Reviews in Computational Chemistry Volume 18

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References 87 212. LeadQuest Chemical Compound Libraries, Vol. 1–3, 2000, Tripos Inc., St. Louis, MO, USA. http://www.tripos.com. 213. J. Sadowski, C. Rudolph, and J. Gasteiger, Tetrahedron Comput. Methodol., 3, 537 (1990). Automatic Generation of 3D Atomic Coordinates for Organic Molecules. 214. J. Sadowski, C. H. Schwab, and J. Gasteiger, Corina, 1998, Molecular Networks GmbH Computerchemie, Erlangen, Germany. http://www.mol-net.de/. 215. Unity Chemical Information Software, Version 4.1.1., Tripos, Inc., St. Louis, MO, USA. 216. A. Maxwell, Biochem. Soc. Trans., 27, 48 (1999). DNA Gyrase as a Drug Target. 217. D. Bailey and D. Brown, Drug Discovery Today, 6, 57 (2001). High-Throughput Chemistry and Structure-Based Design: Survival of the Smartest. 218. R. M. Eglen, G. Scheider, and H.-J. Boehm, in Virtual Screening for Bioactive Molecules, G. Schneider and H.-J. Boehm, Eds., Wiley-VCH, Weinheim, 2000, pp. 1–14. High- Throughput Screening and Virtual Screening: Entry Points to Drug Discovery. 219. R. Lahana, Drug Discovery Today, 4, 447 (1999). How Many Leads from HTS?
CHAPTER 3 Potentials and Algorithms for Incorporating Polarizability in Computer Simulations Steven W. Rick* and Steven J. Stuart y *Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148 and Chemistry Department, Southern University of New Orleans, New Orleans, Louisiana 70126, and y Department of Chemistry, Clemson University, Clemson, South Carolina 29634 INTRODUCTION Reviews in Computational Chemistry, Volume 18 E dited by K enny B. L ipkowitz and D onald B. Boyd Copyr ight © 2002 John Wiley & Sons, I nc. ISBN: 0-471-21576-7 Polarization refers to the redistribution of a particle’s electron density due to an electric field. In terms of molecular interactions, polarization leads to nonadditivity, since a molecule polarized by another molecule will interact differently with a third molecule than it would if it were not polarized. The change in the electron density can be characterized by changes in the monopole charges, dipole moments, or higher order moments. Methods for treating polarizability in molecular dynamics or Monte Carlo simulations achieve this goal through inducible dipole moments (the polarizable point dipole and shell models) or through fluctuating charges (the electronegativity equalization and semiempirical models). This chapter describes these models, with a focus on those methods that have been developed for molecular dynamics and Monte 89
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Reviews in Computational Chemistry
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Kenny B. Lipkowitz Department of Ch
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vi Preface three-dimensional struct
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viii Preface some descriptors and i
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Epilogue and Dedication My associat
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Contents 1. Clustering Methods and
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Contents xv Electron Transfer in Po
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Contributors John M. Barnard, Barna
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Contributors to Previous Volumes *
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Volume 3 (1992) Tamar Schlick, Opti
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Volume 7 (1996) Geoffrey M. Downs a
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Volume 11 (1997) Mark A. Murcko, Re
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T. Daniel Crawford* and Henry F. Sc
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Topics Covered in Volumes 1-18 * Ab
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Reviews in Computational Chemistry
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2 Clustering Methods and Their Uses
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10 Clustering Methods and Their Use
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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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