Revisiting the carboxylic acid dimers in aqueous solution: Interplay of hydrogen bonding, hydrophobic interactions and entropy

Journal of Physical Chemistry B

Volumn 112, Issue 2, 2008, Pages 242-249

  Chen, Jianhan ^a   Brooks III, Charles L ^a   Scheraga, Harold A ^b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMERIZATION; DIMERS; ENTROPY; HYDROGEN BONDS; MATHEMATICAL MODELS; THERMODYNAMICS;

AQUEOUS SOLUTION; DIMERIZATION CONSTANTS; HYDROPHOBIC INTERACTIONS;

CARBOXYLIC ACIDS;

EID: 38749123475     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp074355h     Document Type: Article

References (41)

1. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics; John Wiley and Sons: New York, 1987.
2. Dyson, H. J.; Wright, P. E.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 13057-13061.
3. Chandler, D. Nature 2005, 437, 640-647.
4. Deechongkit, S.; Nguyen, H.; Powers, E. T.; Dawson, P. E.; Gruebele, M.; Kelly, J. W. Nature 2004, 430, 101-105.
5. Rose, G. D.; Fleming, P. J.; Banavar, J. R. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 16623-16633.
6. Ghosh, A.; Elber, R.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A 2002, 99, 10394-10398.
7. Jacob, J.; Krantz, B.; Dothager, R. S.; Thiyagarajan, P.; Sosnick, T. R. J. Mol. Biol. 2004, 338, 369-382.
8. Jagielska, A.; Scheraga, H. A. J. Comput. Chem. 2007, 28, 1068-1082.
9. Schrier, E. E.; Pottle, M.; Scheraga, H. A. J. Am. Chem. Soc. 1964, 86, 3444-3449.
10. Suzuki, E.; Taniguchi, Y.; Watanabe, T. J. Phys. Chem. 1973, 77, 1918-1922.
11. Yamamoto, K.; Nishi, N. J. Am. Chem. Soc. 1990, 112, 549-558.
12. Chocholousova, J.; Vacek, J.; Hobza, P. J. Phys. Chem. A 2003, 107, 3086-3092.
13. Némethy, G.; Scheraga, H. A. J. Phys. Chem. 1962, 66, 1773-1789.
14. Scheraga, H. A. J. Biomol. Struct. Dyn. 1998, 16, 447-460.
15. Hill, T. L. Statistical Mechanics. Principles and Selected Applications; McGraw-Hill: New York, 1956.
16. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72, 1047-1069.
17. Luo, H.; Sharp, K. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 10399-10404.
18. Yu, Y. B.; Privalov, P. L.; Hodges, R. S. Biophys. J. 2001, 81, 1632-1642.
19. Lazaridis, T. Curr. Org. Chem. 2002, 6, 1319-1332.
20. Carlsson, J.; Aqvist, J. Phys. Chem. Chem. Phys. 2006, 8, 5385-5395.
21. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Sttaub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
22. Joregensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
23. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
24. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897-5908.
25. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667-683.
26. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341.
27. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199.
28. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
29. Roux, B. Comput. Phys. Commun. 1995, 91, 275-282.
30. Paci, E.; Ciccotti, G.; Ferrano, D.; Kapral, R. Chem. Phys. Lett. 1991, 176, 581-587.
31. Shannon, C. E. Bell System Tech. J. 1948, 27, 379-423, 623-656.
32. Steinberg, I. Z.; Scheraga, H. A. J. Biol. Chem. 1963, 238, 172-181.
33. Perera, A.; Sokolic, F. J. Chem. Phys. 2004, 121, 11272-11282.
34. Kang, D.; Smith, P. E. J. Comput. Chem. 2006, 27, 1477-1485.
35. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipies. C: The Art of Scientific Computing, 2nd ed.; Cambridge University Press: Cambridge, U.K., 1992.
36. Nash, G. R.; Monk, C. B. J. Chem. Soc. 1957, 4274-4280.
37. Steinberg, I. Z.; Scheraga, H. A. J. Am. Chem. Soc. 1962, 84, 2890-2892.
38. de Araujo, A. F. P.; Pochapsky, T. C.; Joughin, B. Biophys. J. 1999, 76, 2319-2328.
39. Ross, P. D.; Rekharsky, M. V. Biophys. J. 1996, 71, 2144-2154.
40. Privalov, P. L.; Makhatadze, G. I. J. Mol. Biol. 1993, 232, 660-679.
41. Huang, D. M.; Chandler, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 8324-8327.