Reviews in Computational Chemistry Volume 18

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142 Polarizability in Computer Simulations 158. S.-B. Zhu, S. Singh, and G. W. Robinson, J. Chem. Phys., 95, 2791–2799 (1991). A New Flexible/Polarizable Water Model. 159. M. Wilson and P. A. Madden, J. Phys.: Condens. Matter, 5, 2687–2706 (1993). Polarization Effects in Ionic Systems from First Principles. 160. T. Campbell, R. K. Kalia, A. Nakano, P. Vashista, S. Ogata, and S. Rodgers, Phys. Rev. Lett., 82, 4866–4869 (1999). Dynamics of Oxidation of Aluminum Nanoclusters Using Variable Charge Molecular-Dynamics Simulation on Parallel Computers. 161. D. J. Keffer and J. W. Mintmire, Int. J. Quantum Chem., 80, 733–742 (2000). Efficient Parallel Algorithms for Molecular Dynamics Simulations Using Variable Charge Transfer Electrostatic Potentials. 162. M. Medeiros and M. E. Costas, J. Chem. Phys., 107, 2012–2019 (1997). Gibbs Ensemble Monte Carlo Simulation of the Properties of Water with a Fluctuating Charges Model. 163. A. Nakano, Comput. Phys. Commun., 104, 59–69 (1997). Parallel Multilevel Preconditioned Conjugate-Gradient Approach to Variable-Charge Molecular Dynamics. 164. S. W. Rick, in Simulation and Theory of Electrostatic Interactions in Solution, L. R. Pratt and G. Hummer, Eds., American Institute of Physics, Melville, NY, 1999, pp. 114–126. The Influence of Electrostatic Truncation on Simulations of Polarizable Systems. 165. B. Chen, J. J. Potoff, and J. I. Siepmann, J. Phys. Chem. B, 104, 2378–2390 (2000). Adiabatic Nuclear and Electronic Sampling Monte Carlo Simulations in the Gibbs Ensemble: Application to Polarizable Force Fields for Water. 166. H. A. Stern, F. Rittner, B. J. Berne, and R. A. Friesner, J. Chem. Phys., 115, 2237–2251 (2001). Combined Fluctuating-Charge and Polarizable Dipole Models: Application to a Five-Site Water Potential Function. 167. U. Dinur, J. Phys. Chem., 97, 7894–7898 (1993). Molecular Polarizabilities from Electronegativity Equalization Models. 168. S. W. Rick and B. J. Berne, J. Phys. Chem. B, 101, 10488 (1997). The Free Energy of the Hydrophobic Interaction from Molecular Dynamics Simulations: the Effects of Solute and Solvent Polarizability. 169. R. G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules, Oxford University Press, Oxford, UK, 1989. 170. L. J. Bartolotti and K. Flurchick, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, Vol. 7, pp. 187–216 (1996). An Introduction to Density Functional Theory. A. St-Amant, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, Vol. 7, pp. 217–259. Density Functional Methods in Biomolecular Modeling. 171. P. Itskowitz and M. L. Berkowitz, J. Phys. Chem. A, 101, 5687–5691 (1997). Chemical Potential Equalization Principle: Direct Approach from Density Functional Theory. 172. D. Borgis and A. Staib, Chem. Phys. Lett., 238, 187–192 (1995). A Semiempirical Quantum Polarization Model for Water. 173. J. Gao, J. Phys. Chem. B, 101, 657–663 (1997). Toward a Molecular Orbital Derived Empirical Potential for Liquid Simulations. 174. J. Gao, J. Chem. Phys., 109, 2346–2354 (1998). A Molecular-Orbital Derived Polarization Potential for Liquid Water. 175. B. D. Bursulaya and H. J. Kim, J. Chem. Phys., 108, 3277–3285 (1998). Generalized Molecular Mechanics Including Quantum Electronic Structure Variation of Polar Solvents. I. Theoretical Formulation via a Truncated Adiabatic Basis Set Description. 176. B. D. Bursulaya, J. Jeon, D. A. Zichi, and H. J. Kim, J. Chem. Phys., 108, 3286–3295 (1998). Generalized Molecular Mechanics Including Quantum Electronic Structure Variation of Polar Solvents. II. A Molecular Dynamics Simulation Study of Water. 177. A. E. Lefohn, M. Ovchinnikov, and G. A. Voth, J. Phys. Chem. B, 105, 6628–6637 (2001). A Multistate Empirical Valence Bond Approach to a Polarizable and Flexible Water Model.
References 143 178. J. J. P. Stewart, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 45–81. Semiempirical Molecular Orbital Methods. M. C. Zerner, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1991, Vol. 2, pp. 313–365. Semiempirical Molecular Orbital Methods. 179. D. E. Williams, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1991, Vol. 2, pp. 219–271. Net Atomic Charge and Multipole Models for the Ab Initio Molecular Orbital Potential. 180. R. S. Mulliken, J. Chem. Phys., 23, 1833, 1841 (1955). Electronic Population Analysis on LCAO-MO Molecular Wave Functions. I. and II. Overlap Populations, Bond Orders, and Covalent Bond Energies. See also: S. M. Bachrach, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1994, Vol. 5, pp. 171– 227. Population Analysis and Electron Densities from Quantum Mechanics. 181. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc., 107, 3902–3909 (1985). AM1: A New General Purpose Quantum Mechanical Molecular Model. 182. W. J. Hehre, R. F. Stewart, and J. A. Pople, J. Chem. Phys, 51, 2657–2664 (1969). Self- Consistent Molecular-Orbital Methods. I. Use of Gaussian Expansions of Slater-Type Atomic Orbitals. See also: D. Feller and E. R. Davidson, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 1–43. Basis Sets for Ab Initio Molecular Orbital Calculations and Intermolecular Interactions. 183. S. W. Rick and R. E. Cachau, J. Chem. Phys., 112, 5230–5241 (2000). The Non-Planarity of the Peptide Group: Molecular Dynamics Simulations with a Polarizable Two-State Model for the Peptide Bond. 184. G. Corongiu, Int. J. Quantum Chem., 42, 1209–1235 (1992). Molecular Dynamics Simulation for Liquid Water Using a Polarizable and Flexible Potential. 185. M. Sprik, J. Chem. Phys., 95, 6762–6769 (1991). Hydrogen Bonding and the Static Dielctric Constant in Liquid Water. 186. P. G. Kusalik, F. Liden, and I. M. Svishchev, J. Chem. Phys., 103, 10169–10175 (1995). Calculation of the Third Virial Coefficient for Water. 187. S.-B. Zhu, S. Singh, and G. W. Robinson, Adv. Chem. Phys., 85, 627–731 (1994). Field- Perturbed Water. 188. A. Wallqvist and R. D. Mountain, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1999, Vol. 13, pp. 183–247. Molecular Descriptions of Water: Derivation and Description. 189. J. C. Shelley and D. R. Bérard, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1998, Vol. 12, pp. 137–205. Computer Simulation of Water Physisorption at Metal–Water Interfaces. 190. A. A. Chialvo and P. T. Cummings, J. Phys. Chem., 100, 1309–1316 (1996). Microstructure of Ambient and Supercritical Water: Direct Comparison Between Simulation and Neutron Scattering Experiments. 191. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans, in Intermolecular Forces, B. Pullman, Ed., Reidel, Dordrecht, The Netherlands, 1981, pp. 331–342. Interaction Models for Water in Relation to Protein Hydration. 192. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys., 79, 926–935 (1983). Comparison of Simple Potential Functions for Simulating Liquid Water. 193. C. Millot and A. J. Stone, Mol. Phys., 77, 439–462 (1992). Towards an Accurate Intermolecular Potential for Water. 194. U. Niesar, G. Corongiu, M.-J. Huang, M. Dupuis, and E. Clementi, Int. J. Quantum. Chem. Symp., 23, 421–443 (1989). Preliminary Observations on a New Water–Water Potential.
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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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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
Page 127 and 128: two to three orders of magnitude sl
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
Page 133 and 134: minimization can be replaced by mor
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
Page 147 and 148: is treated using variable charges.
Page 149 and 150: water have been developed, includin
Page 151 and 152: Applications 123 classical and rigi
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Page 155 and 156: Comparison of the Polarization Mode
Page 157 and 158: negligible errors in such propertie
Page 159 and 160: ecome significant at field strength
Page 161 and 162: noteworthy in this regard because t
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: References 141 139. J. Hinze and H.
Page 173 and 174: References 145 216. M. W. Mahoney a
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
Page 187 and 188: In Eqs. [18] and [19], F0i is the e
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Page 201 and 202: βF i (X ) 40 20 0 −20 1 2 βλ 1
Page 203 and 204: Table 1 Main Features of the Two-Pa
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Page 207 and 208: λ i /eV 4 3 2 1 0 0 10 20 30 40 Bo
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Page 211 and 212: Table 3 Mapping of the Q Model on S
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Page 215 and 216: F ± (Y ad )/λ I 0.8 0.4 0 −0.4
Page 217 and 218: it by choosing the GMH basis set 7
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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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