Free-energy analysis of solvation with the method of energy representation

Frontiers in Bioscience

Volumn 14, Issue 9, 2009, Pages 3536-3549

  Matubayasi, Nobuyuki ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Biomolecular hydration; Distribution function; Energy representation; Free energy; Membrane; Micelle; Review; Solution; Solvation; Supercritical fluid; Water

Indexed keywords

ARTIFICIAL MEMBRANE; MICELLE; REVIEW; SOLUBILITY; THERMODYNAMICS;

MEMBRANES, ARTIFICIAL; MICELLES; SOLUBILITY; THERMODYNAMICS;

EID: 63849324314     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2735/3469     Document Type: Article

References (26)

1. J. P. Hansen and I. R. McDonald: Theory of Simple Liquids, 2nd ed., Academic Press London (1986)
2. M. P. Allen and D. J. Tildesley: Computer Simulation of Liquids, Oxford University Press Oxford (1987)
3. nd ed., Academic Press London (2002)
4. T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber and W. F. van Gunsteren: Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem Phys Lett 222, 529-539(1994)
5. H. Resat and M. Mezei: Studies on free energy calculations. II. A theoretical approach to molecular solvation. J Chem Phys 101, 6126-6140(1994)
6. M. Zacharias, T. P. Straatsma and J. A. McCammon: Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration. J Chem Phys 100, 9025(1994)
7. N. Lu, J. K. Singh and D. A. Kofke: Appropriate methods to combine forward and reverse free-energy perturbation averages. J Chem Phys 118, 2977-2984(2003)
8. M. R. Shirts and V. S. Pande: Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. J Chem Phys 122, 144107 (16 pages) (2005)
9. N. Matubayasi, L. H. Reed and R. M. Levy: Thermodynamics of Hydration Shell. 1. Excess Energy of a Hydrophobic Solute. J Phys Chem 98, 10640-10649(1994)
10. N. Matubayasi: Matching-mismatching of Water Geometry and Hydrophobic Hydration. J Am Chem Soc 116, 1450-1456(1994) (Pubitemid 24980615)
11. D. Chandler and H. C. Andersen: Optimized Cluster Expansions for Classical Fluids. II. Theory of Molecular Liquids. J Chem Phys 57, 1930-1937(1972)
12. F. Hirata and P. J. Rossky: An extended rism equation for molecular polar fluids. Chem Phys Lett 83, 329-334(1981)
13. S. J. Singer and D. Chandler: Free energy functions in the extended RISM approximation. Mol Phys 55, 621-625(1985)
14. A. Kovalenko and F. Hirata: Self-consistent description of a metal-water interface by the Kohn-Sham density functional theory and the three-dimensional reference interaction site model. J Chem Phys 110, 10095-10112(1999)
15. S. M. Kast: Combinations of simulation and integral equation theory. Phys Chem Chem Phys 3, 5087-5092(2001)
16. H. Freedman and T. N. Truong: A coupled RISM/MD or MC simulation methodology for solvation free energies. Chem Phys Lett 381, 362-367(2003)
17. H. Freedman and T. N. Truong: Coupled reference interaction site model'simulation approach for thermochemistry of solvation: Theory and prospects. J Chem Phys 121, 2187-2198(2004)
18. N. Matubayasi and M. Nakahara: Theory of solutions in the energetic representation. I. Formulation. J Chem Phys 113, 6070-6081(2000)
19. N. Matubayasi and M. Nakahara: Theory of solutions in the energy representation. II. Functional for the chemical potential. J Chem Phys 117, 3605-3616(2002) ; (Pubitemid 34992645)
20. erratum, J Chem Phys 118, 2446(2003)
21. N. Matubayasi and M. Nakahara: Theory of solutions in the energy representation. III. Treatment of the molecular flexibility. J Chem Phys 119, 9686-9702(2003)
22. H. Takahashi, N. Matubayasi, M. Nakahara and T. Nitta: A quantum chemical approach to the free energy calculations in condensed systems: The QM/MM method combined with the theory of energy representation. J Chem Phys 121, 3989-3999(2004)
23. P. B. Balbuena, K. P. Johnston and P. J. Rossky: Computer Simulation Study of an sN2 Reaction in Supercritical Water. J Phys Chem 99, 1554-1565(1995)
24. P. B. Balbuena, K. P. Johnston and P. J. Rossky: Molecular Dynamics Simulation of Electrolyte Solutions in Ambient and Supercritical Water. 1. Ion Solvation. J Phys Chem 100, 2706-2715(1996) (Pubitemid 126793225)
25. N. Matubayasi, K. K. Liang and M. Nakahara: Free-energy analysis of solubilization in micelle. J Chem Phys 124, 154908 (13 pages) (2006)
26. M. Matubayasi, W. Shinoda and M. Nakahara: Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation. J Chem Phys 128, 195107 (13 pages) (2008)