Dimensional Molecular Body: The Shape of Molecular Surfaces -- Simple Descriptors: Volume, Surface Area, and Fractality -- Geometrical and Topological Characterizations -- Shape Group Analysis of Surfaces and Related Techniques -- Elastic Surfaces and Shape Equations -- Some Comments on Shape Dynamics of Flexible Molecules -- Some Comments on Descriptors of Relative Shape -- Relative Descriptors for OD and 1D Models -- Relative Descriptors for 2D and 3D Models -- Summary -- Acknowledgments -- Appendix: Moments of Inertia and Radius of Gyration -- References -- Author Index -- Subject Index.

Note: Reviews in Computational Chemistry II -- Contents -- A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules -- Introduction -- Conformational Analysis: Some Concepts -- Conformational Searching: Statement of the Problem -- Systematic Search Methods -- Tree Representations and Their Use in Systematic Search -- Implementations of the Systematic Search -- Model Building Approaches and Symbolic Representations of Conformation -- Molecular Models -- The "Build-up" Approach: Polypeptides and DNA -- Symbolic Representations of Conformation and Their Use in Searching Conformational Space -- Crystallographic Databases and Conformational Analysis -- Random Search Methods -- Cartesian and Internal Coordinate Random Search Methods -- Random Simulations and the Metropolis Algorithm -- Further Uses of the Metropolis Algorithm in Random Searching Methods -- Simulated Annealing -- Distance Geometry and Related Methods -- The Representation of Conformations Using Interatomic Distances -- Detailed Description of the Distance Geometry Method -- The Generation of Conformations of a Simple Molecule Using Distance Geometry and Some Applications of the Method -- Energy Embedding -- Related Approaches: Target Function Minimization, the Diffusion Equation Method, and the Ellipsoid Algorithm -- Molecular Dynamics -- The Molecular Dynamics Method -- Using Molecular Dynamics to Search Conformational Space -- Restrained Molecular Dynamics -- Summary and Conclusions -- References -- Simplified Models for Understanding and Predicting Protein Structure -- Introduction -- Molecular Mechanics Modeling -- Knowledge-Based Modeling -- Semiempirical and Polymer Models -- Conclusion -- References -- Molecular Mechanics: The Art and Science of Parameterization -- Introduction -- Molecular Mechanics Theory -- History of Molecular Mechanics. , Formulation of Molecular Mechanics -- Bond Stretching -- Angle Bending -- Torsional Angles -- van der Waals -- Electrostatics -- Cross Terms -- Heats of Formation -- Parameterization -- References -- New Approaches to Empirical Force Fields -- Force Fields and Their Physical Significance -- Introduction -- The Basic Paradigm -- System of Coordinates, Spectroscopic versus Empirical Force Fields, and the Assumption of Transferability -- The Energy Expression -- Determining Force Constants -- Derivation of "Quantum Mechanical" Force Fields from Ab Initio Data: The Theory of Energy Derivatives -- Specific Force Constant Analysis and Computational Observables -- Applications of the Theory of Energy Second Derivatives -- An lnitio Dihedral Potentials -- Nonbonded Interactions -- Conclusions -- References -- Calculating the Properties of Hydrogen Bonds by ab Initio Methods -- Definition of a Hydrogen Bond -- Geometry -- Energetics -- Electronic Rearrangement -- Spectroscopic Criteria -- Exceptions Make the Rules -- Theoretical Framework -- Perturbation Theory vs. Supermolecular Approach -- Components of Interaction Energy -- Computational Issues -- Superposition Error -- Historical Perspective -- Secondary Effects -- Conclusions -- Geometry -- Simple Predictive Models -- Basis Set Dependence -- Anisotropy of Correlated Components -- Interaction Energy -- Hartree-Fock Level -- Correlation Contributions -- Level of Correlation -- Potential Energy Surfaces -- Water Dimer -- HF Dimer -- Ammonia Dimer -- Flexibility and Vibrational Frequencies -- Energetic Requirements for Geometric Deformation -- Vibrational Frequencies -- Influence of Basis Set, Correlation, and Anharmonicity -- Summary and Recommendations -- References -- Net Atomic Charge and Multipole Models for the ab Initio Molecular Electric Potential -- Introduction. , Electronegativity, Net Atomic Charges, and Molecular Multipoles -- Calculation of ab lnitio Wavefunctions -- Observed and Calculated Dipole Moments -- Population Analysis of the Wavefunction -- Calculation and Display of the Electric Potential -- Multipole Expansion of the Wavefunction -- Calculation of Potential-Derived Point Charges and Multipoles in Molecules -- Least-Squares Derivation of PD Net Atomic Charges -- Location of Grid Points for the Electric Potential -- Goodness-of-Fit Parameters -- Results for Potential-Derived Net Atomic Charges -- Hydrocarbons -- Halogen Compounds -- Oxygen Compounds -- Nitrogen Compounds (Except Amides) -- Amides -- Miscellaneous Compounds -- Potential-Derived Monopole Models with Additional Nonatomic Sites -- Lone Pair Sites in Azabenzenes -- Lone Pair and Bond Charge Models for Fluorohydrocarbons -- Lone Pair Sites in Water Monomer and Dimer -- Potential-Derived Multicenter Multipole Models -- PD Atomic Multipole Models -- PD Bond Dipole Models -- Electrostatics in Molecular Mechanics -- Conclusion -- References -- Molecular Electrostatic Potentials and Chemical Reactivity -- Introduction -- The Electrostatic Potential: Definition and Significance -- Historical Survey -- Electrophilic Processes -- Biological Recognition Processes -- Hydrogen Bonding -- Computational Methodology -- Rigorous Evaluation of V(r) -- Approximate Evaluation of V(r) -- Some Recent Applications -- Nucleophilic Processes -- Correlations with Other Properties -- Strained Molecules -- Summary -- References -- Semiempirical Molecular Orbital Methods -- Introduction -- Hartree-Fock Theory -- Approximate Formulations of the Fock Equations -- Zero Differential Overlap Methods -- Extended Huckel Schemes -- Parameterization -- Complete Neglect of Differential Overlap Schemes -- Intermediate Neglect of Differential Overlap. , Neglect of Diatomic Differential Overlap -- Extended Huckel Theories -- Current Reliability of Semiempirical Methods -- MIND0 / 3 -- MNDO, AM1, and PM3 -- SINDO1 -- INDO/S -- Semiempirical Quantum Chemistry -- Properties -- Reactions -- Summary -- References -- The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Modeling -- Introduction -- Background for Molecular Connectivity -- Development of Molecular Connectivity -- Molecular Connectivity Approach -- Molecular Connectivity Method -- Order Zero: 0x -- Order One: 1x -- Higher Order Chi Indexes: mxr and mxvt -- QSAR Applications of Molecular Connectivity Chi Indexes -- Chromatographic Retention -- Molar Volume -- Heat of Atomization of Hydrocarbons and Alcohols -- Ionization Potential -- Molar Refraction -- QSAR of General Anesthetics -- Phenol Toxicity to Fathead Minnows -- Inhibition of Microsomal p-Hydroxylation of Anilines by Alcohols -- Antiviral Activity of Benzimidazoles against Flu Virus -- Bioconcentration Factor for Phenyl and Biphenyl Compounds -- Physical Significance of Molecular Connectivity Indexes -- Characterization of Molecular Shape -- Background: Steric or Shape Influence -- Methods for Steric Quantification -- Quantitation of Influence on Properties -- Geometric Models -- Object Comparisons -- Structure Description Based on Topology or Chemical Graph Theory -- Model of Molecular Shape Based on Chemical Graph Theory -- General Model -- First-Order Shape Attribute -- Second-Order Shape Attribute -- Third-Order Shape Attribute -- A Shape Index from Zero-Order Paths -- Shape Information in the Kappa Values -- Encoding Atom Identity -- Modified Atom Count -- Effect of Alpha Inclusion in Kappas -- Kappa Index Values for Small Molecules -- Molecular Shape Quantitation -- General Model -- Higher Order Indexes -- Additivity -- General Applications. , Shape Similarity -- Cavity Definition -- Molecular Flexibility -- Specific Application of Kappa Indexes -- The Pitzer Acentric Factor -- Comparison with the Taft Steric Parameter -- Enzyme Inhibitors -- Toxicity Analysis -- Characterization of Skeletal Atoms, the Topological State -- References -- The Electron-Topological Approach to the QSAR Problem -- Introduction -- Background -- Brief Review of QSAR Methods -- Basic Ideas of the Electron-Topological Approach -- Algorithms and Computer Implementation -- Applications to Specific Problems -- Concluding Remarks -- References -- The Computational Chemistry Literature -- Introduction -- Nobel Laureates -- Most Cited Long-standing Papers -- Most Cited Papers in 1984 and 1985 -- Some Papers Recently Receiving Recognition -- Comparison of Computational Chemistry Journals -- Conclusion -- References -- Appendix: Compendium of Software for Molecular Modeling -- Introduction -- Themes -- References -- Software -- Personal Computers -- Minicornputers-Superrninicomputers-Supercomputers- Workstations -- Author Index -- Subject Index.

Note: Intro -- Reviews in Computational Chemistry Volume 12 -- Contents -- Calculation of the Free Energy and the Entropy of Macromolecular Systems by Computer Simulation -- Introduction -- Statistical Mechanics of Fluids and Chain Systems -- The Partition Function and the Boltzmann Probability Density -- The Absolute Entropy and Free Energy as Ensemble Averages -- Fluctuations -- Entropy and Free Energy Differences by "Calorimetric" Thermodynamic Integration -- The Kirkwood and Zwanzig Equations -- Basic Sampling Theory and Simulation -- Importance Sampling -- The Monte Carlo and Molecular Dynamics Methods -- Application of the MC and MD Methods to Macromolecular Systems -- Direct Methods for Calculating the Entropy of Proteins -- The Harmonic Approximation -- The Quasi-Harmonic Approximation -- Free Energy from < -- exp[+E/kBT] > -- -- Applications of Integration and Importance Sampling Techniques -- Calculations by Calorimetric Integration and Perturbation Methods -- Umbrella Sampling and the Potential of Mean Force -- Thermodynamic Cycles -- Historical Perspective -- Free Energy of Enzyme-Ligand Binding -- Application of Thermodynamic Cycles -- New Perturbation-Related Procedures -- Entropy from Linear Buildup Procedures -- Step-by-Step Construction Methods for Polymers -- Direct Methods for Calculating the Entropy from MC and MD Samples -- The Stochastic Models Method of Alexandrowicz and Its Implications -- Additional Methods for Calculating the Entropy -- The Multicanonical Approach -- Calculation of Entropy by Adiabatic Switching -- Four Additional Methods -- Summary -- Acknowledgments -- References -- Molecular Dynamics with General Holonomic Constraints and Application to Internal Coordinate Constraints -- Introduction -- The Analytical Method of Constraint Dynamics -- Computation of the Forces of Constraints and Their Derivatives. , Numerical Integration of the Equations of Motion -- Error Analysis of the Analytical Method -- Method of Edberg, Evans, and Morriss in Context -- The Method of Undetermined Parameters -- Computation of the Partially Constrained Coordinates -- Computation of the Undetermined Parameters and the Constrained Coordinates -- Error Analysis of the Method of Undetermined Parameters -- Using the Method of Undetermined Parameters with the Basic Verlet Integration Algorithm -- The Matrix Method -- SHAKE -- Physical Picture of SHAKE for Internal Coordinate Constraints -- Method of Tobias and Brooks in Context -- Application to Internal Coordinate Constraints -- Bond-Stretch Constraints -- Angle-Bend Constraints -- Torsional Constraints -- Angle Constraint Versus Triangulation -- Using the Method of Undetermined Parameters with the Velocity Verlet Integration Algorithm -- RATTLE for General Holonomic Constraints -- Application to Bond-Stretch, Angle-Bend, and Torsional Constraints -- Further Developments and Future Prospects -- Acknowledgments -- References -- Computer Simulation of Water Physisorption at Metal-Water Interfaces -- Introduction -- Modeling -- Treatment of Water -- Treatment of Metal-Water Interactions -- Simulation Methods -- Common Aspects of the Methods -- Molecular Dynamics -- Monte Carlo Methods -- Analysis and Results for Metal-Water Interfaces -- Visualization -- Electron Density for Jellium -- Structure -- Dynamics -- Miscellaneous Properties -- General Discussion of the Properties of Metal-Water Interfaces -- Summary and Perspective -- Future Developments -- Acknowledgments -- References -- Quantum-Based Analytic Interatomic Forces and Materials Simulation -- Introduction and Background -- Historical Perspective -- Analytic Potentials and Materials Simulation -- Framework for Bonding: Density Functional Theory. , Bridge to Analytic Forms: The Harris Functional -- Tight Binding Method -- Second Moment Approximation and Finnis-Sinclair Potential -- Empirical Bond-Order Model -- EffectiveMedium Theory -- Embedded-Atom Method -- Fitting Databases -- Acknowledgments -- References -- Quantum Mechanical Methods for Predicting Nonlinear Optical Properties -- Introduction -- Nonlinear Optical Property Basics -- Examples of Applications of Nonlinear Optics -- Second Harmonic Generation (SHG) -- Electrooptic Modulation -- Optical Bistability (Optical Signal Processing) -- Degenerate Four-Wave MixingPhase Conjugation (Imaging Enhancements) -- Frequency Upconversion Lasing -- Definitions of Molecular Properties -- Methods for Molecular Electronic (Hyper)Polarizability Calculations -- Finite Field Method -- Sum-Over-States Methods -- Time-Dependent Hartree-Fock -- Other Methods -- Practical Considerations -- Basis Sets -- Other Considerations -- Beyond MoIecular Electronic Calculations -- Molecular Vibrational Calculations -- Condensed Phase Problems -- Summary -- Acknowledgments -- References -- Sensitivity Analysis in Biomolecular Simulation -- Introduction -- Methods -- Dependence of Sensitivity Results on the Choice of Force Fields -- Convergence Issues -- Applications -- Determinants of (Bio)molecular Properties -- Molecular Recognition -- Green's FunctiodPrincipal Component Analysis and Essential Dynamics -- Error Propagation -- Potential Energy Function Refinement -- Conclusions -- Acknowledgments -- References -- Computer Simulation to Predict Possible Crystal Polymorphs -- Introduction -- Theory and Computational Approaches -- Crystals -- Thermodynamics -- Computational Techniques -- Crystal Structure Prediction Methods -- Related Software -- Comparison of Different Techniques -- Using Experimental Data -- Predicting and Evaluating Crystal Structures. , Example: Polymorph Prediction for Estrone -- Application Examples -- Acknowledgments -- References -- Computational Chemistry in France: A Historical Survey -- Introduction -- Early Age of Theoretical Chemistry -- Computational Quantum Chemistry -- Statistical Mechanics -- Software Development -- Computational Facilities -- Industry -- Teaching Computational Chemistry -- Government Funding -- Conclusion -- Acknowledgments -- References -- Author Index -- Subject Index.

Note: Reviews in Computational Chemistry 8 -- Contents -- Computations in Treating Fullerenes and Carbon Aggregates -- Introduction -- Relevant Methodology -- Hypersurface Stationary Points -- Semiempirical Methods -- Ab Initio Computations -- Algebraic Enumerations -- Absolute and Relative Stabilities of Fullerenes -- Illustrative Applications -- Small Carbon Clusters -- Higher Fullerenes -- Functionalized Fullerenes -- Acknowledgment -- References -- Pseudopotential Calculations of Transition Metal Compounds: Scope and Limitations -- Introduction -- Scope -- Application of Quantum Mechanical Methods -- Heavy-Atom Molecules -- Pseudopotential Methods: An Overview -- Technical Aspects of Pseudopotential Calculations -- General Rules for Calculating Transition Metal Complexes with ECP Methods -- Some Remarks About Calculating Transition Metal Compounds and Molecules of Main Group Elements -- Results and Discussion of Selected Examples -- Carbonyl Complexes -- Methyl and Phenyl Compounds of Late Transition Metals -- Carbene and Carbyne Complexes -- Oxo and Nitrido Complexes -- Alkyne and Vinylidene Complexes in High Oxidation States -- Chelate Complexes of TiCl, and CH3TiCl3 -- Conclusion and Outlook -- Acknowledgment -- References -- Effective Core Potential Approaches to the Chemistry of the Heavier Elements -- Introduction -- 0bjective -- The Challenges of Computational Chemistry of the Heavier Elements -- Increasing Numbers of Electrons and Orbitals -- The Electron Correlation Problem -- Relativistic Effects -- The Promise of Computational Chemistry Across the Periodic Table -- Effective Core Potential Methods -- Derivation of Effective Core Potentials and Valence Basis Sets -- Selecting a Generator State -- Nodeless Pseudo-orbitals -- Relativistic Effective Potentials (REPs) and Averaged REPs -- Analytical Representation for the Pseudo-orbitals. , Analytical Forms for the Potentials -- Optimized Valence Basis Sets -- Computational Methods -- Representative Examples: Main Group Chemistry -- Alkali and Alkaline Earth Metals -- Triels -- Tetrels -- Pnictogens -- Representative Examples: Transition Metal and Lanthanide Chemistry -- Core Size -- Valence Basis Sets -- Energetics -- Metal-Oxo Complexes -- Multiply Bonded Transition Metal Complexes of Heavier Main Group Elements -- Bonding in Heavily loaded Complexes -- Methane Activation -- Summary and Prospectus -- Acknowledgments -- References -- Relativistic Effects in Chemistry -- Introduction -- Nonrelativistic Quantum Mechanics -- General Theory -- The LCAO Expansion -- Electron Correlation -- Relativistic Quantum Mechanics -- General Principles -- The Klein-Gordon Equation -- The Dirac Equation -- Transformation to Two- and One-Component Theory -- The Foldy-Wouthuysen Transformation -- The "Douglas-Kroll" Transformation -- Applications -- Four-Component Methods -- Comparison of Methods -- Conclusions -- References -- The Ab Initio Computation of Nuclear Magnetic Resonance Chemical Shielding -- Introduction -- The General Problem -- Theory -- The Basic Quantum Mechanics -- The Gauge Problem -- What Is Observed? -- Shift and Shielding Scales -- How Well Can We Do? -- A Sample Calculation -- Examples -- A Calculation on a Large Molecule -- Deshielding in the Phospholide Ion -- Some Approaches to Treating Large Systems -- An Ab Initio Approach to Secondary and Tertiary Effects in Proteins -- A Molecular Dynamics and Quantum Mechanical Study of Water -- Effects of Correlation -- Concluding Remarks -- References -- Author Index -- Subject Index.

Note: Intro -- Reviews in Computational Chemistry Volume 22 -- Preface -- Contents -- Contributors -- Contributors to Previous Volumes -- 1. Protein Structure Classification -- Introduction -- Classification and Biology -- The Biomolecular Revolution -- Basic Principles of Protein Structure -- Visualization -- Protein Building Blocks -- Protein Structure Hierarchy -- Three Types of Proteins -- Geometry of Globular Proteins -- Protein Domains -- Resources on Protein Structures -- Protein Structure Comparison -- Automatic Identification of Protein Structural Domains -- The Rigid-Body Transformation Problem -- Protein Structure Superposition -- cRMS: An Ambiguous Measure of Similarity -- Differential Geometry and Protein Structure Comparison -- Upcoming Challenges for Protein Structure Comparison -- Protein Structure Classification -- The Structure Classification of Proteins (SCOP) -- The CATH Classification -- The DALI Domain Dictionary (DDD) -- Comparing SCOP, CATH, and DDD -- Conclusions -- Acknowledgments -- Appendix -- References -- 2. Comparative Protein Modeling -- Introduction -- Anatomy of a Comparative Model -- Step 1: Searching for Related Sequences and Structures -- Expert Protein Analysis System (ExPASy) -- BLAST and PSI-BLAST -- Protein Data Bank (PDB) -- Sequence Alignment and Modeling System with Hidden Markov Models -- Threading -- Threader -- Example: Finding Related Sequences and 3-D Structures -- Step 2: Sequence Alignment -- Preparing the Sequences -- Alignment Basics -- Similarity Matrices -- Clustal -- Tree-Based Consistency Objective Function for Alignment Evaluation (T-Coffee) -- Divide-and-Conquer Alignment (DCA) -- Example: Aligning Sequences -- Step 3: Selecting Templates and Improving Alignments -- Selecting Templates -- Improving Sequence Alignments With Primary and Secondary Structure Analysis. , Example: Aligning the Target to the Selected Template -- Step 4: Constructing Protein Models -- Satisfaction of Spatial Restraints -- Segment Match Modeling -- Multiple Template Method -- 3D-JIGSAW -- Overall Protein Model Construction Methods -- Example: Constructing a Protein Model -- Step 5: Refinement of Protein Models -- Side-Chains with Rotamer Library (SCWRL) -- Energy Minimization -- Molecular Dynamics -- Molecular Dynamics with Simulated Annealing -- Step 6: Evaluating Protein Models -- PROCHECK -- Verify3D -- ERRAT -- Protein Structure Analysis (ProSa) -- Protein Volume Evaluation (PROVE) -- Model Clustering Analysis -- Example: Evaluation of Protein Models -- Conclusions -- References -- 3. Simulations of Protein Folding -- Introduction -- Theoretical Framework -- Energy Landscape Theory -- Thermodynamics and Kinetics of Folding: Two-State and Multistate Folders -- Protein Models -- Introduction and General Simulation Techniques -- Coarse-Grained Protein Models -- Fully Atomic Simulations -- Advanced Topics: The Transition State Ensemble for Folding -- Transition State and Two-State Kinetics -- Methods for Identifying the TSE -- Conclusions and Future Directions -- Acknowledgments -- References -- 4. The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methods -- Introduction -- System Components -- Time and Space Scale -- Experiments -- Electrostatics -- Long-Range Interaction -- Short-Range Interaction -- Boundary Conditions -- Particle-Based Simulation -- Implicit Solvent: Brownian Dynamics -- Explicit Solvent: Molecular Dynamics -- Flux-Based Simulation -- Nernst-Planck Equation -- The Poisson-Nernst-Planck (NP) Method -- Hierarchical Simulation Schemes -- Future Directions and Concluding Remarks -- References -- 5. Wavelets in Chemistry and Chemoinformatics -- Preface. , Introduction to Wavelets -- Fourier Transform -- Continuous Fourier Transform -- Short-Time Fourier Transformation -- Wavelet Transform -- Continuous Wavelet Transform -- Discrete Wavelet Transform -- Wavelet Packet Transform -- Wavelets vs. Fourier Transforms: A Summary -- Application of Wavelets in Chemistry -- Smoothing and Denoising -- Signal Feature Isolation -- Signal Compression -- Quantum Chemistry -- Classification, Regression, and QSAR/QSPR -- Summary -- References -- Author Index -- Subject Index.