Note: Reviews in Computational Chemistry Volume 14 -- Contents -- The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials -- Introduction -- Where Are the Electrons? -- Finding an Atom-Based Index -- Why Choose the Molecular Electrostatic Potential? -- Fitting the Charges -- Larger Molecules Provide Challenges -- Wobbly Charges: The Problem of "Conformational Instability" -- A Sampling of Point Distribution Schemes -- Variation with Conformation: How Much Is Too Much? -- Getting to the Root of the Problem -- A Closer Look at the Linear Least Squares Problem -- Linear Least-Squares Fit to the Molecular Electrostatic Potential -- Conclusions and Recommendations -- References -- An Introduction to Coupled Cluster Theory for Computational Chemists -- Introduction -- Fundamental Concepts -- Cluster Expansion of the Wavefunction -- Cluster Functions and the Exponential Ansatz -- Wavefunction Separability and Size Consistency of the Energy -- Formal Coupled Cluster Theory -- Truncation of the Exponential Ansatz -- The Hausdorff Expansion -- A Variational Coupled Cluster Theory? -- An Eigenvalue Approach to Coupled Cluster Theory -- Derivation of the Coupled Cluster Equations -- Normal-Ordered Second-Quantized Operators -- Wick's Theorem for the Evaluation of Matrix Elements -- The Fermi Vacuum and the Particle-Hole Formalism -- The Normal-Ordered Electronic Hamiltonian -- Simplification of the Coupled Cluster Hamiltonian -- The CCSD Energy Equation -- The CCSD Amplitude Equations -- An Introduction to Coupled Cluster Diagrams -- Diagrammatic Representation of the CCSD Energy Equation -- Diagrammatic Representation of the CCSD Amplitude Equations -- Size Extensivity of the Coupled Cluster Energy -- Connection to Many-Body Perturbation Theory -- Perturbational Decomposition of the Cluster Operators. , Perturbation Theory Energies from the Coupled Cluster Hamiltonian -- The (T) Correction -- Computer Implementation of Coupled Cluster Theory -- Factorization of the Coupled Cluster Equations -- Matrix-Based Storage of Integrals and Amplitudes -- Spatial Symmetry Simplifications -- Spin Factorization of the Coupled Cluster Equations -- Atomic-Orbital-Basis Algorithms -- Current Research and Future Directions -- Coupled Cluster Theory for Open-Shell Molecules -- Spin-Restricted Triple-Excitation Corrections -- Brueckner Orbitals in Coupled Cluster Theory -- Future Research Prospects -- Acknowledgments -- References -- Introduction to Zeolite Modeling -- Introduction -- Approaches to Zeolite Modeling -- Computational Approaches -- Scope of Zeolite Modeling -- Models -- Quantum Mechanical Models -- Potential Models for Framework Modeling -- Hybrid Models -- Methods -- Structure and Periodicity -- Summation of Long-Range Interactions -- Energy Minimization -- Method of Molecular Dynamics -- Monte Carlo Methods -- Car-Parrinello Approach -- Some Selected Applications -- Framework Dynamics -- Zeolite/Template Interactions: Tetrabutylammonium and Tetrapropylammonium in MEL and MFI Structures -- Isomorphic Substitution -- Chemical Reactivity -- Future Developments -- Acknowledgments -- References -- Toward More Accurate Model Intermolecular Potentials for Organic Molecules -- Introduction -- Definitions and Limitations of Intermolecular Potential Theory -- Coordinate Systems -- Molecule-Centered Expansions Versus Atom-Atom Models -- The Pairwise Additive Approximation -- Contributions to the Intermolecular Pair Potential -- Long-Range Contributions to the Intermolecular Energy -- Contributions to the Intermolecular Potential from Molecular Overlap -- Methods of Deriving Model Intermolecular Potentials -- Empirical Model Potentials for Organic Molecules. , Ab Initio Potential Energy Surfaces -- Lessons from Intermolecular Perturbation Theory Calculations on Organic Molecules -- Systematic Potentials -- Electrostatic Contribution: Distributed Multipoles -- Induction and Dispersion Contributions: Distributed Polarizabilities -- Short-Range Terms -- Damping Terms -- Examples of Systematic Potentials -- Model Potentials for Organic Molecules Constructed from Ab Initio Charge Distributions and Empirical Fitting -- Computer Coding of Anisotropic Potentials -- Transferability of Potentials for Organic Molecules -- Transferability of Atom-Atom Nonbonded Parameters Between Molecules -- Transferability Between Conformations -- Future Model Potentials -- Acknowledgments -- References -- Nonequilibrium Molecular Dynamics -- Introduction -- Why Nonequilibrium Molecular Dynamics? -- Homogeneous Versus Inhomogeneous Methods -- Molecular Dynamics and Equilibrium Statistical Mechanics -- Microscopic Motion and Macroscopic Observables -- Relation to Microcanonical Ensemble -- Non-Hamiltonian Dynamics -- Dynamical Generation of the NVT Ensemble -- Dynamical Generation of the NPT Ensemble -- Nonequilibrium Molecular Dynamics and Linear Response -- Generalized Equations of Motion -- Linear Response Theory -- The SLLOD Equations of Motion -- Other Types of Flow: GSLLOD Equations of Motion -- Numerical Implementation of SLLOD Dynamics -- Numerically Integrating the SLLOD Equations -- Boundary Conditions -- Applications of Shear Flow -- Viscosity -- Hydrodynamic Boundary Conditions -- Profile-Unbiased Thermostat and String Phases -- Small-Field Methods -- Crack Propagation -- Conclusions and Future Prospects -- Appendix 1: Time Evolution of the Jacobian -- Appendix 2: Geometric Derivation of the Generalized Liouville Equation -- References -- History of the Gordon Research Conferences on Computational Chemistry. , Introduction -- Laying the Groundwork for a Gordon Research Conference on Computational Chemistry -- The First Gordon Research Conference on Computational Chemistry -- The Second Gordon Research Conference on Computational Chemistry -- Recent Developments -- Pictorial History -- Acknowledgments -- Appendix 1: 1986 Program -- Appendix 2: 1988 Program -- References -- Appendix: Published Force Field Parameters for Molecular Mechanics, Molecular Dynamics, and Monte Carlo Simulations -- Introduction -- Sources of Force Field Parameters -- Cited Literature -- References -- Author Index -- Subject Index.

Note: Reviews in Computational Chemistry Volume 13 -- Contents -- Calculations on Open-Shell Molecules: A Beginner's Guide -- Introduction -- Some Background: Closed-Shell Systems -- Hartree-Fock Calculations for Open-Shell Systems: Navigating Between Scylla and Charybdis -- UHF: The Scylla of Spin Contamination -- ROHF: The Charybdis of Symmetry Breaking -- CASSCF: A Panacea? -- Post-SCF Methods: How to Avoid Building Castles on Sand -- Variational Methods (CI) -- Many-Body Perturbation Theory (MBPT) -- Coupled-Cluster (CC) Methods -- Density Functional Methods: An Affordable Alternative -- Problems Associated with Close-Lying Electronic States -- Watch Your Wavefunction! -- Never Take Symmetry for Granted in Open-Shell Molecules! -- Diradicals: More Configurations and More Problems -- Twisted Ethylene (TE) -- Square Cyclobutadiene (CB) -- Trimethylenemethane (TMM) -- Calculated Singlet-Triplet Gaps in Square Cyclobutadiene and Trimethylenemethane -- Lessons to Be Learned from the Calculations -- More Examples -- Geometries -- Thermodynamics -- Kinetics -- Vibrational Spectra -- Excited States -- Electron Spin Resonance Spectra -- Conclusions -- Epilogue -- Acknowledgments -- Glossary -- References -- Basis Set Superposition Errors: Theory and Practice -- Introduction -- Origin and Magnitude of BSSE -- Magnitude of Error -- Attempts at an Exact Theory -- Counterpoise Correction Method -- Energy Decomposition -- Evaluation of Polarization and Charge Transfer Terms -- Increased Functional Space -- Localized Orbital Approach -- Many-Body Perturbation Theory Versus Symmetry-Adapted Perturbation Theory -- Secondary Corrections -- Bond Functions -- Basis Set Recommendations -- Case Studies -- Geometries -- Dipole Moments -- Interaction Energies -- BSSE Corrected Interaction Energies -- Many-Body Counterpoise Correction -- Summary -- Appendix. , Sample Input Deck for Counterpoise Corrections Using Gaussian 92 or 94 -- Sample Input Deck for Counterpoise Corrections Using GAMESS -- References -- Quantum Monte Carlo: Atoms, Molecules, Clusters, Liquids, and Solids -- Introduction -- History and Overview -- Variational Quantum Monte Carlo -- Diffusion Quantum Monte Carlo -- Green's Function Quantum Monte Carlo -- Node Structure -- Importance Sampling -- Trial Wavefunctions -- Fixed-Node Calculations -- Released-Node Calculations -- Exact Cancellation Method -- Difference Schemes -- Excited States -- Use of Pseudopotentials -- A Sampling of Applications -- Potential Energy Surface for the Reaction H + H2 -- H2 + H -- Binding Energies for Silicon Hydrides -- CuH Spectroscopic Constants -- Clusters of Argon and HF: Energies, Structures, and Vibrational Frequency Shifts -- Metallic Lithium -- Homogeneous Electron Gas -- Hydrocarbon Energetics -- Vibrational States of Formaldehyde -- Approaching Liquid Water -- Reaction Path Zero-Point Energy -- Transition State for Cyclooctatetraene Bond Shifting -- Conclusions -- Acknowledgments -- References -- Molecular Models of Water: Derivation and Description -- Introduction -- Properties of Neat Water Systems -- Experimental Results -- Results from Quantum Chemistry -- Intermolecular Interactions -- Electrostatics -- Polarization and Dispersion Interactions -- Exchange Repulsion -- Dimer Interactions -- Model Considerations -- Empirical Versus Nonempirical Parameter Fitting -- Molecular Geometries and Interaction Sites -- Electrostatic Interactions -- Polarizability -- Dimer Potential Surfaces -- Intramolecular Motion -- Quantum Mechanical Corrections -- Molecular Models -- Pre-Computer Era Models -- Computer Era Models -- Observations on Computational Methodology and Model Choice -- Concluding Remarks -- Acknowledgments -- References. , Simulation of pH-Dependent Properties of Proteins Using Mesoscopic Models -- Introduction -- Theory -- Thermodynamics of Protonation Equilibria -- Electrostatics -- Finite Difference Solutions to the Poisson-Boltzmann Equation -- Models -- Treatment of the Multiple Ionization State Problem -- Current Standard pKa, Algorithm -- Improvements -- Experimental Determination of pKa in Proteins -- Nuclear Magnetic Resonance Spectroscopy -- Dependence of Enzyme Kinetics on pH -- Experimental and Theoretical Investigation of pH-Dependent Properties of Proteins -- pH-Dependent Inhibitor Binding -- Protein Stability and Folding -- Amide Hydrogen Exchange -- Dipole Moments of Proteins -- Sample Applications -- Overall Efficiency of the Methodology -- pKa of Hen Egg White Lysozyme Predicted by Different Research Groups -- Total Charge of BPTI Along a Molecular Dynamics Trajectory -- pH-Dependence of Barnase Stability -- Binding of Inhibitors by HIV Protease -- Amide Hydrogen Exchange -- Dipole Moments of Proteins -- Conclusions -- Acknowledgments -- References -- Structure Diagram Generation -- Introduction -- Illustrating the Challenges -- Straightforward Example -- Problems -- Concepts -- Control Flags and Preservation of Styles -- Design Modes -- Selective Redesign -- Circular Free Sweep -- Prefabricated Units -- Coordinate Systems and Units -- Redraw Queue -- Input and Output -- Program Flow -- Preassembly Analysis -- Atom Prioritization -- Recording Incoming Orientations -- Rings -- Chains -- Assembly -- The Head Atom -- Placing Neighbors -- Substituent Placement -- Postassembly -- Molecule Flipping -- Preservation of Molecular Macroorientation -- Making Rings and Chains Horizontal or Symmetrical -- Rotation to Maximum Bond Alignment -- Individual Bond Alignment -- Special Features -- Combating Overlap -- Stereochemistry -- Label Expansion. , Multiattached Atom Labels -- Variable Attachment Points: Bonding to Pi Bonds -- Annotations: Charges, Delocalized Rings, and Arcs -- Fragment Interpositioning -- Ring Template Databases -- RTDs: Some Specifics -- Survey of SDG Programs -- Attributes of Some Notable SDG Programs -- Future Advances -- Classes of Compound Not Treated -- Heuristics for Macrocycles and Condensed Ring Systems -- Use of Fuzzy Symmetry -- Reaction Layout -- Conclusion -- Acknowledgments -- Glossary and Abbreviations -- 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: 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 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 -- Reviews in Computational Chemistry V -- Contents -- The Development of Computational Chemistry in the United States -- Introduction -- Beginnings -- Stored Program Digital Computers -- The Introduction of Computers to Chemistry -- The Development of Model-Based Computationally Intensive Methods -- Expansion and Extension -- Number Crunching -- Artificial Intelligence -- Questions of Patronage -- The Quantum Chemistry Program Exchange -- Government Funding of Chemistry -- The Westheimer Report -- A Bid for Big Science -- Computational Support for Theoretical Chemistry -- Efforts to Create a National Center for Computation in Chemistry -- The National Resource for Computation in Chemistry -- Epilogue -- Acknowledgments -- References -- Applications of Post-Hartree-Fock Methods: A Tutorial -- Introduction -- Independent Particle Model -- Correlation Problem -- Methods for Electron Correlation -- Methods -- Numerical Results for Potential Energy Curves -- Basis Sets -- Molecular Geometries -- Vibrational Spectra -- Photoelectron Spectra -- Ionization Potentials -- Electron Afinities -- Electronic Spectra -- Molecular Properties -- First-Order Properties -- Second-Order Properties -- Nuclear Magnetic Resonance -- Acknowlegments -- Appendix on Quadratic Configuration Interaction (QCl) -- References -- Population Analysis and Electron Densities from Quantum Mechanics -- Introduction: Defining the Grail -- Computational Approaches: Pathways to the Grail -- Orbital-Based Methods -- Spatially Based Methods -- Alternative Methods -- Examples, Comparisons, Benefits, and Faults: Where Is the Grail? -- Basis Set Dependence -- Effect of Electron Correlation on Populations -- Comparisons of Population Analysis of Small Organic Compounds -- Organolithium Compounds -- Resonance in hides , Carboxylic Acids, and Related Compounds. , Suggestions for the User: Avoiding Traps Along the Path -- Conclusion: Is the Pursuit of the Grail Doomed? -- References -- Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations -- Introduction -- Electrostatics -- Theory of Poisson-Boltzmann (PB) Methods -- Short-Range Electrostatic Interactions -- Brownian Dynamics Simulations -- Theory -- Examples -- Conclusion -- Acknowledgments -- References -- Computer Simulation of Lipid Systems -- Introduction -- Polymorphism in Lipid-Water Systems -- Modeling Strategies -- Monte Carlo Importance Sampling38 -- Molecular Dynamics41 -- Brownian Dynamics and Stochastic Boundary Molecular Dynamics -- Interaction Potentials -- Parameterization -- Modeling of Lipid-Water Systems -- Lipid Aggregation Studies -- Dynamic Simulations with Atom-Atom Potentials -- Bilayer Simulations -- Membrane Transport -- Nonlamellar Phases -- Long-Time Dynamics of Bilayers -- Lipid-Cholesterol Interactions -- Conclusions and Future Prospects -- Acknowledgment -- References -- Distance Geometry in Molecular Modeling -- Introduction -- Overview of Distance Geometry as a General Model Builder -- Where Do Distance Constraints Come from? -- Distance Geometry Methods -- Metric Matrix, Linearized Embedding, and Torsional Space Methods -- Metric Matrix Method -- Triangle Inequality Bounds Smoothing -- Distance Selection -- Improving Random Sampling: Metrization -- Refinement -- Distance Error Functions -- Chiral Constraints and the Chiral Error Function -- Four-Dimensional Refinement -- Minimization -- Dynamics -- Generation of Random Conformers for Conformational Analysis -- Cluster Analysis of Conformations -- Pharmacophore Modeling Using the Ensemble Approach -- Examples: Ligand-Receptor Docking -- Substrate Binding to Chymotrypsin -- Interaction of a Macrocyclic Bisintercalator with DNA. , What To Do When Constraints Are Not Satisfied -- Summary -- Acknowledgments -- References -- A Perspective of Modern Methods in Computer-Aided Drug Design -- Introduction -- Overview -- Develop Strategy for Drug Intervention -- Build Model of the Active Site -- Find or Build Potential Ligands -- Dock Ligands and Quantitate Interaction Energy -- Test Hypotheses -- Iteratively Refine Active Site Model -- Implicit Assumptions and Limitations -- Drug Discovery and Applicable Methods and Programs -- Modeling the Receptor -- Finding Binding Pockets -- Evaluating the Model -- Other Aspects of Protein Modeling -- Refining a Model with Molecular Dynamics -- Building New Molecules to Fill a Receptor Site -- Docking Ligands -- Quantitating Affinity -- Defining the Pharmacophore and Comparing Molecular Volumes -- Measuring Molecular Similarity -- Analyzing Data: QSAR -- Generating Pharmacophores by Distance Geometry -- Three-Dimensional Database Searching -- Finding All-Purpose CADD Software -- Conclusions -- Acknowledgments -- References -- Compendium of Software for Molecular Modeling -- Introduction -- Software for Personal Computers -- General Purpose Molecular Modeling -- Quantum Chemistry Calculations -- Databases of Molecular Structures -- Molecular Graphics and Other Applications -- Software for Minicomputers, Superminicomputers, Workstations, and Supercomputers -- General Purpose Molecular Modeling -- Quantum Chemistry Calculations -- Databases of Molecular Structures -- Molecular Graphics and Other Applications -- Author Index -- Subject Index.

Note: Intro -- Reviews in Computational Chemistry 6 -- Contents -- Continuum Solvation Models: Classical and Quantum Mechanical Implementations -- Introduction -- Aqueous Solvation Components -- Aqueous Solvation Modeling -- Thermodynamics of Solvation -- Continuum Solvation Models: Theory and Applicability -- Classical Models -- Quantum Mechanical Models -- Comparison of Continuum Models -- Survey of Selected SMx Results -- Organic Chemistry -- Biochemistry -- Future Directions and Concluding Remarks -- Acknowledgments -- References -- Molecular Mechanics Force Fields for Modeling Inorganic and Organometallic Compounds -- Introduction -- Molecular Mechanics Force Fields and Inorganic Problems -- Reviews -- What Makes Inorganic Problems Different? -- The Valence Force Field and Organic Molecular Mechanics Computations -- Problems in Extending Molecular Mechanics Methods to Inorganic Systems -- Alternatives to the Standard Molecular Mechanics Force Fields -- Applications of Molecular Mechanics to Transition Metal Complexes -- Macrocyclic Ligands -- Open-Chain Ligands -- Ligand Steric Effects -- Organometallic Complexes -- Catalysis -- Transition Metal Clusters -- Main Group Molecular Mechanics -- Small Molecules -- Large Systems -- Summary -- References -- Computational Methods for Modeling Polymers: An Introduction -- Going From Small Molecules to Large Ones -- Overview of the Literature -- The Scope of Quantum Mechanical Calculations for Polymers -- Molecular Mechanics and Atomistic Simulations -- General Principles of Molecular Dynamics -- General Principles of the Monte Carlo Method -- Not All Macromolecules are Alike: What Works for Proteins May Not Work for Synthetic Polymers -- Single Chain Studies -- Simple Polymer Chain Models -- The Venerable Rotational Isomeric State Model -- Dynamic Rotational Isomeric State (DRIS) Model. , Monte Carlo Simulations of Single Chains -- Applications of Molecular Dynamics Studies of Single Chains -- Modeling Amorphous Polymers in the Bulk -- Applications Based on Molecular Dynamics Methods -- Applications Based on Monte Carlo Methods -- Polymer Reference Site Interaction Model (PRISM) -- Concluding Remarks -- Acknowledgments -- References -- High Performance Computing in Computational Chemistry: Methods and Machines -- Introduction -- Background Concepts and Nomenclature -- Nonuniform Memory Access (NUMA) -- Granularity of Tasks -- Load Balance -- Amdahl's Law -- Application Performance Modeling -- Programming Models and Tools -- Parallel Programming Languages and Environments -- High Performance FORTRAN -- Message Passing -- Ada -- Occam -- Linda -- Strand and PCN -- Requisite Computer Science Efforts -- Parallel Linear Algebra -- Performance Analysis -- Large-Scale Software and Message Passing -- Partial Review of Chemistry Applications Development -- General Overview -- The LCAP Project -- Molecular Electronic Structure -- Survey of Parallel Electronic Structure Developments -- Molecular Dynamics -- Reactive Scattering and Quantum Dynamics -- Conclusions -- Concept Glossary -- Appendix -- MPP Systems -- MPP Hardware and Software -- MasPar, MP-1 and MP-2 (DECmpp 12000) -- Moderately Parallel Computers -- Computational Chemistry Efforts of Vendors -- Acknowledgments -- References -- Molecular Modeling Software in Use: Publication Trends -- Introduction: Gauging Usefulness of Computational Chemistry Software -- The Publication Record Provides an Answer -- Limitations of Database Searching -- Results from the CJACS File: Onward and Upward -- General Molecular Modeling -- Empirical Force Fields -- Quantum Chemistry -- Molecular Database Management -- Other Comparisons: Drawing, De Novo Design, QCPE. , Corroboration from Other Literature Sources -- The Changing Face of Computational Chemistry -- Conclusions: The Software Market and Software Usage Revealed by the Literature -- References -- Appendix 1: Published Force Field Parameters -- References -- Appendix 2: Compendium of Software for Molecular Modeling -- Introduction -- References -- Software for Personal Computers -- General Purpose Molecular Modeling -- Quantum Chemistry Calculations -- Databases of Molecular Structures -- Molecular Graphics and Other Applications -- Software for Minicomputers, Superminicomputers, Workstations, and Supercomputers -- General Purpose Molecular Modeling -- Quantum Chemistry Calculations -- Databases of Molecular Structures -- Molecular Graphics and Other Applications -- Author Index -- Subject Index.

Note: Intro -- Reviews in computational Chemistrv IV -- Contents -- Ab Initio Calculations on Large Molecules: Methodology and Applications -- Introduction -- Historical Overview -- Software for Large-Scale ab Inirio Calculations -- Time and Hardware Requirements of Large-Scale ab Initio Calculations -- Methodology -- Computation of Two-Electron Repulsion Integrals -- Screening and Approximate Evaluation of Two-Electron Repulsion Integrals -- Symmetry Blocking and Assembly of the Fock Matrix -- Post-SCF Calculations -- Selected Applications -- Inorganic Molecules -- Large Carbon Clusters and Related Species -- Organic Molecules -- Extended Systems -- Conclusions -- Acknowledgments -- References -- Computing Reaction Pathways on Molecular Potential Energy Surfaces -- Introduction -- Potential Energy Surfaces -- Locating Minima and Saddle Point on the PES -- Computer Programs for Calculating Stationary Points -- Defining Geometry -- Locating a Saddle Point -- Optimization Methods -- Examples -- Calculating Minimum Energy Paths (MEPS) -- Mass-Weighted Cartesian Coordinates -- The Minimum Energy Path -- The Reaction Path Hamiltonian and Variational Transition State Theory -- Acknowledgment -- References -- Computational Molecular Dynamics of Chemical Reactions in Solution -- Introduction -- Techniques for Simulating Reaction Dynamics in Solution -- Potential Energy Surfaces and Intermolecular Forces -- Periodic Boundary Conditions -- Initial Conditions -- Integrators -- Data Analysis -- Thermally Activated Reactions -- Simulation of Chemical Reactions with Low Barriers -- Simulation of Chemical Reactions with High Barriers -- Molecular Dynamics Simulations of Ion Pair Association -- Molecular Dynamics Simulations of SN1 Reactions -- Molecular Dynamics Simulations of Proton Transfer Reactions in Solution -- Nonthermally Activated Reactions. , Computer Simulation of I2 Photodissociation -- Diatomic Halo en Photodissociation in Rare Gas Solids -- Other Studies -- Some Related Subjects -- Quantum Transition State Theory -- Steric Effects -- Isomerization Reactions at Liquid Interfaces -- Related Molecular Dynamics Studies -- The Interaction Between Simulation and Models for Solution Reaction Dynamics -- Reaction Epochs -- Recrossing Dynamics and the Grote-Hynes Equation -- The Significance of Gas Phase Dynamics -- The Rise from and Decay to Equilibrium and Linear Response Theory -- Modeling the Full Reaction Dynamics: Stochastic Dynamics and the Generalized Langevin Equation -- Concluding Remarks -- Acknowledgments -- References -- Computational Chemistry in the Undergraduate Curriculum -- Introduction -- Background of Molecular Modeling in the Curriculum -- Curriculum Issues Related to Computers and Quantum Chemistry -- General Curriculum Issues -- A Survey of Monographs, Periodicals, and Sources of Software -- Quantum Chemistry -- Ab Initio Theory39-42,57 -- Semiempirical Theory39,41,69,70 -- Molecular mechanics2,39,41,78-80 -- Molecular Dynamics -- A Review of Molecular Mechanics in the Curriculum -- Computational Chemistry at University of South Alabama -- Computational Chemistry at Calvin College -- Computational Chemistry in the Introductory Course -- Beyond the First Year Level -- Numerical Simulation and Chemical Kinetics -- Quantum Chemistry and Computers at St. John's University -- Math Tool Box for Quantum Chemistry -- A Laboratory Manual for Theoretical Chemistry -- Numerical Solutions for Newtonian Physics -- Numerical Solutions for Schrodinger's Equation -- Quantum Mechanics of Two-Electron Atoms and Ions -- Self-consistent Field Theory -- A Molecular Orbital Calculation on the Hydrogen Molecule Ion -- MO, VB, and CI Variational Calculations on Molecular Hydrogen. , The Visible Spectra of Cyanine Dyes -- NMR-A Quantum Mechanical Treatment of a Three Proton System -- Computers and Chemistry at California State University, Los Angeles -- Introductory -- Intermediate -- Advanced -- Some Comments about Software -- A Molecular Mechanics Calculation followed by a Semiempirical Quantum Chemical Calculation -- An Application Involving Mathematica to Display Orbital Contours -- A Look to the Future of Molecular Modeling -- Conclusion -- Acknowledgments -- References -- Appendix: Compendium of Software for Molecular Modeling -- Introduction -- References -- Software for Personal Computers -- General Purpose Molecular Modeling -- Quantum Chemistry Calculations -- Databases of Molecular Structures -- Molecular Graphics and Other Applications -- Software for Minicomputers, Superminicomputers, Workstations, and Supercomputers -- General Purpose Molecular Modeling -- Quantum Chemistry Calculations -- Databases of Molecular Structures -- Molecular Graphics and Other Applications -- Author Index -- Subject Index.