Chemical Modelling: Applications and Theory comprises critical literature reviews of molecular modelling, both theoretical and applied. Molecular modelling in this context refers to modelling the structure, properties and reactions of atoms, molecules & materials. Each chapter is compiled by experts in their fields and provides a selective review of recent literature. With chemical modelling covering such a wide range of subjects, this Specialist Periodical Report serves as the first port of call to any chemist, biochemist, materials scientist or molecular physicist needing to acquaint themselves of major developments in the area. Specialist Periodical Reports provide systematic and detailed review coverage in major areas of chemical research. Compiled by teams of leading authorities in the relevant subject areas, the series creates a unique service for the active research chemist, with regular, in-depth accounts of progress in particular fields of chemistry. Subject coverage within different volumes of a given title is similar and publication is on an annual or biennial basis. Current subject areas covered are Amino Acids, Peptides and Proteins, Carbohydrate Chemistry, Catalysis, Chemical Modelling. Applications and Theory, Electron Paramagnetic Resonance, Nuclear Magnetic Resonance, Organometallic Chemistry. Organophosphorus Chemistry, Photochemistry and Spectroscopic Properties of Inorganic and Organometallic Compounds. From time to time, the series has altered according to the fluctuating degrees of activity in the various fields, but these volumes remain a superb reference point for researchers.

Chapter 1: Computer-Aided Drug Design 2003-2005; 1: Introduction; 2: ADME/Tox and Druggability; 2.1: Druggability and Bioavailability; 2.2: Metabolism, Inhibitors and Substrates; 2.3: Toxicity; 3: Docking and Scoring; 3.1: Ligand Database Preparation; 3.2: Target Preparation; 3.3: Water Molecules; 3.4: Comparison of Docking Methods; 3.5: Scoring; 3.6: New Methods; 3.7: Application of Virtual Screening; 4: De Novo, Inverse QSAR and Automated Iterative Design; 5: 3D-QSAR; 6: Pharmacophores; 7: Library Design; 8: Cheminformatics and Data Mining; 8.1: Scaffold Hopping; 8.2: Descriptors and Atom Typing; 8.3: Tools; 9: Structure-Based Drug Design; 9.1: Analysis of Active Sites and Target Tracability; 9.2: Kinase Modelling; 9.3: GPCR Modelling; 10: Conclusions; References; Chapter 2: Modelling Biological Systems; 1: Introduction; 2: Empirical Force Fields for Biomolecular Simulation: Molecular Mechanics (MM) Methods; 3: Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods; 3.1: Interactions Between the QM and MM Regions; 3.2: Basic Theory of QM/MM Methods; 3.3: Treatment of Long-range Electrostatic Interactions in QM/MM Simulations; 3.4: QM/MM Partitioning Methods and Schemes; 4: Some Comments on Experimental Approaches to the Determination of Biomolecular Structure; 5: Computational Enzymology; 5.1: Goals in Modelling Enzyme Reactions; 5.2: Methods for Modelling Enzyme-catalysed reaction Mechanisms; 5.3: Quantum Chemical Approaches to Modelling Enzyme Reactions: Cluster (or Supermolecule) Approaches, and Linear-scaling QM Methods; 5.4: Empirical Valence Bond Methods; 5.5: Examples of Recent Modelling Studies of Enzymic Reactions; 6: Ab Initio (Car-Parrinello) Molecular Dynamics Simulations; 7: Conclusions; Acknowledgements; References; Chapter 3: Polarizabilities, Hyperpolarizabilities and Analogous Magnetic Properties; 1: Introduction; 2: Electric Field Related Effects; 2.1: Atoms; 2.2: Diatomic Molecules: Non-relativistic; 2.3: Diatomic Molecules: Relativistic; 2.4: Atom-Atom Interactions; 2.5: Inert Gas Compounds; 2.6: Water; 2.7: Small Polyatomic Molecules; 2.8: Medium-size Organic Molecules; 2.9: Organo-metallic Complexes; 2.10: Open Shells and Ionic Structures; 2.11: Clusters, Intermolecular and Solvent Effects, Fullerenes, Nanotubes; 2.12: One and Two Photon Absorption, Scattering, Luminescence etc.; 2.13: Theoretical Developments; 2.14: Oligomers and Polymers; 2.15: Molecules in Crystals; 3: Magnetic Effects; 3.1: Inert Gases, atoms, Diatomics; 3.2: Molecular Magnetizability, Nuclear Shielding, Aromaticity, Gauge Invariance; References; Chapter 4: Applications of Density Functional Theory to Heterogeneous Catalysis; 1: Introduction; 2: Success Stories; 2.1: Success Story Number One: CO Oxidation Over Ru2(110); 2.2: Success Story Number Two: Ammonia Synthesis on Ru Catalysts; 2.3: Success Story Number Three: Ethylene Epoxidation; 3: Areas of Recent Activity; 3.1: Ab Initio Thermodynamics; 3.2: Catalytic Activity of Supported Gold Nanoclusters; 3.3: Bimetallic Catalysts; 4: Areas Poised For Future Progress; 4.1: Catalysis In Reversible Hydrogen Storage; 4.2: Electrocatalysis; 4.3: Zeolite Catalysis; 5: Conclusion and Outlook; Acknowledgements; References; Chapter 5: Numerical Methods in Chemistry; 1: Introduction; 2: Partitioned Trigonometrically-fitted Multistep Methods; 2.1: First Method of the Partitioned Multistep Method; 2.2: Second Method of the Partitioned Multistep Method; 2.3: Numerical Results; 3: Dispersion and Dissipation Properties for Explicit Runge-Kutta Methods; 3.1: Basic Theory; 3.2: Construction of Runge-Kutta Methods Which is Based on Dispersion and Dissipation Properties; 3.3: Numerical results; 4: Four-Step P-Stable Methods with Minimal Phase-Lag; 4.1: Phase-Lag Analysis of General Symmetric 2k - Step, Methods; 4.2: Development of the New Method; 4.3: Numerical Results; 5: Trigonometrically Fitted Fifth-Order Runge-Kutta Methods for the Numerical Solution of the Schr÷dinger Equation; 5.1: Explicit Runge-Kutta Methods for the Schr÷dinger Equation; 5.2: Exponentially Fitted Runge-Kutta Methods; 5.3: Construction of Trigonometrically-fitted Runge-Kutta Methods; 6: Four-step P-stable Trigonometrically-fitted Methods; 6.1: Development of the New Method; 6.2: Numerical results; 7: Comments on the Recent Bibliography; References; Appendix A: Partitioned Multistep Methods - Maple Programme of Construction of the Methods; Appendix B: Maple Program for the Development of Dispersive-fitted and Dissipative-fitted Explicit Runge-Kutta Method; Appendix C: Maple Program for the Development of Explicit Runge-Kutta Method with Minimal Dispersion; Appendix D: Maple Program for the Development of Explicit Runge-Kutta Method With Minimal Dissipation; Appendix E: Maple Program for the Development of the New Four-Step P-Stable Method with Minimal Phase-lag; Appendix F: Maple Program for the Development of the Trigonometrically Fitted Fifth-Order Runge-Kutta Methods; Appendix G: Maple Program for the Development of the New Four-Step P-Stable Trigonometrically-Fitted Method; Chapter 6: Determination of Structure in Electronic Structure Calculations; 1: Introduction; 2: Determining the Global Total-energy Minima for Clusters; 2.1: Random vs Selected Structures; 2.2: Molecular-dynamics and Monte-Carlo Simulations; 2.3: The Car-Parrinello Method; 2.4: Eigenmode Methods; 2.5: GDIIS; 2.6: Lattice Growth; 2.7: Cluster Growth; 2.8: Aufbau/Abbau Method; 2.9: The Basin Hopping Method; 2.10: Genetic Algorithms; 2.11: Tabu Search; 2.12: Combining the Methods; 3: Descriptors for Cluster Properties; 3.1: Energetics; 3.2: Shape; 3.3: Atomic Positions; 3.4: Structural Similarity; 3.5: Structural Motifs; 3.6: Phase Transitions; 4: Examples for Optimizing the Structures of Clusters; 4.1: One-component Lennard-Jones Clusters; 4.2: Two-component Lennard-Jones Clusters; 4.3: Morse Clusters; 4.4: Sodium Clusters; 4.5: Other Metal Clusters; 4.6: Non-metal Clusters; 4.7: Metal Clusters with More Types of Atoms; 4.8: Non-Metal Clusters with More Types of Atoms; 4.9: Clusters on Surfaces; 5: Determining Saddle Points and Reaction Paths; 5.1: Interpolation; 5.2: Eigenmode Methods; 5.3: The Intrinsic Reaction Path; 5.4: Changing the Fitness Function; 5.5: Chain-of-States Methods; 5.6: Nudged Elastic-band Methods; 5.7: String Methods; 5.8: Approximating the Total-energy Surface; 6: Examples for Saddle-point and Reaction-path Calculations; 7: Conclusions; References; Chapter 7: Simulation of Liquids; 1: Introduction; 2: Classical Simulation Techniques; 2.1: Statistical Mechanical Ensembles and Equilibrium Techniques; 2.2: Nonequilibrium MD Simulations and Hybrid Atomistic-continuum Schemes; 3: Potential Energy Hypersurfaces for Liquid State Simulations; 3.1: Quantum Mechanical Interaction Potentials for Weak Interactions; 3.2: Three-Body Interactions; 3.3: Potential Energy Functions for Confined Fluids; 4: Quantum Mechanical Considerations; 4.1: Born-Oppenheimer, Car-Parrinello and Atom-centred Density Matrix Propagation Methods; 4.2: Hybrid Methods; 4.3: Cluster Calculations; 4.4: Dynamical Quantum Effects; 5: Lyapunov Exponents; 6: Thermodynamic and Transport Properties; 6.1: Thermodynamic Properties; 6.2: Free Energies and Entropy Production; 6.3: Transport Properties; 7: Phase Diagrams and Phase Transitions; 7.1: Bulk Fluids; 7.2: Phase Transitions in Confined Systems; 8: Complex Fluids; 8.1: Colloids, Dendrimers, Alkanes, Biomolecular Systems, etc.; 8.2: Polymers; 9: Confined Fluids; 9.1: Nanofluidics, Friction, Stick-slip Boundary Conditions, Transport and Structure; 9.2: Confined Complex Fluids; 9.3: Simple Models; 10: Water and Aqueous Solutions; 11: Conclusions; References; Chapter 8: Combinatorial Enumeration in Chemistry; 1: Introduction; 2: Current Results; 2.1: Isomer Enumeration; 2.2: KekulÚ Structures; 2.3: Walks; 2.4: Structural Complexity; 2.5: Other Enumerations; 3: Conclusion; References; Chapter 9: Many-body Perturbation Theory and Its Application to the Molecular Structure Problem; 1: Introduction; 2: Computation and Supercomputation; 2.1: The Role of Computation; 2.2: Supercomputational Science; 2.3: Literate Programming; 2.4: A Literate Programme for Many-body Perturbation Theory; 3: Increasingly Complex Molecular Systems; 3.1: Large Molecular Systems; 3.2: Relativistic Formulations; 3.3: Multireference Formalisms; 3.4: Multicomponent Formulations; 4: Diagrammatic Many-body Perturbation Theory of Molecular Electronic Structure: A Review of Applications; 4.1: Incidence of the String "MP2" in Titles and/or Keywords and/or Abstracts; 4.2: Comparison with Other Methods; 4.3: Synopsis of Applications of Second Order Many-body Perturbation Theory; 5: Summary and Prospects; References