Reviews in computational chemistry  [1]VCH Publishers ~ 31

edited by Kenny B. Lipkowitz and Donald B. Boyd

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.

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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. "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 non-specialists (in general)." "Journal of American Chemical Society".

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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

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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

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One of the top ten most frequently cited journals, this series 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. Detailed author and subject indices in each volume help the reader to quickly discover particular topics. The chapters are laid out 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.

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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

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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.

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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

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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

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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

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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.

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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.

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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.

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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.

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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.

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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).

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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."

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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

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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

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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

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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

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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

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[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.

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[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 Schrodinger 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.

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[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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[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. Ca'rdenas 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.

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[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. Mu ser ). 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 Re 2 Cl 2- 8 and Related Systems. The Cr-Cr Multiple Bond. Cu 2 O 2 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.

「Nielsen BookData」より

[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.

「Nielsen BookData」より

[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.

「Nielsen BookData」より

[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 Sa rbu 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.

「Nielsen BookData」より

[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.

「Nielsen BookData」より

[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.

「Nielsen BookData」より

[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.

「Nielsen BookData」より

[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 Bohm 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.

「Nielsen BookData」より

[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.

「Nielsen BookData」より

[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

「Nielsen BookData」より

[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

「Nielsen BookData」より

[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.

「Nielsen BookData」より

[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.

「Nielsen BookData」より

[目次]

  • Similarity Searching in Databases of Chemical Structures (G. Downs & P. Willett). Three--Dimensional Structure Database Searches (A. Good & J. Mason). Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials (J. Gao). An Introduction to Density Functional Theory (L. Bartolotti & K. Flurchick). Density Functional Methods in Biomolecular Modeling (A. St--Amant). The A Priori Calculation of Vibrational Circular Dichroism Intensities (D. Yang & A. Rauk). Appendix. Indexes.

「Nielsen BookData」より

[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.

「Nielsen BookData」より

[目次]

  • 1. Linear-Scaling Methods in Quantum Chemistry (Christian Ochsenfeld, Jorg 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 JUrgen 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.

「Nielsen BookData」より

この本の情報

書名 Reviews in computational chemistry
著作者等 Boyd, Donald B.
Lipkowitz, Kenny B.
Parrill, Abby L.
Gillet Valerie J.
Larter Raima
Cundari Thomas R.
巻冊次 [1]VCH Publishers
[1]VCH Verlagsgesellschaft
[1]Wiley-VCH
2. VCH Publishers
2. VCH Verlagsgesellschaft
2. Wiley-VCH
3. VCH Publishers
3. VCH Verlagsgesellschaft
3. Wiley-VCH
4. VCH Publishers
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
14. Wiley-VCH
15. Wiley-VCH
16. Wiley-VCH
17. Wiley-VCH
18. Wiley-VCH
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出版元 VCH;VCH Verlagsgesellschaft
刊行年月 c1990-
版表示 14 ed
ページ数 v.
大きさ 25 cm
ISBN 0471186287
0471187283
0471188107
0471188530
0471188549
0471192481
0471215767
0471235857
0471246719
047133135X
0471354953
0471361682
0471386677
0471398454
0471445258
047168239X
0471779385
1560815159
1560816198
1560816201
1560816678
1560819154
1560819294
1560819308
156081957X
3527278451
3527283382
3527896198
3527896201
089573754X
9780470112816
9780470179987
9780470388396
9780470587140
9781118407776
9781119103936
9781119355434
9781119518020
9780470082010
NCID BA10970029
※クリックでCiNii Booksを表示
言語 英語
出版国 アメリカ合衆国
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