Polarizable water models from mixed computational and empirical optimization

Journal of Physical Chemistry B

Volumn 117, Issue 32, 2013, Pages 9486-9500

  Tröster, Philipp ^a   Lorenzen, Konstantin ^a   Schwörer, Magnus ^a   Tavan, Paul ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EMPIRICAL OPTIMIZATION; MOLECULAR DYNAMICS SIMULATIONS; PARAMETER OPTIMIZATION; POLARIZABLE MOLECULAR MECHANICS; POLARIZABLE WATER MODELS; RADIAL DISTRIBUTION FUNCTIONS; SOLVENT ENVIRONMENTS; THERMODYNAMIC CONDITIONS;

DIPOLE MOMENT; GASES; MOLECULAR DYNAMICS; MOLECULES; OPTIMIZATION;

COMPUTER SIMULATION;

WATER;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; QUANTUM THEORY; THEORETICAL MODEL;

COMPUTER SIMULATION; MODELS, THEORETICAL; QUANTUM THEORY; WATER;

EID: 84882364347     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp404548k     Document Type: Article

References (120)

1. Guillot, B. J. Mol. Liq. 2002, 101, 219-260
2. van Gunsteren, W. F. Angew. Chem., Int. Ed. 2006, 45, 4064-4092
3. Tavan, P.; Carstens, H.; Mathias, G. In Protein Folding Handbook; Buchner, J.; Kiefhaber, T., Eds.; Wiley-VCH: Weinheim, 2005; Vol. 1; pp 1170-1195.
4. MacKerell, A. D. J. Phys. Chem. B 1998, 102, 3586-3616
5. Pearlman, D.; Case, D.; Caldwell, J.; Ross, W.; Cheatham, T., III; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1-41
6. Christen, M.; Hünenberger, P.; Bakowies, D.; Baron, R.; Bürgi, R.; Geerke, D.; Heinz, T.; Kastenholz, M.; Kräutler, V.; Oostenbrink, C.; Peter, C.; Trzesniak, D.; van Gunsteren, W. J. Comput. Chem. 2005, 26, 1719-1751
7. Jorgensen, W.; Chandrasekhar, J.; Madura, J.; Impey, R.; Klein, M. J. Phys. Chem. 1983, 79, 926-935
8. Berendsen, H.; Postma, J.; Van Gunsteren, W.; Hermans, J. Intermol. Forces 1981, 11, 331-342
9. Berendsen, H.; Grigera, J.; Straatsma, T. J. Phys. Chem. 1987, 91, 6269-6271
10. Soper, A. Chem. Phys. 2000, 258, 121-137
11. Soper, A. J. Phys.: Condens. Matter 2007, 19, 335206
12. Hura, G.; Sorenson, J.; Glaeser, R.; Head-Gordon, T. J. Chem. Phys. 2000, 113, 9140-9148
13. Hura, G.; Russo, D.; Glaeser, R.; Head-Gordon, T.; Krack, M.; Parrinello, M. Phys. Chem. Chem. Phys. 2003, 5, 1981-1991
14. Skinner, L. B.; Huang, C.; Schlesinger, D.; Pettersson, L. G.; Nilsson, A.; Benmore, C. J. J. Chem. Phys. 2013, 138, 074506
15. Vega, C.; Abascal, J. Phys. Chem. Chem. Phys. 2011, 13, 19663-19688
16. Lennard-Jones, J. E. Proc. Phys. Soc. 1931, 43, 461-482
17. Verlet, L. Phys. Rev. 1967, 159, 98-103
18. VandeVondele, J.; Tröster, P.; Tavan, P.; Mathias, G. J. Phys. Chem. A 2012, 116, 2466-2474
19. Sorenson, J.; Hura, G.; Glaeser, R.; Head-Gordon, T. J. Chem. Phys. 2000, 113, 9149-9161
20. Clough, S.; Beers, Y.; Klein, G.; Rothman, L. J. Chem. Phys. 1973, 59, 2254-2259
21. Sprik, M. J. Phys. Chem. 1991, 95, 2283-2291
22. Silvestrelli, P.; Bernasconi, M.; Parrinello, M. Chem. Phys. Lett. 1997, 277, 478-482
23. Silvestrelli, P.; Parrinello, M. J. Chem. Phys. 1999, 111, 3572-3570
24. Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M. J. Chem. Phys. 1999, 110, 10452-10467
25. Gubskaya, A.; Kusalik, P. J. Chem. Phys. 2002, 117, 5290-5302
26. Schropp, B.; Tavan, P. J. Phys. Chem. B 2008, 112, 6233-6240
27. Badyal, Y.; Saboungi, M.; Price, D.; Shastri, S.; Haeffner, D.; Soper, A. J. Chem. Phys. 2000, 112, 9206-9208
28. Babitzki, G.; Denschlag, R.; Tavan, P. J. Phys. Chem. B 2009, 113, 10483-10495
29. Lopes, P.; Roux, B.; MacKerell, A. Theor. Chem. Acc. 2009, 124, 11-28
30. Mahoney, M.; Jorgensen, W. J. Chem. Phys. 2000, 112, 8910-8922
31. Horn, H.; Swope, W.; Pitera, J.; Madura, J.; Dick, T.; Hura, G.; Head-Gordon, T. J. Chem. Phys. 2004, 120, 9665-9678
32. Sanz, E.; Vega, C.; Abascal, J.; MacDowell, L. J. Chem. Phys. 2004, 121, 1165-1166
33. Abascal, J.; Vega, C. J. Chem. Phys. 2005, 123, 234505
34. Huggins, D. J. J. Chem. Phys. 2012, 136, 064518
35. Niesar, U.; Corongiu, G.; Clementi, E.; Kneller, G.; Bhattacharya, D. J. Phys. Chem. 1990, 94, 7949-7956
36. Kozack, R.; Jordan, P. J. Chem. Phys. 1992, 96, 3120-3130
37. Corongiu, G. Int. J. Quantum Chem. 1992, 42, 1209-1235
38. Brodholt, J.; Sampoli, M.; Vallauri, R. Mol. Phys. 1995, 86, 149-158
39. Chialvo, A.; Cummings, P. J. Chem. Phys. 1996, 105, 8274-8281
40. Chialvo, A.; Cummings, P. Fluid Phase Equilib. 1998, 150, 73-81
41. Dang, L.; Chang, T. J. Chem. Phys. 1997, 106, 8149-8159
42. Kiyohara, K.; Gubbins, K. E.; Panagiotopoulos, A. Z. Mol. Phys. 1998, 94, 803-808
43. Svishchev, I.; Kusalik, P.; Wang, J.; Boyd, R. J. Chem. Phys. 1996, 105, 4742-4750
44. van Maaren, P. J.; van der Spoel, D. J. Phys. Chem. B 2001, 105, 2618-2626
45. Yu, H.; van Gunsteren, W. J. Chem. Phys. 2004, 121, 9549-9564
46. Lamoureux, G.; MacKerell, A., Jr.; Roux, B. J. Chem. Phys. 2003, 119, 5185-5197
47. Lamoureux, G.; Harder, E.; Vorobyov, I.; Roux, B.; MacKerell, A. Chem. Phys. Lett. 2006, 418, 245-249
48. Paricaud, P.; Předota, M.; Chialvo, A.; Cummings, P. J. Chem. Phys. 2005, 122, 244511
49. Kunz, A.; van Gunsteren, W. J. Phys. Chem. A 2009, 113, 11570-11579
50. Baranyai, A.; Kiss, P. J. Chem. Phys. 2010, 133, 144109
51. Baranyai, A.; Kiss, P. J. Chem. Phys. 2011, 135, 234110
52. Sprik, M.; Klein, M. J. Chem. Phys. 1988, 89, 7556-7554
53. Rick, S.; Stuart, S.; Berne, B. J. Chem. Phys. 1994, 101, 6141-6167
54. Chen, B.; Xing, J.; Siepmann, J. J. Phys. Chem. B 2000, 104, 2391-2401
55. Cieplak, P.; Kollman, P.; Lybrand, T. J. Chem. Phys. 1990, 92, 6755-6760
56. Burnham, C. J.; Li, J.; Xantheas, S. S.; Leslie, M. J. Chem. Phys. 1999, 110, 4566-4581
57. Burnham, C. J.; Xantheas, S. S. J. Chem. Phys. 2002, 116, 1500-1510
58. Ishiyama, T.; Morita, A. J. Phys. Chem. C 2007, 111, 721-737
59. Stern, H.; Rittner, F.; Berne, B.; Friesner, R. J. Chem. Phys. 2001, 115, 2237-2251
60. Viererblová, L.; Kolafa, J. Phys. Chem. Chem. Phys. 2011, 13, 19925-19935
61. Zhu, S.; Singh, S.; Robinson, G. J. Chem. Phys. 1991, 95, 2791-2799
62. Nada, H.; van der Eerden, J. J. Chem. Phys. 2003, 118, 7401-7413
63. Wang, L.-P.; Chen, J.; Van Voorhis, T. J. Chem. Theory Comput. 2012, 9, 452-460
64. Yu, W.; Lopes, P. E. M.; Roux, B.; MacKerell, A. D., Jr. J. Chem. Phys. 2013, 138, 034508
65. Ren, P.; Ponder, J. W. J. Phys. Chem. B 2003, 107, 5933-5947
66. Kiss, P. T.; Baranyai, A. J. Chem. Phys. 2012, 137, 084506
67. Dyke, T.; Muenter, J. J. Chem. Phys. 1973, 59, 3125-3127
68. Murphy, W. J. Chem. Phys. 1977, 67, 5877-5882
69. Buckingham, R. A.; Corner, J. Proc. R. Soc. London, Ser. A 1947, 189, 118-129
70. Wallqvist, A.; Berne, B. J. Phys. Chem. 1993, 97, 13841-13851
71. de Pablo, J. J.; Prausnitz, J. M.; Strauch, H. J.; Cummings, P. T. J. Chem. Phys. 1990, 93, 7355-7359
72. Straatsma, T. P.; McCammon, J. A. Mol. Simul. 1990, 5, 181-192
73. Yu, H.; Hansson, T.; Van Gunsteren, W. J. Chem. Phys. 2003, 118, 221-234
74. Caldwell, J.; Dang, L.; Kollman, P. J. Am. Chem. Soc. 1990, 112, 9144-9147
75. Dang, L. J. Chem. Phys. 1992, 97, 2659-2667
76. Caldwell, J. W.; Kollman, P. A. J. Phys. Chem. 1995, 99, 6208-6219
77. Elking, D.; Darden, T.; Woods, R. J. J. Comput. Chem. 2007, 28, 1261-1274
78. Schropp, B.; Tavan, P. J. Phys. Chem. B 2010, 114, 2051-2057
79. Thole, B. Chem. Phys. 1981, 59, 341-350
80. Benedict, W. S.; Gailar, N.; Plyler, E. K. J. Chem. Phys. 1956, 24, 1139-1165
81. Ichikawa, K.; Kameda, Y.; Yamaguchi, T.; Wakita, H.; Misawa, M. Mol. Phys. 1991, 73, 79-86
82. Thiessen, W. E.; Narten, A. H. J. Chem. Phys. 1982, 77, 2656-2662
83. Schwörer, M.; Breitenfeld, B.; Tröster, P.; Lorenzen, K.; Tavan, P.; Mathias, G. J. Chem. Phys. 2013, 138, 244103
84. Lorenzen, K.; Schwörer, M.; Tröster, P.; Mates, S.; Tavan, P. J. Chem. Theory Comput. 2012, 8, 3628-3636
85. Laio, A.; VandeVondele, J.; Rothlisberger, U. J. Chem. Phys. 2002, 116, 6941-6947
86. Kell, G. J. Chem. Eng. Data 1967, 12, 66-69
87. Jancso, G.; Van Hook, W. A. Chem. Rev. 1974, 74, 689-750
88. Berweger, C.; van Gunsteren, W.; Müller-Plathe, F. Chem. Phys. Lett. 1995, 232, 429-436
89. Eichinger, M.; Grubmüller, H.; Heller, H.; Tavan, P. J. Comput. Chem. 1997, 18, 1729-1749
90. Mathias, G.; Egwolf, B.; Nonella, M.; Tavan, P. J. Chem. Phys. 2003, 118, 10847-10860
91. Niedermeier, C.; Tavan, P. J. Chem. Phys. 1994, 101, 734-748
92. Niedermeier, C.; Tavan, P. Mol. Simul. 1996, 17, 57-66
93. Allen, M. P.; Tildesley, D. Computer Simulations of Liquids; Clarendon: Oxford, 1987.
94. Kirkwood, J. G. J. Chem. Phys. 1934, 2, 351-361
95. Kaatze, U. J. Chem. Eng. Data 1989, 34, 371-374
96. Kräutler, V.; Van Gunsteren, W.; Hünenberger, P. J. Chem. Phys. 2001, 22, 501-508
97. Bussi, G.; Parrinello, M. Comput. Phys. Commun. 2008, 179, 26-29
98. Becke, A. D. Phys. Rev. A 1988, 38, 3098-3100
99. Perdew, J. P. Phys. Rev. B 1986, 33, 8822-8824
100. Troullier, N.; Martins, J. Phys. Rev. B 1991, 43, 1993-2006
101. CPMD V3.9; Copyright IBM Corp 1990-2008, Copyright MPI für Festkörperforschung Stuttgart 1997-2001; see also www.cpmd.org.
102. Pugliano, N.; Saykally, R. Science 1992, 257, 1937-1940
103. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
104. Lingenheil, M.; Denschlag, R.; Reichold, R.; Tavan, P. J. Chem. Theory Comput. 2008, 4, 1293-1306
105. Neumann, M. Mol. Phys. 1983, 50, 841-858
106. Smith, P. E.; van Gunsteren, W. F. J. Chem. Phys. 1994, 100, 3169-3174
107. Dünweg, B.; Kremer, K. J. Chem. Phys. 1993, 99, 6983-6997
108. Yeh, I.-C.; Hummer, G. J. Phys. Chem. B 2004, 108, 15873-15879
109. Motakabbir, K. A.; Berkowitz, M. J. Phys. Chem. 1990, 94, 8359-8362
110. Tironi, I. G.; Van Gunsteren, W. F. Mol. Phys. 1994, 83, 381-403
111. Weigend, F.; Köhn, A.; Hättig, C. J. Chem. Phys. 2002, 116, 3175-3183
112. Verhoeven, J.; Dymanus, A. J. Chem. Phys. 1970, 52, 3222-3233
113. Dyke, T. R.; Mack, K. M.; Muenter, J. S. J. Chem. Phys. 1977, 66, 498-510
114. Odutola, J. A.; Dyke, T. R. J. Chem. Phys. 1980, 72, 5062-5070
115. Sprik, M. J. Chem. Phys. 1991, 95, 6762-6769
116. Rapaport, D. C. The art of molecular dynamics simulation; Cambridge University Press: Cambridge, U.K., 2004.
117. Krynicki, K.; Green, C.; Sawyer, D. Faraday Discuss. Chem. Soc. 1978, 66, 199-208
118. Harris, K.; Woolf, L. J. Chem. Eng. Data 2004, 49, 1064-1069
119. Tazi, S.; Botan, A.; Salanne, M.; Marry, V.; Turq, P.; Rotenberg, B. J. Phys.: Condens. Matter 2012, 24, 284117
120. Weast, R. C. Handbook of Chemistry and Physics; CRC: Boca Raton, 1983.