Reviews in Computational Chemistry Volume 18

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xiv Contents Application of Scoring Functions in Virtual Screening 63 Seeding Experiments 64 Hydrogen Bonding versus Hydrophobic Interactions 65 Finding Weak Inhibitors 69 Consensus Scoring 70 Successful Identification of Novel Leads through Virtual Screening 72 Outlook 75 Acknowledgments 76 References 76 3. Potentials and Algorithms for Incorporating Polarizability in Computer Simulations 89 Steven W. Rick and Steven J. Stuart Introduction 89 Nonpolarizable Models 90 Polarizable Point Dipoles 91 Shell Models 99 Electronegativity Equalization Models 106 Semiempirical Models 116 Applications 120 Water 120 Proteins and Nucleic Acids 125 Comparison of the Polarization Models 127 Mechanical Polarization 127 Computational Efficiency 129 Hyperpolarizability 130 Charge-Transfer Effects 131 The Electrostatic Potential 132 Summary and Conclusions 133 References 134 4. New Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases 147 Dmitry V. Matyushov and Gregory A. Voth Introduction 147 Paradigm of Free Energy Surfaces 155 Formulation 156 Two-State Model 160 Heterogeneous Discharge 165 Beyond the Parabolas 167 Bilinear Coupling Model 169
Contents xv Electron Transfer in Polarizable Donor–Acceptor Complexes 175 Nonlinear Solvation Effects 182 Electron-Delocalization Effects 184 Nonlinear Solvation versus Intramolecular Effects 190 Optical Band Shape 191 Optical Franck–Condon Factors 192 Absorption Intensity and Radiative Rates 195 Electron-Transfer Matrix Element 197 Electronically Delocalized Chromophores 198 Polarizable Chromophores 201 Hybrid Model 202 Summary 205 Acknowledgments 206 References 206 5. Linear Free Energy Relationships Using Quantum Mechanical Descriptors 211 George R. Famini and Leland Y. Wilson Introduction 211 LFER Methodology 212 Background 214 Computational Methods 214 Linear Free Energy Relationships 215 Descriptors 218 Classifications 218 Quantum Mechanical Descriptors 219 Quantum Mechanical Calculations 220 Statistical Procedures 227 Multiple Regression Analysis 227 Examples of LFER Equations 231 Model-Based Methods 232 Nonmodel-Based Methods 246 Conclusions 250 References 251 6. The Development of Computational Chemistry in Germany 257 Sigrid D. Peyerimhoff Introduction 257 Computer Development 260 The ZUSE Computers 260 The G1, G2, and G3 of Billing in Göttingen 261
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: Contents 1. Clustering Methods and
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 and 26: T. Daniel Crawford* and Henry F. Sc
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
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34 Clustering Methods and Their Use
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42 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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Reviews in Computational Chemistry Volume 18

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