An effective force field for molecular dynamics simulations of dimethyl sulfone

Molecular Physics

Volumn 109, Issue 22, 2011, Pages 2593-2605

  Hansen, Niels ^a   Kraus, Peter ^a   Samannshausen, Heiner ^a   Timmerscheidt, Tobias ^a   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

dimethyl sulfone; force field; liquid model; molecular dynamics

Indexed keywords

AQUEOUS MIXTURES; DIELECTRIC PERMITTIVITIES; DIMETHYL SULFONE; EFFECTIVE FORCE FIELDS; EXCESS FREE ENERGY; FORCE FIELDS; GROMOS FORCE FIELDS; HEAT OF VAPORIZATION; INTERACTION PARAMETERS; LIQUID DENSITY; LIQUID MODEL; LOW CONCENTRATIONS; MOLECULAR DYNAMICS SIMULATIONS; PURE-COMPONENT PROPERTIES; UNITED ATOMS;

OXYGEN; PERMITTIVITY;

MOLECULAR DYNAMICS;

EID: 84856885086     PISSN: 00268976     EISSN: 13623028     Source Type: Journal    
DOI: 10.1080/00268976.2011.624128     Document Type: Article

References (88)

1. W.F. Van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, D.P. Geerke, A. Glättli, P.H. Hünenberger, M.A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N.F.A. Van Der Vegt and H.B. Yu, Angew. Chem. Int. Ed. 45, 4064 (2006).
2. R. Zhou and B.J. Berne, Proc. Natl. Acad. Sci. USA 99, 12777 (2002).
3. R. Zhou, PROTEINS: Struct., Funct., Genet. 53, 148 (2003).
4. H. Wang and C.A. Laughton, Phys. Chem. Chem. Phys. 11, 10722 (2009).
5. R.A. Rivero, W.J. Greenlee and A.A. Patchett, Tetrahedron Lett. 32, 5263 (1991).
6. T. Sommerfeld and D. Seebach, Angew. Chem. Int. Ed. 34, 553 (1995).
7. W.T. Hughes, Clin. Infect. Dis. 27, 191 (1998).
8. A.N. Skvortsov, V.E. Zavodnik, A.I. Stash, V.K. Bel'skii and N.K. Skvortsov, Russ. J. Org. Chem. 39, 170 (2003).
9. R. Sowada, Z. Chem. 8, 361 (1968).
10. J. Bergman, B. Pettersson, V. Hasimbegovic and P.H. Svensson, J. Org. Chem. 76, 1546 (2011).
11. P.G. Varlashkin and J.R. Peterson, J. Less Comm. Metals 94, 333 (1983).
12. J.P. Pereira-Ramos, R. Messina and J. Perichon, J. Appl. Electrochem. 16, 379 (1986).
13. M.S. Tesconi, K. Sepassi and S.H. Yalkowsky, J. Pharm. Sci. 88, 501 (1999).
14. D.L. Teagarden and D.S. Baker, Eur. J. Pharm. Sci. 15, 115 (2002).
15. V. Jansons and K. Dahl, Makromol. Chem., Macromol. Symp. 51, 87 (1991).
16. F.-M. Lee, Ind. Eng. Chem. Process Des. Dev. 25, 949 (1986).
17. E. Clark, Sulfolane and Sulfones, in Kirk-Othmer Encyclopedia of Chemical Technology (Wiley-Blackwell, Hoboken, 2001), pp. 1-11.
18. R.J. Herschler, U.S. Patent No. 4,514,421 (30 April 1985).
19. R. J. Herschler, U.S. Patent No. 4,914,135 (3 April 1990).
20. N.L. Allinger and Y. Fan, J. Comput. Chem. 14, 655 (1993).
21. C.S. Ewig, R. Berry, U. Dinur, J.-R. Hill, M.-J. Hwang, H. Li, C. Liang, J. Maple, Z. Peng, T.P. Stockfisch, T.S. Thacher, L. Yand, X. Ni and A.T. Hagler, J. Comput. Chem. 22, 1782 (2001).
22. G. Filippini and A. Gavezzoti, Acta Cryst. B49, 868 (1993).
23. E.S. Henriques, M.A.C. Nascimento and M.J. Ramos, Int. J. Quantum Chem. 106, 2107 (2006).
24. G. Bitan, B. Tarus, S.S. Vollers, H.A. Lashuel, M.M. Condron, J.E. Straub and D.B. Teplow, J. Am. Chem. Soc. 125, 15359 (2003).
25. M.L. Strader and S.E. Feller, J. Phys. Chem. A 106, 1074 (2002).
26. N. Schmid, A. Eichenberger, A. Choutko, S. Riniker, M. Winger, A.E. Mark and W.F. Van Gunsteren, Eur. Biophys. J. 40, 843 (2011).
27. M. Christen, P.H. Hünenberger, D. Bakowies, R. Baron, R. Bürgi, D.P. Geerke, T.N. Heinz, M.A. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak and W.F. Van Gunsteren, J. Comput. Chem. 26, 1719 (2005).
28. D.P. Geerke, C. Oostenbrink, N.F.A. Van Der Vegt and W.F. Van Gunsteren, J. Phys. Chem. B 108, 1436 (2004).
29. H.J.C. Berendsen, J.P.M. Postma, W.F. Van Gunsteren and J. Hermans, in Intermolecular Forces, edited by B. Pullmann (Reidel, Dordrecht, The Netherlands, 1981), pp. 331-342.
30. J.-P. Ryckaert, G. Ciccotti and H.J.C. Berendsen, J. Comput. Phys. 23, 327 (1977).
31. H.J.C. Berendsen, J.P.M. Postma, W.F. Van Gunsteren, A. DiNola and J.R. Haak, J. Chem. Phys 81, 3684 (1984).
32. J.A. Riddick, W.B. Bunger and T.K. Sakand, Organic Solvents: Physical Properties and Methods of Purification (John Wiley, New York, 1986).
33. G.S. Kell, J. Chem. Eng. Data 12, 66 (1967).
34. M. Neumann, J. Chem. Phys. 82, 5663 (1985).
35. I.G. Tironi, R. Sperb, P.E. Smith and W.F. Van Gunsteren, J. Chem. Phys. 102, 5451 (1995).
36. J.P.M. Postma, Ph.D. thesis, Rijksuniversiteit Groningen, 1985.
37. T. Uno, K. Machida and K. Hanai, Spectrochim. Acta 27A, 107 (1971).
38. G. Geiseler and G. Hanschmann, J. Mol. Structure 11, 283 (1972).
39. B. Regelmann and A. Schmidt, Z. Anorg. Allg. Chem. 626, 1038 (2000).
40. W.R. Feairheller and J.E. Katon, Spectrochim. Acta 20, 1099 (1964).
41. NIST Computational Chemistry Comparison and Benchmark Database, NIST Standard Reference Database Number 101, Release 15a, edited by R.D. Johnson III (April 2010), http://cccbdb.nist.gov/
42. G.J. Safford, P.C. Schaffer and P.S. Leung, J. Chem. Phys 50, 2140 (1969).
43. W.R.P. Scott, P.H. Hünenberger, I.G. Tironi, A.E. Mark, S.R. Billeter, J. Fennen, A.E. Torda, T. Huber, P. Krüger and W.F. Van Gunsteren, J. Phys. Chem. A 103, 3596 (1999).
44. R. Walser, A.E. Mark and W.F. Van Gunsteren, Biophys. J. 78, 2752 (2000).
45. W.K. Busfield, K.J. Ivin, H. Mackle and P.A.G. O'Hare, Trans. Faraday Soc. 57, 1058 (1961).
46. A.P. Eichenberger, J.R. Allison, J. Dolenc, D.P. Geerke, B.A.C. Horta, K. Meier, C. Oostenbrink, N. Schmid, D. Steiner, D. Wang and W.F. Van Gunsteren, J. Chem. Theory. Comput. 7, 3379 (2011).
47. S. Riniker, A.-P.E. Kunz and W.F. Van Gunsteren, J. Chem. Theory Comput. 7, 1469 (2011).
48. M. Hargittai and I. Hargittai, J. Mol. Struc. 20, 283 (1974).
49. S. Saito and F. Makino, Bull. Chem. Soc. Jpn. 45, 92 (1972).
50. T. Clark, J.S. Murray, P. Lane and P. Politzer, J. Mol. Model. 14, 689 (2008).
51. J.A. Dobado, H. Martinez-Garcia, J.M. Molina and M.R. Sundberg, J. Am. Chem. Soc. 121, 3156 (1999).
52. A.D. MacKerell, in Computational Biochemistry and Biophysics, edited by O.M. Becker, A.D. MacKerell, B. Roux, and M. Watanabe (Marcel Dekker, New York, 2001), p. 7.
53. W. Strecker and R. Spitaler, Ber. dtsch. chem. Ges. 59, 1754 (1926).
54. J.F. Casteel and P.G. Sears, J. Chem. Eng. Data 19, 196 (1974).
55. W. Acree and J.S. Chickos, J. Phys. Chem. Ref. Data 39, 043101 (2010).
56. H.L. Clever and E.F. Westrum, J. Phys. Chem. 74, 1309 (1970).
57. C. Wohlfarth and B. Wohlfarth, in Landolt-Börnstein. Numerical Data and Functional Relationships in Science and Technology. Group IV: Physical Chemistry. Subvolume B: Pure Organic Liquids, edited by M.D. Lechner (Springer, Berlin, 2002), Vol. 18, p. 20.
58. D.R. Lide, CRC Handbook of Chemistry and Physics, 77th ed. (CRC Press, Boca Raton, 1996).
59. C. Wohlfarth, in Landolt-Börnstein. Numerical Data and Functional Relationships in Science and Technology. Group IV: Macroscopic and Technical Properties of Matter, edited by O. Madelung (Springer, Berlin, 1991), Vol. 6, p. 34.
60. B. Bry and B. Tremillon, J. Chem. Research (M) 0146 (1979).
61. R. Walser, A.E. Mark and W.F. Van Gunsteren, J. Chem. Phys. 112, 10450 (2000).
62. P.J. Gee and W.F. Van Gunsteren, Mol. Phys. 104, 477 (2006).
63. F. Sokolić , Y. Guissani and B. Guillot, J. Phys. Chem. 89, 3023 (1985).
64. M.H. Ketko, G. Kamath and J.J. Potoff, J. Phys. Chem. B 115, 4949 (2011).
65. E. El Ahmar, B. Creton, A. Valtz, C. Coquelet, V. Lachet, D. Richon and P. Ungerer, Fluid Phase Equil. 304, 21 (2011).
66. C. Reichardt, Solvents and Solvent Effects in Organic Chemistry, 3rd ed. (Wiley-VCH, Weinheim, Germany, 2003).
67. B. Kirchner and M. Reiher, J. Am. Chem. Soc. 124, 6206 (2001).
68. B. Kirchner and J. Hutter, Chem. Phys. Lett. 364, 497 (2002).
69. B. Kirchner and J. Hutter, J. Chem. Phys. 121, 5133 (2004).
70. A. Givan, H. Grothe, A. Loewenschuss and C.J. Nielsen, Phys. Chem. Chem. Phys. 4, 255 (2002).
71. Dimethyl Sulfone Technical Bulletin (James River Corporation, Camas, WA, 1990).
72. P.A. Lee and S.J. De Mora, J. Phycol. 35, 8 (1999).
73. L.E. McGann and M.L. Walterson, Cryobiology 24, 11 (1987).
74. S.M. Puranik, A.C. Kumbharkhane and S.C. Mehrotra, J. Chem. Soc. Faraday Trans. 88, 433 (1992).
75. I.A. Borin and M.S. Skaf, J. Chem. Phys. 110, 6412 (1999).
76. A.K. Soper and A. Luzar, J. Phys. Chem. 100, 1357 (1996).
77. A.K. Soper, Faraday Discuss. 103, 41 (1996).
78. M.S. Skaf, J. Phys. Chem. A 103, 10719 (1999).
79. P.P. Wiewiór, H. Shirota and E.W. Castner, J. Chem. Phys. 116, 4643 (2002).
80. A. Vishnyakov, A.P. Lyubartsev and A. Laaksonen, J. Phys. Chem. A 105, 1702 (2001).
81. A. Luzar, Faraday Discuss. 103, 29 (1996).
82. W.J. De Bruyn, J.A. Shorter, P. Davidovits, D.R. Worsnop, M.S. Zahniser and C.E. Kolb, J. Geophys. Res. 99D, 16927 (1994).
83. T.L. Tarbuck and G.L. Richmond, J. Phys. Chem. B 109, 20868 (2005).
84. N. Furukawa and H. Fujihara, in The Chemistry of Sulphones and Sulphoxides, edited by S. Patai, Z. Rappoport, and C. Stirling (John Wiley, New York, 1988), pp. 541-581.
85. K. Remerie, W.F. Van Gunsteren and J.B.F.N. Engberts, Mol. Phys. 56, 1393 (1985).
86. I.I. Vaisman and M.L. Berkowitz, J. Am. Chem. Soc. 114, 7889 (1992).
87. S. Roy, S. Banerjee, N. Biyani, B. Jana and B. Bagchi, J. Phys. Chem. B 115, 685 (2011).
88. D. Martin, A. Weise and H.-J. Niclas, Angew. Chem. 79, 340 (1967).