Reviews in computational chemistry

著者

• Lipkowitz, Kenny B.
• Boyd, Donald B.
• Parrill, Abby L.

書誌事項

Reviews in computational chemistry

edited by Kenny B. Lipkowitz and Donald B. Boyd

VCH , VCH Verlagsgesellschaft, c1990-

• [1]VCH Publishers
• [1]VCH Verlagsgesellschaft
• [1]Wiley-VCH
• 2. VCH Publishers
• 2. VCH Verlagsgesellschaft
• 2. Wiley-VCH
• 3. VCH Publishers
• 3. VCH Verlagsgesellschaft
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• 4. VCH Verlagsgesellschaft
• 4. Wiley-VCH
• 5. VCH Publishers
• 5. VCH Verlagsgesellschaft
• 6. VCH Publishers
• 7. VCH Publishers
• 7. Wiley-VCH
• 8. VCH Publishers
• 9. VCH Publishers
• 10. VCH Publishers
• 11. Wiley-VCH
• 12. Wiley-VCH
• 13. Wiley-VCH
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注記

Imprint varies: Wiley-VCH (v. 11-)

Includes bibliographical references and indexes

v. 28-: edited by Abby L. Parrill, Kenny B. Lipkowitz

Size: v. 31: 24 cm

内容説明・目次

巻冊次

23 ISBN 9780470082010

内容説明

THIS VOLUME, LIKE THOSE PRIOR TO IT, FEATURES CHAPTERS BY EXPERTS IN VARIOUS FIELDS OF COMPUTATIONAL CHEMISTRY. Volume 23 COVERS LINEAR SCALING METHODS FOR QUANTUM CHEMISTRY, VARIATIONAL TRANSITION STATE THEORY, COARSE GRAIN MODELING OF POLYMERS, SUPPORT VECTOR MACHINES, CONICAL INTERSECTIONS, ANALYSIS OF INFORMATION CONTENT USING SHANNON ENTROPY, AND HISTORICAL INSIGHTS INTO HOW COMPUTING EVOLVED IN THE PHARMACEUTICAL INDUSTRY. FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry." -JOURNAL OF MOLECULAR GRAPHICS AND MODELLING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)." -JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

目次

1. Linear-Scaling Methods in Quantum Chemistry (Christian Ochsenfeld, Joerg Kussmann, and Daniel S. Lambrecht). Introduction. Some Basics of SCF Theory. Direct SCF Methods and Two-Electron Integral Screening. Schwarz Integral Estimates. Multipole-Based Integral Estimates (MBIE). Calculation of Integrals via Multipole Expansion. A First Example. Derivation of the Multipole Expansion. The Fast Multipole Method: Breaking the Quadratic Wall. Fast Multipole Methods for Continuous Charge Distributions. Other Approaches. Exchange-Type Contractions. The Exchange-Correlation Matrix of KS-DFT. Avoiding the Diagonalization Step-Density Matrix-Based SCF. General Remarks. Tensor Formalism. Properties of the One-Particle Density Matrix. Density Matrix-Based Energy Functional. ''Curvy Steps'' in Energy Minimization. Density Matrix-Based Quadratically Convergent SCF (D-QCSCF). Implications for Linear-Scaling Calculation of SCF Energies. SCF Energy Gradients. Molecular Response Properties at the SCF Level. Vibrational Frequencies. NMR Chemical Shieldings. Density Matrix-Based Coupled Perturbed SCF (D-CPSCF). Outlook on Electron Correlation Methods for Large Systems. Long-Range Behavior of Correlation Effects. Rigorous Selection of Transformed Products via Multipole-Based Integral Estimates (MBIE). Implications. Conclusions. References. 2. Conical Intersections in Molecular Systems (Spiridoula Matsika). Introduction. General Theory. The Born-Oppenheimer Approximation and its Breakdown: Nonadiabatic Processes. Adiabatic-Diabatic Representation. The Noncrossing Rule. The Geometric Phase Effect. Conical Intersections and Symmetry. The Branching Plane. Characterizing Conical Intersections: Topography. Derivative Coupling. Electronic Structure Methods for Excited States. Multiconfiguration Self-Consistent Field (MCSCF). Multireference Configuration Interaction (MRCI). Complete Active Space Second-Order Perturbation Theory (CASPT2). Single Reference Methods. Choosing Electronic Structure Methods for Conical Intersections. Locating Conical Intersections. Dynamics. Applications. Conical Intersections in Biologically Relevant Systems. Beyond the Double Cone. Three-State Conical Intersections. Spin-Orbit Coupling and Conical Intersections. Conclusions and Future Directions. Acknowledgments. References. 3. Variational Transition State Theory with Multidimensional Tunneling (Antonio Fernandez-Ramos, Benjamin A. Ellingson, Bruce C. Garrett, and Donald G. Truhlar). Introduction. Variational Transition State Theory for Gas-Phase Reactions. Conventional Transition State Theory. Canonical Variational Transition State Theory. Other Variational Transition State Theories. Quantum Effects on the Reaction Coordinate. Practical Methods for Quantized VTST Calculations. The Reaction Path. Evaluation of Partition Functions. Harmonic and Anharmonic Vibrational Energy Levels. Calculations of Generalized Transition State Number of States. Quantum Effects on Reaction Coordinate Motion. Multidimensional Tunneling Corrections Based on the Adiabatic Approximation. Large Curvature Transmission Coefficient. The Microcanonically Optimized Transmission Coefficient. Building the PES from Electronic Structure Calculation. Direct Dynamics with Specific Reaction Parameters. Interpolated VTST. Dual-Level Dynamics. Reactions in Liquids. Ensemble-Averaged Variational Transition State Theory. Gas-Phase Example: H +CH4. Liquid-Phase Example: Menshutkin Reaction. Concluding Remarks. Acknowledgments. References. 4. Coarse-Grain Modeling of Polymers (Roland Faller). Introduction. Defining the System. Choice of Model. Interaction Sites on the Coarse-Grained Scale. Static Mapping. Single-Chain Distribution Potentials. Simplex. Iterative Structural Coarse-Graining. Mapping Onto Simple Models. Dynamic Mapping. Mapping by Chain Diffusion. Mapping through Local Correlation Times. Direct Mapping of the Lennard-Jones Time. Coarse-Grained Monte Carlo Simulations. Reverse Mapping. A Look Beyond Polymers. Conclusions. Acknowledgments. References. 5. Analysis of Chemical Information Content Using Shannon Entropy (Jeffrey W. Godden and JUErgen Bajorath). Introduction. Shannon Entropy Concept. Descriptor Comparison. Influence of Boundary Effects. Extension of SE Analysis for Profiling of Chemical Libraries. Information Content of Organic Molecules. Shannon Entropy in Quantum Mechanics, Molecular Dynamics, and Modeling. Examples of SE and DSE Analysis. Conclusions. References. 6. Applications of Support Vector Machines in Chemistry (Ovidiu Ivanciuc). Introduction. A Nonmathematical Introduction to SVM. Pattern Classification. The Vapnik-Chervonenkis Dimension. Pattern Classification with Linear Support Vector Machines. SVM Classification for Linearly Separable Data. Linear SVM for the Classification of Linearly Non-Separable Data. Nonlinear Support Vector Machines. Mapping Patterns to a Feature Space. Feature Functions and Kernels. Kernel Functions for SVM. Hard Margin Nonlinear SVM Classification. Soft Margin Nonlinear SVM Classification. n-SVM Classification. Weighted SVM for Imbalanced Classification. Multi-class SVM Classification. SVM Regression. Optimizing the SVM Model. Descriptor Selection. Support Vectors Selection. Jury SVM. Kernels for Biosequences. Kernels for Molecular Structures. Practical Aspects of SVM Classification. Predicting the Mechanism of Action for Polar and Nonpolar Narcotic Compounds. Predicting the Mechanism of Action for Narcotic and Reactive Compounds. Predicting the Mechanism of Action from Hydrophobicity and Experimental Toxicity. Classifying the Carcinogenic Activity of Polycyclic Aromatic Hydrocarbons. Structure-Odor Relationships for Pyrazines. Practical Aspects of SVM Regression. SVM Regression QSAR for the Phenol Toxicity to Tetrahymena pyriformis. SVM Regression QSAR for Benzodiazepine Receptor Ligands. SVM Regression QSAR for the Toxicity of Aromatic Compounds to Chlorella vulgaris. SVM Regression QSAR for Bioconcentration Factors. Review of SVM Applications in Chemistry. Recognition of Chemical Classes and Drug Design. QSAR. Genotoxicity of Chemical Compounds. Chemometrics. Sensors. Chemical Engineering. Text Mining for Scientific Information. SVM Resources on the Web. SVM Software. Conclusions. References. 7. How Computational Chemistry Became Important in the Pharmaceutical Industry (Donald B. Boyd). Introduction. Germination: The 1960s. Gaining a Foothold: The 1970s. Growth: The 1980s. Gems Discovered: The 1990s. Final Observations. Acknowledgments. References. Author Index. Subject Index.

巻冊次

24 ISBN 9780470112816

内容説明

Reviews In Computational Chemistry Martin Schoen and Sabine Klapp Kenny B. Lipkowitz and Thomas Cundari, Series Editors This volume, unlike those prior to it, consists of a single monograph covering the timely topic of confined fluids. Volume 24 features the thermodynamics of confined phases, elements of statistical thermodynamics, one-dimensional hard-rod fluids, mean-field theory, treatments of confined fluids with short-range and long-range interactions, and the statistical mechanics of disordered confined fluids. Six appendices are included, which cover the mathematical derivation of equations used throughout the book. From Reviews Of The Series "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry." -Journal Of Molecular Graphics And Modelling "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)." -Journal Of The American Chemical Society

巻冊次

25 ISBN 9780470179987

内容説明

VOLUME 25 Reviews in Computational Chemistry Kenny B. Lipkowitz and Thomas R. Cundari This Volume, Like Those Prior To It, Features Pedagogically Driven Reviews By Experts In Various Fields Of Computational Chemistry. Volume 25 Contains: Eight Chapters Covering The Glass Transition In Polymer Melts, Atomistic Modeling Of Friction, The Computation Of Free Volume, Structural Order And Entropy Of Liquids And Glasses, The Reactivity Of Materials At Extreme Conditions, Magnetic Properties Of Transition Metal Clusters, Multiconfigurational Quantum Methods For The Treatment Of Heavy Metals, Recursive Solutions To Large Eigenvalue Problems, And The Development And Uses Of Artificial Intelligence In Chemistry. From Reviews of the Series "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry." -JOURNAL OF MOLECULAR GRAPHICS AND MODELLING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)." -JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

目次

1. Determining the Glass Transition in Polymer Melts (Wolfgang Paul). Introduction. Phenomenology of the Glass Transition. Model Building. Chemically Realistic Modeling. Coarse-Grained Models. Coarse-Grained Models of the Bead-Spring Type. The Bond-Fluctuation Lattice Model. Simulation Methods. Monte Carlo Methods. Molecular Dynamics Method. Thermodynamic Properties. Dynamics in Super-Cooled Polymer Melts. Dynamics in the Bead-Spring Model. Dynamics in 1,4-Polybutadiene. Dynamic Heterogeneity. Summary. Acknowledgments. References. 2. Atomistic Modeling of Friction (Nicholas J. Mosey and Martin H. Muser). Introduction. Theoretical Background. Friction Mechanisms. Load-Dependence of Friction. Velocity-Dependence of Friction. Role of Interfacial Symmetry. Computational Aspects. Surface Roughness. Imposing Load and Shear. Imposing Constant Temperature. Bulk Systems. Computational Models. Selected Case Studies. Instabilities, Hysteresis, and Energy Dissipation. The Role of Atomic-Scale Roughness. Superlubricity. Self-Assembled Monolayers. Tribochemistry. Concluding Remarks. Acknowledgments. References. 3. Computing Free Volume, Structural Order, and Entropy of Liquids and Glasses (Jeetain Mittal, William P. Krekelberg, Jeffrey R. Errington, and Thomas M. Truskett). Introduction. Metrics for Structural Order. Crystal-Independent Structural Order Metrics. Structural Ordering Maps. Free Volume. Identifying Cavities and Computing Their Volumes. Computing Free Volumes. Computing Thermodynamics from Free Volumes. Relating Dynamics to Free Volumes. Entropy. Testing the Adam-Gibbs Relationship. An Alternative to Adam-Gibbs? Conclusions. Acknowledgments. References. 4. The Reactivity of Energetic Materials at Extreme Conditions (Laurence E. Fried). Introduction. Chemical Equilibrium. Atomistic Modeling of Condensed-Phase Reactions. First Principles Simulations of High Explosives. Conclusions. Acknowledgments. References. 5. Magnetic Properties of Atomic Clusters of the Transition Elements (Julio A. Alonso). Introduction. Basic Concepts. Experimental Studies of the Dependence of the Magnetic Moments with Cluster Size. Simple Explanation of the Decay of the Magnetic Moments with Cluster Size. Tight Binding Method. Tight Binding Approximation for the d Electrons. Introduction of s and p Electrons. Formulation of the Tight Binding Method in the Notation of Second Quantization. Spin-Density Functional Theory. General Density Functional Theory. Spin Polarization in Density Functional Theory. Local Spin-Density Approximation (LSDA). Noncollinear Spin Density Functional Theory. Measurement and Interpretation of the Magnetic Moments of Nickel Clusters. Interpretation Using Tight Binding Calculations. Influence of the s Electrons. Density Functional Calculations for Small Nickel Clusters. Orbital Polarization. Clusters of Other 3d Elements. Chromium and Iron Clusters. Manganese Clusters. Clusters of the 4d Elements. Rhodium Clusters. Ruthenium and Palladium Clusters. Effect of Adsorbed Molecules. Determination of Magnetic Moments by Combining Theory and Photodetachment Spectroscopy. Summary and Prospects. Appendix. Calculation of the Density of Electronic States within the Tight Binding Theory by the Method of Moments. Acknowledgments. References. 6. Transition Metal- and Actinide-Containing Systems Studied with Multiconfigurational Quantum Chemical Methods (Laura Gagliardi). Introduction. The Multiconfigurational Approach. The Complete Active Space SCF Method. Multiconfigurational Second-Order Perturbation Theory, CASPT2. Treatment of Relativity. Relativistic AO Basis Sets. The Multiple Metal-Metal Bond in Re2Cl2-8 and Related Systems. The Cr-Cr Multiple Bond. Cu2O2 Theoretical Models. Spectroscopy of Triatomic Molecules Containing One Uranium Atom. Actinide Chemistry in Solution. The Actinide-Actinide Chemical Bond. Inorganic Chemistry of Diuranium. Conclusions. Acknowledgments. References. 7. Recursive Solutions to Large Eigenproblems in Molecular Spectroscopy and Reaction Dynamics (Hua Guo). Introduction. Quantum Mechanics and Eigenproblems. Discretization. Direct Diagonalization. Scaling Laws and Motivation for Recursive Diagonalization. Recursion and the Krylov Subspace. Lanczos Recursion. Exact Arithmetic. Finite-Precision Arithmetic. Extensions of the Original Lanczos Algorithm. Transition Amplitudes. Expectation Values. Chebyshev Recursion. Chebyshev Operator and Cosine Propagator. Spectral Method. Filter-Diagonalization. Filter-Diagonalization Based on Chebyshev Recursion. Low-Storage Filter-Diagonalization. Filter-Diagonalization Based on Lanczos Recursion. Symmetry Adaptation. Complex-Symmetric Problems. Propagation of Wave Packets and Density Matrices. Applications. Bound States and Spectroscopy. Reaction Dynamics. Lanczos vs. Chebyshev. Summary. Acknowledgments. References. 8. Development and Uses of Artificial Intelligence in Chemistry (Hugh Cartwright). Introduction. Evolutionary Algorithms. Principles of Genetic Algorithms. Genetic Algorithm Implementation. Why Does the Genetic Algorithm Work? Where Is the Learning in the Genetic Algorithm? What Can the Genetic Algorithm Do? What Can Go Wrong with the Genetic Algorithm? Neural Networks. Neural Network Principles. Neural Network Implementation. Why Does the Neural Network Work? What Can We Do with Neural Networks? What Can Go Wrong? Self-Organizing Maps. Where Is The Learning? Some Applications of SOMs. Expert Systems. Conclusion. References. Author Index. Subject Index.

巻冊次

26 ISBN 9780470388396

内容説明

Computational chemistry is increasingly used in conjunction with organic, inorganic, medicinal, biological, physical, and analytical chemistry, biotechnology, materials science, and chemical physics. This series is essential in keeping those individuals involved in these fields abreast of recent developments in computational chemistry.

目次

1. Computations of Noncovalent p Interactions (C. David Sherrill). Introduction. Challenges for Computing p Interactions. Electron Correlation Problem. Basis Set Problem. Basis Set Superposition Errors and the Counterpoise Correction. Additive Basis/Correlation Approximations. Reducing Computational Cost. Truncated Basis Sets. Pauling Points. Resolution of the Identity and Local Correlation. Approximations. Spin-Component-Scaled MP2. Explicitly Correlated R12 and F12 Methods. Density Functional Approaches. Semiempirical Methods and Molecular Mechanics. Analysis Using Symmetry-Adapted Perturbation Theory. Concluding Remarks. Appendix: Extracting Energy Components from the SAPT2006 Program. Acknowledgments. References. 2. Reliable Electronic Structure Computations for Weak Noncovalent Interactions in Clusters (Gregory S. Tschumper). Introduction and Scope. Clusters and Weak Noncovalent Interactions. Computational Methods. Weak Noncovalent Interactions. Historical Perspective. Some Notes about Terminology. Fundamental Concepts: A Tutorial. Model Systems and Theoretical Methods. Rigid Monomer Approximation. Supermolecular Dissociation and Interaction Energies. Counterpoise Corrections for Basis Set Superposition Error. Two-Body Approximation and Cooperative/Nonadditive Effects. Size Consistency and Extensivity of the Energy. Summary of Steps in Tutorial. High-Accuracy Computational Strategies. Primer on Electron Correlation. Primer on Atomic Orbital Basis Sets. Scaling Problem. Estimating Eint at the CCSD(T) CBS Limit: Another Tutorial. Accurate Potential Energy Surfaces. Less Demanding Computational Strategies. Second-Order Moller-Plesset Perturbation Theory. Density Functional Theory. Guidelines. Other Computational Issues. Basis Set Superposition Error and Counterpoise Corrections. Beyond Interaction Energies: Geometries and Vibrational Frequencies. Concluding Remarks. Acknowledgments. References. 3. Excited States from Time-Dependent Density Functional Theory (Peter Elliott, Filipp Furche, and Kieron Burke). Introduction. Overview. Ground-State Review. Formalism. Approximate Functionals. Basis Sets. Time-Dependent Theory. Runge-Gross Theorem. Kohn-Sham Equations. Linear Response. Approximations. Implementation and Basis Sets. Density Matrix Approach. Basis Sets. Convergence for Naphthalene. Double-Zeta Basis Sets. Polarization Functions. Triple-Zeta Basis Sets. Diffuse Functions. Resolution of the Identity. Summary. Performance. Example: Naphthalene Results. Influence of the Ground-State Potential. Analyzing the Influence of the XC Kernel. Errors in Potential vs. Kernel. Understanding Linear Response TDDFT. Atoms as a Test Case. Quantum Defect. Testing TDDFT. Saving Standard Functionals. Electron Scattering. Beyond Standard Functionals. Double Excitations. Polymers. Solids. Charge Transfer. Other Topics. Ground-State XC Energy. Strong Fields. Electron Transport. 4. Computing Quantum Phase Transitions (Thomas Vojta). Preamble: Motivation and History. Phase Transitions and Critical Behavior. Landau Theory. Scaling and the Renormalization Group. Finite-Size Scaling. Quenched Disorder. Quantum vs. Classical Phase Transitions. How Important Is Quantum Mechanics? Quantum Scaling and Quantum-to-Classical Mapping. Beyond the Landau-Ginzburg-Wilson Paradigm. Impurity Quantum Phase Transitions. Quantum Phase Transitions: Computational Challenges. Classical Monte Carlo Approaches. Method: Quantum-to-Classical Mapping and Classical Monte Carlo Methods. Transverse-Field Ising Model. Bilayer Heisenberg Quantum Antiferromagnet. Dissipative Transverse-Field Ising Chain. Diluted Bilayer Quantum Antiferromagnet. Random Transverse-Field Ising Model. Dirty Bosons in Two Dimensions. Quantum Monte Carlo Approaches. World-Line Monte Carlo. Stochastic Series Expansion. Bilayer Heisenberg Quantum Antiferromagnet. Diluted Heisenberg Magnets. Superfluid-Insulator Transition in an Optical Lattice. Fermions. Other Methods and Techniques. Summary and Conclusions. 5. Real-Space and Multigrid Methods in Computational Chemistry (Thomas L. Beck). Introduction. Physical Systems: Why Do We Need Multiscale Methods? Why Real Space? Real-Space Basics. Equations to Be Solved. Finite-Difference Representations. Finite-Element Representations. Iterative Updates of the Functions, or Relaxation. What Are the Limitations of Real-Space Methods on a Single Fine Grid? Multigrid Methods. How Does Multigrid Overcome Critical Slowing Down? Full Approximations Scheme (FAS) Multigrid, and Full Multigrid (FMG). Eigenvalue Problems. Multigrid for the Eigenvalue Problem. Self-Consistency. Linear Scaling for Electronic Structure? Other Nonlinear Problems: The Poisson-Boltzmann and Poisson-Nernst-Planck Equations. Poisson-Boltzmann Equation. Poisson-Nernst-Planck (PNP) Equations for Ion Transport. Some Advice on Writing Multigrid Solvers. Applications of Multigrid Methods in Chemistry, Biophysics, and Materials Nanoscience. Electronic Structure. Electrostatics. Transport Problems. Existing Real-Space and Multigrid Codes. Electronic Structure. Electrostatics. Transport. Some Speculations on the Future. Chemistry and Physics: When Shall the Twain Meet? Elimination of Molecular Orbitals? Larger Scale DFT, Electrostatics, and Transport. Reiteration of ''Why Real Space?'' 6. Hybrid Methods for Atomic-Level Simulations Spanning Multiple-Length Scales in the Solid State (Francesca Tavazza, Lyle E. Levine, and Anne M. Chaka). Introduction. General Remarks about Hybrid Methods. Complete-Spectrum Hybrid Methods. About this Review. Atomistic/Continuum Coupling. Zero-Temperature Equilibrium Methods. Finite-Temperature Equilibrium Methods. Dynamical Methods. Classical/Quantum Coupling. Static and Semistatic Methods. Dynamics Methodologies. 7. Extending the Time Scale in Atomically Detailed Simulations (Alfredo E. Cardenas and Eric Barth). Introduction. The Verlet Method. Molecular Dynamics Potential. Multiple Time Steps. Reaction Paths. Multiple Time-Step Methods. Splitting the Force. Numerical Integration with Force Splitting: Extrapolation vs. Impulse. Fundamental Limitation on Size of MTS Methods. Langevin Stabilization. Further Challenges and Recent Advances. An MTS Tutorial. Extending the Time Scale: Path Methodologies. Transition Path Sampling. Maximization of the Diffusive Flux (MaxFlux). Discrete Path Sampling and String Method. Optimization of Action. Boundary Value Formulation in Length. Use of SDEL to Compute Reactive Trajectories: Input Parameters, Initial Guess, and Parallelization Protocol. Applications of the Stochastic Difference Equation in Length. Recent Advances and Challenges. 8. Atomistic Simulation of Ionic Liquids (Edward J. Maginn). Introduction. Short (Pre)History of Ionic Liquid Simulations. Earliest Ionic Liquid Simulations. More Systems and Refined Models. Force Fields and Properties of Ionic Liquids Having Dialkylimidazolium Cations. Force Fields and Properties of Other Ionic Liquids. Solutes in Ionic Liquids. Implications of Slow Dynamics when Computing Transport Properties. Computing Self-Diffusivities, Viscosities, Electrical Conductivities, and Thermal Conductivities for Ionic Liquids. Nonequilibrium Methods for Computing Transport Properties. Coarse-Grained Models. Ab Initio Molecular Dynamics. How to Carry Out Your Own Ionic Liquid Simulations. What Code? Force Fields. Data Analysis. Operating Systems and Parallel Computing. Summary and Outlook. Acknowledgments. References. Author Index. Subject Index.

巻冊次

27 ISBN 9780470587140

内容説明

This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Volume 27 covers brittle fracture, molecular detailed simulations of lipid bilayers, semiclassical bohmian dynamics, dissipative particle dynamics, trajectory-based rare event simulations, and understanding metal/metal electrical contact conductance from the atomic to continuum scales. Also included is a chapter on career opportunities in computational chemistry and an appendix listing the e-mail addresses of more than 2500 people in that discipline. FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry." -JOURNAL OF MOLECULAR GRAPHICS AND MODELLING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)." -JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

目次

1. Brittle Fracture: From Elasticity Theory to Atomistic Simulations (Stefano Giordano, Alessandro Mattoni, and Luciano Colombo). Introduction. Essential Continuum Elasticity Theory. Conceptual Layout. The Concept of Strain. The Concept of Stress. The Formal Structure of Elasticity Theory. Constitutive Equations. The Isotropic and Homogeneous Elastic Body. Governing Equations of Elasticity and Border Conditions. Elastic Energy. Microscopic Theory of Elasticity. Conceptual Layout. Triangular Lattice with Central Forces Only. Triangular Lattice with Two-Body and Three-Body Interactions. Interatomic Potentials for Solid Mechanics. Atomic-Scale Stress. Linear Elastic Fracture Mechanics. Conceptual Layout. Stress Concentration. The Griffith Energy Criterion. Opening Modes and Stress Intensity Factors. Some Three-Dimensional Configurations. Elastic Behavior of Multi Fractured Solids. Atomistic View of Fracture. Atomistic Investigations on Brittle Fracture. Conceptual Layout. Griffith Criterion for Failure. Failure in Complex Systems. Stress Shielding at Crack-Tip. Acknowledgments. Appendix: Notation. References. 2. Dissipative Particle Dynamics (Igor V. Pivkin, Bruce Caswell, and George Em Karniadakis). Introduction. Fundamentals of DPD. Mathematical Formulation. Units in DPD. Thermostat and Schmidt Number. Integration Algorithms. Boundary Conditions. Extensions of DPD. DPD with Energy Conservation. Fluid Particle Model. DPD for Two-Phase Flows. Other Extensions. Applications. Polymer Solutions and Melts. Binary Mixtures. Amphiphilic Systems. Red Cells in Microcirculation. Summary. References. 3. Trajectory-Based Rare Event Simulations (Peter G. Bolhuis and Christoph Dellago). Introduction. Simulation of Rare Events. Rare Event Kinetics from Transition State Theory. The Reaction Coordinate Problem. Accelerating Dynamics. Trajectory-Based Methods. Outline of the Chapter. Transition State Theory. Statistical Mechanical Definitions. Rate Constants. Rate Constants from Transition State Theory. Variational TST. The Harmonic Approximation. Reactive Flux Methods. The Bennett-Chandler Procedure. The Effective Positive Flux. The Ruiz-Montero-Frenkel-Brey Method. Transition Path Sampling. Path Probability. Order Parameters. Sampling the Path Ensemble. Shooting Move. Sampling Efficiency. Biasing the Shooting Point. Aimless Shooting. Stochastic Dynamics Shooting Move. Shifting Move. Flexible Time Shooting. Which Shooting Algorithm to Choose? The Initial Pathway. The Complete Path Sampling Algorithm. Enhancement of Sampling by Parallel Tempering. Multiple-State TPS. Transition Path Sampling Applications. Computing Rates with Path Sampling. The Correlation Function Approach. Transition Interface Sampling. Partial Path Sampling. Replica Exchange TIS or Path Swapping. Forward Flux Sampling. Milestoning. Discrete Path Sampling. Minimizing the Action. Nudged Elastic Band. Action-Based Sampling. Transition Path Theory and the String Method. Identifying the Mechanism from the Path Ensemble. Reaction Coordinate and Committor. Transition State Ensemble and Committor Distributions. Genetic Neural Networks. Maximum Likelihood Estimation. Conclusions and outlook. Acknowledgments. References. 4. Understanding Metal/Metal Electrical Contact Conductance from the Atomic to Continuum Scales (Douglas L. Irving). Introduction. Factors That Influence Contact Resistance. Surface Roughness. Local Heating. Intermixing and Interfacial Contamination. Dimensions of Contacting Asperities. Computational Considerations. Atomistic Methods. Calculating Conductance of Nanoscale Asperities. Hybrid Multiscale Methods. Characterization of Defected Atoms. Selected Case Studies. Conduction Through Metallic Nanowires. Multiscale Methods Applied to Metal/Metal Contacts. Concluding Remarks. Acknowledgments. References. 5. Molecular Detailed Simulations of Lipid Bilayers (Max L. Berkowitz and James T. Kindt). Introduction. Membrane Simulation Methodology. Force Fields. Choice of the Ensemble. Verification of the Force Field. Monte Carlo Simulation of Lipid Bilayers. Detailed Simulations of Bilayers Containing Lipid Mixtures. Conclusions. References. 6. Semiclassical Bohmian Dynamics (Sophya Garashchuk, Vitaly Rassolov, and Oleg Prezhdo). Introduction. The Formalism and Its Features. The Trajectory Formulation. Features of the Bohmian Formulation. The Classical Limit of the Schroedinger Equation and the Semiclassical Regime of Bohmian Trajectories. Using Quantum Trajectories in Dynamics of Chemical Systems. Bohmian Quantum-Classical Dynamics. Mean-Field Ehrenfest Quantum-Classical Dynamics. Quantum-Classical Coupling via Bohmian Particles. Numerical Illustration of the Bohmian Quantum-Classical Dynamics. Properties of the Bohmian Quantum-Classical Dynamics. Hybrid Bohmian Quantum-Classical Phase-Space Dynamics. The Independent Trajectory Methods. The Derivative Propagation Method. The Bohmian Trajectory Stability Approach. Calculation of Energy Eigenvalues by Imaginary Time Propagation. Bohmian Mechanics with Complex Action. Dynamics with the Globally Approximated Quantum Potential (AQP). Global Energy-Conserving Approximation of the Nonclassical Momentum. Approximation on Subspaces or Spatial Domains. Nonadiabatic Dynamics. Toward Reactive Dynamics in Condensed Phase. Stabilization of Dynamics by Balancing Approximation Errors. Bound Dynamics with Tunneling. Conclusions. Acknowledgments. Appendix A: Conservation of Density within a Volume Element. Appendix B: Quantum Trajectories in Arbitrary Coordinates. Appendix C: Optimal Parameters of the Linearized Momentum on Spatial Domains in Many Dimensions. References. 7. Prospects for Career Opportunities in Computational Chemistry (Donald B. Boyd). Introduction and Overview. Methodology and Results. Proficiencies in Demand. Analysis. An Aside: Economics 101. Prognosis. Acknowledgments. References. Appendix: List of Computational Molecular Scientists. Subject Index.

巻冊次

7. Wiley-VCH ISBN 9780471186281

内容説明

This is the seventh volume in the successful series designed to help the chemistry community keep current with the many new developments in computational techniques. The writing style is refreshingly pedagogical and non-mathematical, allowing students and researchers access to computational methods outside their immediate area of expertise. Each invited author approaches a topic with the aim of helping the reader understand the material, solve problems, and locate key references quickly.

目次

From the Contents: Similarity Searching in Databases of Chemical Structures/Three-Dimensional Structure Database Searches/ Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials/ An Introduction to Density Functional Theory/ Density Functional Methods in Biomolecular Modeling/ The A Priori Calculation of Vibrational Circular Dichroism Intensities.

巻冊次

[1]Wiley-VCH ISBN 9780471187288

内容説明

This book is an account of current developments in computational chemistry, a new multidisciplinary area of research. Experts in computational chemistry, the editors use and develop techniques for computer-assisted molecular design. The core of the text itself deals with techniques for computer-assisted molecular design. The book is suitable for both beginners and experts. In addition, protocols and software for molecular recognition and the relationship between structure and biological activity of drug molecules are discussed in detail. Each chapter includes a mini-tutorial, as well as discussion of advanced topics. Special Feature: The appendix to this book contains an extensive list of available software for molecular modeling.

目次

1. Basis Sets for Ab Initio Molecular Orbital Calculations and Intermolecular Interactions 1 David Feller and Ernest R. Davidson Introduction 1 Some Terminology 4 Gaussian Compared to Exponential Functions 4 Contracted Gaussians 4 Polarization Functions 7 Complete Sets 8 The Basis Set Superposition Error 9 Choosing a Basis Set 10 Molecular Geometries 11 Energy Differences 15 One-Electron Properties 20 In-Depth Discussion 20 Sources of Gaussian Primitives and Contraction Coefficients 20 Even-Tempered Gaussians 21 Well-Tempered Gaussians 22 MINI-/, MIDI-/ and MAXI-/ etc. 26 Still Others 27 Atomic Natural Orbitals 27 Functions for Augmenting Basis Sets 29 Weak Interactions 34 Conclusion 36 References 37 2. Semiempirical Molecular Orbital Methods 45 James J. P. Stewart Introduction 45 History of Semiempirical Methods 46 Complete Neglect of Differential Overlap 47 Complete Neglect of Differential Overlap Version 2 50 Intermediate Neglect of Differential Overlap 51 Neglect of Diatomic Differential Overlap (NDDO) 52 Modified Neglect of Diatomic Overlap 55 Austin Model 1 57 Parametric Method Number 3 58 Self-Consistent Field Convergers 58 Strong and Weak Points of NDDO Semiempirical Methods 61 MINDO/3 62 MNDO, AMI, and PM3 62 Theoretical Experiments 73 Stationary Points 74 General Procedure for Characterizing a Reaction 74 Reaction Path 75 Time-Dependent Phenomena 76 Future of Semiempirical Methods 77 Summary 78 References 78 3. Properties of Molecules by Direct Calculation 83 Clifford E. Dykstra, Joseph D. Augspurger, Bernard Kirtman, and David J. Malik Introduction 83 Overview of Quantum Mechanical Properties 84 Correspondence between Energy Derivatives and Properties 84 Differentiation of the Schrodinger Equation 85 The Development of Methods for Property Determinations 87 Semiempirical Approaches 87 Ab Initio Methods 89 Detailed View of Ab Initio Methods 92 Hamiltonians and Operators 92 Computational Organization of the Differentiation Process 95 Derivatives of Electronic Wavefunctions 97 Local Space Concepts for Extended Systems 99 Vibrations and Rotations 100 Direct Property Calculations 103 Electrical Properties 103 Magnetic Properties 107 Force Constants 109 Transition Probabilities and Optical Properties 110 Summary 111 References 112 4. The Application of Quantitative Design Strategies in Pesticide Discovery 119 Ernest L. Plummer Introduction 119 The Selection of a Strategy 122 The Well-Designed Substituent Set 126 The Ideal Substituent Set Should Cover All Factors That Control Activity 127 The Ideal Substituent Set Should Cover the Selected Factor Space as Completely as Possible 128 The Ideal Substituent Set Should Span Orthogonal Dimensions of Parameter Space 129 The Ideal Set Should Contain the Minimum Number of Substituents Necessary to Avoid Chance Correlations and Still Meet the Desired Goal 130 Target Compounds Should Be Chosen to Preserve Synthetic Resources But Should Not Be Chosen Just Because They Are Easy to Synthesize 131 The Derivatives Must Be Stable under the Conditions of Bioevaluation 131 Analysis Strategies 132 The Topliss Tree 132 Free-Wilson Analysis 135 A Strategy for Lead Optimization Using Multiple Linear Regression Analysis 138 Choose the Optimal Pattern for Substitution 139 Choose the Factors (Parameters) That Are Likely to Be Important 142 Select a Substituent Set 143 Synthesize and Submit for Biological Evaluation 152 Plot Each Parameter versus Activity 154 Generate Squared Terms if Justified by the Single Parameter Plots 157 Run All Combinations of the Chosen Parameters through Linear Regression Analysis to the Limits of Statistical Significance 158 Repeat the Process Until the QSAR Is Stable 160 Sequential Simplex Optimization (SSO) 161 Conclusion 164 References 165 5. Chemometrics and Multivariate Analysis in Analytical Chemistry 169 Peter C. Jurs Introduction 169 Response Surfaces, Sampling, and Optimization 170 Signal Processing 173 Principal Components Analysis and Factor Analysis 175 Calibration and Mixture Analysis 178 Classification and Clustering 182 Classification 183 Clustering 184 Library Searching 186 Molecular Structure-Property Relationships 188 Gas Chromatographic Retention Indices for Diverse Drug Compounds 192 Simulation of Carbon-13 Nuclear Magnetic Resonance Spectra of Methyl-Substituted Norbornan-2-ols 198 Summary and Conclusions 207 References 208 6. Searching Databases of Three-Dimensional Structures 213 Yvonne C. Martin, Mark G. Bures, and Peter Willet Why Are Such Methods Needed? 213 Tools for Searching Two-Dimensional Chemical Structures of Small Molecules 217 Computer Representation of Two-Dimensional Chemical Structures 218 Searching Files of Two-Dimensional Chemical Structures 220 Languages for Chemical Programming 222 System Design for Chemical Information Systems 224 Similarity of Small Molecules Based on Two-Dimensional Structure 225 Substituent Effects on Molecular Properties 225 Two-Dimensional Topological Descriptors of Molecular Shape 226 Similarity of Small Molecules Based on Three-Dimensional Structure 226 Three-Dimensional Similarity Based on Geometric Properties 227 Three-Dimensional Similarity Based on Steric Properties 231 Databases of Three-Dimensional Structures of Molecules 234 Searching Files of Three-Dimensional Structures of Small Molecules 236 Programs from the Cambridge Crystallographic Data Centre 236 Searching Based Principally on Shape Properties 237 Strategies Based on Screen Searching 238 Strategies Based on a Substructure Specification Language 243 Databases and Searching of Multiple Three-Dimensional Pharmacophoric Patterns 248 Searching Files of Three-Dimensional Protein Structures 249 The Protein Data Bank 249 Identification of Patterns of Atoms 249 Identification of Secondary Structure Motifs 252 Conclusions 253 Appendix: Sources of Databases and Programs 255 References 256 7. Molecular Surfaces 265 Paul G. Mezey Introduction 265 Molecular Body and Molecular Surface 266 Classical Models for Molecular Surfaces: Hard Spheres and van der Waals Surfaces (VDWSs) 267 Electron Density Contour Surfaces 269 The Density Domain Approach to Chemical Bonding (DDA) 271 Molecular Electrostatic Potential 274 Molecular Orbitals 276 Solvent Accessible Surfaces 278 Union Surfaces 279 Interpenetration of Molecular Contour Surfaces 281 Shape Analysis of Molecular Surfaces 282 Conclusions 288 References 289 8. Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Peturbation Methods 295 Terry P. Lybrand Introduction 295 Models 296 Methods 297 Energy Minimization 298 Normal Mode Analysis 298 Monte Carlo 299 Molecular Dynamics 300 Free Energy Pertubation Methods 308 Summary 314 References 315 9. Aspects of Molecular Modeling 321 Donald B. Boyd Introduction 321 Quantum Mechanics 323 Why Use Quantum Mechanics? 323 Theory 325 Approximations 326 Comparison of Ab Initio and Semiempirical MO Methods 328 Input 329 Output 331 Basis Sets for Ab Initio Calculations 332 Caveats on Basis Sets 334 Post-Hartree-Fock Treatments 334 Selection of an MO Method 336 Numerical Sensitivity of Geometry Optimization Procedures 337 Quality of Results from Quantum Mechanical Methods 339 Information from X-Ray Databases for Molecular Modeling 341 Standard Geometries 345 Distance Geometry 345 Summary 348 References 351 10. Successes of Computer-Assisted Molecular Design 355 Donald B. Boyd Levels of Success 355 Norfloxacin 359 Metamitron 360 Bromobutide 361 Myclobutanil 362 Conclusion 364 References 365 11. Perspectives on Ab Initio Calculations 373 Ernest R. Davidson Atomic Orbitals Do Not Work 375 The Error in 'P Is Largest Where 'P Is Largest 376 The Number of Electron Pairs Is N(N - l)/2 377 The Computer Cost, at Fixed Accuracy, Grows Like N! 378 Computers Do Not Solve Problems, People Do 379 Appendix: Compendium of Software for Molecular Modeling 383 Donald B. Boyd Personal Computers 384 Minicomputers-Superminicomputers-Workstations 387 Supercomputers 392 Subject Index 393

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2. Wiley-VCH ISBN 9780471188100

内容説明

This second volume of the series 'Reviews in Computational Chemistry' explores new applications, new methodologies, and new perspectives. The topics covered include conformational analysis, protein folding, force field parameterizations, hydrogen bonding, charge distributions, electrostatic potentials, electronic spectroscopy, molecular property correlations, and the computational chemistry literature. Methodologies described include conformational search strategies, distance geometry, molecular mechanics, molecular dynamics, ab initio and semiempirical molecular orbital calculations, and quantitative structure-activity relationships (QSAR) using topological and electronic descriptors. A compendium of molecular modeling software will help users select the computational tools they need. Each chapter in 'Reviews in Computational Chemistry' serves as a brief tutorial for organic, physical, pharmaceutical, and biological chemists new to the field. Practitioners will be interested in the recent advances.

目次

A Survey of Methods for Searching thr Conformational Space of Small and Medium-Sized Molecules (A. Leach). Simplified Models for Understanding and Predicting Protein Structure (J. Troyer and F. Cohen). Moleculaar Mechanics: The Art and Science of Parameterization (J. Bowen and N. Allinger). New Approaches to Empirical Force Fields (U. Dinur and A. Hagler). Calculating the Properties of Hydrogen Bonds by ab Initio Methods (S. Scheiner). Net Atomic Charge and Multiple Models for the ab Initio Molecular Electric Potential (D. Williams). Molecular Electrostatic Potentials and Chemical Reactivity (P. Politzer and J. Murray). Semiempirical Molecular Orbital Methods (M. Zerner). The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Modeling (L. Hall and L. Kier). The Electron-Topological Approach to the QSAR Problem (I. Bersuker and A. Dimoglo). The Computational Chemistry Literature (D. Boyd). Appendix: Compendium of Software for Molecular Modeling (D. Boyd). Author Index. Subject Index.

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3. Wiley-VCH ISBN 9780471188537

内容説明

From reviews of the series: 'Many of the articles are indeed accessible to any interested nonspecialist, even without theoretical background.' Journal of the American Chemical Society '...an invaluable resource for the serious molecular modeler.' Chemical Design Automation News

目次

From the Contents: Optimization Methods in Computational Chemistry/ Predicting Three-Dimensional Structures of Oligopeptides/ Molecular Modeling Using Nuclear Magnetic Resonance Data/ Computer-Assisted Methods in the Evaluation of Chemical Toxicity

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4. Wiley-VCH ISBN 9780471188544

内容説明

This volume in the series brings together reknowned experts in the field to present the reader with an account of the latest developments in quantum mechanics, molecular dynamics, and the teaching of computational chemistry. There are so many developments in the field of computational chemistry that it is difficult to keep track of them. The series was established to review the high volume of developments in the field. Rather than create a traditional article, each author approaches a topic to enable the reader to understand and solve problems and locate key references quickly. Each article has tutorial value. An updated compendium of software for molecular modeling appears as an appendix as in previous volumes. To the editors' knowledge, this is the most complete listing of sources of software for computational chemistry anywhere.

目次

From the Contents: A Survey of Methods for Searching the Conformational Space of small and Medium-Sized Molecules/ Simplified Models for Understanding and Predicting Protein Stucture/ Molecular Mechanics: The Art and Science of Parameterization/ Approaches to Empirical Force Fields/ Calcualating the Properties of Hydrogen Bonds by Ab Initio Methods/ Net Atomic Charge and Multipole Models for the Ab Initio Molecular Electric Potential/ Molecular Electrostatic Potentials and Chemical Reactivity/ Semiempirical Molecular Orbital Methods/ The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure-Property Modeling/ The Electron-Topological Approach to the QSAR Problem/ The Computational Chemistry Literature/ Appendix: Compendium of Software for Molecular Modeling

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11. Wiley-VCH ISBN 9780471192480

内容説明

Volume 11 Reviews in Computational Chemistry Kenny B. Lipkowitz and Donald B. Boyd The Theme of this Eleventh Volume is Computer-Aided Ligand Design and Modeling of Biomolecules. A Stellar Group of Scientists from Around the World Join in this Volume to Provide Tutorials for Beginners and Experts. Chapters 1 and 2 Take A Detailed Look at De Novo Design Methodologies for Discovering New Ligands which May Become Pharmaceuticals. Chapters 3 and 4 Cover the Methods and Applications of Three-Dimensional Quantitative Structure-Activity Relationships (3D-QSAR) Currently Used in Drug Discovery. Ways to Compute the Correct Lipophilic/Hydrophilic Behavior of Molecules are Taught in Chapter 5. Chapter 6 is an Exposition of Realistically Simulating DNA in the Complex Milieu of Ions that Surround it. An Appendix to this Volume Gives A Compendium of Software and Internet Tools for Computational Chemistry. -From Reviews of the Series . This Well-Respected Series Continues the Fine Selection of Topics and Presentation Qualities Set Forth by the Previous Members. For Example, Each Chapter Contains Thorough Treatment of the Theory Behind the Topic Being Covered. Moreover, the Background Material is Followed by Ample Timely Examples Culled From Recent Literature. Journal of Medicinal Chemistry

目次

Recent Advances in Ligand Design Methods (M. Murcko). Current Issues in De Novo Molecular Design (D. Clark, et al.). Theoretical and Practical Aspects of Three-Dimensional Quantitative Structure-Activity Relationships (T. Oprea & C. Waller). Approaches to Three-Dimensional Quantitative Structure-Activity Relationships (G. Greco, et al.). Computational Approaches to Lipophilicity: Methods and Applications (P. Carrupt, et al.). Treatment of Counterions in Computer Simulations of DNA (G. Ravishanker, et al.). Appendix. Indexes.

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18. Wiley-VCH ISBN 9780471215769

内容説明

This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics covered in Volume 18 include molecular modeling, computer-assisted molecular design (camd), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (qsar).

目次

Clustering Methods and Their Uses in Computational Chemistry (Geoff M. Downs and John M. Barnard). The Use of Scoring Functions in Drug Discovery Applications (Hans-Joachim Boehm and Martin Stahl). Potentials and Algorithms for Incorporating Polarizability in Computer Simulations (Steven W. Rick and Steven J. Stuart). New Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases (Dmitry V. Matyushov and Gregory A. Voth). Linear Free Energy Relationships Using Quantum Mechanical Descriptors (George R. Famini and Leland Y. Wilson). The Development of Computational Chemistry in Germany (Sigrid D. Peyerimhoff). Appendix. Examination of the Employment Environment for Computational Chemistry (Donald B. Boyd and Kenny B. Lipkowitz). Author Index. Subject Index.

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19 ISBN 9780471235859

内容説明

The Reviews in Computational Chemistry series brings together leading authorities in the field. The chapters in this book series are written to teach the newcomer and update the expert. Topics include computational chemistry, molecular modeling, computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). Detailed author and subject indices on each volume help the reader to quickly discover particular topics. The chapters are approached in a tutorial manner and written in a non-mathematical style allowing students and researchers to access computational methods outside their immediate area of expertise.

目次

1. Computational Techniques and Strategies for Monte Carlo Thermodynamic Calculations, with Applications to Nanoclusters (Robert Q. Topper, et al.). 2. Computing Hydrophobicity (David E. Smith and Anthony D.J. Haymet). 3. Born-Oppenheimer Direct Dynamics Classical Trajectory Simulations (Lipeng Sun and William L. Hase). 4. The Poisson-Boltzmann Equation (Gene Lamm). Author Index. Subject Index.

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12. Wiley-VCH ISBN 9780471246718

内容説明

VOLUME 12 REVIEWS IN COMPUTATIONAL CHEMISTRY Kenny B. Lipkowitz and Donald B. Boyd HOW DOES ONE COMPUTE FREE ENERGY AND ENTROPY FROM MOLECULAR SIMULATIONS? WHAT HAPPENS WHEN SIMULATIONS ARE RUN WITH CONSTRAINTS? HOW SHOULD SIMULATIONS BE PERFORMED TO MODEL INTERFACIAL PHENOMENA? HOW IS DENSITY FUNCTIONAL THEORY USED TO SIMULATE MATERIALS? WHAT QUANTUM MECHANICAL METHODS SHOULD BE USED TO COMPUTE NONLINEAR OPTICAL PROPERTIES OF MATERIALS? WHICH PARAMETERS ARE MOST INFLUENTIAL IN A MOLECULAR SIMULATION? HOW CAN CRYSTAL STRUCTURES BE PREDICTED? TUTORIALS PROVIDING ANSWERS TO THESE QUESTIONS ARE THE FOCUS OF THIS BOOK. FROM REVIEWS OF THE SERIES "The series continues to be one of the most useful information sources." -JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

目次

Calculation of the Free Energy and the Entropy of Macromolecular Systems by Computer Simulation (H. Meirovitch). Molecular Dynamics with General Holonomic Constraints and Application to Internal Coordinate Constraints (R. Kutteh & T. Straatsma). Computer Simulation of Water Physisorption at Metal-Water Interfaces (J. Shelley & D. Berard). Quantum-Based Analytic Interatomic Forces and Materials Simulation (D. Brenner, et al.). Quantum Mechanical Methods for Predicting Nonlinear Optical Properties (H. Kurtz & D. Dudis). Sensitivity Analysis in Biomolecular Simulation (C. Wong, et al.). Computer Simulation to Predict Possible Crystal Polymorphs (P. Verwer & F. Leusen). Computational Chemistry in France: A Historical Survey (J.-L Rivail & B. Maigret). Indexes.

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13. Wiley-VCH ISBN 9780471331353

内容説明

THIS BOOK HAS SIX TUTORIALS AND REVIEWS WRITTEN BY INVITED EXPERTS. FIVE CHAPTERS TEACH TOPICS IN QUANTUM MECHANICS AND MOLECULAR SIMULATIONS. THE SIXTH CHAPTER EXPLAINS HOW PROGRAMS FOR CHEMICAL STRUCTURE DRAWING WORK. AN EDITORIAL DISCUSSES SOME OF THE MOST WELL-KNOWN PERSONAGES IN COMPUTATIONAL CHEMISTRY. FROM REVIEWS OF THE SERIES "Anyone who is doing or intends to do computational research on molecular structure and design should seriously consider purchasing this book for his or her personal library."-JOURNAL OF COMPUTATIONAL CHEMISTRY. "These reviews are becoming regarded as the standard reference among both specialists and novices in the expanding field of computational chemistry." -JOURNAL OF MOLECULAR GRAPHICS AND MODELLING. "[This book is] written for newcomers learning about molecular modeling techniques as well as for seasoned professionals who need to acquire expertise in areas outside their own."-JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCE.

目次

Calculations on Open-Shell Molecules: A Beginner's Guide (T. Bally & W. Borden). Basis Set Superposition Errors: Theory and Practice (N. Kestner & J. Combariza). Quantum Monte Carlo: Atoms, Molecules, Clusters, Liquids, and Solids (J. Anderson). Molecular Models of Water: Derivation and Description (A. Wallqvist & R. Mountain). Simulation of pH-Dependent Properties of Proteins Using Mesoscopic Models (J. Briggs & J. Antosiewicz). Structure Diagram Generation (H. Helson). Indexes.

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14. Wiley-VCH ISBN 9780471354956

内容説明

THIS VOLUME, WHICH IS DESIGNED FOR STAND-ALONE USE IN TEACHING AND RESEARCH, FOCUSES ON QUANTUM CHEMISTRY, AN AREA OF SCIENCE THAT MANY CONSIDER TO BE THE CENTRAL CORE OF COMPUTATIONAL CHEMISTRY. TUTORIALS AND REVIEWS COVER * HOW TO OBTAIN SIMPLE CHEMICAL INSIGHT AND CONCEPTS FROM DENSITY FUNCTIONAL THEORY CALCULATIONS, * HOW TO MODEL PHOTOCHEMICAL REACTIONS AND EXCITED STATES, AND * HOW TO COMPUTE ENTHALPIES OF FORMATION OF MOLECULES. * A FOURTH CHAPTER TRACES CANADIAN RESEARCH IN THE EVOLUTION OF COMPUTATIONAL CHEMISTRY. * ALSO INCLUDED WITH THIS VOLUME IS A SPECIAL TRIBUTE TO QCPE. FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry proves itself an invaluable resource to the computational chemist. This series has a place in every computational chemist's library."-JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

目次

The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials (M. Francl & L. Chirlian). An Introduction to Coupled Cluster Theory for Computational Chemists (T. Crawford & H. Schaefer). Introduction to Zeolite Modeling (B. van de Graaf, et al.). Towards More Accurate Model Intermolecular Potentials for Organic Molecules (S. Price). Nonequilibrium Molecular Dynamics (C. Mundy, et al.). History of the Gordon Research Conferences on Computational Chemistry (D. Boyd & K. Lipkowitz). Appendix. Indexes.

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15. Wiley-VCH ISBN 9780471361688

内容説明

THIS VOLUME, WHICH IS DESIGNED FOR STAND-ALONE USE IN TEACHING AND RESEARCH, FOCUSES ON QUANTUM CHEMISTRY, AN AREA OF SCIENCE THAT MANY CONSIDER TO BE THE CENTRAL CORE OF COMPUTATIONAL CHEMISTRY. TUTORIALS AND REVIEWS COVER * HOW TO OBTAIN SIMPLE CHEMICAL INSIGHT AND CONCEPTS FROM DENSITY FUNCTIONAL THEORY CALCULATIONS, * HOW TO MODEL PHOTOCHEMICAL REACTIONS AND EXCITED STATES, AND * HOW TO COMPUTE ENTHALPIES OF FORMATION OF MOLECULES. A FOURTH CHAPTER TRACES CANADIAN RESEARCH IN THE EVOLUTION OF COMPUTATIONAL CHEMISTRY. ALSO INCLUDED WITH THIS VOLUME IS A SPECIAL TRIBUTE TO QCPE.FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry proves itself an invaluable resource to the computational chemist. This series has a place in every computational chemist's library."-Journal of the American Chemical Society

目次

Kohn-Sham Density Functional Theory: Predicting and Understanding Chemistry (F. Bickelhaupt & E. Baerends). A Computational Strategy for Organic Photochemistry (M. Robb, et al.). Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds (L. Curtiss, et al.). The Development of Computational Chemistry in Canada (R. Boyd). Indexes.

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16. Wiley-VCH ISBN 9780471386674

内容説明

Volume 16 Reviews In Computational Chemistry Kenny B. Lipkowitz and Donald B. Boyd The focus of this book is on methods useful in molecular design. Tutorials and reviews span (1) methods for designing compound libraries for combinatorial chemistry and high throughput screening, (2) the workings of artificial neural networks and their use in chemistry, (3) force field methods for modeling materials and designing new substances, and (4) free energy perturbation methods of practical usefulness in ligand design. From Reviews of the Series "This series spans all the subdisciplines in the field, from techniques to practical applications, and includes reviews from many of the acknowledged leaders in the field. the reviews cross many subdisciplines yet are both general enough to be of wide interest while including detailed information of use to workers in particular subdisciplines." -Journal of the American Chemical Society

目次

Cumputer-Aided Molecular Diversity Analysis and Combinatorial Library Design (R. Lewis, et al.). Artificial Neural Networks and Their Use in Chemistry (K. Peterson). Use of Force Fields in Materials Modeling (J.-R. Hill, et al.). Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities (M. Reddy, et al.). Indexes.

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17. Wiley-VCH ISBN 9780471398455

内容説明

Computational chemistry is increasingly used in most areas of molecular science including organic, inorganic, medicinal, biological, physical, and analytical chemistry. Researchers in these fields who do molecular modelling need to understand and stay current with recent developments. This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Two chapters focus on molecular docking, one of which relates to drug discovery and cheminformatics and the other to proteomics. In addition, this volume contains tutorials on spin-orbit coupling and cellular automata modeling, as well as an extensive bibliography of computational chemistry books. FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry."-JOURNAL OF MOLECULAR GRAPHICS AND MODELLING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)."-JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

目次

1. Small Molecule Docking and Scoring (Ingo Muegge and Matthias Rarey). Introduction. Algorithms for Molecular Docking. Appendix. Books Published on the Topics of Computational Chemistry (Kenny B. Lipkowitz and Donald B. Boyd). Introduction. Computers in Chemistry. Chemical Information. Computational Chemistry. Artificial Intelligence and Chemometrics. Crystallography, Spectroscopy, and Thermochemistry. Quantum Chemistry. Fundamentals of Quantum Theory. Applied Quantum Chemistry. Crystals, Polymers, and Materials. Selected Series and Proceedings from Long-Running Conferences. Molecular Modeling. Molecular Simulation. Molecular Design and Quantitative Structure-Activity Relationships. Graph Theory in Chemistry. Trends. Concluding Remarks. References. Author Index. Subject Index. The Docking Problem. Placing Fragments and Rigid Molecules. Flexible Ligand Docking. Handling Protein Flexibility. Docking of Combinatorial Libraries. Scoring. Shape and Chemical Complementary Scores. Force Field Scoring. Empirical Scoring Functions. Knowledge-Based Scoring Functions. Comparing Scoring Functions in Docking Experiments: Consensus Scoring. From Molecular Docking to Virtual Screening. Protein Data Preparation. Ligand Database Preparation. Docking Calculation. Postprocessing. Applications. Docking as a Virtual Screening Tool. Docking as a Ligand Design Tool. Concluding Remarks. Acknowledgments. References. 2. Protein-Protein Docking (Lutz P. Ehrlich and Rebecca C. Wade). Introduction. Why This Topic? Protein-Protein Binding Data. Challenges for Computational Docking Studies. Computational Approaches to the Docking Problem. Docking = Sampling + Scoring. Rigid-Body Docking. Flexible Docking. Example. Estimating the Extent of Conformational Change upon Binding. Rigid-Body Docking. Flexible Docking with Side-Chain Flexibility. Flexible Docking with Full Flexibility. Future Directions. Conclusions. References. 3. Spin-Orbit Coupling in Molecules (Christel M. Marian). What It Is All About. The Fourth Electronic Degree of Freedom. The Stern-Gerlach Experiment. Zeeman Spectroscopy. Spin Is a Quantum Effect. Angular Momenta. Orbital Angular Momentum. General Angular Momenta. Spin Angular Momentum. Spin-Orbit Hamiltonians. Full One- and Two-Electron Spin-Orbit Operators. Valence-Only Spin-Orbit Hamiltonians. Effective One-Electron Spin-Orbit Hamiltonians. Symmetry. Transformation Properties of the Wave Function. Transformation Properties of the Hamiltonian. Matrix Elements. Examples. Summary. Computational Aspects. General Considerations. Evaluation of Spin-Orbit Integrals. Perturbational Approaches to Spin-Orbit Coupling. Variational Procedures. Comparison of Fine-Structure Splittings with Experiment. First-Order Spin-Orbit Splitting. Second-Order Spin-Orbit Splitting. Spin-Forbidden Transitions. Radiative Transitions. Nonradiative Transitions. Summary and Outlook. Acknowledgments. References. 4. Cellular Automata Models of Aqueous Solution Systems (Lemont B. Kier, Chao-Kun Cheng, and Paul G. Seybold). Introduction. Cellular Automata. Historical Background. The General Structure. Cell Movement. Movement (Transition) Rules. Collection of Data. Aqueous Solution Systems. Water as a System. The Molecular Model. Significance of the Rules. Studies of Water and Solution Phenomena. A Cellular Automata Model of Water. The Hydrophobic Effect. Solute Dissolution. Aqueous Diffusion. Immiscible Liquids and Partitioning. Micelle Formation. Membrane Permeability. Acid Dissociation. Percolation. Solution Kinetic Models. First-Order Kinetics. Kinetic and Thermodynamic Reaction Control. Excited-State Kinetics. Second-Order Kinetics. Enzyme Reactions. An Anticipatory Model. Chromatographic Separation. Conclusions. Appendix. References.

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20 ISBN 9780471445258

内容説明

THIS VOLUME, LIKE THOSE PRIOR TO IT, FEATURES CHAPTERS BY EXPERTS IN VARIOUS FIELDS OF COMPUTATIONAL CHEMISTRY. TOPICS COVERED IN VOLUME 20 INCLUDE VALENCE THEORY, ITS HISTORY, FUNDAMENTALS, AND APPLICATIONS; MODELING OF SPIN-FORBIDDEN REACTIONS; CALCULATION OF THE ELECTRONIC SPECTRA OF LARGE MOLECULES; SIMULATING CHEMICAL WAVES AND PATTERNS; FUZZY SOFT-COMPUTING METHODS AND THEIR APPLICATIONS IN CHEMISTRY; AND DEVELOPMENT OF COMPUTATIONAL MODELS FOR ENZYMES, TRANSPORTERS, CHANNELS, AND RECEPTORS RELEVANT TO ADME/TOX. FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry." -JOURNAL OF MOLECULAR GRAPHICS AND MODELING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)." -JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

目次

1. Valence Bond Theory, Its History, Fundamentals, and Applications: A Primer (Sason Shaik and Philippe C. Hiberty). Introduction. A Story of Valence Bond Theory, Its Rivalry with Molecular Orbital Theory, Its Demise, and Eventual Resurgence. Roots of VB Theory. Origins of MO Theory and the Roots of VB-MO Rivalry. The ''Dance'' of Two Theories: One Is Up, the Other Is Down. Are the Failures of VB Theory Real Ones? Modern VB Theory: VB Theory Is Coming of Age. Basic VB Theory. Writing and Representing VB Wave Functions. The Relationship between MO and VB Wave Functions. Formalism Using the Exact Hamiltonian. Qualitative VB Theory. Some Simple Formulas for Elementary Interactions. Insights of Qualitative VB Theory. Are the ''Failures'' of VB Theory Real? Can VB Theory Bring New Insight into Chemical Bonding? VB Diagrams for Chemical Reactivity. VBSCD: A General Model for Electronic Delocalization and Its Comparison with the Pseudo-Jahn-Teller Model. What Is the Driving Force, s or p, Responsible for the D6h Geometry of Benzene? VBSCD: The Twin-State Concept and Its Link to Photochemical Reactivity. The Spin Hamiltonian VB Theory. Theory. Applications. Ab Initio VB Methods. Orbital-Optimized Single-Configuration Methods. Orbital-Optimized Multiconfiguration VB Methods. Prospective. Appendix. A.1 Expansion of MO Determinants in Terms of AO Determinants. A.2 Guidelines for VB Mixing. A.3 Computing Mono-Determinantal VB Wave Functions with Standard Ab Initio Programs. Acknowledgments. References. 2. Modeling of Spin-Forbidden Reactions (Nikita Matsunaga and Shiro Koseki). Overview of Reactions Requiring Two States. Spin-Forbidden Reaction, Intersystem Crossing. Spin-Orbit Coupling as a Mechanism for Spin-Forbidden Reaction. General Considerations. Atomic Spin-Orbit Coupling. Molecular Spin-Orbit Coupling. Crossing Probability. Fermi Golden Rule. Landau-Zener Semiclassical Approximation. Methodologies for Obtaining Spin-Orbit Matrix Elements. Electron Spin in Nonrelativistic Quantum Mechanics. Klein-Gordon Equation. Dirac Equation. Foldy-Wouthuysen Transformation. Breit-Pauli Hamiltonian. Zeff Method. Effective Core Potential-Based Method. Model Core Potential-Based Method. Douglas-Kroll Transformation. Potential Energy Surfaces. Minimum Energy Crossing-Point Location. Available Programs for Modeling Spin-Forbidden Reactions. Applications to Spin-Forbidden Reactions. Diatomic Molecules. Polyatomic Molecules. Phenyl Cation. Norborene. Conjugated Polymers. CH(2II) + N2 -- HCN + N(4S). Molecular Properties. Dynamical Aspects. Other Reactions. Biological Chemistry. Concluding Remarks. Acknowledgments. References. 3. Calculation of the Electronic Spectra of Large Molecules (Stefan Grimme). Introduction. Types of Electronic Spectra. Types of Excited States. Theory. Excitation Energies. Transition Moments. Vibrational Structure. Quantum Chemical Methods. Case Studies. Vertical Absorption Spectra. Circular Dichroism. Vibrational Structure. Summary and Outlook. Acknowledgments. References. 4. Simulating Chemical Waves and Patterns (Raymond Kapral). Introduction. Reaction-Diffusion Systems. Cellular Automata. Coupled Map Lattices. Mesoscopic Models. Summary. References. 5. Fuzzy Soft-Computing Methods and Their Applicationsin Chemistry (Costel Sarbu and Horia F. Pop). Introduction. Methods for Exploratory Data Analysis. Visualization of High-Dimensional Data. Clustering Methods. Projection Methods. Linear Projection Methods. Nonlinear Projection Methods. Artificial Neural Networks. Perceptron. Multilayer Nets: Backpropagation. Associative Memories: Hopfield Net. Self-Organizing Map. Properties. Mathematical Characterization. Relation between SOM and MDS. Multiple Views of the SOM. Other Architectures. Evolutionary Algorithms. Genetic Algorithms. Canonical GA. Evolution Strategies. Evolutionary Programming. Fuzzy Sets and Fuzzy Logic. Fuzzy Sets. Fuzzy Logic. Fuzzy Clustering. Fuzzy Regression. Fuzzy Principal Component Analysis (FPCA). Fuzzy PCA (Optimizing the First Component). Fuzzy PCA (Nonorthogonal Procedure). Fuzzy PCA (Orthogonal). Fuzzy Expert Systems (Fuzzy Controllers). Hybrid Systems. Combinations of Fuzzy Systems and Neutral Networks. Fuzzy Genetic Algorithms. Neuro-Genetic Systems. Fuzzy Characterization and Classification of the Chemical Elements and Their Properties. Hierarchical Fuzzy Classification of Chemical Elements Based on Ten Physical Properties. Hierarchical Fuzzy Classification of Chemical Elements Based on Ten Physical, Chemical, and Structural Properties. Fuzzy Hierarchical Cross-Classification of Chemical Elements Based on Ten Physical Properties. Fuzzy Hierarchical Characteristics Clustering. Fuzzy Horizontal Characteristics Clustering. Characterization and Classification of Lanthanides and Their Properties by PCA and FPCA. Properties of Lanthanides Considered in This Study. Classical PCA. Fuzzy PCA. Miscellaneous Applications of FPCA. Fuzzy Modeling of Environmental, SAR and QSAR Data. Spectral Library Search and Spectra Interpretation. Fuzzy Calibration of Analytical Methods and Fuzzy Robust Estimation of Location and Spread. Application of Fuzzy Neural Networks Systems in Chemistry. Applications of Fuzzy Sets Theory and Fuzzy Logic in Theoretical Chemistry. Conclusions and Remarks. References. 6. Development of Computational Models for Enzymes, Transporters, Channels, and Receptors Relevant to ADME/Tox (Sean Ekins and Peter W. Swaan). Introduction. ADME/Tox Modeling: An Expansive Vision. The Concerted Actions of Transport and Metabolism. Metabolism. Transporters. Approaches to Modeling Enzymes, Transporters, Channels, and Receptors. Classical QSAR. Pharmacophore Models. Homology Modeling. Transporter Modeling. Applications of Transporters. The Human Small Peptide Transporter, hPEPT1. The Apical Sodium-Dependent Bile Acid Transporter. P-Glycoprotein. Vitamin Transporters. Organic Cation Transporter. Organic AnionTransporters. Nucleoside Transporter. Breast Cancer Resistance Protein. Sodium Taurocholate Transporting Polypeptide. Enzymes. Cytochrome P450. Epoxide Hydrolase. Monoamine Oxidase. Flavin-Containing Monooxygenase. Sulfotransferases. Glucuronosyltransferases. Glutathione S-transferases. Channels. Human Ether-a-gogo Related Gene. Receptors. Pregnane X-Receptor. Constitutive Androstane Receptor. Future Developments. Acknowledgments. Abbreviations. References. Author Index. Subject Index.

巻冊次

21 ISBN 9780471682394

内容説明

REVIEWS IN COMPUTATIONAL CHEMISTRY Kenny B. Lipkowitz, Raima Larter, and Thomas R. Cundari This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. TOPICS COVERED IN Volume 21 iNCLUDE AB INITIO QUANTUM SIMULATION IN SOLID STATE CHEMISTRY; MOLECULAR QUANTUM SIMILARITY; ENUMERATING MOLECULES; VARIABLE SELECTION; BIOMOLECULAR APPLICATIONS OF POISSON-BOLTZMANN METHODS; AND DATA SOURCES AND COMPUTATIONAL APPROACHES FOR GENERATING MODELS OF GENE REGULATORY NETWORKS. FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry." --JOURNAL OF MOLECULAR GRAPHICS AND MODELLING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)." --JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

目次

1. Ab Initio Quantum Simulation in Solid State Chemistry 1 (Roberto Dovesi, Bartolomeo Civalleri, Roberto Orlando, Carla Roetti, and Victor R. Saunders). 2. Molecular Quantum Similarity: Theory and Applications (Patrick Bultinck, Xavier Girones, and Ramon Carbo-Dorca). 3. Enumerating Molecules (Jean-Loup Faulon, Donald P. Visco, Jr., and Diana Roe). 4. Variable Selection-Spoilt for Choice? (David J. Livingstone and David W. Salt). 5. Biomolecular Applications of Poisson-Boltzmann Methods (Nathan A. Baker). 6. Data Sources and Computational Approaches for Generating Models of Gene Regulatory Networks (Baltazar D. Aguda, Georghe Craciun, and Rengul Cetin-Atalay). Author Index. Subject Index.

巻冊次

22 ISBN 9780471779384

内容説明

FROM REVIEWS OF THE SERIES "Reviews in Computational Chemistry remains the most valuable reference to methods and techniques in computational chemistry." -JOURNAL OF MOLECULAR GRAPHICS AND MODELLING "One cannot generally do better than to try to find an appropriate article in the highly successful Reviews in Computational Chemistry. The basic philosophy of the editors seems to be to help the authors produce chapters that are complete, accurate, clear, and accessible to experimentalists (in particular) and other nonspecialists (in general)." -JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

目次

1. Protein Structure Classification (Patrice Koehl). 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 (Emilio Xavier Esposito, Dror Tobi, and Jeffry D. Madura). 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 (Joan-Emma Shea, Miriam R. Friedel, and Andrij Baumketner). 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 (Marco Saraniti, Shela Aboud, and Robert Eisenberg). 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 (C. Matthew Sundling, Nagamani Sukumar, Hongmei Zhang, Mark J. Embrechts, and Curt M. Breneman). 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.

巻冊次

28 ISBN 9781118407776

内容説明

The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered around molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 28 include: Free-energy Calculations with Metadynamics Polarizable Force Fields for Biomolecular Modeling Modeling Protein Folding Pathways Assessing Structural Predictions of Protein-Protein Recognition Kinetic Monte Carlo Simulation of Electrochemical Systems Reactivity and Dynamics at Liquid Interfaces

目次

Preface xi List of Contributors xv Contributors to Previous Volumes xvii 1. Free-Energy Calculations with Metadynamics: Theory and Practice 1 Giovanni Bussi and Davide Branduardi Introduction 1 Molecular Dynamics and Free-Energy Estimation 3 Molecular Dynamics 3 Free-Energy Landscapes 4 A Toy Model: Alanine Dipeptide 6 Biased Sampling 8 Adaptive Biasing with Metadynamics 9 Reweighting 12 Well-Tempered Metadynamics 12 Reweighting 14 Metadynamics How-To 14 The Choice of the CV(s) 15 The Width of the Deposited Gaussian Potential 17 The Deposition Rate of the Gaussian Potential 18 A First Test Run Using Gyration Radius 19 A Better Collective Variable: Dihedral Angle 23 Well-Tempered Metadynamics Using Gyration Radius 24 Well-Tempered Metadynamics Using Dihedral Angle 27 Advanced Collective Variables 28 Path-Based Collective Variables 30 Collective Variables Based on Dimensional Reduction Methods 32 Template-Based Collective Variables 34 Potential Energy as a Collective Variable 35 Improved Variants 36 Multiple Walkers Metadynamics 36 Replica Exchange Metadynamics 37 Bias Exchange Metadynamics 38 Adaptive Gaussians 39 Conclusion 41 Acknowledgments 42 Appendix A: Metadynamics Input Files with PLUMED 42 References 44 2. Polarizable Force Fields for Biomolecular Modeling 51 Yue Shi, Pengyu Ren, Michael Schnieders, and Jean-Philip Piquemal Introduction 51 Modeling Polarization Effects 52 Induced Dipole Models 52 Classic Drude Oscillators 54 Fluctuating Charges 54 Recent Developments 55 AMOEBA 55 SIBFA 57 NEMO 58 CHARMM-Drude 58 CHARMM-FQ 59 X-Pol 60 PFF 60 Applications 61 Water Simulations 61 Ion Solvation 62 Small Molecules 63 Proteins 64 Lipids 66 Continuum Solvents for Polarizable Biomolecular Solutes 66 Macromolecular X-ray Crystallography Refinement 67 Prediction of Organic Crystal Structure, Thermodynamics, and Solubility 70 Summary 71 Acknowledgment 71 References 72 3. Modeling Protein Folding Pathways 87 Clare-Louise Towse and Valerie Daggett Introduction 87 Outline of this Chapter 90 Protein Simulation Methodology 90 Force Fields, Models and Solvation Approaches 90 Unfolding: The Reverse of Folding 97 Elevated Temperature Unfolding Simulations 100 Biological Relevance of Forced Unfolding 103 Biased or Restrained MD 108 Characterizing Different States 111 Protein Folding and Refolding 115 Folding in Families 118 Conclusions and Outlook 121 Acknowledgment 122 References 122 4. Assessing Structural Predictions of Protein-Protein Recognition: The CAPRI Experiment 137 Joel Janin, Shoshana J. Wodak, Marc F. Lensink, and Sameer Velankar Introduction 137 Protein-Protein Docking 138 A Short History of Protein-Protein Docking 138 Major Current Algorithms 141 The CAPRI Experiment 144 Why Do Blind Predictions? 144 Organizing CAPRI 145 The CAPRI Targets 146 Creating a Community 149 Assessing Docking Predictions 150 The CAPRI Evaluation Procedure 150 A Survey of the Results of 12 Years of Blind Predictions on 45 Targets 154 Recent Developments in Modeling Protein-Protein Interaction 160 Modeling Multicomponent Assemblies. The Multiscale Approach 160 Genome-Wide Modeling of Protein-Protein Interaction 161 Engineering Interactions and Predicting Affinity 162 Conclusion 164 Acknowledgments 165 References 165 5. Kinetic Monte Carlo Simulation of Electrochemical Systems 175 C. Heath Turner, Zhongtao Zhang, Lev D. Gelb, and Brett I. Dunlap Background 175 Introduction to Kinetic Monte Carlo 176 Electrochemical Relationships 180 Applications 184 Transport in Li-ion Batteries 184 Solid Electrolyte Interphase (SEI) Passive Layer Formation 187 Analysis of Impedance Spectra 189 Electrochemical Dealloying 189 Electrochemical Cells 190 Solid Oxide Fuel Cells 193 Other Electrochemical Systems 197 Conclusions and Future Outlook 198 Acknowledgments 199 References 199 6. Reactivity and Dynamics at Liquid Interfaces 205 Ilan Benjamin Introduction 205 Simulation Methodology for Liquid Interfaces 207 Force Fields for Molecular Simulations of Liquid Interfaces 207 Boundary Conditions and the Treatment of Long-Range Forces 210 Statistical Ensembles for Simulating Liquid Interfaces 213 Comments About Monte Carlo Simulations 214 The Neat Interface 214 Density, Fluctuations, and Intrinsic Structure 215 Surface Tension 221 Molecular Structure 223 Dynamics 230 Solutes at Interfaces: Structure and Thermodynamics 235 Solute Density 236 Solute-Solvent Correlations 240 Solute Molecular Orientation 242 Solutes at Interfaces: Electronic Spectroscopy 243 A Brief General Background on Electronic Spectroscopy in the Condensed Phase 243 Experimental Electronic Spectroscopy at Liquid Interfaces 245 Computer Simulations of Electronic Transitions at Interfaces 249 Solutes at Interfaces: Dynamics 253 Solute Vibrational Relaxation at Liquid Interfaces 253 Solute Rotational Relaxation at Liquid Interfaces 258 Solvation Dynamics 263 Summary 269 Reactivity at Liquid Interfaces 270 Introduction 270 Electron Transfer Reactions at Liquid/Liquid Interfaces 271 Nucleophilic Substitution Reactions and Phase Transfer Catalysis (PTC) 277 Conclusions 283 Acknowledgments 284 References 284 7. Computational Techniques in the Study of the Properties of Clathrate Hydrates 315 John S. Tse Historical Perspective 315 Structures 317 The van der Waals-Platteeuw Solid Solution Theory 318 Computational Advancements 322 Thermodynamic Modelling 322 Atomistic Simulations 327 Thermodynamic Stability 344 Hydrate Nucleation and Growth 355 Guest Diffusion Through Hydrate Cages 368 Ab Initio Methods 371 Outlook 381 References 382 8. The Quantum Chemistry of Loosely-Bound Electrons 391 John M. Herbert Introduction and Overview 391 What Is a Loosely-Bound Electron? 391 Scope of This Review 392 Chemical Significance of Loosely-Bound Electrons 394 Challenges for Theory 400 Terminology and Fundamental Concepts 402 Bound Anions 402 Metastable (Resonance) Anions 415 Quantum Chemistry for Weakly-Bound Anions 425 Gaussian Basis Sets 425 Wave Function Electronic Structure Methods 439 Density Functional Theory 456 Quantum Chemistry for Metastable Anions 471 Maximum Overlap Method 474 Complex Coordinate Rotation 477 Stabilization Methods 483 Concluding Remarks 495 Acknowledgments 495 Appendix A: List of Acronyms 496 References 497 Index 519

巻冊次

29 ISBN 9781119103936

内容説明

The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered on molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 29 include: Noncovalent Interactions in Density-Functional Theory Long-Range Inter-Particle Interactions: Insights from Molecular Quantum Electrodynamics (QED) Theory Efficient Transition-State Modeling using Molecular Mechanics Force Fields for the Everyday Chemist Machine Learning in Materials Science: Recent Progress and Emerging Applications Discovering New Materials via a priori Crystal Structure Prediction Introduction to Maximally Localized Wannier Functions Methods for a Rapid and Automated Description of Proteins: Protein Structure, Protein Similarity, and Protein Folding

目次

Contributors x Preface xii Contributors to Previous Volumes xv 1 Noncovalent Interactions in Density Functional Theory 1 Gino A. DiLabio and Alberto Otero-de-la-Roza Introduction 1 Overview of Noncovalent Interactions 3 Theory Background 9 Density -Functional Theory 9 Failure of Conventional DFT for Noncovalent Interactions 17 Noncovalent Interactions in DFT 20 Pairwise Dispersion Corrections 20 Potential-Based Methods 42 Minnesota Functionals 47 Nonlocal Functionals 54 Performance of Density Functionals for Noncovalent Interactions 59 Description of Noncovalent Interactions Benchmarks 59 Performance of Dispersion-Corrected Methods 66 Noncovalent Interactions in Perspective 74 Acknowledgments 78 References 79 2 Long -Range Interparticle Interactions: Insights from Molecular Quantum Electrodynamics (QED) Theory 98 Akbar Salam Introduction 98 The Interaction Energy at Long Range 101 Molecular QED Theory 104 Electrostatic Interaction in Multipolar QED 112 Energy Transfer 114 Mediation of RET by a Third Body 119 Dispersion Potential between a Pair of Atoms or Molecules 123 Triple-Dipole Dispersion Potential 128 Dispersion Force Induced by External Radiation 132 Macroscopic QED 136 Summary 141 References 143 3 Efficient Transition State Modeling Using Molecular Mechanics Force Fields for the Everyday Chemist 152 Joshua Pottel and Nicolas Moitessier Introduction 152 Molecular Mechanics and Transition State Basics 154 Molecular Mechanics 154 Transition States 157 Ground State Force Field Techniques 158 Introduction 158 ReaxFF 159 Reaction Force Field 161 Seam 163 Empirical Valence Bond/Multiconfiguration Molecular Dynamics 166 Asymmetric Catalyst Evaluation 169 TSFF Techniques 173 Introduction 173 Q2MM 175 Conclusion and Prospects 178 References 178 4 Machine Learning in Materials Science: Recent Progress and Emerging Applications 186 Tim Mueller, Aaron Gilad Kusne, and Rampi Ramprasad Introduction 186 Supervised Learning 188 A Formal Probabilistic Basis for Supervised Learning 189 Supervised Learning Algorithms 199 Unsupervised Learning 213 Cluster Analysis 215 Dimensionality Reduction 226 Selected Materials Science Applications 237 Phase Diagram Determination 237 Materials Property Predictions Based on Data from Quantum Mechanical Computations 240 Development of Interatomic Potentials 245 Crystal Structure Predictions (CSPs) 249 Developing and Discovering Density Functionals 250 Lattice Models 251 Materials Processing and Complex Materials Behavior 256 Automated Micrograph Analysis 257 Structure-Property Relationships in Amorphous Materials 260 Additional Resources 263 Summary 263 Acknowledgments 264 References 264 5 Discovering New Materials via A Priori Crystal Structure Prediction 274 Eva Zurek Introduction and Scope 274 Crystal Lattices and Potential Energy Surfaces 276 Calculating Energies and Optimizing Geometries 281 Methods to Predict Crystal Structures 282 Following Soft Vibrational Modes 283 Random (Sensible) Structure Searches 284 Simulated Annealing 285 Basin Hopping and Minima Hopping 287 Metadynamics 288 Particle Swarm Optimization 289 Genetic Algorithms and Evolutionary Algorithms 291 Hybrid Methods 292 The Nitty -Gritty Aspects of Evolutionary Algorithms 294 Workflow 294 Selection for Procreation 295 Evolutionary Operators 297 Maintaining Diversity 299 The XtalOpt Evolutionary Algorithm 300 Practical Aspects of Carrying out an Evolutionary Structure Search 303 Crystal Structure Prediction at Extreme Pressures 312 Note in Proof 315 Conclusions 316 Acknowledgments 317 References 317 6 Introduction to Maximally Localized Wannier Functions 327 Alberto Ambrosetti and Pier Luigi Silvestrelli Introduction 327 Theory 329 Bloch States 329 Wannier Functions 331 Maximally Localized Wannier Functions: -Point Formulation 333 Extension to Brillouin-Zone k ]Point Sampling 336 Degree of WF Localization 337 Entangled Bands and Subspace Selection 338 Applications 340 Charge Visualization 340 Charge Polarization 344 Bonding Analysis 348 Amorphous Phases and Defects 351 Electron Transport 354 Efficient Basis Sets 356 Hints About MLWFs Numerical Computation 361 Brief Review of the Presently Available Computational Tools 361 MLWF Generation 362 References 363 7 Methods for a Rapid and Automated Description of Proteins: Protein Structure, Protein Similarity, and Protein Folding 369 Zhanyong Guo and Dieter Cremer Introduction 369 Protein Structure Description Methods Based on Frenet Coordinates and/or Coarse Graining 373 The Automated Protein Structure Analysis (APSA) 375 The Curvature-Torsion Description for Idealized Secondary Structures 378 Identification of Helices, Strands, and Coils 384 Difference between Geometry -Based and H ]Bond -Based Methods 385 Combination of Geometry -Based and H -Bond ]Based Methods 388 Chirality of SSUs 388 What is a Regular SSU? 389 A Closer Look at Helices: Distinction between - and 310 -Helices 391 Typical Helix Distortions 395 Level 2 of Coarse Graining: The Curved Vector Presentation of Helices 398 Identification of Kinked Helices 402 Analysis of Turns 406 Introduction of a Structural Alphabet 409 Derivation of a Protein Structure Code 411 Description of Protein Similarity 416 Qualitative and Quantitative Assessment of Protein Similarity 417 The Secondary Code and Its Application in Connection with Protein Similarity 423 Description of Protein Folding 423 Concluding Remarks 426 Acknowledgments 428 References 428 Index 439

巻冊次

30 ISBN 9781119355434

内容説明

The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered on molecular modeling. * Provides background and theory, strategies for using the methods correctly, pitfalls to avoid, applications, and references * Contains updated and comprehensive compendiums of molecular modeling software that list hundreds of programs, services, suppliers and other information that every chemist will find useful * Includes detailed indices on each volume help the reader to quickly discover particular topics * Uses a tutorial manner and non-mathematical style, allowing students and researchers to access computational methods outside their immediate area of expertise

目次

List of Contributors xi Foreword xiii Contributors to Previous Volumes xvii 1 Chemical Bonding at High Pressure 1 Andreas Hermann High-Pressure Science 1 Motivation 1 Pressure in Industrial Processes 2 High-Pressure Experiments 2 Pressure Effects in Materials 5 Close Packing and Metallicity-or Not 6 Hydrogen and Hydrogen-Rich Compounds 7 Molecular Crystals 8 Closed-Shell Reactivity 9 Unusual Chemistry 9 New Electronic States 10 Electronic Structure Calculations on Materials Under Pressure 10 Density and Wave Function-Based Approaches 11 Basis Sets and Pseudopotentials 13 Identifying High-Pressure Crystal Structures 14 Stability of High-Pressure Phases 16 Properties of Materials Under Pressure 20 Mechanical Properties 21 Electronic Properties 23 Spectroscopic Properties 28 Conclusions 29 Acknowledgments 31 References 31 2 Molecular Dynamics Simulations of Shock Loading of Materials: A Review and Tutorial 43 Mitchell A. Wood, Mathew J. Cherukara, Edwin Antillon, and Alejandro Strachan Introduction 43 Shock Loading of Solids 101 44 Chapter Organization 46 Molecular Simulations of Shockwaves in Solids 46 Molecular Dynamics and Coarse Grain Dynamics 46 Direct Shock Simulations 48 Indirect Shock Simulations: Achieving Longer Timescales 49 Shock-Induced Plasticity and Failure 51 Plastic Deformation 51 Preexisting Defects: Voids and Vacancies 54 Preexisting Defects: Polycrystalline Materials 56 Granular Materials 56 Dynamical Failure 57 Critical Phenomena in Spallation and Cluster Formation 60 Ejecta Formation and the Richtmyer-Meshkov Instability 61 Shock-Induced Phase Transformation and Materials Synthesis 62 Phase Transformations 63 Shock-Induced and Shock-Assisted Chemical Reactions 69 Reactive Composites 70 Energetic Materials and Detonation 73 Model Explosives: Shock to Detonation 74 Reactive MD Simulations of Explosives 75 Electronic Structure-Based Modeling 79 Coarse-Grained Descriptions of Shock-Induced Chemistry 80 Summary and Outlook 83 Acknowledgments 84 Appendix 84 References 85 3 Basis Sets in Quantum Chemistry 93 Balazs Nagy, and Frank Jensen Introduction 93 The Basis Set Approximation 94 Basis Set Desiderata 96 Types of Basis Functions 98 Slater and Gaussian Type Functions 98 Plane-Wave Functions 101 Real-Space Functions 103 Other Functions 104 Structure and Classification of Gaussian Type Basis Sets 105 Contracted Basis Functions 108 Optimization of Basis Set Parameters 111 Basis Set Augmentation 113 Diffuse Functions 113 Tight Functions 114 Fitting Functions 115 Nonatom-Centered Basis Sets 115 Examples of Basis Sets 116 Segmented Contracted Basis Sets 116 General Contracted Basis Sets 117 Property Basis Sets 119 Electric Properties 121 Magnetic Properties 126 Mixed Properties 128 Relativistic Basis Sets 129 Pseudopotentials 130 Basis Set Convergence 131 Convergence of Electronic Structure Methods with Gaussian Type Basis Sets 132 Composite Extrapolation Methods 133 Basis Set Incompleteness and Superposition Errors 134 Aspects of Choosing A Suitable Basis Set 136 Availability of Basis Sets 139 Acknowledgment 139 References 139 4 The Quantum Chemistry of Open-Shell Species 151 Anna I. Krylov Introduction and Overview 151 Quantum Chemistry Methods for Open- and Closed-Shell Species 155 Some Aspects of Electronic Structure of Open-Shell Species 159 Spin Contamination of Approximate Open-Shell Wave Functions 159 Jahn-Teller Effect 160 Vibronic Interactions and Pseudo-Jahn-Teller Effect 162 High-Spin Open-Shell States 165 Open-Shell States with Multiconfigurational Character 167 EOM-IP and EOM-EA Methods for Open-Shell Systems 167 Examples 169 Diradicals, Triradicals, and Beyond 174 Excited States of Open-Shell Species 181 Metastable Radicals 186 Bonding in Open-Shell Species 187 Dyson Orbitals 188 Density-Based Wave Function Analysis 189 Insight into Bonding from Physical Observables 192 Properties and Spectroscopy 193 Vibrational Spectroscopy 194 Electronic and Photoelectron Spectroscopy 194 Electronic Transitions 200 Outlook 207 Acknowledgments 208 Appendix: List of Acronyms 209 References 210 5 Machine Learning, Quantum Chemistry, and Chemical Space 225 Raghunathan Ramakrishnan, and O. Anatole von Lilienfeld Introduction 225 Paradigm 228 Kernel Ridge Regression 230 Representation 232 Data 234 Kernel 236 Electrons 239 -Machine Learning 241 Atoms in Molecules 245 Crystals 247 Conclusions and Outlook 248 Acknowledgments 250 References 250 6 The Master Equation Approach to Problems in Chemical and Biological Physics 257 Dmitrii E. Makarov Introduction 257 The General Form of A Master Equation and its Solution 260 Microscopic Reversibility, Detailed Balance, and Their Consequences 262 The Kinetic Monte Carlo (KMC) Method 265 Quantum Master Equations 270 The Reduced Density Matrix as a Description of a Molecule Interacting with Its Surroundings 270 Diagonal and Off-Diagonal Elements of the Density Matrix and Significance of Dephasing 273 Relaxation 275 Kinetic Monte Carlo for Quantum Master Equations 277 Physical Significance of The Quantum Kinetic Monte Carlo Scheme 282 Concluding Remarks 283 Acknowledgments 284 References 284 7 Continuous Symmetry Measures: A New Tool in Quantum Chemistry 289 Pere Alemany, David Casanova, Santiago Alvarez, Chaim Dryzun, and David Avnir Introduction 289 Symmetry as a Fundamental Concept in Quantum Chemistry 289 Symmetry, Pseudosymmetry, and Quasisymmetry 292 Continuous Symmetry Measures 295 General Definition of CSMs 295 CSMs in Molecular Quantum Chemistry 299 CSM for the Nuclear Framework 300 CSMs for Matrices and Operators 303 CSM for Functions: Electron Density, Wave Functions, and Molecular Orbitals 304 CSMs for Irreducible Representations of a Group 307 Pseudosymmetry Analysis of Molecular Orbitals 313 Applications 315 The Nature of the Chemical Bond from the Point of View of CSMs 315 CSM Analysis of the Electronic Structure of Conjugated Hydrocarbons and Related Compounds 321 Pseudosymmetry Analysis of the d-Block Molecular Orbitals of "Octahedral" ML6 Transition Metal Compounds 328 Symmetry, Pseudosymmetry and Walsh Diagrams for ML4 Compounds along the Planarization Path 334 Conclusions 343 Acknowledgment 344 References 344 Index 353

巻冊次

31 ISBN 9781119518020

内容説明

The Reviews in Computational Chemistry series brings together leading authorities in the field to teach the newcomer and update the expert on topics centered on molecular modeling, such as computer-assisted molecular design (CAMD), quantum chemistry, molecular mechanics and dynamics, and quantitative structure-activity relationships (QSAR). This volume, like those prior to it, features chapters by experts in various fields of computational chemistry. Topics in Volume 31 include: Lattice-Boltzmann Modeling of Multicomponent Systems: An Introduction Modeling Mechanochemistry from First Principles Mapping Energy Transport Networks in Proteins The Role of Computations in Catalysis The Construction of Ab Initio Based Potential Energy Surfaces Uncertainty Quantification for Molecular Dynamics

目次

List of Contributors ix Preface xi Contributors to Previous Volumes xv 1 Lattice-Boltzmann Modeling of Multicomponent Systems: An Introduction 1 Ulf D. Schiller and Olga Kuksenok Introduction 1 The Lattice Boltzmann Equation: A Modern Introduction 4 A Brief History of the LBM 5 The Lattice Boltzmann Equation 7 The Fluctuating Lattice Boltzmann Equation 23 Boundary Conditions 25 Fluid-Particle Coupling 30 LBM for Multiphase Fluids 37 Governing Continuum Equations 37 Lattice Boltzmann Algorithm for Binary Fluid: Free-Energy Approach 42 Minimizing Spurious Velocities 47 Conclusions 50 References 51 2 Mapping Energy Transport Networks in Proteins 63 David M. Leitner and Takahisa Yamato Introduction 63 Thermal and Energy Flow in Macromolecules 65 Normal Modes of Proteins 65 Simulating Energy Transport in Terms of Normal Modes 69 Energy Diffusion in Terms of Normal Modes 70 Energy Transport from Time Correlation Functions 73 Energy Transport in Proteins is Inherently Anisotropic 75 Locating Energy Transport Networks 77 Communication Maps 77 CURrent calculations for Proteins (CURP) 80 Applications 83 Communication Maps: Illustrative Examples 83 CURP: Illustrative Examples 89 Future Directions 98 Summary 99 Acknowledgments 100 References 100 3 Uncertainty Quantification for Molecular Dynamics 115 Paul N. Patrone and Andrew Dienstfrey Introduction 115 From Dynamical to Random: An Overview of MD 118 System Specification 119 Interatomic Potentials 121 Hamilton's Equations 123 Thermodynamic Ensembles 128 Where Does This Leave Us? 131 Uncertainty Quantification 131 What is UQ? 132 Tools for UQ 136 UQ of MD 143 Tutorial: Trajectory Analysis 143 Tutorial: Ensemble Verification 148 Tutorial: UQ of Data Analysis for the Glass-Transition Temperature 151 Concluding Thoughts 161 References 162 4 The Role of Computations in Catalysis 171 Horia Metiu, Vishal Agarwal, and Henrik H. Kristoffersen Introduction 171 Screening 172 Sabatier Principle 173 Scaling Relations 175 BEP Relationship 176 Volcano Plots 180 Some Rules for Oxide Catalysts 189 Let Us Examine Some Industrial Catalysts 191 Sometimes Selectivity is More Important than Rate 191 Sometimes We Want a Smaller Rate! 191 Sometimes Product Separation is More Important than the Reaction Rate 193 Some Reactions are Equilibrium-limited 193 The Cost of Making the Catalyst is Important 194 The Catalyst Should Contain Abundant Elements 194 A Good Catalyst Should not be Easily Poisoned 195 Summary 195 References 196 5 The Construction of Ab Initio-Based Potential Energy Surfaces 199 Richard Dawes and Ernesto Quintas-Sanchez Introduction and Overview 199 What is a PES? 199 Significance and Range of Applications of PESs 204 Challenges for Theory 207 Terminology and Concepts 209 The Schroedinger Equation 209 The BO Approximation 210 Mathematical Foundations of (Linear) Fitting 215 Quantum Chemistry Methods 221 General Considerations 221 Single Reference Methods 223 Multireference Methods 225 Compound Methods or Protocols 227 Fitting Methods 229 General Considerations and Desirable Attributes of a PES 229 Non-Interpolative Fitting Methods 231 Interpolative Fitting Methods 239 Applications 242 The Automated Construction of PESs 242 Concluding Remarks 248 Acknowledgements 250 Acronyms/Abbreviations 250 References 251 6 Modeling Mechanochemistry from First Principles 265 Heather J. Kulik Introduction and Scope 265 Potential Energy Surfaces and Reaction Coordinates 266 Theoretical Models of Mechanochemical Bond Cleavage 268 Linear Model (Kauzmann, Eyring, and Bell) 268 Tilted Potential Energy Profile Model 270 First-Principles Models for Mechanochemical Bond Cleavage 271 Constrained Geometries Simulate External Force (COGEF) 271 Force-Modified Potential Energy Surfaces 273 Covalent Mechanochemistry 278 Overview of Characterization Methods 278 Representative Mechanophores 280 Representative Mechanochemistry Case Studies 281 Benzocyclobutene 281 gem-Difluorocyclopropane 285 PPA: Heterolytic Bond Cleavage 288 Mechanical Force for Sampling: Application to Lignin 292 Best Practices for Mechanochemical Simulation 296 Conclusions 298 Acknowledgments 299 References 300 Index 313

巻冊次

6. VCH Publishers ISBN 9781560816676

内容説明

This is the sixth volume in a series that reviews advances in the rapidly growing and evolving field of computational chemistry. Each volume has an updated and comprehensive listing of software sources.

目次

• Continuum solvation models - classical and quantum mechanical implementations
• molecular mechanics force fields for modelling inorganic and organometallic compounds
• computational methods for modelling polymers - an introduction
• high performance computing in computational chemistry - methods and machines
• molecular modelling software in use - publication trends
• appendix 1 - published force field parameters
• appendix 2 - compendium of software for molecular modelling.

巻冊次

7. VCH Publishers ISBN 9781560819158

内容説明

This volume in computational chemistry includes aspects of: theoretical chemistry, physical chemistry, computer graphics in chemistry, molecular structure, and pharmaceutical chemistry.

目次

• An introduction to density functional theory
• density functional methods in biomolecular modelling
• similarity searching in databases of chemical structures
• methods and applications of combined quantum mechanical and molecular mechanical potentials
• the a priori calculations of vibrational circular dichroism intensities
• effective core potential approaches to the chemistry of the heavier elements
• computations in treating fullerenes and carbon aggregates
• appendix - compendium of software for molecular modelling.

巻冊次

8. VCH Publishers ISBN 9781560819295

内容説明

This volume provides reviews in computational chemistry, which is increasingly used in conjunction with organic, inorganic, medicinal, biological, physical and analytical chemistry, biotechnology, materials science and chemical physics.

巻冊次

9. VCH Publishers ISBN 9781560819301

内容説明

This volume is part of a series presenting research developments in the field of computational chemistry.

巻冊次

10. VCH Publishers ISBN 9781560819578

内容説明

Part of a series containing updated and comprehensive compendiums of molecular modelling software, listing hundreds of programs, services, suppliers, and other information. The chapters are approached in a tutorial manner and written in a non-mathematical style.

巻冊次

[1]VCH Verlagsgesellschaft ISBN 9783527278459

内容説明

This book is an account of current developments in the field of computational chemistry and may be of interest to any chemists involved in molecular modelling, including biochemists, medicinal chemists, organic and physical chemists. The core of the book deals with techniques for computer assisted design and the book also discusses software for molecular recognition and the relationship between structure and biological activity of drug molecules.

目次

• Basic sets for Ab initio molecular orbital calculations and intermolecular interactions
• semiempirical molecular orbital methods
• properties of molecules by direct calculation
• the application of quantitative design strategies in pesticide design
• chemometrics and multivariate analysis in analytical chemistry
• searching databases of three-dimensional structures
• molecular surfaces
• computer simulation of biomolecular systems using molecular dynamics and free energy perturbation methods
• aspects of molecular modelling
• successes of computer-assisted molecular design
• perspectives on Ab initio calculations
• compendium of software for molecular modelling.

巻冊次

2. VCH Verlagsgesellschaft ISBN 9783527283385

内容説明

Topics covered include conformational analysis, molecular dynamics and quantitative structure-activity relationships (QSAR). Attention is also given to recent advances in computational chemistry with a focus on new and important literature. An updated appendix provides information on the software available for molecular modelling. The series is designed to help the scientist understand and apply the newest computer technology in the search to better understand the molecule. "Reviews in Computational Chemistry: Volume 2" brings together renowned experts in the field to present the reader with an account of the latest developments in computational chemistry.

巻冊次

3. VCH Verlagsgesellschaft ISBN 9783527896196

内容説明

This third volume in the series brings together experts in the field to present the reader with an account of recent developments in computational chemistry. Rather than create a traditional review article, each author approaches a topic to enable the reader to understand and solve problems and locate key references quickly. An updated compendium of software for molecular modelling appears as an appendix as in previous volumes.

目次

• Optimization methods in computational chemistry
• predicting three-dimensional structures of oligopeptides
• molecular modelling using NMR data
• computer-assisted methods in the evaluation of chemical toxicity
• compendium of software for molecular modelling.

巻冊次

4. VCH Verlagsgesellschaft ISBN 9783527896202

内容説明

This fourth volume in the series brings together experts in the field to present the reader with an account of recent developments in computational chemistry. Rather than create a traditional review article, each author approaches a topic to enable the reader to understand and solve problems and locate key references quickly. An updated compendium of software for molecular modelling appears as an appendix as in previous volumes.

目次

• Basis sets from ab initio molecular orbital calculations and intermolecular interactions
• semiempirical molecular orbital methods
• properties of molecules by direct calculation
• the application of quantitative design strategies in pesticide discovery
• chemometrics and multivariate analysis in analytical chemistry
• searching databases of three-dimensional structures
• molecular surfaces
• computer simulation of biomolecular systems using molecular dynamics and free energy peturbation methods
• aspects of molecular modelling
• successes of computer-assisted molecular design
• perspectives on ab initio calculations. Appendix: compendium of software for molecular modelling.

「Nielsen BookData」 より

詳細情報

• NII書誌ID(NCID): BA10970029
• ISBN:
  • 089573754X
  • 3527278451
  • 0471187283
  • 1560815159
  • 3527283382
  • 0471188107
  • 1560816198
  • 3527896198
  • 0471188530
  • 1560816201
  • 3527896201
  • 0471188549
  • 1560816678
  • 1560819154
  • 0471186287
  • 1560819294
  • 1560819308
  • 156081957X
  • 0471192481
  • 0471246719
  • 047133135X
  • 0471354953
  • 0471361682
  • 0471386677
  • 0471398454
  • 0471215767
  • 0471235857
  • 0471445258
  • 047168239X
  • 0471779385
  • 9780470082010
  • 9780470112816
  • 9780470179987
  • 9780470388396
  • 9780470587140
  • 9781118407776
  • 9781119103936
  • 9781119355434
  • 9781119518020
• LCCN: 89021466
• 出版国コード: us
• タイトル言語コード: eng
• 本文言語コード: eng
• 出版地: New York, N.Y.,Weinheim
• ページ数/冊数: v.
• 大きさ: 25 cm
• 分類:
  • LCC : QD39.3.E46
  • DC20 : 542/.8
• 件名:
  • LCSH : Chemistry -- Data processing
  • LCSH : Chemistry -- Mathematics