Conformational equilibria of alkanes in aqueous solution: Relationship to water structure near hydrophobic solutes

Biophysical Journal

Volumn 77, Issue 2, 1999, Pages 645-654

  Ashbaugh, Henry S ^a,d   Garde, Shekhar ^b   Hummer, Gerhard ^b   Kaler, Eric W ^a   Paulaitis, Michael E ^c  

^a University of Delaware   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c Johns Hopkins University   (United States)

^d LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALKANE DERIVATIVE; BUTANE; HEXANE; PENTANE; WATER;

AQUEOUS SOLUTION; ARTICLE; CONFORMATION; CONTROLLED STUDY; ENERGY; HYDRATION; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; SIMULATION; THERMODYNAMICS; WATER STRUCTURE;

EID: 0032814970     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)76920-1     Document Type: Article

References (78)

1. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Oxford University Press, Oxford, U.K.
2. Ashbaugh, H. S., E. W. Kaler, and M. E. Paulaitis. 1998. Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes. Biophys. J. 75:755-768.
3. Ashbaugh, H. S., and M. E. Paulaitis. 1996. Entropy of hydrophobic hydration: extension to hydrophobic chains. J. Phys. Chem. 100: 1900-1913.
4. Beglov, D., and B. Roux. 1994. Finite representation of an infinite bulk system: solvent boundary potential for computer simulations. J. Chem. Phys. 100:9050-9063.
5. Ben-Naim, A. 1974. Water and Aqueous Solutions. Plenum Press, New York.
6. Berendsen, H. J, C., J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models of water in relation to protein hydration. In Intermolecular Forces: Proceedings of the Fourteenth Jerusalem Symposium on Quantum Chemistry and Biochemistry. B. Pullman, editor. D. Reidel Publishing Company, Dordrecht, The Netherlands. 331-342.
7. Blokzijl, W., and J. B. F. N. Engberts. 1993. Hydrophobic effects. Opinions and facts. Agnew. Chem. Int. Ed. Engl. 32:1545-1579.
8. Chandler, D. 1987. Introduction to Modern Statistical Mechanics. Oxford University Press, New York.
9. Cheng, Y.-K., and P. J. Rossky. 1998. Surface topography dependence of biomolecular hydrophobic hydration. Nature. 392:696-699.
10. Chothia, C. 1974. Hydrophobic bonding and accessible surface area in proteins. Nature. 248:338-339.
11. Dill, K. A. 1990. Dominant forces in protein folding. Biochemistry. 29: 7133-7155.
12. Frank, H. S., and M. W. Evans. 1945. Free volume and entropy in condensed systems. III. Entropy in binary liquid mixtures; partial molal entropy in dilute solutions; structure and thermodynamics in aqueous electrolytes. J. Chem. Phys. 13:507-532.
13. García, A. E., G. Hummer, and D. M. Soumpasis. 1997. Hydration of an alpha-helical peptide: comparison of theory and molecular dynamics simulation. Proteins Strut. Funct. Genet. 27:471-480.
14. Garde, S., G. Hummer, A. E. García, M. E. Paulaitis, and L. R. Pratt. 1996a. Origin of the entropy convergence in hydrophobic hydration and protein folding. Phys. Rev. Lett. 77:4966-4968.
15. Garde, S., G. Hummer, A. E. García, L. R. Pratt, and M. E. Paulaitis. 1996b. Hydrophobic hydration: inhomogeneous water structure near nonpolar molecular solutes. Phys. Rev. E. 53:R4310-R4313.
16. Garde, S., G. Hummer, and M. E. Paulailis. 1996c. Hydrophobic interactions: conformational equilibria and the association of non-polar molecules in water. Faraday Disc. 103:125-139.
17. Garde, S., G. Hummer, M. E. Paulaitis, and A. E. García. 1997. Hydration of biological macromolecules: from small solutes to proteins and nucleic acids. In Proceedings of the 1996 Materials Research Society Fall Meeting Symposium on Statistical Mechanics in Physics and Biology. D. Wirtz, T. C. Halsey, editors. Materials Research Society, Pittsburgh. 463:21-28.
18. Garde, S., A. E. García, L. R. Pratt, and G. Hummer. 1999. Temperature dependence of the solubility of nonpolar gases in water. Biophys. Chem. 78:21-32.
19. Green, H. S. 1952. The Molecular Theory of Fluids. North-Holland Publishing Company, Amsterdam, The Netherlands.
20. Hermann, R. B. 1972. Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility with solvent cavity surface area. J. Phys. Chem. 76:2754-2759.
21. Hummer, G., A. E. García, and D. M. Soumpasis. 1995a. Hydration of nucleic-acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes. Biophys. J. 68:1639-1652.
22. Hummer, G., A. E. García, and D. M. Soumpasis. 1996a. A statistical mechanical description of biomolecular hydration. Faraday Disc. 103: 175-189.
23. Hummer, G., and S. Garde. 1998. Cavity expulsion and weak dewetting of hydrophobic solutes in water. Phys. Rev. Lett. 80:4193-4196.
24. Hummer, G., S. Garde, A. E. García, M. E. Paulaitis, and L. R. Pratt. 1998. The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proc. Natl. Acad. Sci. USA. 95:1552-1555.
25. Hummer, G., S. Garde, A. E. García, A. Pohorille, and L. R. Pratt. 1996b. An information theory model of hydrophobic interactions. Proc. Natl. Acad. Sci. USA. 93:8951-8955.
26. Hummer, G., L. R. Pratt, and A. E. García. 1995b. The hydration free energy of water. J. Phys. Chem. 99:14188-14194.
27. Hummer, G., L. R. Pratt, and A. E. García. 1996c. The free energy of ionic hydration. J. Phys. Chem. 100:1206-1215.
28. Hummer, G., and D. M. Soumpasis. 1994a. Computation of the water density distribution at the ice-water interface using the potentials-of-mean-force expansion. Phys. Rev. E. 49:591-596.
29. Hummer, G., and D. M. Soumpasis. 1994b. A statistical mechanical treatment of the structural hydration of biological macromolecules: results for B-DNA. Phys. Rev. E. 50:5085-5095.
30. Hummer, G., D. M. Soumpasis, and M. Neumann. 1994. Computer simulation of aqueous Na-Cl electrolytes. J. Phys.: Condens. Matt. 6:A141-A144.
31. Hunter, R. J. 1987. Foundations of Colloid Science. Oxford University Press, Oxford, U.K.
32. Israelachvili, J. 1992. Intermolecular and Surface Forces. Academic Press Limited, London.
33. Jorgensen, W. L. 1982. Monte Carlo simulation of n-butane in water: conformational evidence for the hydrophobic effect. J. Chem. Phys. 77:5757-5765.
34. Jorgensen, W. L., and J. K. Buckner. 1987. Use of statistical perturbation theory for computing solvent effects on molecular conformation. Butane in water. J. Phys. Chem. 91:6083-6085.
35. Jorgensen, W. L., J. D. Madura, and C. J. Swenson. 1984. Optimized intermolecular potential functions for liquid hydrocarbons. J. Am. Chem. Soc. 106:6638-6646.
36. Kaminski, G., E. M. Duffy, T. Matusui, and W. L. Jorgensen. 1994. Free energies of hydration and pure liquid properties of hydrocarbons from the OPLS all-atom model. J. Phys. Chem. 98:13077-13082.
37. Kauzmann, W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1-63.
38. Klement, R., D. M. Soumpasis, and T. M. Jovin. 1991. Computation of ionic distributions around charged biomolecular structures: results for right-handed and left-handed DNA. Proc. Natl. Acad. Sci. USA. 88: 4631-4635.
39. Kubo, R. 1962. Generalized cumulant expansion method. J. Phys. Soc. Jpn. 17:1100-1120.
40. Lazaridis, T., and M. E. Paulaitis. 1992. Entropy of hydrophobic hydration: a new statistical mechanical formulation. J. Phys. Chem. 96:3847-3855.
41. Lazaridis, T., and M. E. Paulaitis. 1993. Reply to the comment on "Entropy of hydrophobic hydration: a new statistical mechanical formulation". J. Phys. Chem. 97:5789-5790.
42. Lazaridis, T., and M. E. Paulaitis. 1994. Simulation studies of the hydration entropy of simple, hydrophobic solutes. J. Phys. Chem. 98:635-642.
43. Lee, B., and F. M. Richards. 1971. Protein structures: estimation of static accessibility. J. Mol. Bio. 55:379-400.
44. Lüdemann, S., R. Abseher, H. Schreiber, and O. Steinhauser. 1997. The temperature dependence of hydrophobic association in water. Pair versus bulk hydrophobic interactions. J. Am. Chem. Soc. 119:4206-4213.
45. Lüdemann, S., H. Schreiber, R. Abseher, and O. Steinhauser. 1996. The influence of temperature on pairwise hydrophobic interactions of methane-like particles: a molecular dynamics study of the free energy. J. Chem. Phys. 104:286-295.
46. Lum, K., and A. Luzar. 1997. Pathway to surface-induced phase-transition of a confined fluid. Phys. Rev. E 56:R6283-R6286.
47. Lum, K., and D. Chandler, 1998. Phase-diagram and free energies of vapor films and tubes for a confined fluid. Int. J. Thermophysics. 19:845-855.
48. Lum, K., D. Chandler, and J. D. Weeks. 1999. Hydrophobicity at small and large length scales. J. Phys. Chem. in press.
49. Makarov, V. A., B. K. Andrews, and B. M. Pettitt. 1998. Reconstructing the protein-water interface. Biopolymers. 45:469-478.
50. Mattice, W. L., and U. W. Suter. 1994. Conformational Theory of Large Molecules: The Rotational Isomeric State Model in Macromolecular Systems. John Wiley and Sons, Inc., New York.
51. aq at 25°C. J. Am. Chem. Soc. 102:4287-4294.
52. Mezei, M., and D. L. Beveridge. 1986. Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion. Methods Enzymol. 127:21-47.
53. New, M. H., and B. J. Berne. 1995. Molecular dynamics calculation of the effect of solvent polarizability on the hydrophobic interaction. J. Am. Chem. Soc. 117:7172-7179.
54. Pangali, C, M. Rao, and B. J. Berne. 1979. A Monte Carlo simulation of the hydrophobic interaction. J. Chem. Phys. 71:2975-2981.
55. Paulaitis, M. E., H. S. Ashbaugh, and S, Garde. 1994. The entropy of hydration of simple hydrophobic solutes. Biophys. Chem. 51:349-357.
56. Payne, V. A., N. Matubayasi, L. R. Murphy, and R. M. Levy. 1997. Monte Carlo study of the effect of pressure on hydrophobic association. J. Phys. Chem. B. 101:2054-2060.
57. Pelligrini, M., and S. Doniach. 1995. Modeling solvation contributions to conformational free energy changes of biomolecules using a potential of mean force expansion. J. Chem. Phys. 103:2696-2702.
58. Pelligrini, M., N. Grønbech-Jensen, and S. Doniach. 1996. Potentials of mean force for biomolecular simulations: theory and test on alanine dipeptide. J. Chem. Phys. 104:8639-8648.
59. Pettitt, M. B., V. A. Makarov, and B. K. Andrews. 1998. Protein hydration density: theory, simulations and crystallography. Curr. Opin. Struct. Biol. 8:218-221.
60. Pohorille, A., and L. R. Pratt. 1990. Cavities in molecular liquids and the theory of hydrophobic solubilities. J. Am. Chem. Soc. 112: 5066-5074.
61. Pratt, L. R., and D. Chandler. 1977. Theory of the hydrophobic effect. J. Chem. Phys. 67:3683-3704.
62. Pratt, L. R., and A. Pohorille. 1992. Theory of hydrophobicity: transient cavities in molecular liquids. Proc. Natl. Acad. Sci. USA. 89:2995-2999.
63. Reynolds, J. A., D. B. Gilbert, and C. Tanford. 1974. Empirical correlation between hydrophobic free energy and aqueous cavity surface area. Proc. Natl. Acad. Sci. USA. 71:2925-2927.
64. Richards, F. M. 1977. Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioeng. 6:151-176.
65. Rosenberg, R. O., R. Mikkilineni, and B. J. Berne. 1982. Hydrophobic effect of chain folding. The trans to gauche isomerization of n-butane in water. J. Am. Chem. Soc. 104:7647-7649.
66. Sitkoff, D., K. A. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988.
67. Smith, D., and A. D. J. Haymet. 1993. Free energy, entropy, and internal energy of hydrophobic interactions: computer simulations. J. Chem. Phys. 98:6445-6454.
68. Smith, P. E., and W. F. van Gunsteren. 1994. Predictions of free energy differences from a single simulation of the initial state. J. Chem. Phys. 100:577-585.
69. Soumpasis, D. M. 1984. Statistical mechanics of the B → Z transition of DNA: contribution of diffuse ionic interactions. Proc. Natl. Acad. Sci. USA. 81:5116-5119.
70. Stillinger, F. H. 1973. Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory. J. Solut. Chem. 2:141-158.
71. Tanford, C. 1980. The Hydrophobic Effect. Wiley, New York.
72. Tobias, D. J., and C. L. Brooks, III. 1990. The thermodynamics of solvaphobic effects: a molecular-dynamics study of n-butane in carbon tetra chloride and water. J. Chem. Phys. 92:2582-2592.
73. van Belle, D., and S. J. Wodak. 1993. Molecular dynamics study of methane hydration and methane association in a polarizable water phase. J. Am. Chem. Soc. 115:647-652.
74. Wallqvist, A., and B. J. Berne. 1995. Computer simulation of hydrophobic forces on stacked plates at short range. J. Phys. Chem. 99:2893-2899.
75. Weeks, J. D., D. Chandler, and H. C. Andersen. 1971. Role of repulsive forces in determining the equilibrium structure of simple liquids. J. Chem. Phys. 54:5237-5247.
76. Young, W. S., and C. L. Brooks, III. 1997. A reexamination of the hydrophobic effect: exploring the role of the solvent model in computing the methane-methane potential of mean force. J. Chem. Phys. 106: 9265-9269.
77. Zichi, D. A., and P. J. Rossky. 1986. Molecular conformational equilibria in liquids. J. Chem. Phys. 84:1712-1723.
78. Zwanzig, R. W. 1954. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J. Chem. Phys. 22:1420-1426.