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1.

図書

図書
volume editor, E. Steckhan ; with contributions by R.D. Little ... [et al.]
出版情報: Berlin : Springer, c1997  184 p. ; 25 cm
シリーズ名: Topics in current chemistry = Fortschritte der chemischen Forschung ; 185 . Electrochemistry ; 6
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2.

図書

図書
editors, M. Guisnet ... [et al.]
出版情報: Amsterdam ; Tokyo : Elsevier, 1991  xviii, 608 p.
シリーズ名: Studies in surface science and catalysis ; 59
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3.

図書

図書
J.C. Elliott
出版情報: Amsterdam : Elsevier, 1994  xiii, 389 p. ; 25 cm
シリーズ名: Studies in inorganic chemistry ; 18
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4.

図書

図書
edited by Joseph J. Pesek, Ivan E. Leigh
出版情報: Cambridge : Royal Society of Chemistry, 1994  xi, 223 p. ; 24 cm
シリーズ名: Special publication / Royal Society of Chemistry ; no. 139
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5.

図書

図書
edited by Aleš Koller
出版情報: Amsterdam : Elsevier, 1994  587 p. ; 25 cm
シリーズ名: Materials science monographs ; 80
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目次情報: 続きを見る
Introduction / A. Koller1:
Thermodynamics and ceramic systems / P. Holba2:
The formation of ceramic body / 3:
Methods for studying the structure of ceramics / S. Civia ; I. Sanc4:
Symmetry and crystallography / V. Kopsky5:
Crystal structure / 6:
The glass phase / I. Fanderlik7:
The effect of structure on the mechanical properties of ceramics / F. Kroupa8:
The effect of the structure on the electric properties of ceramics / A. Kubovy9:
Structure and magnetic properties of ferrites / E. Pollert10:
Structure and thermal properties of ceramics / 11:
Subject Index
Introduction / A. Koller1:
Thermodynamics and ceramic systems / P. Holba2:
The formation of ceramic body / 3:
6.

図書

図書
M. Toda, R. Kubo, N. Saitô
出版情報: Berlin ; Tokyo : Springer-Verlag, c1992  xvi, 252 p. ; 24 cm
シリーズ名: Springer series in solid-state sciences ; 30 . Statistical physics ; 1
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7.

図書

図書
edited by Maurice H. Francombe and John L. Vossen
出版情報: San Diego ; Tokyo : Academic Press, 1993  xiii, 397 p. ; 24 cm
シリーズ名: Physics of thin films : advances in research and development ; v. 17
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8.

図書

図書
board of editors, Andrew S. Kende ... [et al.]
出版情報: New York : Wiley, 1993-  v. ; 24 cm
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目次情報: 続きを見る
Partial table of contents:Preparation of (R,R)-1,2:4,5-Diepoxypentane / S. Rychnovsky, et al.
Synthesis and Diastereoselective Alkylation of Pseudoephedrine Amides / A. Myers ; B. Yang
(R)-(+)-2-Hydroxy-1,2,2-Triphenylethyl Acetate / J. Macor, et al.
Synthesis of 1,1-Dimethylethyl (S)-4-Formyl-2,2-Dimethyl-3-Oxazolidinecarboxylate By Reduction of the Alcohol / A. Dondoni ; D. Perrone
Synthesis of (S,E)-1-(Methoxymethoxy)-1-Tributylstannyl-2-Butene / J. Marshall, et al.
Allylindation in Aqueous Media: Methyl 3-(Hydroxymethyl)-4-Methyl-2-Methylenepentanoate / G. Bennett ; L. Paquette
The Synthesis of 2-Alkyl-4-Pyrones From Meldrum's Acid / M. Crimmins, et al.
9-Ethyl-3,6-Dimethylcarbazole (DMECZ) / J. Buck, et al.
Bis(Pinacolato)Diboron / T. Ishiyama, et al.
Alpha;-Tosylbenzyl Isocyanide / J. Sisko, et al.
Methyl 2,3-O-(6,6'-Octahydro-6,6'-Bi-2H-Pyran-2,2'-Diyl)-alpha;-D-Galactopyranoside / S. Ley ; H. Osborn
Cyclopropylacetylene / E. Corley, et al.
3-Nitropropanal, 3-Nitropropanol, and 3-Nitropropanal Dimethyl Acetal / H. Griesser, et al.
Cyclopropene: A New Synthesis and Its Diels-Alder Reaction with Cyclopentadiene / P. Binger, et al.
Unchecked Procedures
Indexes
Partial table of contents
Resolution of 1,1'-Bl-2-Naphthol / D. Cai, et al.
1S-(-)-1,3-Dithiane 1-Oxide / P. Page, et al.
(1S, 2R)-1-Aminoindan-2-OL / J. Larrow, et al.
Methyl (S)-2-Phthalimido-4-Oxobutanoate / P. Meffre, et al.
(tert-Butyldimethylsilyl)Allen / B. Zheng
6-Chloro-1-Hexene and 8-Chloro-1-Octene / P. Mazerolles, et al.
2-Chlorophenyl Phosphorodi-Chloridothioate / V. Ravikumar ; B. Ross
9,10-Diphenylphenanthrene / G. Olah, et al.
Partial table of contents:(-)-2-0-Benzyl-L-Glyceraldehyde and Ethyl (R,E)-4-0-Benzyl-4,5-Dihydroxy-2-Pentenoate / B. Steuer, et al.
Bis(Trimethylsilyl) Peroxide (BTMSPO) / P. Dembech, et al.
Synthesis of Epoxides Using Dimethyldioxirane: trans-Stilbene Oxide / R. Murray ; M. Singh
Phenyl Vinyl Sulfide / D. Reno ; R. Pariza
Regio- and Stereoselective Carboxylation of Allylic Barium Reagents: (E)-4,8- Di-Methyl-3,7-Nonadienoic Acid / A. Yanagisawa, et al.
Preparation of 3-Bromopropiolic Esters: Methyl and tert-Butyl 3-Bromopropiolates / J. Leroy
Regioselective Synthesis of 3-Substituted Indoles: 3-Ethylindole / M. Amat, et al.
Catalytic Asymmetric Allylation Reactions
S)-1-Phenylmethoxy)-4-Penten-2-OL / G. Keck ; D. Krishnamurthy
Ethyl (R)-2-Azidopropionate / A. Thompson, et al.
(4R,5S)-4,5-Diphenyl-3-Vinyl-2-Oxazolidinone / T. Akiba, et al.
3-Chloro-2-(Chloromethyl)-1-Propene / K. Lynch ; W. Dailey
[1.1.1]Propellane
N-Benzyl-2,3-Azetidinedione / C. Behrens
Preparation of Cyanoalkynes
3-Phenyl-2-Propynenitrile / F.-T. Luo, et al.
2-Trimethylsilylethane-Sulfonyl Chloride (SES-Cl) / S. Weinreb, et al.
4-Dimethylamino-N-Triphenyl-Methylpyridinium Chloride / A. Bhatia, et al.
6,7-Dihydrocyclopenta-1,3-Dioxin-5(4H)-One / K. Chen, et al.
3-Cyclopentene-1-Carboxylic Acid / J.-P. Depres ; A. Greene
Partial table of contents:?
L-(S)-Glyceraldehyde Acetonide / C. Hubschwerlen ; J.-L Specklin
D-(R)-Glyceraldehyde Acetonide / C. Schmid ; J. Bryant
(1R,5R)-(+)-Verbenone of High Optical Purity / M. Braun, et al. ; M. Sivik, et al.
Benzocyclobutenone by Flash Vacuum Pyrolysis / P. Schiess, et al.
An Efficient Synthesis of Indole-2-Acetic Acid Methyl Esters / S. Modi, et al.
7-Methoxyphthalide / X. Wang, et al.
Phenylthioacetylene / P. Magriotis ; J. Brown
Warning
Roger Adams / I:
James Bryant Conant / II:
Hans Thacher Clarke / III:
Oliver Kamm / IV:
Carl Shipp Marvel / V:
Henry Gilman / VI:
Frank C. Whitmore / VII:
A revised edition of Annual Volumes I-IX / VIII:
Wallace H. Carothers / X:
William W. Hartman / XIV:
Carl R. Noller / XV:
John R. Johnson / XVI:
L. F. Fieser / XVII:
Reynold C. Fuson / XVIII:
A revised edition of Annual Volumes X-XIX / XIX:
Charles F. H. Allen / 20:
Nathan L. Drake / 21:
Lee Irvin Smith / 22:
Werner E. Bachmann / 23:
Homer Adkins / 26:
R. L. Shriner / 27:
H. R. Snyder / 28:
Cliff S. Hamilton / 29:
A revised edition of Annual Volumes 20-29 / Collective Vol. III:
Arthur C. Cope / 30:
R. S. Schreiber / 31:
Richard T. Arnold / 32:
Charles C. Price / 33:
William S. Johnson / 34:
T. L. Cairns / 35:
N. J. Leonard / 36:
James Cason / 37:
John C. Sheehan / 38:
Max Tishler / 39:
A revised edition of Annual Volumes 30-39 / Collective Vol. IV:
Melvin S. Newman / 40:
John D. Roberts / 41:
Virgil Boekelheide / 42:
B. C. McKusick / 43:
William E. Parham / 44:
William G. Dauben / 45:
E. J. Corey / 46:
William D. Emmons / 47:
Peter Yates / 48:
Kenneth B. Wiberg / 49:
A revised edition of Annual Volumes 40-49 / Collective Vol. V:
Cumulative Indices to Collective Volumes, I, II, III, IV, V
Ronald Breslow / 50:
Richard E. Benson / 51:
Herbert O. House / 52:
Arnold Brossi / 53:
Robert E. Ireland / 54:
Satoru Masamune / 55:
George H. Buchi / 56:
Carl R. Johnson / 57:
William A. Sheppard / 58:
Robert M. Coates / 59:
A revised edition of Annual Volumes 50-59 / Collective Vol. VI:
Orville L. Chapman / 60:
Robert V. Stevens / 61:
Martin F. Semmelhack / 62:
Gabriel Saucy / 63:
Andrew S. Kende / 64:
A revised edition of Annual Volumes 60-64 / Collective Vol. VII:
Edwin Vedejs / 65:
Clayton H. Heathcock / 66:
Bruce E. Smart / 67:
James D. White / 68:
Leo A. Paquette / 69:
Reaction Guide to Collective Volumes I-VII and Annual Volumes 65-68
A revised edition of Annual Volumes 65-69 / Collective Vol. VIII:
Cumulative Indices to Collective Volumes, I, II, III, IV, V, VI, VII, VIII
Albert I. Meyers / 70:
Larry E. Overman / 71:
David L. Coffen / 72:
Robert K. Boeckman, Jr. / 73:
Ichiro Shinkai / 74:
A revised edition of Annual Volumes 70-74 / Collective Vol. IX:
Amos B. Smith, III / 75:
Stephen F. Martin / 76:
David S. Hart / 77:
William R. Roush / 78:
Louis S. Hegedus / 79:
A revised edition of Annual Volumes 75-79 / Collective Vol. X:
Steven Wolff / 80:
Rick L. Danheiser / 81:
Edward J. J. Grabowski / 82:
Amos B. Smith III / Roger Adams ; James Bryant Conant ; Hans Thacher Clarke ; Oliver Kamm ; Carl Shipp Marvel ; Henry Gilman ; Frank C. Whitmore ; Wallace H. Carothers ; William W. Hartman ; Carl R. Noller ; John R. Johnson ; L. F. Fieser ; Reynold C. Fuson ; Charles F. H. Allen ; Nathan L. Drake ; Lee Irvin Smith ; Werner E. Bachmann ; Homer Adkins ; R. L. Shriner ; H. R. Snyder ; Cliff S. Hamilton ; Arthur C. Cope ; R. S. Schreiber ; Richard T. Arnold ; Charles C. Price ; William S. Johnson ; T. L. Cairns ; N. J. Leonard ; James Cason ; John C. Sheehan ; tMax Tishler ; Melvin S. Newman ; John D. Roberts ; Virgil Boekelheide ; B. C. McKusick ; William E. Parham ; William G. Dauben ; E. J. Corey ; William D. Emmons ; Peter Yates ; Kenneth B. Wiberg ; Ronald Breslow ; Richard E. Benson ; Herbert O. House ; Arnold Brossi ; Robert E. Ireland ; Satoru Masamune ; George H. Buchi ; Carl R. Johnson ; William A. Sheppard ; Robert M. Coates ; Orville L. Chapman ; Robert V. Stevens ; Martin F. Semmelhack ; Gabriel Saucy ; Andrew S. Kende ; Edwin Vedejs ; Clayton H. Heathcock ; Bruce E. Smart ; James D. White ; Leo A. Paquette ; Albert I. Meyers ; Larry E. Overman ; David L. Coffen ; Robert K. Boeckman, Jr. ; Ichiro Shinkai ; Amos B. Smith III ; Stephen F. Martin ; David J. Hart ; William R. Roush ; Louis S. Hegedus ; Steven Wolff
David J. Hart
Asymmetric Hydrogenation of 3-OXO Carboxylates Using Binapruthenium Complexes: (R)-(-)-Methyl 3-Hydroxybutanoate / M. Kitamura, et al.
Direct Degradation of the Biopolymer Poly [(R)-3-Hydroxybutyric Acid] to (R)-3-Hydroxybutanoic Acid and Its Methyl Ester / D. Seebach, et al.
3-(S)-[(tert-Butyldiphenylsilyl)-Oxy]-2-Butanone / L. Overman ; G. Rishton
Schwartz's Reagent / S. Buchwald, et al.
4-Methoxy-4'-Nitrobiphenyl / J. Stille, et al.
Ubiquinone-1 / Y. Naruta ; K. Maruyama
Benzoannelation of Ketones: 3,4-Cyclododeceno-1-Methylbenzene / M. Tius ; G. Kannangara
2-Methylene-1, 3-Dithiolane / K. Dahnke
Methoxycarbonylmethylation of Aldehydes Via Siloxycyclopropanes: Methyl 3,3-Dimethyl-4-Oxobutanoate H.-U / Reissig, et al.
9-Bromo-9-Phenylfluorene / T. Jamison, et al.
A revised edition of Annual Volumes, 75-79 / A. H. Blatt ; E. C. Horning ; Max Tishler ; Norman Rabjohn ; Henry E. Baumgarten ; Ralph L. ; Rachel H. Shriner ; Wayland E. Noland ; Jeremiah P. Freeman ; Dennis C. Liotta ; Mark Volmer ; Amos B. Smith, III ; David S. Hart
3-[(1S)-1,2-Dihydroxyethyl]-1,5-Dihydro-3H-2,4-Benzo-Dioxepine / Rick L. Danheiser ; Edward J. J. Grabowski ; Dennis P. Curran ; R. Oi ; K. Sharpless83:
(4R)-(+)-tert-Butyldimethylsiloxy-2-Cyclopenten-1-One / L. Paquette, et al.
(4S)-(-)-tert-Butyldimenthylsiloxy-2-Cyclopenten-1-One / T. Heidelbaugh
Alkylidenation of Ester Carbonyl Groups
(Z)-1-Ethoxy-1-Phenyl-1-Hexene / K. Takai, et al.
4-Dodecylbenzenesulfonyl Azides / G. Hazen, et al.
Bis(Trifluoroethyl) (Carbo-Ethoxymethyl)
Phosphonate / C. Patois, et al.
Diethyl
4-Ketoundecanoic Acid / S. Saito, et al. ; M. Tschantz, et al.
3-Pyrroline / M. Oda, et al.|!2 ; A. Meyers, et al.
2-Cyclohexene-1,4-Dione / M. Oda, et al.
4,5-Dibenzoyl-1,3-Dithiole-1-Thione / T. Hansen, et al.
Editorial: Organic Syntheses: The ôGold Standardö for Experimental Synthetic Organic Chemistry
Partial table of contents:Preparation of (R,R)-1,2:4,5-Diepoxypentane / S. Rychnovsky, et al.
Synthesis and Diastereoselective Alkylation of Pseudoephedrine Amides / A. Myers ; B. Yang
(R)-(+)-2-Hydroxy-1,2,2-Triphenylethyl Acetate / J. Macor, et al.
9.

図書

図書
R. Kubo, M. Toda, N. Hashitsume
出版情報: Berlin ; New York : Springer-Verlag, c1991  xvi, 279 p. ; 24 cm
シリーズ名: Springer series in solid-state sciences ; 31 . Statistical physics ; 2
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10.

図書

図書
edited by Y. Tzeng ... [et al.]
出版情報: Amsterdam ; New York : Elsevier, 1991  xxv, 874 p. ; 25 cm
シリーズ名: Materials science monographs ; 73
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11.

図書

図書
editor, G. Szenes
出版情報: Aedermannsdorf, Switzerland : Trans Tech Publications, c1992  789 p. ; 25 cm
シリーズ名: Materials science forum ; v.97-99
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12.

図書

図書
Stephen Maybank
出版情報: Berlin ; New York : Springer-Verlag, c1993  xi, 261 p. ; 24 cm
シリーズ名: Springer series in information sciences ; 28
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13.

図書

図書
editors, Robert W. Hay, Jon R. Dilworth, Kevin B. Nolan
出版情報: London ; Greenwich, Conn. : JAI Press, 1991-  v. ; 24 cm
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目次情報: 続きを見る
Preface
Lithium in biology
Ceruloplasmin: the beginning if the end of an enigma
The chemistry of rhenium in nuclear medicine
Macrocyclic polyamines and their metal complexes: a novel type of anti-HIV agent
Chemistry of platinum anticancer drugs
Functional model complexes for dinuclear phospoesterase enzymes
Preface
Lithium in biology
Ceruloplasmin: the beginning if the end of an enigma
14.

図書

図書
edited by P.J.T. Morris, W.A. Campbell, H.L. Roberts
出版情報: Cambridge : Royal Society of Chemistry, c1991  viii, 307 p. ; 21 cm
シリーズ名: Special publication / Royal Society of Chemistry ; no. 96
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15.

図書

図書
editor, J.L.G. Fierro
出版情報: Amsterdam ; Tokyo : Elsevier, 1990  xii, 384 p. ; 25 cm
シリーズ名: Studies in surface science and catalysis ; v. 57 . Spectroscopic characterization of heterogeneous catalysts ; pt. A
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16.

図書

図書
R. Glaser, D. Gingell (eds)
出版情報: Berlin ; Tokyo : Springer-Verlag, c1990  viii, 366 p. ; 25 cm
シリーズ名: Springer series in biophysics ; v. 5
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17.

図書

図書
editors, M. Misono, Y. Moro-oka and S. Kimura
出版情報: Amsterdam ; New York : Elsevier, 1990  vii, 381 p. ; 25 cm
シリーズ名: Studies in surface science and catalysis ; v. 54
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18.

図書

図書
editor, J. Mattay
出版情報: Berlin ; Tokyo : Springer-Verlag, c1990-<c1993 >  v. <1-5 > ; 23-25 cm
シリーズ名: Topics in current chemistry = Fortschritte der chemischen Forschung ; 156, 158, 159, 163, 168
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19.

図書

図書
Volkmar Brückner, Karl-Heinz Feller, Ulrich-Walter Grummt
出版情報: Amsterdam ; New York : Elsevier, 1990  xii, 244 p. ; 24 cm
シリーズ名: Studies in physical and theoretical chemistry ; 66
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20.

図書

図書
editor, J.L.G. Fierro
出版情報: Amsterdam ; Tokyo : Elsevier, 1990  xiv, 394 p. ; 25 cm
シリーズ名: Studies in surface science and catalysis ; v. 57 . Spectroscopic characterization of heterogeneous catalysts ; pt. B
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21.

図書

図書
R. Wiesendanger, H.-J. Güntherodt (eds.) ; with contributions by W. Baumeister ... [et al.]
出版情報: Berlin ; New York : Springer-Verlag, c1992  xiv, 308 p. ; ill. : 24 cm
シリーズ名: Springer series in surface sciences ; 28 . Scanning tunneling microscopy ; 2
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22.

図書

図書
C.P. Slichter
出版情報: Berlin ; Tokyo : Springer-Verlag, c1990  xi, 655 p. ; 25 cm
シリーズ名: Springer series in solid-state sciences ; 1
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23.

図書

図書
R.C. Ropp
出版情報: Amsterdam ; Tokyo : Elsevier , New York, NY, U.S.A. : Distributors for the U.S. and Canada, Elsevier Science Pub. Co., 1991  xv, 453 p. ; 25 cm
シリーズ名: Studies in inorganic chemistry ; 12
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24.

図書

図書
edited by Kenny B. Lipkowitz and Donald B. Boyd
出版情報: New York, N.Y. : VCH , Weinheim : VCH Verlagsgesellschaft, c1990-  v. ; 25 cm
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目次情報: 続きを見る
Computations in Treating Fullerenes and Carbon Aggregates / Christian Ochsenfeld ; Patrice Koehl1:
Peptide Mimetic Design with the Aid of Computational Chemistry
Pseudopotential Calculations of Transitions Metals Compounds-Scope and Limitation / R. Judson ; M. Murcko ; M. Francl ; Geoff M. Downs
Free Energy by Molecular Simulation
Effective Core Potential Approaches to the Chemistry of the Heavier Elements / Sason Shaik ; Roberto Dovesi ; Jorg Kussmann
The Application of Molecular Modeling Techniques to the Determination of Oligosaccaride Solution Conformations
Genetic Algorithms and Their Use in Chemistry
Recent Advances in Ligand Design Methods
Protein Structure Classification / L. Chirlian ; John M. Barnard
Relativistic Effects in Chemistry
Molecular Mechanics Calculated Conformational Energies of Organic Molecules
The Ab Initio Computation of Nuclear Magnetic Resonance Chemical Shielding / E. Martin, et al. ; D. Clark, et al. ; Philippe C. Hiberty ; Bartolomeo Civalleri ; Daniel S. Lambrecht
A Comparison of Force Fields
The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials
Clustering Methods and Their Uses in Computational Chemistry
Introduction
Indexes
Molecular Shape Descriptors
Does Combinatorial Chemistry Obviate Computer-Aided Drug Design?
Current Issues in De Novo Molecular Design
Valence Bond Theory, Its History, Fundamentals, and Applications: A Primer / T. Crawford ; Hans-Joachim Bouml;hm
Classification and Biology / Roberto Orlando
The Biomolecular Revolution / R. Topper ; T. Oprea
Linear-Scaling Methods in Quantum Chemistry
A Story of Valence Bond Theory, Its Rivalry with Molecular Orbital Theory, Its Demise, and Eventual Resurgence / H. Schaefer ; Martin Stahl
Basic Principles of Protein Structure / Carla Roetti
Visualizing Molecular Phase Space: Nonstatistical Effects in Reaction Dynamics
Roots of VB Theory / C. Waller
Visualization
An Introduction to Coupled Cluster Theory for Computational Chemists / R. Larter
The Use of Scoring Functions in Drug Discovery Applications
Origins of MO Theory and the Roots of VB-MO Rivalry
Protein Building Blocks / Victor R. Saunders
Theoretical and Practical Aspects of Three-Dimensional Quantitative Structure-Activity Relationships
The ''Dance'' of Two Theories: One Is Up, the Other Is Down / B. van de Graaf, et al. ; Steven W. Rick
Protein Structure Hierarchy
Some Basics of SCF Theory
Are the Failures of VB Theory Real Ones? / K. Showalter ; G. Greco, et al.
Ab Initio Quantum Simulation in Solid State Chemistry 1
Three Types of Proteins
Introduction to Zeolite Modeling
Modern VB Theory: VB Theory Is Coming of Age / Steven J. Stuart
Geometry of Globular Proteins / 2:
Direct SCF Methods and Two-Electron Integral Screening
Computational Studies in Nonlinear Dynamics
Approaches to Three-Dimensional Quantitative Structure-Activity Relationships
Basic VB Theory / S. Price
Protein Domains / Patrick Bultinck
Potentials and Algorithms for Incorporating Polarizability in Computer Simulations / S. Smith ; P. Carrupt, et al.
Writing and Representing VB Wave Functions
Resources on Protein Structures
Schwarz Integral Estimates
Towards More Accurate Model Intermolecular Potentials for Organic Molecules
The Relationship between MO and VB Wave Functions / Dmitry V. Matyushov
Protein Structure Comparison / Xavier Girones
Computational Approaches to Lipophilicity: Methods and Applications / B. Sutcliffe
Formalism Using the Exact Hamiltonian / C. Mundy, et al.
Automatic Identification of Protein Structural Domains
Multipole-Based Integral Estimates (MBIE)
Qualitative VB Theory / G. Ravishanker, et al. ; Gregory A. Voth
The Rigid-Body Transformation Problem / Ramon Carbo-Dorca
The Development of Computational Chemistry in the United Kingdom
Nonequilibrium Molecular Dynamics
Some Simple Formulas for Elementary Interactions
Protein Structure Superposition
Calculation of Integrals via Multipole Expansion
Treatment of Counterions in Computer Simulations of DNA
New Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases / D. Boyd
Insights of Qualitative VB Theory
Molecular Quantum Similarity: Theory and Applications
cRMS: An Ambiguous Measure of Similarity
Appendix
Are the ''Failures'' of VB Theory Real? / George R. Famini
Differential Geometry and Protein Structure Comparison / 3:
A First Example
Can VB Theory Bring New Insight into Chemical Bonding? / K. Lipkowitz
Upcoming Challenges for Protein Structure Comparison / Jean-Loup Faulon
VB Diagrams for Chemical Reactivity / Leland Y. Wilson
Derivation of the Multipole Expansion
History of the Gordon Research Conferences on Computational Chemistry
VBSCD: A General Model for Electronic Delocalization and Its Comparison with the Pseudo-Jahn-Teller Model
The Structure Classification of Proteins (SCOP) / Donald P. Visco, Jr.
Linear Free Energy Relationships Using Quantum Mechanical Descriptors
What Is the Driving Force, s or p, Responsible for the D6h Geometry of Benzene?
The CATH Classification
The Fast Multipole Method: Breaking the Quadratic Wall
VBSCD: The Twin-State Concept and Its Link to Photochemical Reactivity / Sigrid D. Peyerimhoff
The DALI Domain Dictionary (DDD) / Diana Roe
The Spin Hamiltonian VB Theory
Comparing SCOP, CATH, and DDD
Fast Multipole Methods for Continuous Charge Distributions
The Development of Computational Chemistry in Germany
Theory
Enumerating Molecules
Conclusions
Applications
Acknowledgments / 4:
Other Approaches
Ab Initio VB Methods / Donald B. Boyd
Orbital-Optimized Single-Configuration Methods / David J. Livingstone
References
Exchange-Type Contractions
Orbital-Optimized Multiconfiguration VB Methods / Kenny B. Lipkowitz
Prospective / David W. Salt
The Exchange-Correlation Matrix of KS-DFT / Emilio Xavier Esposito
Examination of the Employment Environment for Computational Chemistry
Variable Selection-Spoilt for Choice?
Author Index
Avoiding the Diagonalization Step-Density Matrix-Based SCF / Dror TobiA.1:
Subject Index
Expansion of MO Determinants in Terms of AO Determinants
General Remarks / Nathan A. Baker ; Jeffry D. MaduraA.2:
Guidelines for VB Mixing
Biomolecular Applications of Poisson-Boltzmann Methods
Comparative Protein Modeling / A.3:
Tensor Formalism
Computing Mono-Determinantal VB Wave Functions with Standard Ab Initio Programs
Anatomy of a Comparative Model / Baltazar D. Aguda
Properties of the One-Particle Density Matrix
Searching for Related Sequences and Structures / Georghe CraciunStep 1:
Density Matrix-Based Energy Functional
Expert Protein Analysis System (ExPASy) / Nikita Matsunaga ; Rengul Cetin-Atalay
BLAST and PSI-BLAST
"Curvy Steps" in Energy Minimization
Data Sources and Computational Approaches for Generating Models of Gene Regulatory Networks / Shiro Koseki
Protein Data Bank (PDB)
Sequence Alignment and Modeling System with Hidden Markov Models
Density Matrix-Based Quadratically Convergent SCF (D-QCSCF)
Modeling of Spin-Forbidden Reactions
Index Subject
Threading
Overview of Reactions Requiring Two States
Threader
Implications for Linear-Scaling Calculation of SCF Energies
Spin-Forbidden Reaction, Intersystem Crossing
Example: Finding Related Sequences and 3-D Structures
Spin-Orbit Coupling as a Mechanism for Spin-Forbidden Reaction
SCF Energy Gradients / Step 2:
General Considerations
Sequence Alignment
Atomic Spin-Orbit Coupling
Preparing the Sequences
Molecular Response Properties at the SCF Level
Molecular Spin-Orbit Coupling
Alignment Basics
Crossing Probability
Similarity Matrices
Vibrational Frequencies
Fermi Golden Rule
Clustal
Landau-Zener Semiclassical Approximation
Tree-Based Consistency Objective Function for Alignment Evaluation (T-Coffee)
NMR Chemical Shieldings
Methodologies for Obtaining Spin-Orbit Matrix Elements
Divide-and-Conquer Alignment (DCA)
Electron Spin in Nonrelativistic Quantum Mechanics
Example: Aligning Sequences
Density Matrix-Based Coupled Perturbed SCF (D-CPSCF)
Klein-Gordon Equation
Dirac Equation / Step 3:
Selecting Templates and Improving Alignments
Outlook on Electron Correlation Methods for Large Systems
Foldy-Wouthuysen Transformation
Selecting Templates
Breit-Pauli Hamiltonian
Improving Sequence Alignments With Primary and Secondary Structure Analysis
Long-Range Behavior of Correlation Effects
Z eff Method
Example: Aligning the Target to the Selected Template
Effective Core Potential-Based Method
Rigorous Selection of Transformed Products via Multipole-Based Integral Estimates (MBIE) / Step 4:
Model Core Potential-Based Method
Constructing Protein Models
Douglas-Kroll Transformation
Satisfaction of Spatial Restraints
Implications
Potential Energy Surfaces
Segment Match Modeling
Minimum Energy Crossing-Point Location
Multiple Template Method
Available Programs for Modeling Spin-Forbidden Reactions
3D-Jigsaw
Applications to Spin-Forbidden Reactions
Overall Protein Model Construction Methods
Diatomic Molecules
Example: Constructing a Protein Model
Polyatomic Molecules
Phenyl Cation / Spiridoula MatsikaStep 5:
Refinement of Protein Models
Norborene
Side-Chains with Rotamer Library (SCWRL)
Conjugated Polymers
Energy Minimization
Conical Intersections in Molecular Systems
CH( 2 II) + N2 -- HCN + N( 4 S)
Molecular Dynamics
Blast and PSI-Blast
Molecular Properties
Molecular Dynamics with Simulated Annealing
Dynamical Aspects
Other Reactions / Step 6:
Evaluating Protein Models
General Theory
Biological Chemistry
Procheck
Concluding Remarks
Verify3D
The Born-Oppenhemier Approximation and its Breakdown: Nonadiabatic Processes
Errat
Protein Structure Analysis (ProSa)
Adiabatic-Diabatic Representation
Protein Volume Evaluation (PROVE)
Model Clustering Analysis / Stefan Grimme
The Noncrossing Rule
Example: Evaluation of Protein Models
Calculation of the Electronic Spectra of Large Molecules
The Geometric Phase Effect
Types of Electronic Spectra
Conical Intersections and Symmetry
Types of Excited States
The Branching Plane / Joan-Emma Shea
Excitation Energies
Transition Moments / Miriam R. Friedel
Characterizing Conical Intersections: Topography
Vibrational Structure
Quantum Chemical Methods / Andrij Baumketner
Derivative Coupling
Case Studies
Simulations of Protein Folding
Vertical Absorption Spectra
Electronic Structure Methods for Excited States
Circular Dichroism
Theoretical Framework
Energy Landscape Theory
Multiconfiguration Self-Consistent Field (MCSCF)
Summary and Outlook
Thermodynamics and Kinetics of Folding: Two-State and Multistate Folders
Protein Models
Multireference Configuration Interaction (MRCI)
Introduction and General Simulation Techniques
Coarse-Grained Protein Models
Complete Active Space Second-Order Perturbation Theory (CASPT2)
Fully Atomic Simulations / Raymond Kapral
Advanced Topics: The Transition State Ensemble for Folding
Single Reference Methods
Simulating Chemical Waves and Patterns
Transition State and Two-State Kinetics
Methods for Identifying the TSE
Choosing Electronic Structure Methods for Conical Intersections
Reaction-Diffusion Systems
Conclusions and Future Directions
Cellular Automata
Locating Conical Intersections
Coupled Map Lattices
Mesoscopic Models
Dynamics
Summary
Conical Intersections in Biologically Relevant Systems / Marco Saraniti ; Shela Aboud ; Costel Sa?rbu
Beyond the Double Cone / Robert Eisenberg ; Horia F. Pop
The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methods
Fuzzy Soft-Computing Methods and Their Applicationsin Chemistry
Three-State Conical Intersections
System Components
Methods for Exploratory Data Analysis
Time and Space Scale
Spin-Orbit Coupling and Conical Intersections
Visualization of High-Dimensional Data
Experiments
Clustering Methods
Electrostatics
Projection
Long-Range Interaction
Short-Range Interaction
Boundary Conditions
Particle-Based Simulation
Implicit Solvent: Brownian Dynamics
Explicit Solvent: Molecular Dynamics
Flux-Based Simulation / Antonio Fernandez-Ramos
Nernst-Planck Eq"
Variational Transition State Theory with Multidimensional Tunneling / Benjamin A. Ellingson ; Bruce C. Garrett ; Donald G. Truhlar
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 + CH[subscript 4]
Liquid-Phase Example: Menshutkin Reaction
Coarse-Grain Modeling of Polymers / Roland Faller
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
Nernst-Planck Equation
The Poisson-Nernst-Planck (NP) Method
Hierarchical Simulation Schemes / Jeffrey W. Godden
Future Directions and Concluding Remarks / Jurgen Bajorath
Analysis of Chemical Information Content Using Shannon Entropy
Shannon Entropy Concept / C. Matthew Sundling ; Nagamani Sukumar
Descriptor Comparison / Hongmei Zhang
Influence of Boundary Effects / Mark J. Embrechts
Extension or SE Analysis for Profiling of Chemical Libraries / Curt M. Breneman
Information Content of Organic Molecules
Wavelets in Chemistry and Chemoinformatics
Shannon Entropy in Quantum Mechanics, Molecular Dynamics, and Modeling
Preface
Examples of SE and DSE Analysis
Introduction to Wavelets
Fourier Transform
Continuous Fourier Transform
Short-Time Fourier Transformation / Ovidiu Ivanciuc
Wavelet Transform
Applications of Support Vector Machines in Chemistry
Continuous Wavelet Transform
Discrete Wavelet Transform
A Nonmathematical Introduction to SVM
Wavelet Packet Transform
Pattern Classification
Wavelets vs. Fourier Transforms: A Summary
The Vapnik-Chervonenkis Dimension
Application of Wavelets in Chemistry
Pattern Classification with Linear Support Vector Machines
Smoothing and Denoising
SVM Classification for Linearly Separable Data
Signal Feature Isolation
Linear SVM for the Classification of Linearly Non-Separable Data
Signal Compression
Nonlinear Support Vector Machines
Quantum Chemistry
Mapping Patterns to a Feature Space
Classification, Regression, and QSAR/QSPR
Feature Functions and Kernels
Kernel Functions for SVM
Hard Margin Nonlinear SVM Classification
Soft Margin Nonlinear SVM Classification
v-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
How Computational Chemistry Became Important in the Pharmaceutical Industry / 7:
Germination: The 1960s
Gaining a Foothold: The 1970s
Growth: The 1980s
Gems Discovered: The 1990s
Final Observations
Determining the Glass Transition in Polymer Melts / Wolfgang Paul
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
Atomistic Modeling of Friction / Nicholas J. Mosey ; Martin H. Muser
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
Computing Free Volume, Structural Order, and Entropy of Liquids and Glasses / Jeetain Mittal ; William P. Krekelberg ; Jeffrey R. Errington ; Thomas M. Truskett
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?
The Reactivity of Energetic Materials at Extreme Conditions / Laurence E. Fried
Chemical Equilibrium
Atomistic Modeling of Condensed-Phase Reactions
First Principles Simulations of High Explosives
Magnetic Properties of Atomic Clusters of the Transition Elements / Julio A. Alonso
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
Calculation of the Density of Electronic States within the Tight Binding Theory by the Method of Moments / Appendix:
Transition Metal- and Actinide-Containing Systems Studied with Multiconfigurational Quantum Chemical Methods / Laura Gagliardi
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 [Characters not reproducible] and Related Systems
The Cr-Cr Multiple Bond
Cu[subscript 2]O[subscript 2] Theoretical Models
Spectroscopy of Triatomic Molecules Containing One Uranium Atom
Actinide Chemistry in Solution
The Actinide-Actinide Chemical Bond
Inorganic Chemistry of Diuranium
Recursive Solutions to Large Eigenproblems in Molecular Spectroscopy and Reaction Dynamics / Hua Guo
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
Bound States and Spectroscopy
Reaction Dynamics
Lanczos vs. Chebyshev
Development and Uses of Artificial Intelligence in Chemistry / Hugh Cartwright8:
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
Computer-Aided Molecular Diversity Analysis and Combinatorial Library Design / Richard A. Lewis ; Stephen D. Pickett ; David E. Clark1.:
Molecular Recognition: Similarity and Diversity
Describing Diversity Space
Types of Descriptor
Choosing Appropriate Descriptors
Validation of Descriptors
Diversity Analysis
Combinatorial Library Design
Diversity Is Not the Be-All and End-All!
Current Issues and Future Directions
Diversity Descriptors
Library Design
Speed Requirement
"Quick and Dirty" QSAR
Integration with Other Modeling Tools
Persuading the Customers
Artificial Neural Networks and Their Use in Chemistry / Keith L. Peterson2.:
Overview and Goals
What Are Artificial Neural Networks?
Analogy with the Brain
Artificial Neural Networks
Summary of Neural Network Operation
Brief History of Neural Networks
What Can Neural Networks Be Used for and When Should You Use Them?
Classification
Modeling
Mapping and Associations
General Comments on ANNs, Statistics, and Artificial Intelligence
Processing Elements
Summation Functions
Transfer Functions
Output Functions
Error Functions
Learning Rules
Collections of Processing Elements
Different Types of Artificial Neural Network
Adaptive Resonance Theory (ART) Networks
Backpropagation (BP) and Related Networks
Biassociative Memory (BAM) Networks
Counterpropagation Networks
Generalized Regression Networks (GRN)
Hopfield Networks
Kohonen Self-Organizing Map (SOM) Networks
Perceptron Networks
Radial Basis Function (RBF) Networks
Recirculation Networks
Miscellaneous Networks
Practical Considerations in Solving Problems with Neural Networks
What Type of Network?
Data Preprocessing
Variable Selection, Reduction, and Orthogonalization
Training and Testing Sets
Training the Network
Learning Versus Generalization
Performance Metrics
Classification Problems
Nonclassification, Supervised Learning Problems
Miscellaneous Remarks
Analysis of Neural Networks
Neural Network Software
Use of Force Fields in Materials Modeling / Jorg-Rudiger Hill ; Clive M. Freeman ; Lalitha Subramanian3.:
The Force Field Approach to Describing Structures of Materials
What Are Force Fields?
Ion Pair and Shell Model Potentials
Molecular Mechanics Force Fields
Comparison of Ion Pair and Molecular Mechanics Force Fields
Force Field Parameterization
Ab Initio Based Force Fields
Empirical Force Fields
Transferability
Rule-Based Force Fields
Application of Force Fields in Materials Science
Metal Oxides and Ceramics
Superconductors
Zeolites and Related Microporous Materials
Glasses
Polymers
Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities / M. Rami Reddy ; Mark D. Erion ; Atul Agarwal4.:
Methodology Overvie
Computational Details
Treatment of Long-Range Forces
Polarization
Bond Length Constraints
Treatment of Boundaries
Solvent Models
Convergence of Free Energy Results
Free Energy Perturbation Calculations for Small Molecules
Tautomerization
Ionization
Log P
Covalent Hydration
Solvation
Free Energy Perturbation Calculations for Macromolecules
Nonprotein-Ligand Complexes
Protease Inhibitors
Lyases
Oxidases and Reductases
Allosteric Binding Site Ligands
DNA Binding Proteins
Miscellaneous Studies
Guide to Structure-Based Ligand Optimization
Computer Model
Characterization of the Binding Site
Lead Generation
Optimization of Lead Compounds
Optimization of Ligands to HIV-1 Protease: Using the FEP Method
Design Considerations
X-Ray Structures of HIV-1 Protease Complexes
Force Field Parameters
Computational Details for Solvent
Computational Details for Complex
Computer Model Validation
Validation of FEP Methodology
Convergence and Error Analysis
Binding Affinity Predictions
Advantages of Free Energy Calculations
Limitations of Free Energy Calculations
Brief Guide for Free Energy Calculations and Their Use in Ligand Optimization
Small Molecule Docking and Scoring / Ingo Muegge ; Matthias Rarey
Algorithms for Molecular Docking
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
Docking as a Virtual Screening Tool
Docking as a Ligand Design Tool
Protein-Protein Docking / Lutz P. Ehrlich ; Rebecca C. Wade
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
Flexible Docking with Side-Chain Flexibility
Flexible Docking with Full Flexibility
Future Directions
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
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
Cellular Automata Models of Aqueous Solution Systems / Lemont B. Kier ; Chao-Kun Cheng ; Paul G. Seybold
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
Books Published on the Topics of Computational Chemistry
Computers in Chemistry
Chemical Information
Computational Chemistry
Artificial Intelligence and Chemometrics
Crystallography, Spectroscopy, and Thermochemistry
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
Clustering Algorithms
Hierarchical Methods
Nonhierarchical Methods
Progress in Clustering Methodology
Algorithm Developments
Comparative Studies on Chemical Data Sets
How Many Clusters?
Chemical Applications
The use of Scoring Functions in Drug Discovery Applications / Hans-Joachim Bohm
The Process of Virtual Screening
Major Contributions to Protein--Ligand Interactions
Description of Scoring Functions for Receptor--Ligand Interactions
Force Field-Based Methods
Knowledge-Based Methods
Critical Assessment of Current Scoring Functions
Influence of the Training Data
Molecular Size
Other Penalty Terms
Specific Attractive Interactions
Water Structure and Protonation State
Performance in Structure Prediction
Rank Ordering Sets of Related Ligands
Application of Scoring Functions in Virtual Screening
Seeding Experiments
Hydrogen Bonding versus Hydrophobic Interactions
Finding Weak Inhibitors
Consensus Scoring
Successful Identification of Novel Leads through Virtual Screening
Outlook
Nonpolarizable Models
Polarizable Point Dipoles
Shell Models
Electronegativity Equalization Models
Semiempirical Models
Water
Proteins and Nucleic Acids
Comparison of the Polarization Models
Mechanical Polarization
Computational Efficiency
Hyperpolarizability
Charge-Transfer Effects
The Electrostatic Potential
Summary and Conclusions
Paradigm of Free Energy Surfaces
Formulation
Two-State Model
Heterogeneous Discharge
Beyond the Parabolas
Bilinear Coupling Model
Electron Transfer in Polarizable Donor--Acceptor Complexes
Nonlinear Solvation Effects
Electron-Delocalization Effects
Nonlinear Solvation versus Intramolecular Effects
Optical Band Shape
Optical Franck--Condon Factors
Absorption Intensity and Radiative Rates
Electron-Transfer Matrix Element
Electronically Delocalized Chromophores
Polarizable Chromophores
Hybrid Model
LFER Methodology / 5.:
Background
Computational Methods
Linear Free Energy Relationships
Descriptors
Classifications
Quantum Mechanical Descriptors
Quantum Mechanical Calculations
Statistical Procedures
Multiple Regression Analysis
Examples of LFER Equations
Model-Based Methods
Nonmodel-Based Methods
Computer Development / 6.:
The ZUSE Computers
The G1, G2, and G3 of Billing in Gottingen
Computer Development at Universities
The Analog Computer in Chemistry
Quantum Chemistry, A New Start
Theoretical Chemistry 1960-1970
The Deutsche Rechenzentrum at Darmstadt
Formation of Theoretical Chemistry Groups
Deutsche Forschungsgemeinschaft--Schwerpunktprogramm Theoretische Chemie
Theoretical Chemistry Symposia
Scientific Developments
Computational Chemistry 1970-1980
European Efforts
Computer-Aided Synthesis
Progress in Quantum Chemical Methods
Beyond 1980
Hiring Trends / Appendix.:
Skills in Demand
The Broader Context
Salaries
Computations of Noncovalent ? Interactions / C. David Sherrill
Challenges for Computing ? 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
Appendix: Extracting Energy Components from the SAPT2006 Program
Reliable Electronic Structure Computations for Weak Noncovalent Interactions in Clusters / Gregory S. Tschumper
Introduction and Scope
Clusters and Weak Noncovalent Interactions
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 Møller-Plesset Perturbation Theory
Density Functional Theory
Guidelines
Other Computational Issues
Basis Set Superposition Error and Counterpoise Corrections
Beyond Interaction Energies: Geometries and Vibrational Frequencies
Excited States from Time-Dependent Density Functional Theory / Peter Elliott ; Filipp Furche ; Kieron Burke
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
Convergence for Naphthalene
Double-Zeta Basis Sets
Polarization Functions
Triple-Zeta Basis Sets
Diffuse Functions
Resolution of the Identity
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
Solids
Charge Transfer
Other Topics
Ground-State XC Energy
Strong Fields
Electron Transport
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
Spin1/2 Quantum Heisenberg Magnet
Diluted Heisenberg Magnets
Superfluid-Insulator Transition in an Optical Lattice
Fermions
Other Methods and Techniques
Real-Space and Multigrid Methods in Computational Chemistry / Thomas L. Beck
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
Transport Problems
Existing Real-Space and Multigrid Codes
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?"
Hybrid Methods for Atomic-Level Simulations Spanning Multiple-Length Scales in the Solid State / Francesca Tavazza ; Lyle E. Levine ; Anne M. Chaka
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
Conclusions: The Outlook
Appendix: A List of Acronyms
Extending the Time Scale in Atomically Detailed Simulations / Alfredo E. Cárdenas ; Eric Barth
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
Appendix: MATLAB Scripts for the MTS Tutorial
Acknowledgment
Atomistic Simulation of Ionic Liquids / Edward J. Maginn
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
Ab Initio Molecular Dynamics
How to Carry Out Your Own Ionic Liquid Simulations
What Code?
Force Fields
Data Analysis
Operating Systems and Parallel Computing
Brittle Fracture: From Elasticity Theory to Atomistic Simulations / Stefano Giordano ; Alessandro Mattoni ; Luciano Colombo
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
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
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
Griffith Criterion for Failure
Failure in Complex Systems
Stress Shielding at Crack-Tip
Appendix: Notation
Dissipative Particle Dynamics / Igor V. Pivkin ; Bruce Caswell ; George Em Kamiadakis
Fundamentals of DPD
Mathematical Formulation
Units in DPD
Thermostat and Schmidt Number
Integration Algorithms
Extensions of DPD
DPD with Energy Conservation
Fluid Particle Model
DPD for Two-Phase Flows
Other Extensions
Polymer Solutions and Melts
Binary Mixtures
Amphiphilic Systems
Red Cells in Microcirculation
Trajectory-Based Rare Event Simulations / Peter G. Bolhuis ; Christoph Dellago
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
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
Understanding Metal/Metal Electrical Contact Conductance from the Atomic to Continuum Scales / Douglas L. Irving
Factors That Influence Contact Resistance
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
Conduction Through Metallic Nanowires
Multiscale Methods Applied to Metal/Metal Contacts
Molecular Detailed Simulations of Lipid Bilayers / Max L. Berkowitz ; James T. Kindt
Membrane Simulation Methodology
Choice of the Ensemble
Verification of the Force Field
Monte Carlo Simulation of Lipid Bilayers
Detailed Simulations of Bilayers Containing Lipid Mixtures
Semiclassical Bohmian Dynamics / Sophya Garashchuk ; Vitaly Rassolov ; Oleg Prezhdo
The Formalism and Its Features
The Trajectory Formulation
Features of the Bohmian Formulation
The Classical Limit of the Schrödinger 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
Conservation of Density within a Volume Element / Appendix A:
Quantum Trajectories in Arbitrary Coordinates / Appendix B:
Optimal Parameters of the Linearized Momentum on Spatial Domains in Many Dimensions / Appendix C:
Prospects for Career Opportunities in Computational Chemistry
Introduction and Overview
Methodology and Results
Proficiencies in Demand
Analysis
An Aside: Economics 101
Prognosis
Appendix: List of Computational Molecular Scientists
Computations in Treating Fullerenes and Carbon Aggregates / Christian Ochsenfeld ; Patrice Koehl1:
Peptide Mimetic Design with the Aid of Computational Chemistry
Pseudopotential Calculations of Transitions Metals Compounds-Scope and Limitation / R. Judson ; M. Murcko ; M. Francl ; Geoff M. Downs
25.

図書

図書
Joachim Stöhr
出版情報: Berlin ; Tokyo : Springer-Verlag, c1992  xv, 403 p. ; 24 cm
シリーズ名: Springer series in surface sciences ; 25
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26.

図書

図書
edited by E. Wolf
出版情報: Amsterdam ; Tokyo : North-Holland, 1961-[1992]  v. ; 23 cm
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目次情報: 続きを見る
Preface
Ultrafast Solid State Lasers / U. Keller ; V. Mahajan1:
Gaussian Apodization and Beam Propagation
Control of Nonlinear Optical Processes in Multi-level Atomic Systems / A. Shchegrov ; A. Joshi ; A. Maradudin ; M. Xiao ; E. Mendez2:
Multiple Scattering of Light from Randomly Rough Surfaces / 3:
Laser Diode Interferometry / H. Benisty ; Y. Ishii ; C. Weisbuch
Photonic Crystals
Optical Realization of Quantum Teleportation / J. Gea-Banacloche ; C. Brosseu4:
Symmetry Properties and Polarization Descriptors for an Arbitrary Electromagnetic Wavefield / A. Dogariu ; H.J. Carmichael5:
Quantum Cryptography / G.T. Foster ; M. Dusek ; L.A. Orozco ; N. Lutkenhaus ; J.E. Reiner ; M. Hendrych ; P.R. Rice
Intensity-Field Correlations of Non-Classical Light / 6:
Author index / N. Cerf
Subject index
Contents of previous volumes Cumulative index - Volumes 1-46 / J. Fiurasek
Optical Quantum Cloning
Author index for Volume 49
Subject index for Volume 49
Contents of previous volumes Cumulative index - Volumes 1-49
Preface
Ultrafast Solid State Lasers / U. Keller ; V. Mahajan1:
Gaussian Apodization and Beam Propagation
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