Hydrophobicity within the three-dimensional Mercedes-Benz model: Potential of mean force

Journal of Chemical Physics

Volumn 134, Issue 6, 2011, Pages

  Dias, Cristiano L ^a,b   Hynninen, Teemu ^c,d   Ala Nissila, Tapio ^d,e   Foster, Adam S ^c,d   Karttunen, Mikko ^f  

^a UNIVERSITY OF TORONTO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^d AALTO UNIVERSITY   (Finland)

^e BROWN UNIVERSITY   (United States)

^f UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMISTIC MODELS; CONCEPTUAL SIMPLICITY; DESOLVATION; HEAT CAPACITIES; HYDROPHOBIC INTERACTIONS; MERCEDES BENZ; MICROSCOPIC MECHANISMS; MOLECULAR LEVELS; MONTE CARLO SIMULATION; POTENTIAL OF MEAN FORCE; RADIAL DISTRIBUTION FUNCTIONS; TEMPERATURE DEPENDENCE;

DISTRIBUTION FUNCTIONS; HYDROPHOBICITY; MONTE CARLO METHODS; SPECIFIC HEAT; TEMPERATURE DISTRIBUTION; THERMODYNAMICS;

THREE DIMENSIONAL;

WATER;

ARTICLE; CHEMICAL MODEL; CHEMICAL PHENOMENA; CHEMISTRY; MONTE CARLO METHOD; THERMODYNAMICS;

HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, CHEMICAL; MONTE CARLO METHOD; THERMODYNAMICS; WATER;

EID: 79951788733     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3537734     Document Type: Article

References (67)

1. C. Tanford, Science 200, 1012 (1978). 10.1126/science.653353
2. D. Chandler, Nature (London) 437, 640 (2005). 10.1038/nature04162 (Pubitemid 41486526)
3. M. Jensen and O. G. Mouritsen, Biochim. Biohys. Acta 1666, 205 (2006). 10.1016/j.bbamem.2004.06.009
4. R. Zhou, X. Huang, C. J. Margulis, and B. J. Berne, Science 305, 1605 (2004). 10.1126/science.110117
5. C. L. Dias, T. Ala -Nissila, J. Wong -ekkabut, I. Vattulainen, M. Grant, and M. Karttunen, Cryobiology 60, 91 (2010). 10.1016/j.cryobiol.2009.07.005
6. P. De Los Rios and G. Caldarelli, Phys. Rev. E 63, 031802 (2001). 10.1103/PhysRevE.63.031802
7. P. D. L. Rios and G. Caldarelli, Phys. Rev. E 62, 8449 (2000). 10.1103/PhysRevE.62.8449 (Pubitemid 32087907)
8. W. Kauzmann, Adv. Protein Chem. 14, 1 (1959). 10.1016/S0065-3233(08) 60608-7
9. K. A. Dill, Biochemistry 29, 7133 (1990). 10.1021/bi00483a001 (Pubitemid 20230041)
10. P. R. Wolde, J. Phys. Condens. Matter 14, 9445 (2002). 10.1088/0953-8984/14/40/328 (Pubitemid 35275060)
11. G. Hummer, S. Garde, A. E. Garca, and L. R. Pratt, Chem. Phys. 258, 349 (2000). 10.1016/S0301-0104(00)00115-4
12. E. E. Meyer, K. J. Rosenberg, and J. Israelachvili, Proc. Natl. Acad. Sci. U.S.A. 103, 15739 (2006). 10.1073/pnas.0606422103 (Pubitemid 44657537)
13. B. Widom, P. Bhimalapuram, and K. Koga, Phys. Chem. Chem. Phys. 5, 3085 (2003). 10.1039/b304038k
14. N. T. Southall, K. A. Dill, and A. D. J. Haymet, J. Phys. Chem. B 106, 521 (2002). 10.1021/jp015514e (Pubitemid 35276170)
15. C. Tanford, Protein Sci. 6, 1358 (1997). 10.1002/pro.v6:6
16. H. S. Frank and M. W. Evans, J. Chem. Phys. 13, 507 (1945). 10.1063/1.1723985
17. C. L. Dias, T. Ala-Nissila, J. Wong-ekkabut, I. Vattulainen, M. Grant, and M. Karttunen, Cryobiology 60, 356 (2010). 10.1016/j.cryobiol.2010.03.006
18. D. T. Bowron, A. Filipponi, M. A. Roberts, and J. L. Finney, Phys. Rev. Lett. 81, 4164 (1998). 10.1103/PhysRevLett.81.4164
19. Y. Rezus and H. Bakker, Phys. Rev. Lett. 99, 148301 (2007). 10.1103/PhysRevLett.99.148301 (Pubitemid 47519538)
20. L. R. Pratt and D. Chandler, J. Chem. Phys. 67, 3683 (1977). 10.1063/1.435308
21. S. Simizu and H. S. Chan, J. Am. Chem. Soc. 123, 2083 (2001). 10.1021/ja0034390 (Pubitemid 32200040)
22. D. Paschek, J. Chem. Phys. 120, 10605 (2004). 10.1063/1.1737294
23. M. S. Moghaddam, S. Shimizu, and H. S. Chan, J. Am. Chem. Soc. 127, 303 (2005). 10.1021/ja040165y (Pubitemid 40094393)
24. N. T. Southall and K. A. Dill, Biophys. Chem. 101-102, 295 (2002). 10.1016/S0301-4622(02)00167-9 (Pubitemid 35462054)
25. S. Shimizu and H. S. Chan, J. Chem. Phys. 115, 1414 (2001). 10.1063/1.1379765 (Pubitemid 32699324)
26. S. Shimizu and H. S. Chan, Proteins: Struct., Funct., Bioinf. 48, 15 (2002). 10.1002/(ISSN)1097-0134
27. T. Ghosh, A. E. Garca, and S. Garde, J. Phys. Chem. B 107, 612 (2003). 10.1021/jp0220175
28. C. L. Dias, T. Ala-Nissila, M. Grant, and M. Karttunen, J. Chem. Phys. 131, 54505 (2009). 10.1063/1.3183935
29. A. Ben-Naim, J. Chem. Phys. 54, 3682 (1971). 10.1063/1.1675414
30. A. Ben-Naim, Water and Aqueous Solutions (Plenum Press, New York, 1974).
31. A. Ben-Naim, Molecular Theory of Water and Aqueous Solutions, 1st ed. (World Scientific, Singapore, 2009).
32. A. Bizjak, T. Urbic, V. Vlachy, and K. Dill, Acta Chim. Svov. 54, 532 (2007).
33. A. Bizjak, T. Urbic, V. Vlachy, and K. A. Dill, J. Chem. Phys. 131, 194504 (2009). 10.1063/1.3259970
34. T. Hynninen, V. Heinonen, C. L. Dias, M. Karttunen, A. S. Foster, and T. Ala-Nissila, Phys. Rev. Lett. 105, 086102 (2010). 10.1103/PhysRevLett.105.086102
35. K. A. T. Silverstein, A. D. J. Haymet, and K. A. Dill, J. Am. Chem. Soc. 120 (13), 3166 (1998). 10.1021/ja973029k (Pubitemid 28204530)
36. N. T. Southall and K. A. Dill, J. Phys. Chem. B 104, 1326 (2000). 10.1021/jp992860b
37. K. A. Dill, T. M. Truskett, V. Vlachy, and B. Hribar-Lee, Annu. Rev. Biophys. Biomol. Struct. 34, 173 (2005). 10.1146/biophys.2005.34.issue-1
38. J. -P. Becker and O. Collet, J. Mol. Struct.: THEOCHEM 774, 23 (2006). 10.1016/j.theochem.2006.06.033
39. C. L. Dias, T. Ala-Nissila, M. Karttunen, I. Vattulainen, and M. Grant, Phys. Rev. Lett. 100, 118101 (2008). 10.1103/PhysRevLett.100.118101 (Pubitemid 351434247)
40. S. F. Dec, S. J. Gill, J. Solution Chem. 14, 417 (1985). 10.1007/BF00643945
41. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, New York, 1987).
42. D. J. Bonthuis, D. Horinek, L. Bocquet, and R. R. Netz, Phys. Rev. Lett. 103, 144503 (2009). 10.1103/PhysRevLett.103.144503
43. J. Wong-ekkabut, M. S. Miettinen, C. Dias, and M. Karttunen, Nat. Nanotechnol. 5, 555 (2010). 10.1038/nnano.2010.152
44. E. Sobolewski, M. Makowski, C. Czaplewski, A. Liwo, S. Odziej, and H. A. Scheraga, J. Phys. Chem. B 111, 10765 (2007). 10.1021/jp070594t (Pubitemid 47497621)
45. M. S. Cheung, A. E. Garca, and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 99, 685 (2002). 10.1073/pnas.022387699 (Pubitemid 34106571)
46. Z. Liu and H. S. Chan, J. Mol. Biol. 349, 872 (2005). 10.1016/j.jmb.2005.03.084 (Pubitemid 40725960)
47. B. Lee and F. M. Richards, J. Mol. Biol. 55, 379 (1971). 10.1016/0022-2836(71)90324-X
48. D. Paschek, J. Chem. Phys. 120, 6674 (2004). 10.1063/1.1652015
49. S. Shimizu and H. S. Chan, J. Chem. Phys. 113, 4683 (2000). 10.1063/1.1288922
50. D. E. Smith and A. D. J. Haymet, J. Chem. Phys. 98, 6445 (1993). 10.1063/1.464809
51. Solutes are considered to be in the CC state if the distance between them is smaller than 1.65-this corresponds to the first minimum in the solute- solute RDF. The SSC state is defined when the distance between solutes is within [1.65:2.73]. Water is considered to form a shell around the solute if their distance to the solute is smaller than 1.65-this corresponds to the first minimum of the water- solute RDF.
52. S. J. Gill, S. F. Dec, G. Olofsson, and I. Wadso, J. Phys. Chem. 89, 3758 (1985). 10.1021/j100263a034
53. J. H. Griffith and H. A. Scheraga, THEOCHEM 682, 97 (2004). 10.1016/j.theochem.2004.06.003
54. S. Swaminathan, S.W. Harrison, and D. L. Beveridge, J. Am. Chem. Soc. 100, 5705 (1978). 10.1021/ja00486a020
55. C. A. Koh, R. P. Wisbey, X. Wu, R. E. Westacott, and A. K. Soper, J. Chem. Phys. 113, 6390 (2000). 10.1063/1.1288818
56. P. H. K. De Jong, J. E. Wilson, G. W. Neilson, and A. D. Buckingham, Mol. Phys. 91, 99 (1997). 10.1080/002689797171788
57. S. F. Dec, K. E. Bowler, L. L. Stadterman, C. A. Koh, and E. Dendy Sloan Jr., J. Am. Chem. Soc. 128, 414 (2006). 10.1021/ja055283f (Pubitemid 43157526)
58. R. L. Baldwin, Proc. Natl. Acad. Sci. U.S.A. 83, 8069 (1986). 10.1073/pnas.83.21.8069 (Pubitemid 17182445)
59. J. T. Edsall, J. Am. Chem. Soc. 54, 1506 (1935). 10.1021/ja01311a501
60. N. Tsunekawa, H. Miyagawa, K. Kitamura, and Y. Hiwatari, J. Chem. Phys. 116, 6725 (2002). 10.1063/1.1463054 (Pubitemid 34460148)
61. T. Yoshidome and M. Kinoshita, Phys. Rev. E 79, 30905 (2009). 10.1103/PhysRevE.79.030905
62. P. L. Privalov, Y. V. Griko, and S. Y. Venyaminov, J. Mol. Biol., 190, 487 (1986) 10.1016/0022-2836(86)90017-3
63. M. Ikeguchi, S. Shimizu, S. Nakamura, and K. Shimizu, J. Phys. Chem. B 102, 5891 (1998). 10.1021/jp980210m
64. B. Lee, Biopolymers 24, 813 (1985). 10.1002/(ISSN)1097-0282
65. K. J. Soda, J. Phys. Soc. Jpn. 62, 1782 (1993). 10.1143/JPSJ.62.1782
66. T. Ghosh, A. E. Garcia, and S. Garde, J. Chem. Phys. 116, 2480 (2002). 10.1063/1.1431582 (Pubitemid 34167985)
67. T. Ghosh, A. E. Garcia, and S. Garde, J. Am. Chem. Soc. 123, 10997 (2001). 10.1021/ja010446v (Pubitemid 33042014)