Alan Hinchliffe 
Chemical Modelling [PDF ebook] 
Applications and Theory Volume 4

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