計算分子化学(全6巻)<br>Computational Molecular Science (6-Volume Set)

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計算分子化学(全6巻)
Computational Molecular Science (6-Volume Set)

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  • 製本 Hardcover:ハードカバー版/ページ数 3194 p.
  • 言語 ENG
  • 商品コード 9780470723074
  • DDC分類 660

Full Description


Easy access to information on all aspects of molecular computations Order the six-volume set today and benefit from the special introductory price full details below Computational Molecular Science is the successor of the highly acclaimed Encyclopedia of Computational Chemistry, which was published by Wiley in 1998, and is the ultimate resource on all aspects of computational chemistry and its applications in chemistry, biology and materials science. Capturing the interdisciplinary flavour of the field, authors address key topics from differing perspectives such as chemistry, biology and materials science. In order to make the material accessible to students, practitioners and researchers alike the content is presented at different depths and levels in a range of article types: *Overviews provide broad and non-technical treatment of important topics at an accessible level * Key areas of research in the style of leading review journals are presented in Advanced Reviews for researchers and advanced students *Focus Articles present short, technical contributions describing specific real-world issues, e.g. implementations etc.*Software Reviews feature specific software packages of high utility in the field, with an emphasis on their capabilities and implementation rather than methodology *Opinions present individual perspectives from thought leaders in the field A special focus has been placed on computations and modeling of relevant biomolecules which are essential to new developments in medicinal chemistry. Covering all areas relevant to the understanding of computational molecular methods the content is structured in the following sections: *Computer and Information Science includes a wide range of techniques and applications used in cheminformatics, such as artificial intelligence, patent information, semantic web, data mining, automated synthesis design, etc.*Electronic Structure Theory covers computations of molecules based on ab initio quantum molecular methods and density functional theory *Simulation Methods includes free energy methods, molecular dynamics, Monte-Carlo methods and molecular mechanics *Software describes examples of commercial and shareware software packages for molecular computations and modeling *Structure and Mechanism concentrates on applications in the areas of computational biochemistry and biophysics, computational materials science, molecular structures and dynamics, and reaction mechanisms *Theoretical and Physical Chemistry includes reaction dynamics, kinetics and spectroscopy Experience the scope of content in Computational Molecular Science for yourself with a selection of free articles available to download now: WIREs Computational Molecular Science uses all the advantages of the WIREs concept and is the logical online successor of the highly acclaimed Encyclopedia of Computational Chemistry.As a review journal WIREs Computational Molecular Science includes all the material published in the book edition and will continue to publish much more material in the future, establishing itself as THE REVIEW JOURNAL in the field of computational chemistry and biology, offering the following advantages: * An impact factor of 5.783 according to 2012 ISI Journal Citation Reports with the following Ranking: 1/47 (Mathematical & Computational Biology) and 22/152 (Chemistry Multidisciplinary) * Indexed in all major A&I services such as CAS, TRSI and Scopus * Important new forum to promote cross-disciplinary research on computational chemistry, biochemistry and materials science * Authoritative, encyclopedic resource addressing key topics from diverse research perspectives Recommend that your librarian requests a free trial for your institution,

Table of Contents

        List of Contributors                       xxvii
Volume 1 Computer And Information Science 1 (508)
1.1 Chemoinformatics 3 (506)
1.1.1 Algorithms for Chemoinformatics 5 (12)
Nathan Brown
1.1.2 Automated Systematic Nomenclature 17 (12)
Generation for Organic Compounds
Antony John Williams
Andrey Yerin
1.1.3 Automatic Reaction Mapping and 29 (34)
Reaction Center Detection
William Lingran Chen
David Z. Chen
Keith T. Taylor
1.1.4 Cambridge Structural Database: 63 (10)
Experimental Three-Dimensional
Information on Small Molecules is a
Vital Resource for Interdisciplinary
Research and Learning
Colin R. Groom
Frank H. Allen
1.1.5 Chemical Patent Information 73 (16)
Systems
Geoffrey M. Downs
John M. Barnard
1.1.6 Cheminformatics and the Semantic 89 (18)
Web: Adding Value with Linked Data and
Enhanced Provenance
Jeremy G. Frey
Colin L. Bird
1.1.7 Chemoinformatics Applications of 107 (16)
Cluster Analysis
John David MacCuish
Norah Elizabeth MacCuish
1.1.8 Chemoinformatics: a History 123 (12)
Peter Willett
1.1.9 Computational Chemogenomics 135 (12)
Edgar Jacoby
1.1.10 Computational Methods for 147 (26)
Scaffold Hopping
Ansgar Schuffenhauer
1.1.11 Computational Toxicology: a Tool 173 (12)
for All Industries
Carol A. Marchant
1.1.12 Computer-Aided Synthesis Design: 185 (30)
40 Years On
Anthony Cook
A. Peter Johnson
James Law
Mahdi Mirzazadeh Orr Ravitz
Aniko Simon
1.1.13 Diversity Selection Algorithms 215 (10)
Valerie J. Gillet
1.1.14 Druggability Predictions: 225 (12)
Methods, Limitations, and Applications
Xavier Barril
1.1.15 Enabling Future Drug Discovery 237 (18)
by De Novo Design
Markus Hartenfeller
Gisbert Schneider
1.1.16 Enumeration of Chemical Space 255 (18)
Jean-Louis Reymond
Lars Ruddigkeit Lorenz Blum
Ruud van Deursen
1.1.17 Exploring Structure-Activity 273 (14)
Data Using the Landscape Paradigm
Rajarshi Guha
1.1.18 Fragment Library Design 287 (18)
Considerations
Susan M. Boyd
Andrew P. Turnbull
Bjorn Walse
1.1.19 Generation of Three-Dimensional 305 (16)
Pharmacophore Models
John H. Van Drie
1.1.20 Hansch Analysis: 50 Years On 321 (8)
Yvonne Connolly Martin
1.1.21 In Silico Applications of 329 (16)
Bioisosterism in Contemporary Medicinal
Chemistry Practice
George Papadatos
Nathan Brown
1.1.22 Maximum Common Subgraph 345 (12)
Isomorphism Algorithms and Their
Applications in Molecular Science: a
Review
Hans-Christian Ehrlich
Matthias Rarey
1.1.23 Molecular Interaction Fields in 357 (20)
Drug Discovery: Recent Advances and
Future Perspectives
Anna Artese
Simon Cross
Giosue Costa
Simona Distinto
Lucia Parrotta
Stefano Alcaro Francesco Ortuso
Gabriele Cruciani
1.1.24 Outstanding Challenges in 377 (32)
Protein--Ligand Docking and
Structure-Based Virtual Screening
Bohdan Waszkowycz
David E. Clark
Emanuela Gancia
1.1.25 RCSB Protein Data Bank Website, 409 (8)
Evolution of
Philip E. Bourne
Bojan Beran
Chunxiao Bi
Wolfgang F. Bluhm
Dimitris Dimitropoulos
Zukang Feng
David S. Goodsell
Andreas Prlic
Gregory B. Quinn
Peter W. Rose
John Westbrook
Benjamin Yukich
Jasmine Young
Christine Zardecki
Helen M. Berman
1.1.26 Representation of Chemical 417 (24)
Structures
Wendy A. Warr
1.1.27 Shape-Based Similarity Searching 441 (16)
in Chemical Databases
Paul W. Finn
Garrett M. Morris
1.1.28 Similarity Searching 457 (24)
Dagmar Stumpfe
Jurgen Bajorath
1.1.29 Two Personal Perspectives on a 481 (6)
Key Issue in Contemporary 3D QSAR
Robert D. Clark
Ulf Norinder
1.1.30 Understanding Drug-Likeness 487 (22)
Oleg Ursu
Anwar Rayan
Amiram Goldblum
Tudor I. Oprea
List of Contributors xxvii
Volume 2 Electronic Structure Theory 509 (750)
2.1 Ab Initio Electronic Structure Methods 511 (536)
2.1.1 Ab Initio Nonorthogonal Valence 513 (14)
Bond Methods
Peifeng Su
Wei Wu
2.1.2 All-Electron Basis Sets for Heavy 527 (12)
Elements
Dimitrios A. Pantazis
Frank Neese
2.1.3 Analytic Derivative and Response 539 (14)
Theory
Peter Pulay
2.1.4 Anharmonic Molecular Force Fields 553 (18)
Attila G. Csaszar
2.1.5 Atomic Orbital Basis Sets 571 (24)
Frank Jensen
2.1.6 Coupled-Cluster Theory and Its 595 (14)
Equation-of-Motion Extensions
Rodney J. Bartlett
2.1.7 Electron Propagator Theory: an 609 (20)
Approach to Prediction and
Interpretation in Quantum Chemistry
Joseph Vincent Ortiz
2.1.8 Excited State Coupled Cluster 629 (20)
Methods
Kristian Sneskov
Ove Christiansen
2.1.9 Explicitly Correlated Electronic 649 (12)
Structure Theory from R12/F12 Ansatze
Seiichiro Ten-no
Jozef Noga
2.1.10 Gn Theory 661 (16)
Larry A. Curtiss
Paul C. Redfern
Krishnan Raghavachari
2.1.11 Green's Function Methods for 677 (12)
Calculating Ionization Potentials,
Electron Affinities, and Excitation
Energies
David Danovich
2.1.12 Linear-Scaling Self-Consistent 689 (24)
Field Methods for Large Molecules
Jorg Kussmann
Matthias Beer
Christian Ochsenfeld
2.1.13 Low Entanglement Wavefunctions 713 (14)
Garnet Kin-Lie Chan
2.1.14 Møller--Plesset 727 (22)
Perturbation Theory: From Small
Molecule Methods to Methods for
Thousands of Atoms
Dieter Cremer
2.1.15 Multiconfiguration Second-Order 749 (20)
Perturbation Theory Approach to Strong
Electron Correlation in Chemistry and
Photochemistry
Daniel Roca-Sanjuan
Francesco Aquilante
Roland Lindh
2.1.16 Multi-Electron Integrals 769 (14)
Simen Reine
Tiygve Helgaker
Roland Lindh
2.1.17 Natural Bond Orbital Methods 783 (42)
Eric D. Glendening
Clark R. Landis
Frank Weinhold
2.1.18 Polarizable Continuum Model 825 (20)
Benedetta Mennucci
2.1.19 Polarizable Continuum Model for 845 (14)
the Representation of Solvation,
Selected Features of
Jacopo Tomasi
2.1.20 Pseudopotentials and 859 (12)
Modelpotentials
Xiaoyan Cao
Michael Dolg
2.1.21 Quadratic Configuration 871 (22)
Interaction Approach, From
Configuration Interaction to Coupled
Cluster Theory
Dieter Cremer
2.1.22 Quantum Monte Carlo Methods 893 (16)
Arne Luchow
2.1.23 Relativistic Douglas-Kroll-Hess 909 (12)
Theory
Markus Reiher
2.1.24 Resummation Methods 921 (20)
David Z. Goodson
2.1.25 Spin-Component-Scaled Electron 941 (22)
Correlation Methods
Stefan Grimme
Lars Goerigk
Reinhold F. Fink
2.1.26 Spin-Orbit Coupling and 963 (18)
Intersystem Crossing in Molecules
Christel M. Marian
2.1.27 State-Specific Multireference 981 (22)
Coupled-Cluster Theory
Andreas Kohn
Matthias Hanauer
Leonie Anna Muck
Thomas-Christian Jagau
Jurgen Gauss
2.1.28 Symmetry-Adapted Perturbation 1003 (20)
Theory of Intermolecular Forces
Krzysztof Szalewicz
2.1.29 Wavefunction Methods for 1023 (24)
Noncovalent Interactions
Edward G. Hohenstein
C. David Sherrill
2.2 Combined QM/MM Methods 1047 (66)
2.2.1 Description of Electronic 1049 (16)
Processes Inside Proteins from
Car-Parrinello Molecular Dynamics:
Chemical Transformations
Came Rovira
2.2.2 Empirical Valence Bond Model: 1065 (16)
Theory and Applications
Shina C. L. Kamerlin
Arieh Warshel
2.2.3 Mixed Quantum Mechanics and 1081 (8)
Molecular Mechanics Methods: Looking
Inside Proteins
Frank H. Wallrapp
Victor Guallar
2.2.4 ONIOM Method: Its Foundation and 1089 (24)
Applications to Metalloenzymes and
Photobiology
Lung Wa Chung
Hajime Hirao
Xin Li
Keiji Morokuma
2.3 Density Functional Theory 1113 (74)
2.3.1 Density Functional Theory with 1115 (18)
London Dispersion Corrections
Stefan Grimme
2.3.2 Long-Range Corrected Density 1133 (16)
Functionals
Takao Tsuneda
Kimihiko Hirao
2.3.3 Subsystem Density-Functional 1149 (38)
Theory
Christoph R. Jacob
Johannes Neugebauer
2.3 A. Symmetry-Adapted Perturbation 1187 (18)
Theory with Density Functional Methods
Georg Jansen
2.4 Semiempirical Electronic Structure 1205 (54)
Methods
2.4.1 Density Functional Tight Binding: 1207 (14)
Application to Organic and Biological
Molecules
Michael Gaus
Qiang Cui
Marcus Elstner
2.4.2 Density-Functional Tight 1221 (10)
Binding---An Approximate
Density-Functional Theory Method
Gotthard Seifert
Jan-Ole Joswig
2.4.3 Intermediate Neglect of 1231 (14)
Differential Overlap for Spectroscopy
Alexander A. Voityuk
2.4.4 Semiempirical Quantum--Chemical 1245 (14)
Methods
Walter Thiel
List of Contributors xxvii
Volume 3 Simulation Methods 1259 (368)
3.1 Free Energy Methods 1261 (22)
3.1.1 Frontiers in Free-Energy 1263 (20)
Calculations of Biological Systems
Christophe Chipot
3.2 Molecular Dynamics and Monte-Carlo 1283 (224)
Methods
3.2.1 Algorithm Improvements for 1285 (16)
Molecular Dynamics Simulations
Per Larsson
Berk Hess
Erik Lindahl
3.2.2 Atomistic Simulations of 1301 (16)
Nucleosomes
Mithun Biswas
Jorg Langowski
and Thomas C. Bishop
3.2.3 Coarse-Grained Biomolecular 1317 (24)
Simulations
Helgi I. Ingolfsson
Cesar A. Lopez
Jaakko J. Uusitalo
Djurre H. de Jong
Srinivasa M. Gopal
Xavier Petiole
Siewert J. Marrink
3.2.4 Coarse-Grained Methods for 1341 (10)
Polymeric Materials: Enthalpy- and
Entropy-Driven Models
Paola Carbone
Carlos Avendano
3.2.5 Coarse-Grained Models of Protein 1351 (12)
Folding as Detailed Tools to Connect
with Experiments
Athi N. Naganathan
3.2.6 Discrete Molecular Dynamics 1363 (14)
Elizabeth A. Proctor
Feng Ding
Nikolay V. Dokholyan
3.2.7 Essential Dynamics: Foundation 1377 (10)
and Applications
Isabella Daidone
Andrea Amadei
3.2.8 High-Throughput Molecular 1387 (14)
Dynamics Simulations: Toward a Dynamic
View of Macromolecular Structure
Adam Hospital
Josep Ll Gelpi
3.2.9 Low-Resolution Structural 1401 (16)
Approaches to Study Biomolecular
Assemblies
Pau Bernado
3.2.10 Metadynamics 1417 (18)
Alessandro Barducci
Massimiliano Bonomi
Michele Parrinello
3.2.11 New Advances in Metadynamics 1435 (10)
Ludovico Sutto
Simone Marsili
Francesco Luigi Gervasio
3.2.12 NMR and MD Simulations to Study 1445 (14)
the Structural Heterogeneity of
Proteins, Synergistic Use of
Santiago Esteban-Martin
Robert Bryn Fenwick
Xavier Salvatella
3.2.13 Predictions of Protein-RNA 1459 (16)
Interactions
Davide Cirillo
Federico Agostini
Gian Gaetano Tartaglia
3.2.14 Umbrella Sampling 1475 (12)
Johannes Kastner
3.2.15 Understanding Protein Unfolding 1487 (20)
from Molecular Simulations
Rudesh D. Toofanny
Valerie Daggett
3.3 Molecular Mechanics 1507 (120)
3.3.1 Carbohydrate Force Fields 1509 (46)
B. Lachele Foley
Matthew B. Tessier
Robert J. Woods
3.3.2 Coarse-Grained Modeling of DNA, 1555 (16)
Recent Successes in
Davit A. Potoyan
Alexey Savelyev
Garegin A. Papoian
3.3.3 Coarse-Grained Models of Water 1571 (10)
Leonardo Darre
Matias R. Machado
Sergio Pantano
3.3.4 Cooperative Dynamics of Proteins 1581 (14)
Unraveled by Network Models
Eran Eyal
Anindita Dutta
Ivet Bahar
3.3.5 Polarization Effects in Molecular 1595 (12)
Interactions
F. Javier Luque
Francois Dehez
Christophe Chipot
Modesto Orozco
3.3.6 Recent Developments and 1607 (20)
Applications of the CHARMM Force Fields
Xiao Zhu
Pedro E. M. Lopes
Alexander D. MacKerell Jr
List of Contributors xxvii
Volume 4 Structure And Mechanism 1627 (900)
4.1 Computational Biochemistry and 1629 (168)
Biophysics
4.1.1 Atomistic Simulation of DNA 1631 (12)
Charles A. Laughton
Sarah A. Harris
4.1.2 Electron Transfer in DNA 1643 (16)
Khatcharin Siriwong
Alexander A. Voityuk
4.1.3 Next Challenges in 1659 (10)
Protein--Protein Docking: from Proteome
to Interactome and Beyond
Adrien S.J. Melquiond
Ezgi Karaca
Panagiotis L. Kastritis
Alexandre M.J.J. Bonvin
4.1.4 Noncovalent Interactions in 1669 (16)
Biochemistry
Kevin E. Riley
Pavel Hobza
4.1.5 Optimization of Protein Models 1685 (16)
Dominik Gront
Sebastian Kmiecik
Maciej Blaszczyk
Dariusz Ekonomiuk
Andrzej Kolinski
4.1.6 Prediction of Protein Binding 1701 (20)
Sites and Hot Spots
Juan Fernandez-Recio
4.1.7 Quantum Chemical Cluster Approach 1721 (14)
for Modeling Enzyme Reactions
Per E.M. Siegbahn
Fahmi Himo
4.1.8 Receptor Flexibility in 1735 (18)
Small-Molecule Docking Calculations
Daria B. Kokh
Rebecca C. Wade
Wolfgang Wenzel
4.1.9 Resonance Energy Flow Dynamics of 1753 (22)
Coherently Delocalized Excitons in
Biological and Macromolecular Systems:
Recent Theoretical Advances and Open
Issues
Seogjoo Jang
Yuan-Chung Cheng
4.1.10 Theoretical Models of DNA 1775 (10)
Flexibility
Tomas Drsata
Filip Lankas
4.1.11 Theoretical Studies of Nucleic 1785 (12)
Acids Folding
Mahmut Kara
Martin Zacharias
4.2 Computational Materials Science 1797 (42)
4.2.1 Cross-Conjugation 1799 (10)
Peter A. Limacher
Hans P. Luthi
4.2.2 Density Functional Theory in 1809 (12)
Materials Science
Jorg Neugebauer
Tilmann Hickel
4.2.3 DNA Insertion in and Wrapping 1821 (18)
Around Carbon Nanotubes
Flavio F. Contreras-Torres
Erick Martinez-Loran
4.3 Computational Quantum Chemistry 1839 (526)
4.3.1 Carbocations 1841 (22)
Donald H. Aue
4.3.2 Carbodicarbenes---Divalent 1863 (10)
Carbon(O) Compounds Exhibiting
Carbon-Carbon Donor-Acceptor Bonds
Gernot Frenking
Ralf Tonner
4.3.3 Cation--π and Anion--π 1873 (20)
Interactions
Antonio Frontera
David Quinonero
Pere M. Deya
4.3.4 Computational Methods for 1893 (32)
Contemporary Carbene Chemistry
Dennis Gerbig
David Ley
4.3.5 Determination of Enthalpies 1925 (16)
('Heats') of Formation
Donald W. Rogers
Andreas A. Zavitsas
Nikita Matsunaga
4.3.6 Electron Transport and Optical 1941 (12)
Properties of Curved Aromatics
Laura Zoppi
Jay S. Siegel
Kim K. Baldridge
4.3.7 Electrostatic Potential: an 1953 (12)
Overview
Jane S. Murray
Peter Politzer
4.3.8 Enediynes and Related Species 1965 (40)
Elfi Kraka
Dieter Cremer
4.3.9 Energy Decomposition Analysis 2005 (20)
Moritz von Hopffgarten
Gernot Frenking
4.3.10 First-Principles Prediction of 2025 (12)
Acidities in the Gas and Solution Phase
Junming Ho
Michelle L. Coote
4.3.11 Fluctional Molecules 2037 (10)
Michael L. McKee
4.3.12 Fullerenes: Formation, 2047 (18)
Stability, and Reactivity
Antonio Rodriguez-Fortea
Stephan Irle
Josep M. Poblet
4.3.13 Homodesmotic Reactions for 2065 (18)
Thermochemistry
Steven E. Wheeler
4.3.14 Hydrocarbon σ -Radical 2083 (20)
Cations
Tatyana E. Shubina
Andrey A. Fokin
4.3.15 Hyperconjugation 2103 (34)
Igor V. Alabugin
Kerry M. Gilmore
Paul W. Peterson
4.3.16 Mechanical Properties of Silicon 2137 (12)
Nanowires
Al'ona Furmanchuk
Olexandr Isayev
Tandabany C. Dinadayalane
Danuta Leszczynska
Jerzy Leszczynski
4.3.17 Metalloaromaticity 2149 (18)
Ferran Feixas
Eduard Matito
Jordi Poater
Miquel Sola
4.3.18 π-Conjugation 2167 (12)
Begona Milian-Medina
Johannes Gierschner
4.3.19 Photoisomerization of 2179 (12)
Light-Driven Molecular Rotary Motors,
Understanding the Dynamics Behind
Michael Filatov
4.3.20 Polyarene Anions: Interplay 2191 (24)
Between Theory and Experiment
David Eisenberg
Roy Shenhar
4.3.21 Proteins in the Gas Phase 2215 (18)
Tim Meyer
Valerie Gabelica
Helmut Grubmuller
Modesto Orozco
4.3.22 Qualitative Valence Bond Theory 2233 (12)
-- a Theory Coming of Age
Sason Shaik
Philippe C. Hiberty
4.3.23 Recent Trends in Conformational 2245 (30)
Analysis
Andrea Mazzanti
Daniele Casarini
4.3.24 Rotational Barriers in Alkanes 2275 (8)
Yirong Mo
4.3.25 σ-Holes 2283 (8)
Timothy Clark
4.3.26 Structure-Reactivity 2291 (20)
Relationships for Aromatic Molecules:
Electrostatic Potentials at Nuclei and
Electrophile Affinity Indices
Bon's Galabov
Sonia Ilieva
Gergana Koleva
Wesley D. Allen
Henry F. Schaefer III
Paul von R. Schleyer
4.3.27 Tautomerism in Nucleic Acid 2311 (14)
Bases and Base Pairs: a Brief Overview
Manoj K. Shukla
Jerzy Leszczynski
4.3.28 Understanding Palladium 2325 (14)
Complexes Structures and Reactivities:
Beyond Classical Point of View
Etienne Derat
Giovanni Maestri
4.3.29 Wavefunction Methods for the 2339 (26)
Accurate Characterization of Small
Water Clusters
J. Coleman Howard
Gregory S. Tschumper
4.4 Reaction Mechanisms and Catalysis 2365 (162)
4.4.1 Cope Rearrangement---the First 2367 (20)
Born of a Great Family
Nicole Graulich
4.4.2 Correlation Diagram Approach as a 2387 (14)
Tool for Interpreting Chemistry: an
Introductory Overview
Hajime Hirao
4.4.3 Elementary Electron Transfer 2401 (18)
Reactions: From Basic Concepts to
Recent Computational Advances
Raffaele Borrelli
Andrea Peluso
4.4.4 Mechanisms of Branch Formation in 2419 (22)
Metal-Catalyzed Ethene Polymerization
Peter H. M. Budzelaar
4.4.5 Organocatalysis: Acylation 2441 (20)
Catalysts
Evgeny Larionov
Hendrik Zipse
4.4.6 Organocatalysis: Cinchona 2461 (12)
Catalysts
Tommaso Marcelli
4.4.7 Pericyclic Steps in the 2473 (16)
Mechanisms of Gold(I) Catalyzed
Rearrangement of Alkynes,
Characterization of
Adan Gonzalez Perez
Rosana Alvarez
Angel R. de Lera
4.4.8 Proline-Derived Organocatalysis 2489 (12)
and Synergism Between Theory and
Experiments
Raghavan B. Sunoj
4.4.9 Spin-Forbidden Reactions: 2501 (14)
Computational Insight into Mechanisms
and Kinetics
Jeremy N. Harvey
4.4.10 Transition Metal Catalysis by 2515 (12)
Density Functional Theory and Density
Functional Theory/Molecular Mechanics
W. M. C. Sameera
Feliu Maseras
List of Contributors xxvii
Volume 5 Theoretical And Physical Chemistry 2527 (318)
5.1 Reaction Dynamics and Kinetics 2529 (194)
5.1.1 A Refinement of Everyday 2531 (22)
Thinking: the Energetic Span Model for
Kinetic Assessment of Catalytic Cycles
Sebastian Kozuch
5.1.2 Car--Parrinello Molecular Dynamics 2553 (10)
Jurg Butter
5.1.3 Direct Chemical Dynamics 2563 (22)
Simulations: Coupling of Classical and
Quasiclassical Trajectories with
Electronic Structure Theory
Manikandan Paranjothy
Rui Sun
Yu Zhuang
William L. Hase
5.1.4 Excited-State Dynamics 2585 (16)
Benjamin Lasorne
Graham A. Worth
Michael A. Robb
5.1.5 Geometry Optimization 2601 (20)
H. Bernhard Schlegel
5.1.6 Global Optimization 2621 (10)
Bernd Hartke
5.1.7 Nonadiabatic Dynamics with 2631 (14)
Trajectory Surface Hopping Method
Mario Barbatti
5.1.8 Reaction Path Hamiltonian and the 2645 (26)
Unified Reaction Valley Approach
Elfi Kraka
5.1.9 Second Generation Car-Parrinello 2671 (16)
Molecular Dynamics
Thomas D. Kuhne
5.1.10 Studying Molecular Quantum 2687 (24)
Dynamics with the Multiconfiguration
Time-Dependent Hartree Method
Hans-Dieter Meyer
5.1.11 Tunneling Theory 2711 (12)
Johannes Kastner
5.2 Spectroscopy 2723 (122)
5.2.1 Accurate Variational Calculations 2725 (18)
for Line Lists to Model the
Vibration-Rotation Spectra of Hot
Astrophysical Atmospheres
Jonathan Tennyson
5.2.2 Circular Dichroism: Electronic 2743 (18)
Ingolf Warnke
Filipp Furche
5.2.3 Circular Dichroism: Magnetic 2761 (14)
Thomas Kjærgaard
Sonia Coriani
Kenneth Ruud
5.2.4 Circular Dichroism: Vibrational 2775 (24)
Gabor Magyarfalvi
Gyorgy Tarczay
Elemer Vass
5.2.5 Computing Ro-Vibrational Spectra 2799 (12)
of Van Der Waals Molecules
Tucker Carrington Jr.
Xiao-Gang Wang
5.2.6 Local Modes in Vibration-Rotation 2811 (20)
Spectroscopy
Per Jensen
5.2.7 NMR Spectroscopy: 2831 (14)
Quantum-Chemical Calculations
Michael Buhl
Tanja van Mourik
List of Contributors xxvii
Volume 6 Software 2845 (196)
6.1 Computer Algorithms and Programming 2847 (12)
6.1.1 Computational Molecular Science 2849 (10)
Using Graphics Processing Units, a
Survey of
M. J. Harvey
Gianni De Fabritiis
6.2 Molecular Modeling 2859 (44)
6.2.1 Amber Biomolecular Simulation 2861 (14)
Package, an Overview of
Romelia Salomon-Ferrer
David A. Case
Ross C. Walker
6.2.2 ChemShell---A Modular Software 2875 (10)
Package for QM/MM Simulations
Sebastian Metz
Johannes Kastner
Alexey A. Sokol
Thomas W. Keal
Paul Sherwood
6.2.3 COSMO and COSMO-RS Solvation 2885 (12)
Models
Andreas Klamt
6.2.4 GROMACS---The Road Ahead 2897 (6)
David van der Spoel
Berk Hess
6.3 Quantum Chemistry 2903 (138)
6.3.1 ACES III with the Super 2905 (8)
Instruction Architecture, Software
Design of
Erik Deumens
Victor F. Lotrich
Ajith Perera
Mark J. Ponton
Beverly A. Sanders
Rodney J. Bartlett
6.3.2 COLUMBUS---A Program System for 2913 (10)
Advanced Multireference Theory
Calculations
Hans Lischka
Thomas Muller
Peter G. Szalay
Isaiah Shavitt
Russell M. Pitzer
Ron Shepard
6.3.3 CP2K: Atomistic Simulations of 2923 (12)
Condensed Matter Systems
Jurg Hutter
Marcella Iannuzzi
Florian Schiffmann
Joost VandeVondele
6.3.4 Dalton 2935 (16)
Kestutis Aidas
Celestino Angeli
Keld L. Bak
Vebjørn Bakken
Radovan Bast
Linus Boman
Ove Christiansen
Renzo Cimiraglia
Sonia Coriani
Pal Dahle
Erik K. Dalskov
Ulf Ekstrom
Thomas Enevoldsen
Janus J. Eriksen
Patrick Ettenhuber
Berta Fernandez
Lara Ferrighi
Heike Fliegl
Luca Frediani
Kasper Hald
Asger Halkier
Christof Hattig
Hanne Heiberg
Trygve Helgaker
Alf Christian Hennum
Hinne Hettema
Eirik Hjertenæs
Stinne Høst
Ida-Marie Høyvik
Maria Francesca Iozzi
Branislav Jansik
Hans Jørgen Aa. Jensen
Dan Jonsson
Foul Jørgensen
Joanna Kauczor
Sheela Kirpekar
Thomas Kjærgaard
Wim Klopper
Stefan Knecht
Rika Kobayashi
Henrik Koch
Jacob Kongsted
Andreas Krapp
Kasper Kristensen
Andrea Ligabue
Ola B. Lutnæs
Juan I. Melo
Kurt V. Mikkelsen
Rolf H. Myhre
Christian Neiss
Christian B. Nielsen
Patrick Norman
Jeppe Olsen
Jogvan Magnus H. Olsen
Anders Osted
Martin J. Packer
Filip Pawlowski
Thomas B. Pedersen
Patricio F. Provasi
Simen Reine
Zilvinas Rinkevicius
Torgeir A. Ruden
Kenneth Ruud
Vladimir V. Rybkin
Pawel Salek
Claire C. M. Samson
Alfredo Sanchez de Merds
Trond Saue
Stephan P. A. Sauer
Bernd Schimmelpfennig
Kristian Sneskov
Arnfinn H. Steindal
Kristian O. Sylvester-Hvid
Peter R. Taylor
Andrew M. Teale
Erik I. Tellgren
David P. Tew
Andreas J. Thorvaldsen
Lea Thøgersen
Olav Vahtras
Mark A. Watson
David J. D. Wilson
Marcin Ziolkowski
Hans Agren
6.3.5 deMon2k 2951 (8)
Gerald Geudtner
Patrizia Calaminici
Javier Carmona-Espindola
Jorge Martin del Campo
Victor Daniel Dominguez-Soria
Robert Flores Moreno
Gabriel Wises Gamboa
Annick Goursot
Andreas M. Koster
Jose Wises Reveles
Tzonka Mineva
Jose Manuel Vasquez-Perez
Alberto Vela
Bernardo Zuninga-Gutierrez
Dennis R. Salahub
6.3.6 MOLCAS---A Software for 2959 (8)
Multiconfigurational Quantum Chemistry
Calculations
Francesco Aquilante
Thomas Bondo Pedersen
Valera Veryazov
Roland Lindh
6.3.7 Molpro: A General-Purpose Quantum 2967 (12)
Chemistry Program Package
Hans-Joachim Werner
Peter J. Knowles
Gerald Knizia
Frederick R. Manby
Martin Schutz
6.3.8 Newton-X: A Surface-Hopping 2979 (8)
Program for Nonadiabatic Molecular
Dynamics
Mario Barbatti
Matthias Ruckenbauer
Felix Plasser
Jiri Pittner
Giovanni Granucci
Maurizio Persico
Hans Lischka
6.3.9 NWChem: Scalable Parallel 2987 (8)
Computational Chemistry
H.J.J. van Dam
W.A. de Jong
E. Bylaska
N. Govind
K. Kowalski
T.P. Straatsma
M. Valiev
6.3.10 ORCA Program System 2995 (6)
Frank Neese
6.3.11 PQS Program, Recent Developments 3001 (10)
in
Jon Baker
Tomasz Janowski
Krzysztof Wolinski
Peter Pulay
6.3.12 Psi4: an Open-Source Ab Initio 3011 (10)
Electronic Structure Program
Justin M. Turney
Andrew C. Simmonett
Robert M. Parrish
Edward G. Hohenstein
Francesco A. Evangelista
Justin T. Fermann
Benjamin J. Mintz
Lori A. Burns
Jeremiah J. Wilke
Micah L. Abrams
Nicholas J. Russ
Matthew L. Leininger
Curtis L. Janssen
Edward T. Seidl
Wesley D. Allen
Henry F. Schaefer
Rollin A. King
Edward F. Valeev
C. David Sherrill
T. Daniel Crawford
6.3.13 Q-Chem: an Engine for Innovation 3021 (20)
Anna I. Krylov
Peter M.W. Gill
6.3.14 Turbomole
Filipp Furche
Reinhart Ahlrichs
Christof Hattig
Wim Klopper
Marek Sierka
Florian Weigend
Index 3041