Hydration of krypton and consideration of clathrate models of hydrophobic effects from the perspective of quasi-chemical theory

Biophysical Chemistry

Volumn 105, Issue 2-3, 2003, Pages 323-338

  Ashbaugh, Henry S ^a   Asthagiri, D ^a   Pratt, Lawrence R ^a   Rempe, Susan B ^b  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

Ab initio molecular dynamics; Clathrate hydrate; Hydrophobic hydration; Krypton; Quasi chemical theory; Scaled particle theory

Indexed keywords

KRYPTON; WATER;

AB INITIO CALCULATION; ARTICLE; ATOMIC PARTICLE; CHEMICAL STRUCTURE; ENERGY TRANSFER; EXPERIMENTAL MODEL; HYDRATION; HYDROPHOBICITY; MOLECULAR DYNAMICS; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; QUANTUM CHEMISTRY; STRUCTURE ANALYSIS; THEORY;

EID: 0141671993     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(03)00084-X     Document Type: Article

References (79)

1. Kauzmann W. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1959;1-63.
2. Tanford C. How protein chemists learned about the hydrophobia factor. Protein Science. 6:1997;1358-1366.
3. Lazaridis T. Solvent size vs. cohesive energy as the origin of hydrophobicity. Ace. Chem. Res. 34:2001;931-937.
4. Pratt L.R. Molecular theory of hydrophobic effects: 'She is too mean to have her name repeated'. Annu. Rev. Phys. Chem. 53:2002;409-436.
5. Pratt L.R., Pohorille A. Hydrophobic effects and modeling of biophysical aqueous solution interfaces. Chem. Rev. 102:2002;2671-2691.
6. Bowron D.T., Filipponi A., Roberts M.A., Finney J.L. Hydrophobic hydration and the formation of a clathrate hydrate. Phys. Rev. Letts. 81:1998;4164-4167.
7. Frank H.S., Evans M.W. Free volume and entropy in condensed systems. III. Entropy in binary liquid mixtures; partial molar entropy in dilute solutions; structure and thermodynamics of aqueous electrolytes. J. Chem. Phys. 13:1945;507.
8. Hummer G., Garde S., García A.E., Pratt L.R. New perspectives on hydrophobic effects. Chem. Phys. 258:2000;349-370.
9. M.E. Paulaitis, L.R. Pratt, Hydration theory for molecular biophysics, Adv. Prot. Chem. (in press).
10. Swaminathan S., Harrison S.W., Beveridge D.L. Monte Carlo studies on structure of a dilute aqueous-solution of methane. J. Am. Chem. Soc. 100:1978;5705-5712.
11. Swope W.C., Andersen H.C. A molecular-dynamics method for calculating the solubility of gases in liquids and the hydrophobia hydration of inert-gas atoms in aqueous-solution. J. Phys. Chem. 88:1984;6548-6556.
12. Watanabe K., Andersen H.C. Molecular-dynamics study of the hydrophobic interaction in an aqueous-solution of krypton. J. Phys. Chem. 90:1986;795-802.
13. Chandler D., Weeks J.D., Andersen H.C. Van der Waals picture of liquids, solids, and phase-transformations. Science. 220:1983;787-794.
14. Y.A. Dyadin, E.G. Larionov, A.Y. Manakov, F.V. Zhurko, E.Y. Aladko, T.V. Mikina, V.Y. Komarov, Clathrate hydrates of hydrogen and neon, Mendeleev Comm. (1999) 209-210.
15. Kosyakov V.I., Shestakov V.A. Simulation of phase equilibria in the water-helium and water-neon systems. Russ. J. Phys. Chem. 76:2002;716-719.
16. Mao W.L., Mao H.-K., Goncharov A.F., Struzhkin V.V., Guo Q., Hu J., et al. Hydrogen clusters in clathrate hydrate. Science. 297:2002;2247-2249.
17. Sloan E.D. Jr. Clathrate Hydrates of Natural Gases, 2nd ed. 1998;Marcel Dekker, Inc, New York, Revised and expanded edition.
18. Eisenberg D., Kauzmann W. The Structure and Properties of Water. 1969;Oxford University Press, New York.
19. Cheng Y., Rossky P.J. Surface topography dependence of biomolecular hydrophobic hydration. Nature. 392:1998;696-699.
20. Glew D.N. Aqueous solubility and the gas-hydrates. The methane-water system. J. Phys. Chem. 66:1962;605-609.
21. Dill K.A. Dominant forces in protein folding. Biochem. 29:1990;7133-7155.
22. Klotz I.M. Protein hydration and behavior. Science. 128:1958;815-822.
23. Pauling L. The structure of water. Hadzi D. Hydrogen Bonding. 1959;1-6 Pergamon, New York.
24. Southall N.T., Dill K.A., Haymet A.D.J. A view of the hydrophobic effect. J. Phys. Chem. B. 106:2002;521-533.
25. Head-Gordon T. Is water-structure around hydrophobic groups clathrate-like? Proc. Nat. Acad. Sci. USA. 92:1995;8308-8312.
26. Udachin K.A., Ripmeester J.A. A complex clathrate hydrate structure showing bimodal guest hydration. Nature. 397:1999;420-423.
27. Udachin K.A., Ratcliffe C.I., Ripmeester J.A. A dense and efficient clathrate hydrate structure with unusual cages. Angew. Chem. Int. Ed. 40:2001;1303.
28. Teeter M.M. Water-structure of a hydrophobic protein at atomic resolution: pentagon rings of water-molecules on crystals of crambin. Proc. Natl. Acad. Sci. USA. 81:1984;6014-6018.
29. Lipscomb L.A., Zhou F.X., Williams L.D. Clathrate hydrates are poor models of biomolecule hydration. Biopolymers. 38:1996;177-181.
30. Tse J.S., Klein M.L., McDonald I.R. Molecular-dynamics studies of ice Ic and the structure-I clathrate hydrate of methane. J. Phys. Chem. 87:1983;4198-4203.
31. Forrisdahl O.K., Kvamme B., Haymet A.D.J. Methane clathrate hydrates: melting, supercooling, and phase separation from molecular dynamics computer simulations. Mol. Phys. 89:1996;819-834.
32. Owicki J.C., Scheraga H.A. Monte Carlo calculations in isothermal-isobaric ensemble. 2. dilute aqueous-solution of methane. J. Am. Chem. Soc. 99:1977;7413-7418.
33. Alagona G., Tani A. Structure of a dilute aqueous-solution of argon: Monte-Carlo simulation. J. Chem. Phys. 72:1980;580-588.
34. Gomez M.A., Pratt L.R., Hummer G., Garde S. Molecular realism in default models for information theories of hydrophobic effects. J. Phys. Chem. B. 103:1999;3520-3523.
35. Friedman H.L., Krishnan C.V. Water A Comprehensive Treatise. 3: 1973;1-118 Plenum Press, New York.
36. Pratt L.R., Rempe S.B. Quasi-chemical theory and implicit solvent models for simulations. Pratt L.R., Hummer G. Simulation and Theory of Electrostatic Interactions in Solution. Computational Chemistry, Biophysics, and Aqueous Solutions, AIP Conference Proceedings. 492:1999;172-201 American Institute of Physics, Melville, NY.
37. +(aq). J. Phys. Chem. A. 106:2002;9145-9148.
38. H.S. Ashbaugh, L.R. Pratt, A quasi-chemical self-consistent field model for the statistical thermodynamics of the hard sphere fluid, unpublished work.
39. + in liquid water. J. Am. Chem. Soc. 122:2000;966-967.
40. + in liquid water. Fluid Phase Equil. 183:2001;121-132.
41. Wang Y., Perdew J.P. Correlation hole of the spin-polarized electron gas with exact small-wave-vector and high-density scaling. Phys. Rev. B. 44:1991;13298.
42. Kresse G., Hafner J. Ab initio molecular-dynamics for liquid-metals. Phys. Rev. B. 47:1993;RC558.
43. Kresse G., Furthmüller J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B. 54:1996;11169.
44. Vanderbilt D. Soft self-consistent pseudopotentials in a generalized eigenvalue formalism. Phys. Rev. B. 41:1990;7892.
45. Kresse G., Hafner J. Norm-conserving and ultrasoft pseudopotentials for first-row and transition-elements. J. Phys. Condens. Matter. 6:1994;8245.
46. Filipponi A., Bowron D.T., Lobban C., Finney J.L. Structural determination of the hydrophobic hydration shell of Kr. Phys. Rev. Lett. 79:1997;1293-1296.
47. Ashbaugh H.S., Paulaitis M.E. Effect of solute size and solute-water attractive interactions on hydration water structure around hydrophobic solutes. J. Am. Chem. Soc. 123:2001;10721-10728.
48. Stillinger F.H. Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory. J. Sol. Chem. 2:1973;141-158.
49. Long J.P., Sloan E.D. Jr. Quantized water clusters around apolar molecules. Mol. Sim. 11:1993;145-161.
50. Lum K., Chandler D., Weeks J.D. Hydrophobicity at small and large length scales. J. Phys. Chem. B. 103:1999;4570-4577.
51. Pratt L.R., LaViolette R.A., Gomez M.A., Gentile M.E. Quasi-chemical theory for the statistical thermodynamics of the hard-sphere fluid. J. Phys. Chem. B. 105:2001;11662-11668.
52. Allen M.P., Tildesley D.J. Computer Simulation of Liquids. 1987;Oxford Science Publications, Oxford.
53. Clever H.L. Krpton, xenon, and radon-gas solubilities. Clever H.L. Solubility Data Series. 2:1979;Pergamon Press, New York.
54. Ludwig R., Weinhold F. Quantum cluster equilibrium theory of liquids: Freezing of QCE/3-21G water to tetrakaidecahedral 'Bucky-ice'. J. Chem. Phys. 110:1999;508-515.
55. Frisch M.J. Gaussian 98 (Revision A.2). 1998;Gaussian, Inc, Pittsburgh, PA.
56. Yoon B.J., Lenhoff A.M. A boundary element method for molecular electrostatics with electrolyte effects. J. Comp. Chem. 11:1990;1080-1086.
57. Sanner M.F., Spehner J.-C., Olson A.J. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 38:1996;305-320.
58. Pauling L. The structure and entropy of ice and of other crystals with some randomness of atomic arrangement. J. Am. Chem. Soc. 57:1935;2680-2684.
59. Garde S., Hummer G., García A.E., Paulaitis M.E., Pratt L.R. Origin of entropy convergence in hydrophobic hydration and protein folding. Phys. Rev. Lett. 77:1996;4966-4968.
60. Garde S., Ashbaugh H.S. Temperature dependence of hydrophobic hydration and entropy convergence in an isotropic model of water. J. Chem. Phys. 115:2001;977-982.
61. Ashbaugh H.S., Truskett T.M., Debenedetti P.G. A simple molecular thermodynamic theory of hydrophobic hydration. J. Chem. Phys. 116:(7):2002;2907-2921.
62. Pratt L.R., Pohorille A. Theory of hydrophobicity: transient cavities in molecular liquids. Proc. Natl. Acad. Sci. USA. 89:1992;2995-2999.
63. Pratt L.R., Pohorille A. Hydrophobic effects from cavity statistics. Palma M.U., Palma-Vittorelli M.B., Parak F. Proceedings of the EBSA 1992 International Workshop on Water-Biomolecule Interactions. 1993;261-268 Societá Italiana de Fisica, Bologna.
64. Guillot B., Guissani Y. A computer simulation study of the temperature dependence of the hydrophobic hydration. J. Chem. Phys. 99:1993;8075-8094.
65. Pratt L.R., Hummer G., Garde S. Theories of hydrophobic effects and the description of free volume in complex liquids. Caccamo C., Hansen J.-P., Stell G. New Approaches to Problems in Liquid State Theory, NATO Science Series. 529:1999;407-420 Kluwer, Netherlands.
66. Pratt L.R., Chandler D. Theory of the hydrophobic effect. J. Chem. Phys. 67:1977;3683-3704.
67. Murphy K.P., Privalov P.L., Gill S.J. Common features of protein unfolding and dissolution of hydrophobic compounds. Science. 247:1990;559-561.
68. Dill K.A. The meaning of hydrophobicity. Science. 250:1990;297-297.
69. Privalov P.L., Gill S.J., Murphy K.P. Reply to Dill. Science. 250:1990;297-297.
70. Herzfeld J. Understanding hydrophobic behavior. Science. 253:1991;88-88.
71. Li B., Alonso D.O.V., Daggett V. The molecular basis for the inverse temperature transition of elastin. J. Mol. Biol. 305:2001;581-592.
72. Stillinger F.H. Water revisited. Science. 209:1980;451-457.
73. Hummer G., Garde S., García A.E., Paulaitis M.E., Pratt L.R. Hydrophobic effects on a molecular scale. J. Phys. Chem. B. 102:1998; 10469-10482.
74. Head-Gordon T., Stillinger F.H. An orientational perturbation-theory for pure liquid water. J. Chem. Phys. 98:1993;3313-3327.
75. Ben-Naim A., Friedman H.L. On the application of the scale particle theory of aqueous solutions of nonpolar gases. J. Phys. Chem. 71:1967;448-449.
76. Pierotti R.A. The solubility of gases in liquids. J. Phys. Chem. 67:1963;1840-1845.
77. Pierotti R.A. A scaled particle theory of aqueous and nonaqueous solutions. Chem. Rev. 76:1976;717-726.
78. Rowlinson J.S., Swinton F.L. Liquids and Liquid Mixtures. 1982;Butterworths, London.
79. Hoffman R., Minkin V.I., Carpenter B.K. Ockham's razor and chemistry. HYLE: Int. J. Phil. Chem. 3:1997;3-28.