Reviews in Computational Chemistry Volume 18

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xxvi Contributors to Previous Volumes Donald W. Brenner, Olga A. Shenderova, and Denis A. Areshkin, Quantum- Based Analytic Interatomic Forces and Materials Simulation. Henry A. Kurtz and Douglas S. Dudis, Quantum Mechanical Methods for Predicting Nonlinear Optical Properties. Chung F. Wong,* Tom Thacher, and Herschel Rabitz, Sensitivity Analysis in Biomolecular Simulation. Paul Verwer and Frank J. J. Leusen, Computer Simulation to Predict Possible Crystal Polymorphs. Jean-Louis Rivail and Bernard Maigret, Computational Chemistry in France: A Historical Survey. Volume 13 (1999) Thomas Bally and Weston Thatcher Borden, Calculations on Open-Shell Molecules: A Beginner’s Guide. Neil R. Kestner and Jaime E. Combariza, Basis Set Superposition Errors: Theory and Practice. James B. Anderson, Quantum Monte Carlo: Atoms, Molecules, Clusters, Liquids, and Solids. Anders Wallqvist y and Raymond D. Mountain, Molecular Models of Water: Derivation and Description. James M. Briggs and Jan Antosiewicz, Simulation of pH-dependent Properties of Proteins Using Mesoscopic Models. Harold E. Helson, Structure Diagram Generation. Volume 14 (2000) Michelle Miller Francl and Lisa Emily Chirlian, The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials. *Current addrress: Howard Hughes Medical Institute, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0365 (Electronic mail: c4wong@ucsd.edu). y Current address: National Cancer Institute, P.O. Box B, Frederick, Maryland 21702 (Electronic mail: wallqvist@ncifcrt.gov).
T. Daniel Crawford* and Henry F. Schaefer III, An Introduction to Coupled Cluster Theory for Computational Chemists. Bastiaan van de Graaf, Swie Lan Njo, and Konstantin S. Smirnov, Introduction to Zeolite Modeling. Sarah L. Price, Toward More Accurate Model Intermolecular Potentials for Organic Molecules. Christopher J. Mundy, y Sundaram Balasubramanian, Ken Bagchi, Mark E. Tuckerman, Glenn J. Martyna, and Michael L. Klein, Nonequilibrium Molecular Dynamics. Donald B. Boyd and Kenny B. Lipkowitz, History of the Gordon Research Conferences on Computational Chemistry. Mehran Jalaie and Kenny B. Lipkowitz, Appendix: Published Force Field Parameters for Molecular Mechanics, Molecular Dynamics, and Monte Carlo Simulations. Volume 15 (2000) F. Matthias Bickelhaupt and Evert Jan Baerends, Kohn–Sham Density Functional Theory: Predicting and Understanding Chemistry. Michael A. Robb, Marco Garavelli, Massimo Olivucci, and Fernando Bernardi, A Computational Strategy for Organic Photochemistry. Larry A. Curtiss, Paul C. Redfern, and David J. Frurip, Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds. Russell J. Boyd, The Development of Computational Chemistry in Canada. Volume 16 (2000) Contributors to Previous Volumes xxvii Richard A. Lewis, Stephen D. Pickett, and David E. Clark, Computer-Aided Molecular Diversity Analysis and Combinatorial Library Design. *Current address: Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0212 (Electronic mail: crawdad@vt.edu). y Current address: Computational Materials Science, L-371, Lawrence Livermore National Laboratory, Livermore, California 94550 (Electronic mail: mundy2@llnl.gov).
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: Volume 11 (1997) Mark A. Murcko, Re
Page 27 and 28: Topics Covered in Volumes 1-18 * Ab
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
Page 73 and 74: 44 The Use of Scoring Functions in
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46 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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