Potentials and algorithms for incorporating polarizability in computer simulations

Reviews in Computational Chemistry

Volumn 18, Issue , 2002, Pages 89-146

  Rick, Steven J ^a   Stuart, Steven W ^b  

^a UNIVERSITY OF NEW ORLEANS   (United States)

^b CLEMSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77949975511     PISSN: 10693599     EISSN: None     Source Type: Book Series    
DOI: 10.1002/0471433519.ch3     Document Type: Article

References (265)

1. J. A. McCammon and S. C. Harvey, Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, UK, 1987.
2. M. Rigby, E. B. Smith, W. A. Wakeham, and G. C. Maitland, The Forces Between Molecules, Oxford Science Publications, Oxford, UK, 1986.
3. T. A. HalgrenJ. Am. Chem. Soc, 114, 7827-7843 (1992). Representation of van der Waals (vdW) Interactions in Molecular Mechanics Force Fields: Potential Form, Combination Rules, and vdW Parameters.
4. H. J. C. Berendsen,J. R. Grigera, andT. P. Straatsma, J. Phys. Chem., 91,6269-6271 (1987). The Missing Term in Effective Pair Potentials.
5. K. Watanabe and M. L. Klein, Chem. Phys., 131, 157-167 (1989). Effective Pair Potentials and the Properties of Water.
6. L. Kuyper, D. Ashton, K. M. Merz Jr., and P. A. Kollmanj. Phys. Chem., 95, 6661-6666 (1991). Free Energy Calculations on the Relative Solvation Free Energies of Benzene, Anisole, and 1,2,3-Trimethoxybenzene: Theoretical and Experimental Analysis of Aromatic Methoxy Solvation.
7. W. L. Jorgensen and J. Gao, J. Am. Chem. Soc, 110, 4212-4216 (1988). Cis-Trans Energy-Difference for the Peptide Bond in the Gas Phase and in Aqueous Solution.
8. D. E. Williams, Biopolymers, 29,1367-1386 (1990). Alanyl Dipeptide Potential-Derived Net Atomic Charges and Bond Dipoles, and Their Variation with Molecular Conformation.
9. P. Cieplak and P. Kollman, J. Comput. Chem., 12, 1232-1236 (1991). On the Use of Electrostatic Potential Derived Charges in Molecular Mechanics Force Field. The Relative Solvation Free Energy of Cis- and Trans-N-Methyl-Acetamide.
10. S. W. Rick and B. J. Berne, J. Am. Chem. Soc, 118, 672-679 (1996). Dynamical Fluctuating Charge Force Fields: The Aqueous Solvation of Amides.
11. J. J. Urban and G. R. Famini, J. Comput. Chem., 14, 353-362 (1993). Conformational Dependence of the Electrostatic Potential-Derived Charges of Dopamine: Ramifications in Molecular Mechanics Force Field Calculation in the Gas Phase and Aqueous Solution.
12. U. Dinur and A. T. Hagler, J. Comput. Chem., 16, 154-170 (1995). Geometry-Dependent Atomic Charges-Methodology and Application to Alkanes, Aldehydes, Ketones, and Amides.
13. U. Koch, P. L. A. Popelier, and A. J. Stone, Chem. Phys. Lett., 238, 253-260 (1995). Conformational Dependence of Atomic Multipole Moments.
14. C. J. F. Böttcher, Theory of Electric Polarization, 2nd ed., Elsevier, New York, 1973.
15. T. P. Lybrand and P. A. Kollman, J. Chem. Phys., 83, 2923-2933 (1985). Water-Water and Water-Ion Potential Functions Including Terms for Many Body Effects.
16. P. Cieplak, T. P. Lybrand, and P. A. Kollman, J. Chem. Phys., 86, 6393-6403 (1987). Calculations of Free Energy Changes in Ion-Water Clusters Using Nonadditive Potentials and the Monte Carlo Method.
17. B. J. Berne and A. Wallqvist,;. Chem. Phys., 88, 8016-8017 (1988).
18. Comment on: "Water-Water and Water-Ion Potential Functions Including Terms for Many-Body Effects," T. P. Lybrand and P. Kollman, J. Chem. Phys. 83, 2923 (1985),
19. on "Calculation of Free Energy Changes in Ion-Water Clusters Using Nonadditive Potentials and the Monte Carlo Method," P. Cieplak, T. P. Lybrand, and P. Kollman, J. Chem. Phys. 86, 6393 (1987).
20. P. Kollman, T. Lybrand, and P. Cieplak, J. Chem. Phys., 88, 8017 (1988).
21. Reply to "Comment on "Water-Water and Water-Ion Potential Functions Including Terms for Many-Body Effects," T. P. Lybrand and P. Kollman, J. Chem. Phys. 83, 2923 (1985),
22. "Calculation of Free Energy Changes in Ion-Water Clusters Using Nonadditive Potentials and the Monte Carlo Method," P. Cieplak, T. P. Lybrand, and P. Kollman, J. Chem. Phys. 86,6393 (1987)".
23. J. A. C. Rullman and P. T. van Duijnen, Mol. Phys., 63, 451-475 (1988). A Polarizable Water Model for Calculation of Hydration Energies.
24. F. H. Stillinger and C. W. David, J. Chem. Phys., 69,1473-1484 (1978). Polarization Model for Water and Its Ionic Dissociation Products.
25. P. Barnes, J. L. Finney, J. D. Nicholas, and J. E. Quinn, Nature (London), 282, 459-464 (1979). Cooperative Effects in Simulated Water.
26. M. Sprik and M. L. Klein, J. Chem. Phys., 89, 7556-7560 (1988). A Polarizable Model for Water Using Distributed Charge Sites.
27. P. Ahlström, A. Wallqvist, S. Engström, and B. Jönsson, Mol. Phys., 68, 563-581 (1989). A Molecular Dynamics Study of Polarizable Water.
28. P. Cieplak, P. A. Kollman, and T. P. Lybrand, J. Chem. Phys., 92, 6755-6760 (1990). A New Water Potential Including Polarization: Application to Gas-Phase, Liquid, and Crystal Properties of Water.
29. U. Niesar, G. Corongiu, E. Clementi, G. R. Kneller, and D. K. Bhattacharya, J. Phys. Chem., 94, 7949-7956 (1990). Molecular Dynamics Simulations of Liquid Water Using the NCC Ab Initio Potential.
30. S. Kuwajima and A. Warshel, J. Phys. Chem., 94, 460-466 (1990). Incorporating Electric Polarizabilities in Water-Water Interaction Potentials.
31. J. Caldwell, L. X. Dang, and P. A. Kollman, J. Am. Chem. Soc, 112, 9144-9147 (1990). Implementation of Nonadditive Intermolecular Potentials by Use of Molecular Dynamics: Development of a Water-Water Potential and Water-Ion Cluster Interactions.
32. L. X. Dang, J. Chem. Phys., 97, 2659-2660 (1992). The Nonadditive Intermolecular Potential for Water Revised.
33. R. E. Kozack and P. C. Jordan, J. Chem. Phys., 96, 3120-3130 (1992). Polarizability Effects on a Four-Charge Model for Water.
34. A. Wallqvist and B. J. Berne, J. Phys. Chem., 97, 13841-13851 (1993). Effective Potentials for Liquid Water Using Polarizable and Nonpolarizable Models.
35. D. N. Bernardo, Y. Ding, K. Krogh-Jespersen,and R.M. Levy, J. Phys. Chem., 98, 4180-4187 (1994). An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular Mechanics Force Fields.
36. J. W. Caldwell and P. A. Kollman, J. Phys. Chem., 99, 6208-6219 (1995). Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and N-Methylacetamide.
37. J. Brodholt, M. Sampoli, and R. Vallauri, Mol. Phys., 85, 81-90 (1995). Parameterizing Polarizable Intermolecular Potentials for Water with the Ice 1h Phase.
38. T. Chang, K. A. Peterson, and L. X. Dang, J. Chem. Phys., 103, 7502-7513 (1995). Molecular Dynamics Simulations of Liquid, Interface, and Ionic Solvation of Polarizable Carbon Tetrachloride.
39. A. A. Chialvo and P. T. Cummings,;. Chem. Phys., 105, 8274-8281 (1996). Engineering a Simple Polarizable Model for the Molecular Simulation of Water Applicable over Wide Ranges of State Conditions.
40. L. X. Dang and T. Chang, J. Chem. Phys., 106, 8149-8159 (1997). Molecular Dynamics Study of Water Clusters, Liquid, and Liquid-Vapor Interface of Water with Many-Body Potentials.
41. L. Ojamae, I. Shavitt, and S. J. Singer, J. Chem. Phys., 109, 5547-5564 (1998). Potential Models for Simulations of the Solvated Proton in Water.
42. Y. Ding, D. N. Bernardo, K. Krogh-Jespersen, and R. M. Levy, J. Phys. Chem., 99, 11575-11583 (1995). Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials.
43. J. Applequist, J. R. Carl, and K.-K. Fung, J. Am. Chem. Soc, 94, 2952-2960 (1972). An Atom Dipole Interaction Model for Molecular Polarizability. Application to Polyatomic Molecules and Determination of Atom Polarizabilities.
44. J. Applequist, Acc. Chem. Res., 10, 79-85 (1977). An Atom Dipole Interaction Model for Molecular Optical Properties.
45. B. T. Thole, Chem. Phys., 59, 341-350 (1981). Molecular Polarizabilities Calculated with a Modified Dipole Interaction.
46. R. C. Weast, Ed., CRC Handbook of Chemistry and Physics, CRC Press, Boca Raton, FL, Vol.66, 1985.
47. F. H. Stillinger, J. Chem. Phys., 71, 1647-1651 (1979). Dynamics and Ensemble Averages for the Polarization Models of Molecular Interactions.
48. A. Warshel and M. Levitt, J. Mol. Biol., 103, 227-249 (1976). Theoretical Studies of Enzymic Reactions: Dielectric, Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme.
49. S. T. Russell and A. Warshel, J. Mol. Biol., 185, 389-404 (1985). Calculations of Electrostatic Energies in Proteins. The Energetics of Ionized Groups in Bovine Pancreatic Trypsin Inhibitor.
50. D. Van Belle, I. Couplet, M. Prevost, and S. J. Wodak, J. Mol. Biol., 198, 721-735 (1987). Calculations of Electrostatic Properties in Proteins. Analysis of Contributions from Induced Protein Dipoles.
51. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz Jr., D. M. Ferguson, D. C. Spellmeyer.T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc, 117, 5179-5197 (1995). A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules.
52. E. L. Pollock and B. J. Alder, Phys. Rev. Lett., 39, 299-302 (1977). Effective Field of a Dipole in Polarizable Fluids.
53. F. J. Vesely, J. Comput. Phys., 24, 361-371 (1977). N-Particle Dynamics of Polarizable Stockmayer-Type Molecules.
54. A. Toukmaji, C. Sagui.J. Board, and T. DardenJ. Chem. Phys., 113, 10913-10927 (2000). Efficient Particle-Mesh Ewald Based Approach to Fixed and Induced Dipolar Interactions.
55. R. Kutteh and J. B. Nicholas, Comput. Phys. Commun., 86, 227-235 (1995). Efficient Dipole Iteration in Polarizable Charged Systems Using the Cell Multipole Method and Application to Polarizable Water.
56. J. Brodholt, M. Sampoli, and R. Vallauri, Mol. Phys., 86, 149-158 (1995). Parameterizing a Polarizable Intermolecular Potential for Water.
57. I. M. Svishchev, P. G. Kusalik, P. G. Wang, and R. J. Boyd, J. Chem. Phys., 105, 4742-4750 (1996). Polarizable Point-Charge Model for Water: Results Under Normal and Extreme Conditions.
58. A. Wallqvist, P. Ahlström, and G. KarlstromJ. Phys. Chem., 94, 1649-1656 (1990). A New Intermolecular Energy Calculation Scheme: Applications to Potential Surface and Liquid Properties of Water.
59. G. Ruocco and M. Sampoli, Mol. Phys., 82, 875-886 (1994). Computer Simulation of Polarizable Fluids: A Consistent and Fast Way for Dealing with Polarizability and Hyper-polarizability.
60. 4.
61. D. van Belle, M. F. G. Lippens, and S. J. Wodak, Mol. Phys., 77,239-255 (1992). Molecular Dynamics Simulation of Polarizable Water by an Extended Lagrangian Method.
62. J. W. Halley, J. R. Rustad, and A. Rahman, J. Chem. Phys., 98, 4110-4119 (1993). A Polarizable, Dissociating Molecular Dynamics Model for Liquid Water.
63. J. M. Goodfellow, Proc. Natl. Acad. Sci. USA, 79, 4977-4979 (1982). Cooperative Effects in Water-Biomolecule Crystal Systems.
64. B. J. Costo, J. L. Rivail, and B. Bigot,J. Chem. Phys., 86,1467-1473 (1987). A Monte Carlo Simulation Study of a Polarizable Liquid: Influence of the Electrostatic Induction on Its Thermodynamic and Structural Properties.
65. K. Kiyohara, K. E. Gubbins, and A. Z. Panagiotopoulos, Mol. Phys., 94, 803-808 (1998). Phase Coexistence Properties of Polarizable Water Models.
66. P. Jedlovszky and R. Vallauri, Mol. Phys., 97, 1157-1163 (1999). Temperature Dependence of Thermodynamic Properties of a Polarizable Potential Model of Water.
67. M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys., 114, 9337-9349 (2001). Rapid Estimation of Electronic Degrees of Freedom in Monte Carlo Calculations for Polarizable Models of Liquid Water.
68. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Oxford University Press, Oxford, UK, 1987.
69. D. Frenkel and B. Smit, Understanding Molecular Simulation: from Algorithms to Applications, Academic Press, San Diego, 1996.
70. W. Smith, Information Quarterly for Computer Simulation of Condensed Phases, 4, 13-25 (1982). Point Multipoles in the Ewald Summation.
71. T. M. Nymand and P. Linse, J. Chem. Phys., 112, 6386-6395 (2000). Molecular Dynamics Simulations of Polarizable Water at Different Boundary Conditions.
72. D. Fincham, Information Quarterly for Computer Simulation of Condensed Phases, 38, 17-24 (1993). Optimization of the Ewald Sum.
73. R. Kutteh and J. B. Nicholas, Comput. Phys. Commun., 86, 236-254 (1995). Implementing the Cell Multipole Method for Dipolar and Charged Dipolar Systems.
74. M. Born and T. von Kármán, Phys. Z., 13, 297-309 (1912). Vibrations in Space Gratings (Molecular Frequencies).
75. M. Born and K. Huang, Dynamical Theory of Crystal Lattices, Oxford University Press, Oxford, UK, 1954.
76. B. G. Dick and A. W. Overhauser, Phys. Rev., 112, 90 (1958). Theory of the Dielectric Constants of Alkali Halide Crystals.
77. J. E. Hanlon and A. W. Lawson, Phys. Rev., 113, 472-478 (1959). Effective Ionic Charge in Alkali Halides.
78. R. A. Cowley, W. Cochran, B. N. Brockhouse, and A. D. B. Woods, Phys. Rev., 131, 1030-1039 (1963). Lattice Dynamics of Alkali Halide Crystals. III. Theoretical.
79. W. Cochran, CRC Crit. Rev. Solid State Set., 2, 1-14 (1971). Lattice Dynamics of Ionic and Covalent Crystals.
80. A. N. Basu, D. Roy, and S. Sengupta, Phys. Stat. Sol. A, 23, 11-32 (1974). Polarisable Models for Ionic Crystals and the Effective Many-Body Interaction.
81. M. J. L. Sangster and M. Dixon, Adv. Phys., 25, 247-342 (1976). Interionic Potentials in Alkali Halides and Their Use in Simulations of the Molten Salts.
82. J. Shanker and S. Dixit, Phys. Status Solidi A, 123, 17-50 (1991). Dielectric Constants and Their Pressure and Temperature Derivatives for Ionic Crystals.
83. P. Drude, The Theory of Optics, Longmans, Green, and Co., New York, 1901.
84. F. London, Trans. Faraday Soc., 33, 8-26 (1937). The General Theory of Molecular Forces.
85. W. Cochran, in Phonons in Perfect Lattices and in Lattices with Point Imperfections, R. W. H. Stevenson, Ed., Plenum Press, New York, 1966, Vol.6 of Scottish Universities' Summer School, Chapter 2, pp. 53-72. Theory of Phonon Dispersion Curves.
86. S. J. Stuart and B. J. Berne, J. Phys. Chem., 100, 11934-11943 (1996). Effects of Polarizability on the Hydration of the Chloride Ion.
87. C. R. A. Catlow, K. M. Diler, and M. J. Norgett, J. Phys. C, 10, 1395-1412 (1977). Interionic Potentials for Alkali Halides.
88. M. Dixon and M. J. Gillan, Philos. Mag. B, 43, 1099-1112 (1981). Structure of Molten Alkali Chlorides I. A Molecular Dynamics Study.
89. G. V. Lewis and C. R. A. Catlow, J. Phys. G, 18, 1149-1161 (1985). Potential Models for Ionic Oxides.
90. A. M. Stoneham and J. H. Harding, Annu. Rev. Phys. Chem., 37, 53 (1986). Interatomic Potentials in Solid State Chemistry.
91. C. R. A. Catlow and G. D. Price, Nature (London), 347, 243-248 (1990). Computer Modelling of Solid-State Inorganic Materials.
92. J. H. Harding, Rep. Progr. Phys., 53, 1403-1466 (1990). Computer Simulation of Defects in Ionic Solids.
93. S. M. Tomlinson, C. R. A. Catlow, and J. H. Harding, J. Phys. Chem. Solids, 51, 477-506 (1990). Computer Modelling of the Defect Structure of Non-Stoichiometric Binary Transition Metal Oxides.
94. P.J. Mitchell and D. FinchamJ. Phys.: Condens. Matter, 5, 1031-1038 (1993). Shell Model Simulations by Adiabatic Dynamics.
95. P. J. D. Lindan, Mol. Simul., 14, 303-312 (1995). Dynamics with the Shell Model.
96. M. S. Islam, J. Mater. Chem., 10, 1027-1038 (2000). Ionic Transport in ABO(3) Perovskite Oxides: A Computer Modelling Tour.
97. J.-R. Hill, A. R. Minihan, E. Wimmer, and C. J. Adams, Phys. Chem. Chem. Phys., 2, 4255-4264 (2000). Framework Dynamics Including Computer Simulations of the Water Adsorption Isotherm of Zeolite Na-MAP.
98. See also J.-R. Hill, C. M. Freeman, and L. Subramanian, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 2000, Vol.16, pp. 141-216. Use of Force Fields in Materials Modeling.
99. The shell model is also discussed by B. van de Graaf, S. L. Njo, and K. S. Smirnov, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 2000, Vol.14, pp. 137-223. Introduction to Zeolite Modeling.
100. J. Sauer and M. Sierka, J. Comput. Chem., 21, 1470-1493 (2000). Combining Quantum Mechanics and Interatomic Potential Functions in Ab Initio Studies of Extended Systems.
101. H. Saint-Martin, C. Medina-Llanos, and I. Ortega-Blake, J. Chem. Phys., 93, 6448-6452 (1990). Nonadditivity in an Analytical Intermolecular Potential: The Water-Water Interaction.
102. P. C. Jordan, P. J. van Maaren, J. Mavri, D. van der Spoel, and H. J. C. Berendsen, J. Chem. Phys., 103, 2272-2285 (1995). Towards Phase-Transferable Potential Functions: Methodology and Application to Nitrogen.
103. N. H. de Leeuw and S. C. Parker, Phys. Rev. B, 58, 13901-13908 (1998). Molecular-Dynamics Simulation of MgO Surfaces in Liquid Water Using a Shell-Model Potential for Water.
104. H. Saint-Martin, J. Hernández-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys., 113, 10899-10912 (2000). A Mobile Charge Densities in Harmonic Oscillators (MCDHO) Molecular Model for Numerical Simulations: The Water-Water Interaction.
105. P. J. van Maaren and D. van der Spoel, J. Phys. Chem. B, 105, 2618-2626 (2001). Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials.
106. N. Karasawa and W. A. Goddard, Macromolecules, 25, 7268-7281 (1992). Force-Fields, Structures, and Properties of Poly(vinylidene Fluoride) Crystals.
107. M. Dixon and M. J. L. SangsterJ. Phys. C: Solid State Phys., 8, L8-L11 (1975). Simulation of Molten Nal Including Polarization Effects.
108. T. Schlick, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1992, Vol.3, pp. 1-71. Optimization Methods in Computational Chemistry.
109. P. J. D. Lindan and M. J. Gillan, J. Phys.: Condens. Matter, 5, 1019-1030 (1993). Shell-Model Molecular Dynamics Simulation of Superionic Conduction in CaF2.
110. S. J. Stuart and B. J. Berne, J. Phys. Chem. A, 103, 10300-10307 (1999). Surface Curvature Effects in the Aqueous Ionic Solvation of the Chloride Ion.
111. K. F. O'Sullivan and P. A. Madden, J. Phys.: Condens. Matter, 3, 8751-8756 (1991). Light Scattering by Alkali Halides Melts: A Comparison of Shell-Model and Rigid-Ion Computer Simulation Results.
112. J. A. Board and R. J. Elliott, J. Phys.: Condens. Matter, 1, 2427-2440 (1989). Shell Model Molecular Dynamics Calculations of the Raman spectra of Molten Nal.
113. W. Cochran, Philos. Mag., 4, 1082-1086 (1959). Lattice Dynamics of Alkali Halides.
114. J. Cao and B. J. Berne,J. Chem. Phys., 99, 2213-2220 (1993). Theory of Polarizable Liquid Crystals: Optical Birefringence.
115. U. Schröder, Solid State Commun., 4, 347-349 (1966). A New Model for Lattice Dynamics ("Breathing Shell Model").
116. M. P. Verma and R. K. Singh, Phys. Status Solidi, 33, 769 (1969). The Contribution of Three-Body Overlap Forces to the Dynamical Matrix of Alkali Halides.
117. D. K. Fisler, J. D. Gale, and R. T. Cygan, Am. Mineral., 85,217-224 (2000). A Shell Model for the Simulation of Rhombohedral Carbonate Minerals and Their Point Defects.
118. R. Ferneyhough, D. Fincham, G. D. Price, and M. J. Gillan, Model. Simul. Mater. Sci. Eng., 2, 1101-1110 (1994). The Melting of MgO Studied by Molecular-Dynamics Simulation.
119. 2 Using Shell-Model Potentials.
120. 3 Lattice: Dynamic Properties.
121. M. Baudin and K. Hermansson, Surf. Sci., 474, 107-113 (2001). Metal Oxide Surface Dynamics from Molecular Dynamics Simulations: The α-Al2O3(0001) SurfAcc.
122. G. Jacucci, I. R. McDonald, and A. Rahman, Phys. Rev. A, 13,1581-1592 (1976). Effects of Polarization on Equilibrium and Dynamic Properties of Ionic Systems.
123. M. Dixon and M. J. L. Sangster, J. Phys. C: Solid State Phys., 8, 909-925 (1976). Effects of Polarization on Some Static and Dynamic Properties of Molten Nal.
124. M. Dixon, Philos. Mag. B, 47, 509-530 (1983). Molecular Dynamics Studies of Molten Nal. I. Quasi-Elastic Neutron Scattering.
125. M. Dixon, Philos. Mag. B, 47,531-554 (1983). Molecular Dynamics Studies of Molten Nal. II. Mass-, Charge- and Number-Density Fluctuations.
126. M. Dixon, Philos. Mag. B, 48, 13-29 (1983). Molecular Dynamics Studies of Molten Nal. III. Longitudinal and Transverse Currents.
127. J. D. Carbeck, D. J. Lacks, and G. C. Rutledge, J. Chem. Phys., 103, 10347-10355 (1995). A Model of Crystal Polarization in β-Poly(Vinylidene Fluoride).
128. R. S. Mulliken, J. Chem. Phys., 2, 782-793 (1934). A New Electronegativity Scale: Together with Data on Valence States and an Ionization Potential and Electron Affinities.
129. R. G. Parr and R. G. Pearson, J. Am. Chem. Soc, 105,7512-7516 (1983). Absolute Hardness: Companion Parameter to Absolute Electronegativity.
130. R. G. Pearson, Inorg. Chem., 27, 734-740 (1988). Absolute Electronegativity and Hardness: Application to Inorganic Chemistry.
131. A. K. Rappé and W. A. Goddard III, J. Phys. Chem., 95, 3358-3363 (1991). Charge Equilibration for Molecular Dynamics Simulations.
132. S. W. Rick, S. J. Stuart, and B. J. Berne, J. Chem. Phys., 101, 6141-6156 (1994). Dynamical Fluctuating Charge Force Fields: Application to Liquid Water.
133. F. H. Streitz and J. W. Mintmire, Phys. Rev. B, 50, 11996-12003 (1994). Electrostatic Potentials for Metal-Oxide Surfaces and Interfaces.
134. S. Ogata, H. Iyetomi, K. Tsuruta, F. Shimojo, R. K. Kalia, A. Nakano, and P. Vashista, J. Appl. Phys., 86, 3036-3041 (1999). Variable-Charge Interatomic Potentials for Molecular-Dynamics Simulations of TiO2.
135. M. Berkowitz, J. Am. Chem. Soc, 109, 4823-4825 (1987). Density Functional Approach to Frontier Controlled Reactions.
136. D. M. York and W. Yang, J. Chem. Phys., 104, 159-172 (1996). A Chemical Potential Equalization Method for Molecular Simulations.
137. C. Bret, M. J. Field, and L. Hemmingsen, Mol. Phys., 98, 751-763 (2000). A Chemical Potential Equilization Model for Treating Polarization in Molecular Mechanics Force Fields.
138. R. G. Parr, R. A. Donelly, M. Levy, and W. E. Palke, J. Chem. Phys., 68, 3801-3807 (1978). Electronegativity: The Density Functional Viewpoint.
139. L. C. Allen, Acc. Chem. Res., 23, 175-176 (1990). Electronegativity Scales.
140. R. T. Sanderson, Science, 114, 670-672 (1951). An Interpretation of Bond Lengths and a Classification of Bonds.
141. W. J. Mortier, K. V. Genechten, and J. Gasteiger, J. Am. Chem. Soc, 107, 829-835 (1985). Electronegativity Equalization: Application and Parameterization.
142. W. J. Mortier, S. K. Ghosh, and S. Shankar, J. Am. Chem. Soc, 108, 4315-4320 (1986). Electronegativity Equalization: Method for the Calculation of Atomic Charges in Molecules.
143. K. T. No, J. A. Grant, and H. A. Scheraga, J. Phys. Chem., 94, 4732-4739 (1990). Determination of Net Ionic Charges Using a Modified Partial Equalization of Orbital Electronegativity Method. 1. Application to Neutral Molecules as Models for Polypeptides.
144. K. T. No, J. A. Grant, M. S. Jkon, and H. A. Scheraga, J. Phys. Chem., 94, 4740-4746 (1990). Determination of Net Atomic Charges Using a Modified Equalization of Orbital Electro-negativity Method. 2. Application to Ionic an Aromatic Molecules as Models for Polypeptides.
145. J. Hinze and H. H. Jaffe, J. Am. Chem. Soc, 84,540-546 (1962). Electronegativity. I. Orbital Electronegativity of Neutral Atoms.
146. n Molecules.
147. 0 + qH), introducing nonlinearities in the electronegativities. However, rather than using the Mulliken definition of X as mathematical equation presented Rappé and Goddard use the expression for X from Eq. [42] and thereby ignore the nonlinear terms. This means that the charges in this model do not minimize the energy. This fact is not clear from Ref. 125, but it is necessary to use Eq. [42] to reproduce their results.
148. H. Toufar, B. G. Baekelandt, G. O. A. Janssens, W. J. Mortier, and R. A. Schoonheydt, J. Phys. Chem., 99, 13876-13885 (1995). Investigation of Supramolecular Systems by a Combination of the Electronegativity Equalization Method and a Monte Carlo Simulation Technique.
149. B.-C. Perng, M. D. Newton, F. O. Raineri, and H. L. Friedman, J. Chem. Phys., 104, 7153-7176 (1996). Energetics of Charge Transfer Reactions in Solvents of Dipolar and Higher Order Multiplier Character. I. Theory.
150. M. J. Field, Mol. Phys., 91, 835-845 (1997). Hybrid Quantum Mechanical/Molecular Mechanical Fluctuating Charge Models for Condensed Phase Simulations.
151. Y.-P. Liu, K. Kim, B. J. Berne, R. A. Friesner, and S. W. Rick, J. Chem. Phys., 108, 4739 (1998). Constructing Ab Initio Force Fields for Molecular Dynamics Simulations.
152. J. L. Banks, G. A. Kaminski, R. Zhou, D. T. Mainz, B. J. Berne, R. A. Friesner, J. Chem. Phys., 110, 741-754 (1999). Parametrizing a Polarizable Force Field from Ab Initio Data. I. The Fluctuating Point Charge Model.
153. B. Chen, J. Xing, and J. I. SiepmannJ. Phys. Chem. B, 104,2391-2401 (2000). Development of Polarizable Water Force Fields for Phase Equilibria Calculations.
154. M. C. C. Ribeiro and L. C. J. Almeida, J. Chem. Phys., 110, 11445-11448 (1999). Fluctuating Charge Model for Polyatomic Ionic Systems: A Test Case with Diatomic Anions.
155. R. Chelli, P. Procacci, R. Righini, and S. Califano, J. Chem. Phys., 111, 8569-8575 (1999). Electrical Response in Chemical Potential Equilization Schemes.
156. H. A. Stern, G. A. Kaminski, J. L. Banks, R. Zhou, B. J. Berne, and R. A. Friesner, J. Phys. Chem. B, 103, 4730-4737 (1999). Fluctuating Charge, Polarizable Dipole, and Combined Models: Parameterization from Ab Initio Quantum Chemistry.
157. K. Kitaura and K. Morokuma, Int. J. Quantum Chem., 10, 325-340 (1976). A New Energy Decomposition Scheme for Molecular Interactions within the Hartee-Fock Approximation.
158. F. Weinhold, J. Mol. Struct., 399,181-197 (1997). Nature of H-Bondingin Clusters, Liquids, and Enzymes: An Ab Initio, Natural Bond Orbital Perspective.
159. A. van der Vaart and K. M. Merz Jr., J. Am. Chem. Soc, 121, 9182-9190 (1999). The Role of Polarization and Charge Transfer in the Solvation of Biomolecules.
160. J. Korchowiec and T. Uchimaru, J. Chem. Phys., 112, 1623-1633 (2000). New Energy-Partitioning Scheme Based on the Self-Consistent Charge and Configuration Method for Subsystems: Application to Water Dimer System.
161. J. P. Perdew, R. G. Parr, M. Levy, and J. L. Balduz Jr., Phys. Rev. Lett., 49,1691-1694 (1982). Density-Functional Theory for Fractional Particle Number: Derivative Discontinuities of the Energy.
162. R. Car and M. Parrinello, Phys. Rev. Lett., 55, 2471-2474 (1985). Unified Approuch for Molecular Dynamics and Density-Functional Theory.
163. J. Morales and T. J. Martinez, J. Chem. Phys., 105, 2842-2850 (2001). Classical Fluctuating Charge Theories: An Entropy Valence Bond Formalism and Relationships to Previous Models.
164. S.-B. Zhu, S. Singh, and G. W. Robinson,J. Chem. Phys., 95, 2791-2799 (1991). A New Flexible/Polarizable Water Model.
165. M. Wilson and P. A. Madden, J. Phys.: Condens. Matter, 5,2687-2706 (1993). Polarization Effects in Ionic Systems from First Principles.
166. 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.
167. 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.
168. 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.
169. A. Nakano, Comput. Phys. Commun., 104,59-69 (1997). Parallel Multilevel Preconditioned Conjugate-Gradient Approach to Variable-Charge Molecular Dynamics.
170. 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.
171. 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.
172. 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.
173. U. Dinur,J. Phys. Chem., 97, 7894-7898 (1993). Molecular Polarizabilities from Electronegativity Equalization Models.
174. 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.
175. R. G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules, Oxford University Press, Oxford, UK, 1989.
176. 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.
177. 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.
178. P. Itskowitz and M. L. Berkowitz, J. Phys. Chem. A, 101, 5687-5691 (1997). Chemical Potential Equalization Principle: Direct Approach from Density Functional Theory.
179. D. Borgis and A. Staib, Chem. Phys. Lett., 238, 187-192 (1995). A Semiempirical Quantum Polarization Model for Water.
180. J. Gao, J. Phys. Chem. B, 101, 657-663 (1997). Toward a Molecular Orbital Derived Empirical Potential for Liquid Simulations.
181. J. Gao, J. Chem. Phys., 109, 2346-2354 (1998). A Molecular-Orbital Derived Polarization Potential for Liquid Water.
182. 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.
183. 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.
184. 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.
185. 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.
186. 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.
187. 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.
188. 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.
189. 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.
190. 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.
191. 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.
192. 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.
193. 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.
194. G. Corongiu, Int. J. Quantum Chem., 42, 1209-1235 (1992). Molecular Dynamics Simulation for Liquid Water Using a Polarizable and Flexible Potential.
195. M. Sprik J. Chem. Phys., 95, 6762-6769 (1991). Hydrogen Bonding and the Static Dielctric Constant in Liquid Water.
196. P. G. Kusalik, F. Liden, and I. M. Svishchev,J. Chem. Phys., 103, 10169-10175 (1995). Calculation of the Third Virial Coefficient for Water.
197. S.-B. Zhu, S. Singh, and G. W. Robinson, Adv. Chem. Phys., 85, 627-731 (1994). Field-Perturbed Water.
198. 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.
199. 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.
200. 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.
201. 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.
202. 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.
203. C. Millot and A. J. Stone, Mol. Phys., 77, 439-462 (1992). Towards an Accurate Inter-molecular Potential for Water.
204. 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.
205. 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.
206. 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.
207. 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.
208. E. R. Batista,S. S. Xantheas, and H. Jónsson, J. Chem. Phys., 112, 3285-3292 (2000). Electric Fields in Ice and Near Water Clusters.
209. K. Laasonen, M. Sprik, M. Parrinello, and R. Car, J. Chem. Phys., 99, 9080-9089(1993). "Ab Initio" Liquid Water.
210. 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.
211. P. L. Silvestrelli and M. Parrinello, J. Chem. Phys., 111, 3572-3580 (1999). Structural, Electronic, and Bonding Properties of Liquid Water from First Principles.
212. M. Sprik, J. Phys. Chem., 95, 2283-2291 (1991). Computer Simulations of the Dynamics of Induced Polarization Fluctuations.
213. J. R. Reimers, R. O. Watts, and M. L. Klein, Chem. Phys., 64, 95-114 (1982). Intermolecular Potential Functions and the Properties of Water.
214. 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.
215. B. Guillot and Y. Guissani, J. Chem. Phys., 114(15), 6720-6733 (2001). How To Build a Better Pair Potential for Water.
216. 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.
217. 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.
218. F. H. Stillinger and A. Rahman, J. Chem. Phys., 60, 1545-1557 (1974). Improved Simulation of Liquid Water by Molecular Dynamics.
219. P. H. Poole, F. Sciortino, U. Essman, and H. E. Stanley, Nature (London), 360, 324-328 (1992). Phase Behaviour of Liquid Water.
220. 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?
221. L. A. B́aez and P. Clancy, J. Chem. Phys., 101, 9837-9840 (1994). Existence of a Density Maximum in Extended Simple Point Charge Water.
222. A. Wallqvist and P.-O. Åstrand, J. Chem. Phys., 102, 6559-6565 (1995). Liquid Densities and Structural Properites of Molecular Models of Water.
223. 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.
224. 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.
225. 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.
226. 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, Non-polarizable Potential Functions.
227. M. Sprik, M. L. Klein, and K. Watanabe,J. Phys. Chem., 94, 6483-6488 (1990). Solvent Polarization and Hydration of the Chlorine Anion.
228. n (n = 2,3,⋯, 15) Clusters. Molecular Dynamics Computer Simulations.
229. 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.
230. 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.
231. 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 β-Diketone Fragment.
232. G. A. Jeffrey and W. Saenger, Hydrogen Bonding in Biological Structures, Springer-Verlag, Heidelberg, 1991.
233. 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.
234. 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.
235. 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.
236. I. M. Klotz and J. S. Franzen, J. Am. Chem. Soc, 84, 3461-3466 (1962). Hydrogen Bonds Between Model Peptide Groups in Solution.
237. A. Wada, Adv. Biophys., 9, 1-63 (1976). The α-Helix as an Electric MacroDipole.
238. 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?
239. H. Guo and D. R. Salahub, Angew. Chem. Int. Ed., 37, 2985-2990 (1998). Cooperative Hydrogen Bonding and Enzyme Catalysis.
240. J. Šponer, 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.
241. N. Gresh and J. Šponer, J. Phys. Chem. B, 103, 11415-11427(1999). Complexes of Pentahydrated Zn2+ with Guanine, Adenine, and the Guanine-Cytosine and Adenine-Thymine Base Pairs. Structures and Energies Characterized by Polarizable Molecular Mechanics and Ab Initio Calculations.
242. P. Cieplak.J. Caldwell, and P. KollmanJ. 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.
243. E. D. Stevens, Acta Crystallogr., Sect. B, 34,544-551 (1978). Low Temperature Experimental Electron Density Distribution in Formamide.
244. G. A. Jeffrey, An Introduction to Hydrogen Bonding, Oxford University Press, New York and Oxford, 1997.
245. 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.
246. E. J. Dodson, G. J. Davis, V. S. Lamzin, G. N. Murshudov, and K. S. Wilson, Structure, 6, 685-690 (1998). Validation Tools: Can They Indicate the Information Content of Macro-molecular Crystal Structures?
247. P. Hobza and J. Šponer, Chem. Rev., 99, 3247-3276 (1999). Structure, Energies, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio Calculations.
248. J. N. Wilson and R. M. Curtis, J. Phys. Chem., 74, 187-196 (1970). Dipole Polarizabilities of Ions in Alkali Halide Crystals.
249. G. D. Mahan, Solid State Ionics, 1, 29-45 (1980). Polarizability of Ions in Crystals.
250. P. W. Fowler and P. A. Madden, Phys. Rev. B: Condens. Matter, 29, 1035-1042 (1984). In-crystal Polarizabilities of Alkali and Halide Ions.
251. J. K. Badenhoop and F. Weinhold, J. Chem. Phys., 107, 5422-5432 (1997). Natural Steric Analysis: Ab Initio van der Waals Radii of Atoms and Ions.
252. A. Warshel and R. M. Weiss, J. Am. Chem. Soc, 102, 6218-6226 (1980). An Emprical Valence Bond Approach for Comparing Reactions in Solutions and in Enzymes.
253. M. J. L. Sangster, Solid State Commun., 15, 471-474 (1974). Properties of Diatomic Molecules from Dynamical Models for Alkali Halide Crystals.
254. L. Greengard, and V. Rokhlin, J. Comput. Phys., 73, 325-348 (1987). A Fast Algorithm for Particle Simulations.
255. H.-Q. Ding, N. Karasawa, and W. A. Goddard III, J. Chem. Phys., 97, 4309-4315 (1992). Atom Level Simulations of a Million Particles: The Cell Multipole Method for Coulomb and London Nonbond Interactions.
256. R. W. Hockney and J. W. Eastwood, Computer Simulation Using Particles, Institute of Physics Publishing, Bristol, UK, 1988.
257. T.Darden, D. York, and L. Pedersen, J. Chem. Phys., 93, 10089-10092(1993). Particle Mesh Ewald: An Nlog(N) Method for Ewald Sums in Large Systems.
258. P. Ewald, Ann. Phys., 64, 253-287 (1921). Die Berechnung optischer und elektrostatischer Gitterpotentiale.
259. D. M. Heyes, J. Chem. Phys., 74, 1924-1929 (1981). Electrostatic Potentials and Fields in Infinite Point Charge Lattices.
260. M. Tuckerman, B. J. Berne, and G. J. Martyna, J. Chem. Phys., 97, 1990-2001 (1992). Reversible Multiple Time Scale Molecular Dynamics.
261. S. J. Stuart, R. Zhou, and B. J. Berne, J. Chem. Phys., 105, 1426-1436 (1996). Molecular Dynamics with Multiple Timescales: The Selection of Efficient Reference System Propagators.
262. P. Kaatz, E. A. Donley, and D. P. Shelton, J. Chem. Phys., 180, 849-856 (1998). A Comparison of Molecular Hyperpolarizabilities from Gas and Liquid Phase Measurements.
263. 2O.
264. The linear increase in polarization with molecule size assumes that the characteristic polarizability a is small compared to the characteristic volume per polarizable unit: α ≪ r3. See Eqs. [15] and [16]. In cases where this approximation does not hold, the polarizability will increase faster than linearly with system size, leading to a polarization catastrophe.
265. B. L. Bush, C. I. Bayly, and T. A. Halgren, J. Comput. Chem., 20, 1495-1516 (1999). Consensus Bond-Charge Increments Fitted to Electrostatic Potential or Field of Many Compounds: Application to MMFF94 Training Set.