Reviews in Computational Chemistry Volume 18

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xxviii Contributors to Previous Volumes Keith L. Peterson, Artificial Neural Networks and Their Use in Chemistry. Jörg-Rüdiger Hill, Clive M. Freeman, and Lalitha Subramanian, Use of Force Fields in Materials Modeling. M. Rami Reddy, Mark D. Erion, and Atul Agarwal, Free Energy Calculations: Use and Limitations in Predicting Ligand Binding Affinities. Volume 17 (2001) Ingo Muegge and Matthias Rarey, Small Molecule Docking and Scoring. Lutz P. Ehrlich and Rebecca C. Wade, Protein–Protein Docking. Christel M. Marian, Spin-Orbit Coupling in Molecules. Lemont B. Kier, Chao-Kun Cheng, and Paul G. Seybold, Cellular Automata Models of Aqueous Solution Systems. Kenny B. Lipkowitz and Donald B. Boyd, Appendix: Books Published on the Topics of Computational Chemistry.
Topics Covered in Volumes 1–18 * Ab initio calculations, 1, 2, 3, 8, 13, 15 Basis set superposition errors, 13 Basis sets, 1 Brownian dynamics, 5 Cellular automata modeling, 17 Charge distributions, 2, 5, 14 Charge transfer, 18 Cheminformatics, 1, 7, 18 Chemometrics, 1 Clustering methods, 18 Computational chemistry literature, 2, 17 Conformational analysis, 2, 9 Coupled cluster theory, 14 Crystal polymorphs, 12 Databases of structures, 1, 7 De novo design, 11 Density functional theory, 7, 13, 15 Descriptors, 1, 9, 18 Distance geometry, 5 Diversity analysis, 10, 16 DNA, 11 Docking, 16, 18 Drug discovery, 1, 5, 9, 10, 11, 16, 18 Effective core potentials, 8 Electrostatics, 2, 5, 14 Enthalpies of formation, 14 Entropy, 12 Force fields, 2, 6, 9, 14, 16 Free energy calculations, 1, 9, 12, 16 Fullerenes, 8 Genetic algorithms, 10 High performance computing, 6 *This brief index lists topics and volume numbers. History of development of the field, 1, 10, 12, 14, 15, 18 Hydrogen bonding, 2 Inorganics, 6 Intermolecular interactions, 1, 14 Job market, 18 Kohn-Sham orbitals, 15 Library design, 10, 16 Ligand design, 1, 5, 9, 10, 11, 16, 18 Linear free energy relationships, 18 Lipids, 6 Lipophilicity, 11 Materials modeling, 6, 8, 12, 14, 16 Mesoscopic models, 13 Metal–water interfaces, 12 Molecular connectivity, 2 Molecular design, 1, 5 Molecular diversity, 16 Molecular dynamics, 1, 4, 5, 9, 11, 12, 14, 18 Molecular mechanics, 2, 6, 9, 14 Molecular modeling, 1, 3, 9 Molecular orbital calculations, 1, 2, 3, 6, 8, 13 Molecular properties, 1 Molecular shape, 9 Molecular similarity, 7, 16 Molecular simulations, 1, 4, 5, 9, 11, 12, 14, 18 Molecular surfaces, 1 Neural networks, 16 Nonequilibrium molecular dynamics, 14 Nonlinear dynamics, 10 xxix
Page 1 and 2: Reviews in Computational Chemistry
Page 3 and 4: Kenny B. Lipkowitz Department of Ch
Page 5 and 6: vi Preface three-dimensional struct
Page 7 and 8: viii Preface some descriptors and i
Page 9 and 10: Epilogue and Dedication My associat
Page 11 and 12: Contents 1. Clustering Methods and
Page 13 and 14: Contents xv Electron Transfer in Po
Page 15 and 16: Contributors John M. Barnard, Barna
Page 17 and 18: Contributors to Previous Volumes *
Page 19 and 20: Volume 3 (1992) Tamar Schlick, Opti
Page 21 and 22: Volume 7 (1996) Geoffrey M. Downs a
Page 23 and 24: Volume 11 (1997) Mark A. Murcko, Re
Page 25: T. Daniel Crawford* and Henry F. Sc
Page 29 and 30: Reviews in Computational Chemistry
Page 31 and 32: 2 Clustering Methods and Their Uses
Page 39 and 40: 10 Clustering Methods and Their Use
Page 71 and 72: 42 The Use of Scoring Functions in
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48 The Use of Scoring Functions in
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Table 1 Reference List for the Most
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CHAPTER 3 Potentials and Algorithms
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Vn (1 + cos(nω + γ)) 2 K θ (θ
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are modified by their environment w
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Table 1 Polarizability Parameters f
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The polarizable point dipole models
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two to three orders of magnitude sl
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M i z i + q i d i k i and shell cha
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Shell Models 103 on estimates of sh
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minimization can be replaced by mor
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The energy required to create a cha
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for all i ði:e:; 8 iÞ: @U @qi l
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where we have used q Cl ¼ qNa. The
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Electronegativity Equalization Mode
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Electronegativity Equalization Mode
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of N molecules is taken as a Hartre
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is treated using variable charges.
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water have been developed, includin
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Applications 123 classical and rigi
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developing polarizable models. A va
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Comparison of the Polarization Mode
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negligible errors in such propertie
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ecome significant at field strength
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noteworthy in this regard because t
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References 135 9. P. Cieplak and P.
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References 137 48. E. L. Pollock an
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References 139 Computational Chemis
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References 141 139. J. Hinze and H.
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References 143 178. J. J. P. Stewar
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References 145 216. M. W. Mahoney a
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CHAPTER 4 New Developments in the T
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Introduction 149 applications). For
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FCWD(∆E ) FCWD(0) ∆E = 0 ∆E
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Introduction 153 Equations [6]-[12]
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Paradigm of Free Energy Surfaces 15
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Paradigm of Free Energy Surfaces 15
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In Eqs. [18] and [19], F0i is the e
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where ‘‘þ’’ and ‘‘ ’
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is, however, small for the usual co
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solute-solvent coupling through the
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where Z is the electrode overpotent
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energy surfaces of ET. 33,50-56 It
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This result indicates a fundamental
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βF i (X ) 40 20 0 −20 1 2 βλ 1
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Table 1 Main Features of the Two-Pa
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and Hss ¼ U rep ss 1 2 X j;k ðmj
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λ i /eV 4 3 2 1 0 0 10 20 30 40 Bo
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the width/Stokes shift relation (Eq
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Table 3 Mapping of the Q Model on S
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This situation is of course not sat
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F ± (Y ad )/λ I 0.8 0.4 0 −0.4
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it by choosing the GMH basis set 7
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Anharmonic higher order terms gain
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of the radiation is the perturbatio
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individual vibrational excitations
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m 12 /D 6 5.5 5 4.5 4 3.5 17 18 19
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In Eq. [144], the coordinates Y km
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ε/M −1 cm −1 4000 2000 0 analy
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βσ 2 /10 3 cm −1 14 12 10 8 Opt
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0.2 0.1 0 12 16 20 24 28 32 The app
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References 207 7. M. D. Newton, Adv
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References 209 59. R. Kubo and Y. T
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