Reviews in Computational Chemistry Volume 18

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144 Polarizability in Computer Simulations 195. G. C. Lie, G. Corongiu, and E. Clementi, J. Phys. Chem., 89, 4131–4134 (1985). Calculation of the Third Virial Coefficient for Water Using Ab Initio Two-Body and Three-Body Potentials. 196. S. L. Carnie and G. N. Patey, Mol. Phys., 47, 1129–1151 (1982). Fluids of Polarizable Hard Spheres with Dipoles and Tetrahedral Quadrupoles. Integral Equation Results with Application to Liquid Water. 197. E. R. Batista, S. S. Xantheas, and H. Jónsson, J. Chem. Phys., 109, 6011–6015 (1999). Multipole Moments of Water Molecules in Clusters and Ice Ih from First Principles Calculations. 198. E. R. Batista, S. S. Xantheas, and H. Jónsson, J. Chem. Phys., 112, 3285–3292 (2000). Electric Fields in Ice and Near Water Clusters. 199. K. Laasonen, M. Sprik, M. Parrinello, and R. Car, J. Chem. Phys., 99, 9080–9089 (1993). ‘‘Ab Initio’’ Liquid Water. 200. L. Delle Site, A. Alavi, and R. M. Lynden-Bell, Mol. Phys., 96, 1683–1693 (1999). The Electrostatic Properties of Water Molecules in Condensed Phases: An Ab Initio Study. 201. P. L. Silvestrelli and M. Parrinello, J. Chem. Phys., 111, 3572–3580 (1999). Structural, Electronic, and Bonding Properties of Liquid Water from First Principles. 202. M. Sprik, J. Phys. Chem., 95, 2283–2291 (1991). Computer Simulations of the Dynamics of Induced Polarization Fluctuations. 203. J. R. Reimers, R. O.Watts, and M. L. Klein, Chem. Phys., 64, 95–114 (1982). Intermolecular Potential Functions and the Properties of Water. 204. N. Yoshii, S. Miura, and S. Okazaki, Chem. Phys. Lett., 345, 195–200 (2001). A Molecular Dynamics Study of Water from Ambient to Sub- and Supercritical Conditions Using a Fluctuating-Charge Potential Model. 205. B. Guillot and Y. Guissani, J. Chem. Phys., 114(15), 6720–6733 (2001). How To Build a Better Pair Potential for Water. 206. I. M. Svishchev and T. M. Hayward, J. Chem. Phys., 111, 9034–9038 (1999). Phase Coexistence Properties for the Polarizable Point Charge Model of Water and the Effects of Applied Electric Field. 207. S. W. Rick, J. Chem. Phys., 114, 2276–2283 (2001). Simulations of Ice and Liquid Water over a Range of Temperatures Using the Fluctuating Charge Model. 208. F. H. Stillinger and A. Rahman, J. Chem. Phys., 60, 1545–1557 (1974). Improved Simulation of Liquid Water by Molecular Dynamics. 209. P. H. Poole, F. Sciortino, U. Essman, and H. E. Stanley, Nature (London), 360, 324–328 (1992). Phase Behaviour of Liquid Water. 210. S. R. Billeter, P. M. King, and W. F. van Gunsteren, J. Chem. Phys., 100, 6692–6699 (1994). Can the Density Maximum of Water Be Found by Computer Simulation? 211. L. A. Báez and P. Clancy, J. Chem. Phys., 101, 9837–9840 (1994). Existence of a Density Maximum in Extended Simple Point Charge Water. 212. A. Wallqvist and P.-O. A˚ strand, J. Chem. Phys., 102, 6559–6565 (1995). Liquid Densities and Structural Properites of Molecular Models of Water. 213. S. Harrington, P. H. Poole, F. Sciortino, and H. E. Stanley, J. Chem. Phys., 107, 7443–7450 (1997). Equation of State of Supercooled Water Simulated Using the Extended Simple Point Charge Intermolecular Potential. 214. K. Bagchi, S. Balasubramanian, and M. L. Klein, J. Chem. Phys., 107, 8561–8567 (1997). The Effects of Pressure on Structural and Dynamical Properties of Associated Liquids: Molecular Dynamics Calculations for the Extended Simple Point Charge Model of Water. 215. W. L. Jorgensen and C. Jensen, J. Comput. Chem., 19, 1179–1186 (1998). Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum Density.
References 145 216. M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys., 112, 8910–8922 (2000). A Five-Site Model for Liquid Water and the Reproduction of the Density Anomaly by Rigid, Nonpolarizable Potential Functions. 217. M. Sprik, M. L. Klein, and K. Watanabe, J. Phys. Chem., 94, 6483–6488 (1990). Solvent Polarization and Hydration of the Chlorine Anion. 218. L. Perera and M. L. Berkowitz, J. Chem. Phys., 100, 3085–3093 (1994). Structures of Cl ðH2OÞn and F ðH2OÞn ðn ¼ 2; 3; ...; 15Þ Clusters. Molecular Dynamics Computer Simulations. 219. P. Jungwirth and D. J. Tobias, J. Phys. Chem. B, 104, 7702–7706 (2000). Surface Effects on Aqueous Ionic Solvation: A Molecular Dynamics Study of NaCl at the Air/Water Interface from Infinite Dilution to Saturation. 220. I.-C. Yeh and M. L. Berkowitz, J. Chem. Phys., 112, 10491–10495 (2000). Effects of the Polarizability and Water Density Constraint on the Structure of Water Near Charged Surfaces: Molecular Dynamics Simulations. 221. G. Gilli, F. Belluci, V. Ferretti, and V. Berolasi, J. Am. Chem. Soc., 111, 1023–1128 (1989). Evidence for Resonance-Assisted Hydrogen Bonding from Crystal Structure Correlations on the Enol Form of the b-Diketone Fragment. 222. G. A. Jeffrey and W. Saenger, Hydrogen Bonding in Biological Structures, Springer-Verlag, Heidelberg, 1991. 223. H. Guo and M. Karplus, J. Phys. Chem., 98, 7104–7105 (1994). Solvent Influence on the Stability of the Peptide Hydrogen Bond: A Supramolecular Cooperative Effect. 224. R. Ludwig, F. Weinhold, and T. C. Farrar, J. Chem. Phys., 107, 499–507 (1997). Theoretical Study of Hydrogen Bonding in Liquid and Gaseous N-Methylformamide. 225. H. Guo, N. Gresh, B. P. Rogues, and D. R. Salahub, J. Phys. Chem. B, 104, 9746–9754 (2000). Many-Body Effects in Systems of Peptide Hydrogen- Bonded Networks and Their Contributions to Ligand Binding: A Comparison of DFT and Polarizable Molecular Mechanics. 226. I. M. Klotz and J. S. Franzen, J. Am. Chem. Soc., 84, 3461–3466 (1962). Hydrogen Bonds Between Model Peptide Groups in Solution. 227. A. Wada, Adv. Biophys., 9, 1–63 (1976). The a-Helix as an Electric MacroDipole. 228. A. van der Vaart, B. D. Bursulaya, C. L. Brooks III, and K. M. Merz Jr., J. Phys. Chem. B, 104, 9554–9563 (2000). Are Many-Body Effects Important in Protein Folding? 229. H. Guo and D. R. Salahub, Angew. Chem. Int. Ed., 37, 2985–2990 (1998). Cooperative Hydrogen Bonding and Enzyme Catalysis. 230. J. S˘poner, H. A. Gabb, J. Leszczynski, and P. Hobza, Biophys. J., 73, 76–87 (1997). Base-Base and Deoxyribose-Base Stacking Interactions in B-DNA and Z-DNA: A Quantum-Chemical Study. 231. N. Gresh and J. S˘poner, J. Phys. Chem. B, 103, 11415–11427 (1999). Complexes of Pentahydrated Zn 2 þ with Guanine, Adenine, and the Guanine–Cytosine and Adenine–Thymine Base Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and Ab Initio Calculations. 232. P. Cieplak, J. Caldwell, and P. Kollman, J. Comput. Chem., 22, 1048–1057 (2001). Molecular Mechanical Models for Organic and Biological Systems Going Beyond the Atom Centered Two Body Additive Approximation: Aqueous Solution Free Energies of Methanol and N-Methyl Acetamide, Nucleic Acid Base, and Amide Hydrogen Hydrogen Bonding and Chloroform/Water Partition Coefficients of the Nucleic Acid Bases. 233. E. D. Stevens, Acta Crystallogr., Sect. B, 34, 544–551 (1978). Low Temperature Experimental Electron Density Distribution in Formamide. 234. G. A. Jeffrey, An Introduction to Hydrogen Bonding, Oxford University Press, New York and Oxford, 1997. 235. M. W. MacArthur and J. M. Thornton, J. Mol. Biol., 264, 1180–1195 (1996). Deviations from Planarity of the Peptide Bond in Peptides and Proteins.
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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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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
Page 121 and 122: are modified by their environment w
Page 123 and 124: Table 1 Polarizability Parameters f
Page 125 and 126: The polarizable point dipole models
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Page 129 and 130: M i z i + q i d i k i and shell cha
Page 131 and 132: Shell Models 103 on estimates of sh
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Page 135 and 136: The energy required to create a cha
Page 137 and 138: for all i ði:e:; 8 iÞ: @U @qi l
Page 139 and 140: where we have used q Cl ¼ qNa. The
Page 141 and 142: Electronegativity Equalization Mode
Page 143 and 144: Electronegativity Equalization Mode
Page 145 and 146: of N molecules is taken as a Hartre
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Page 149 and 150: water have been developed, includin
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Page 159 and 160: ecome significant at field strength
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Page 163 and 164: References 135 9. P. Cieplak and P.
Page 165 and 166: References 137 48. E. L. Pollock an
Page 167 and 168: References 139 Computational Chemis
Page 169 and 170: References 141 139. J. Hinze and H.
Page 171: References 143 178. J. J. P. Stewar
Page 175 and 176: CHAPTER 4 New Developments in the T
Page 177 and 178: Introduction 149 applications). For
Page 179 and 180: FCWD(∆E ) FCWD(0) ∆E = 0 ∆E
Page 181 and 182: Introduction 153 Equations [6]-[12]
Page 183 and 184: Paradigm of Free Energy Surfaces 15
Page 185 and 186: Paradigm of Free Energy Surfaces 15
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Page 215 and 216: F ± (Y ad )/λ I 0.8 0.4 0 −0.4
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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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