Model-Free "Solvent Modeling" in Chemistry and Biochemistry Based on the Statistical Mechanics of Liquids

Modeling Solvent Environments: Applications to Simulations of Biomolecules

Volumn , Issue , 2010, Pages 31-54

  Yoshida, Norio ^a,b   Kiyota, Yasuomi ^a,b   Ikuta, Yasuhiro ^a,b   Imai, Takashi ^c   Hirata, Fumio ^a,b  

^a INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c RIKEN   (Japan)

Author keywords

Hydrolysis; Molecular recognition; Partial molar volume; RISM; Statistical mechanics

Indexed keywords

EID: 84887178452     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527629251.ch2     Document Type: Chapter

References (42)

1. Watson, J.D., et al. (eds) (1987) Molecular Biology of the Gene, Benjamin/Cummings, Menlo Park, CA.
2. Gurney, R.W. (1953) Ionic Processes in Solution, Dover, New York.
3. Prock, A. and McConkey, G. (eds) (1962) Topics in Chemical Physics: Based on the Harvard Lectures of Peter J.W. Debye, Elsevier, Amsterdam.
4. Kirkwood, J.G. (1934) Theory of solutions of molecules containing widely separated charges with special application to zwitterions. J. Chem. Phys., 2, 351.
5. Onsager, L. (1936) Electric moments of molecules in liquids. J. Am. Chem. Soc., 58, 1486.
6. Frohlich, H. (1958) Theory of Dielectrics, Clarendon Press, Oxford.
7. Born, M. (1920) Volumen und Hydratationswärme der Ionen. Z. Phys., 1, 45.
8. Marcus, R.A. (1964) Chemical and electrochemical electron-transfer theory. Annu. Rev. Phys. Chem., 15, 155.
9. Tapia, O. and Bertran, J. (eds) (1996) Solvent Effects and Chemical Reactivity, Kluwer Academic, Dordrecht.
10. Hill, T. (1987) Statistical Mechanics, Dover, New York.
11. McQuarrie, D.A. (1976) Statistical Mechanics, Harper and Row, New York.
12. Hansen, J.-P. and McDonald, I.R. (2006) Theory of Simple Liquids, 3rd edn, Academic, London.
13. Chandler, D. and Andersen, H.C. (1972) Optimized cluster expansions for classical fluids. II. Theory of molecular liquids. J. Chem. Phys., 57, 1930.
14. Hirata, F. and Rossky, P.J. (1981) An extended Rism equation for molecular polar fluids. Chem. Phys. Lett., 83, 329.
15. Hirata, F. (ed.) (2003) Molecular Theory of Solvation (Understanding Chemical Reactivity), Kluwer, Dordrecht.
16. Kovalenko, A. and Hirata, F. (1998) Three-dimensional density profiles of water in contact with a solute of arbitrary shape: a RISM approach. Chem. Phys. Lett., 290, 237.
17. Beglov, D. and Roux, B. (1997) An integral equation to describe the solvation of polar molecules in liquid water. J. Phys. Chem. B, 101, 7821.
18. Cortis, C.M., Rossky, P.J., and Friesner, R.A. (1997) A three-dimensional reduction of the Ornstein-Zernicke equation for molecular liquids. J. Chem. Phys., 107, 6400.
19. Imai, T., Kovalenko, A., and Hirata, F. (2005) Partial molar volume of proteins studied by the three-dimensional reference. Interaction site model theory. J. Phys. Chem. B, 109, 6658.
20. Imai, T., Hiraoka, R., Kovalenko, A., and Hirata, F. (2005) Water molecules in a protein cavity detected by a statistical-mechanical theory. J. Am. Chem. Soc., 127, 15334.
21. Kovalenko, A. and Hirata, F. (1999) Self-consistent description of a metal-water interface by the Kohn-Sham density functional theory and three-dimensional reference interaction site model. J. Chem. Phys., 110, 10095.
22. Singer, S.J. and Chandler, D. (1985) Free energy functions in the extended RISM approximation. Mol. Phys., 55, 621.
23. Kirkwood, J.G. and Buff, F.D. (1951) The statistical mechanical theory of solutions. J. Chem. Phys., 19, 774.
24. Imai, T., Kinoshita, M., and Hirata, F. (2000) Theoretical study for partial molar volume of amino acids in aqueous solution: implication of ideal fluctuation volume. J. Chem. Phys., 112, 9469.
25. Harano, Y., Imai, T., Kovalenko, A., and Hirata, F. (2001) Theoretical study for partial molar volume of amino acids and polypeptides by the three-dimensional reference interaction site model. J. Chem. Phys., 114, 9506.
26. Sato, H., Hirata, F., and Kato, S. (1996) Analytical energy gradient for the reference interaction site model multiconfigurational self-consistent-field method: application to 1,2-difluoroethylene in aqueous solution. J. Chem. Phys., 105, 1546.
27. Gusarov, S., Ziegler, T., and Kovalenko, A. (2006) Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package. J. Phys. Chem. A, 110, 6083.
28. Yoshida, N. and Hirata, F. (2006) A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions. J. Comput. Chem., 27, 453.
29. Imai, T., Hiraoka, R., Kovalenko, A., and Hirata, F. (2007) Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation. Proteins Struct. Funct. Bioinform., 66, 804.
30. Wilson, K.P., Malcolm, B.A., and Matthews, B.W. (1992) Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme. J. Biol. Chem., 267, 10842.
31. Yoshida, N., Phongphanphanee, S., Maruyama, Y., Imai, T., and Hirata, F. (2006) Selective ion-binding by protein probed with the 3D-RISM theory. J. Am. Chem. Soc., 128, 12042.
32. Yoshida, N., Phongphanphanee, S., and Hirata, F. (2007) Selective ion binding by protein probed with the statistical mechanical integral equation theory. J. Phys. Chem. B, 111, 4588.
33. 2+ binding site engineered into human lysozyme. J. Biol. Chem., 273, 34310.
34. Ikuta, Y., Karita, S., Kitago, Y., Watanabe, N., and Hirata, F. (2008) A water molecule identified as a substrate of enzymatic hydrolysis of cellulose: a statistical-mechanics study. C hem. Phys. Lett., 465, 279.
35. Perutz, M.F. and Matthews, F.S. (1966) An x-ray study of azide methaemoglobin. J. Mol. Biol., 21, 199.
36. Sakakura, M., Yamaguchi, S., Hirota, N., and Terazima, M. (2001) Dynamics of structure and energy of horse carboxymyoglobin after photodissociation of the carbon monoxide. J. Am. Chem. Soc., 123, 4286.
37. Nishihara, Y., Sakakura, M., Kimura, Y., and Terazima, M. (2004) The escape process of carbon monoxide from myoglobin to solution at physiological temperature. J. Am. Chem. Soc., 126, 11877.
38. Kiyota, Y., Hiraoka, R., Yoshida, N., Maruyama, Y., Imai, T., and Hirata, F. (2009) Theoretical study of CO escaping pathway in myoglobin with the 3D-RISM theory. J. Am. Chem. Soc., 131, 3852.
39. Tilton, R.F., Kuntz, I.D., and Petsko, G.A. (1984) Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 Å. Biochemistry, 23, 2849.
40. 2, CO, NO, and Xe inside myoglobin. Biophys. J., 91, 1844.
41. Miyata, T. and Hirata, F. (2008) Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution. J. Comput. Chem., 29, 871.
42. Kim, B.-S., Chong, S.H., Ishizuka, R., and Hirata, F. (2008) An attempt toward the generalized Langevin dynamics simulation. Condens. Matter Phys., 11, 179.