Variational approach for nonpolar solvation analysis

Journal of Chemical Physics

Volumn 137, Issue 8, 2012, Pages

  Chen, Zhan ^a   Zhao, Shan ^b   Chun, Jaehun ^c   Thomas, Dennis G ^c   Baker, Nathan A ^c   Bates, Peter W ^a   Wei, G W ^a,d,e  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b UNIVERSITY OF ALABAMA   (United States)

^c PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^d Michigan State University   (United States)

^e UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MODELING; CONTINUUM DESCRIPTION; DIFFERENTIAL GEOMETRY; ENERGY FUNCTIONALS; EXPERIMENTAL DATA; IMPLICIT SOLVENT MODEL; MODEL PREDICTION; NON-POLAR; SOLVATION ENERGY; SOLVATION FREE ENERGIES; SOLVATION MODELS; VAN DER WAALS INTERACTIONS; VARIATIONAL APPROACHES;

CHEMICAL ANALYSIS; FREE ENERGY; LAPLACE EQUATION; SOLVENTS; VAN DER WAALS FORCES;

SOLVATION;

SOLVENT;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; SURFACE PROPERTY; THERMODYNAMICS;

MODELS, CHEMICAL; SOLVENTS; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 84865794074     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4745084     Document Type: Article

References (61)

1. J. W. Ponder and D. A. Case, Force fields for protein simulations., Adv. Protein Chem. 66, 27-85 (2003). 10.1016/S0065-3233(03)66002-X (Pubitemid 37392314)
2. a, redox reactions and solvation free energies., J. Phys. Chem. B 113, 1253-1272 (2009). 10.1021/jp8071712
3. R. M. Levy, L. Y. Zhang, E. Gallicchio, and A. K. Felts, On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy., J. Am. Chem. Soc. 125 (31), 9523-9530 (2003). 10.1021/ja029833a (Pubitemid 36936069)
4. E. Gallicchio, M. M. Kubo, and R. M. Levy, Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation., J. Phys. Chem. B 104 (26), 6271-6285 (2000). 10.1021/jp0006274
5. R. Ishizuka, S. H. Chong, and F. Hirata, An integral equation theory for inhomogeneous molecular fluids: The reference interaction site model approach., J. Chem. Phys. 128 (3), 34504-34504 (2008). 10.1063/1.2819487
6. C. S. Hsu and D. Chandler, Rism calculation of the structure of liquid acetonitrile., Mol. Phys. 36 (1), 215-224 (1978). 10.1080/00268977800101521
7. 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 (1999). 10.1063/1.478883
8. J. L. Lebowitz and J. K. Percus, Mean spherical model for lattice gases with extended hard cores and continuum fluids., Phys. Rev. 144 (1), 251 (1966). 10.1103/PhysRev.144.251
9. R. Triolo, J. R. Grigera, and L. Blum, Simple electrolytes in the mean spherical approximation., J. Phys. Chem. 80 (17), 1858-1861 (1976). 10.1021/j100558a008
10. J. M. J. Van Leeuwen, J. Groeneveld, and J. De Boer, New method for the calculation of the pair correlation function. I., Physica 25 (7-12), 792-808 (1959). 10.1016/0031-8914(59)90004-7
11. L. S. Ornstein and F. Zernike, Accidental deviations of density and opalescence at the critical point of a single substance., Proc. R. Acad. Sci. Amsterdam 17, 793 (1914).
12. J. K. Percus, H. L. Frisch, and J. L. Lebowitz, The Equilibrium Theory of Classical Fluids, edited by, H. L. Frisch, and, J. L. Lebowitz, (Benjamin, 1964), p. 1133.
13. J. P. Donley, J. G. Curro, and J. D. McCoy, A density functional theory for pair correlation functions in molecular liquids., J. Chem. Phys. 101, 3205 (1994). 10.1063/1.467566
14. J. K. Percus and G. J. Yevick, Analysis of classical statistical mechanics by means of collective coordinates., Phys. Rev. 110 (1), 1 (1958). 10.1103/PhysRev.110.1
15. M. S. Wertheim, Exact solution of the Percus-Yevick integral equation for hard spheres., Phys. Rev. Lett. 10 (8), 321-323 (1963). 10.1103/PhysRevLett.10. 321
16. P. Koehl, H. Orland, and M. Delarue, Beyond Poisson-Boltzmann: Modeling biomolecule-water and water-water interactions., Phys. Rev. Lett. 102 (8), 087801 (2009). 10.1103/PhysRevLett.102.087801
17. S. A. Hassan, Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution., J. Phys. Chem. B 111 (1), 227-241 (2007). 10.1021/jp0647479 (Pubitemid 46277987)
18. A. Rubinstein and S. Sherman, Evaluation of the influence of the internal aqueous solvent structure on electrostatic interactions at the protein-solvent interface by nonlocal continuum electrostatic approach., Biopolymers 87 (2-3), 149-164 (2007). 10.1002/bip.20808 (Pubitemid 47518366)
19. P. Madden and D. Kivelson, A Consistent Molecular Treatment of Dielectric Phenomena, Advances in Chemical Physics Vol. 56, (1984), pp. 467-566.
20. K. A. Sharp and B. Honig, Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equatlon., J. Phys. Chem. 94, 7684-7692 (1990). 10.1021/j100382a068
21. M. K. Gilson, M. E. Davis, B. A. Luty, and J. A. McCammon, Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation., J. Phys. Chem. 97 (14), 3591-3600 (1993). 10.1021/j100116a025
22. F. H. Stillinger, Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory., J. Solution Chem. 2, 141-158 (1973). 10.1007/BF00651970
23. F. Dong, J. A. Wagoner, and N. A. Baker, Assessing the performance of implicit solvation models at a nucleic acid surface., Phys. Chem. Chem. Phys. 10, 4889-4902 (2008). 10.1039/b807384h
24. C. J. Cramer and D. G. Truhlar, Implicit solvation models: Equilibria, structure, spectra, and dynamics., Chem. Rev. 99, 2161-2200 (1999). 10.1021/cr960149m (Pubitemid 129585183)
25. B. Husowitz and V. Talanquer, Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: A density functional approach., J. Chem. Phys. 126 (5), 054508 (2007). 10.1063/1.2432327
26. M. R. Reddy, U. C. Singh, and M. D. Erion, Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies., J. Comput. Chem. 28 (2), 491-494 (2007). 10.1002/jcc.20510 (Pubitemid 46181822)
27. A. V. Marenich, C. J. Cramer, and D. G. Truhlar, Perspective on foundations of solvation modeling: The electrostatic contribution to the free energy of solvation., J. Chem. Theory Comput. 4 (6), 877-887 (2008). 10.1021/ct800029c
28. W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig, Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects., J. Comput. Chem. 23, 128-137 (2002). 10.1002/jcc.1161 (Pubitemid 34063137)
29. B. Lee and F. M. Richards, The interpretation of protein structures: Estimation of static accessibility., J. Mol. Biol. 55 (3), 379-400 (1971). 10.1016/0022-2836(71)90324-X
30. F. M. Richards, Areas, volumes, packing, and protein structure., Annu. Rev. Biophys. Bioeng. 6 (1), 151-176 (1977). 10.1146/annurev.bb.06.060177.001055
31. R. S. Spolar, J. H. Ha, and M. T. Record Jr., Hydrophobic effect in protein folding and other noncovalent processes involving proteins., Proc. Natl. Acad. Sci. U.S.A. 86 (21), 8382-8385 (1989). 10.1073/pnas.86.21.8382 (Pubitemid 19286063)
32. J. R. Livingstone, R. S. Spolar, and M. T. Record Jr., Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area., Biochemistry 30 (17), 4237-4244 (1991). 10.1021/bi00231a019
33. P. B. Crowley and A. Golovin, Cation-π interactions in protein-protein interfaces., Proteins: Struct., Funct., Bioinf. 59 (2), 231-239 (2005). 10.1002/prot.20417 (Pubitemid 40471562)
34. L. A. Kuhn, M. A. Siani, M. E. Pique, C. L. Fisher, E. D. Getzoff, and J. A. Tainer, The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures., J. Mol. Biol. 228 (1), 13-22 (1992). 10.1016/0022-2836(92)90487-5
35. C. A. S. Bergstrom, M. Strafford, L. Lazorova, A. Avdeef, K. Luthman, and P. Artursson, Absorption classification of oral drugs based on molecular surface properties., J. Med. Chem. 46 (4), 558-570 (2003). 10.1021/jm020986i (Pubitemid 36182757)
36. A. I. Dragan, C. M. Read, E. N. Makeyeva, E. I. Milgotina, M. E. Churchill, C. Crane-Robinson, and P. L. Privalov, DNA binding and bending by HMG boxes: Energetic determinants of specificity., J. Mol. Biol. 343 (2), 371-393 (2004). 10.1016/j.jmb.2004.08.035 (Pubitemid 39296872)
37. R. M. Jackson and M. J. Sternberg, A continuum model for protein-protein interactions: Application to the docking problem., J. Mol. Biol. 250 (2), 258-275 (1995). 10.1006/jmbi.1995.0375
38. V. J. Licata and N. M. Allewell, Functionally linked hydration changes in Escherichia coli aspartate transcarbamylase and its catalytic subunit., Biochemistry 36 (33), 10161-10167 (1997). 10.1021/bi970669r (Pubitemid 27357726)
39. M. F. Sanner, A. J. Olson, and J. C. Spehner, Reduced surface: An efficient way to compute molecular surfaces., Biopolymers 38, 305-320 (1996). 10.1002/(SICI)1097-0282(199603)38:3305::AID-BIP4>3.0.CO;2-Y
40. G. W. Wei, Y. H. Sun, Y. C. Zhou, and M. Feig, Molecular multiresolution surfaces., e-print arXiv:math-ph/0511001v1.
41. P. W. Bates, G. W. Wei, and S. Zhao, The minimal molecular surface., e-print arXiv:q-bio/0610038v1 [q-bio.BM].
42. P. W. Bates, G. W. Wei, and S. Zhao, Minimal molecular surfaces and their applications., J. Comput. Chem. 29 (3), 380-391 (2008). 10.1002/jcc.20796
43. P. W. Bates, Z. Chen, Y. H. Sun, G. W. Wei, and S. Zhao, Geometric and potential driving formation and evolution of biomolecular surfaces., J. Math. Biol. 59, 193-231 (2009). 10.1007/s00285-008-0226-7
44. G. W. Wei, Differential geometry based multiscale models., Bull. Math. Biol. 72, 1562-1622 (2010). 10.1007/s11538-010-9511-x
45. Z. Chen, N. A. Baker, and G. W. Wei, Differential geometry based solvation models I: Eulerian formulation., J. Comput. Phys. 229, 8231-8258 (2010). 10.1016/j.jcp.2010.06.036
46. Z. Chen, N. A. Baker, and G. W. Wei, Differential geometry based solvation models II: Lagrangian formulation., J. Math. Biol. 63, 1139-1200 (2011). 10.1007/s00285-011-0402-z
47. Z. Chen and G. W. Wei, Differential geometry based solvation model. III. Quantum formulation., J. Chem. Phys. 135, 194108 (2011). 10.1063/1.3660212
48. J. Dzubiella, J. M. J. Swanson, and J. A. McCammon, Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models., Phys. Rev. Lett. 96, 087802 (2006). 10.1103/PhysRevLett.96.087802 (Pubitemid 43334270)
49. L. T. Cheng, J. Dzubiella, J. A. McCammon, and B. Li, Application of the level-set method to the implicit solvation of nonpolar molecules., J. Chem. Phys. 127 (8), 084503 (2007). 10.1063/1.2757169 (Pubitemid 47352536)
50. G.-W. Wei, Q. Zheng, Z. Chen, and K. Xia, Variational multiscale models for charge transport., SIAM Rev. (to be published).
51. J. A. Wagoner and N. A. Baker, Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms., Proc. Natl. Acad. Sci. U.S.A. 103 (22), 8331-8336 (2006). 10.1073/pnas.0600118103 (Pubitemid 43838455)
52. E. Gallicchio, L. Y. Zhang, and R. M. Levy, The SGB/NP hydration free energy model based on the surface generalized Born solvent reaction field and novel nonpolar hydration free energy estimators., J. Comput. Chem. 23 (5), 517-529 (2002). 10.1002/jcc.10045 (Pubitemid 34409032)
53. E. Gallicchio and R. M. Levy, AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling., J. Comput. Chem. 25 (4), 479-499 (2004). 10.1002/jcc.10400
54. J. D. Weeks, D. Chandler, and H. C. Andersen, Role of repulsive forces in determining the equilibrium structure of simple liquids., J. Chem. Phys. 54 (12), 5237-5247 (1971). 10.1063/1.1674820
55. A. Nicholls, D. L. Mobley, P. J. Guthrie, J. D. Chodera, and V. S. Pande, Predicting small-molecule solvation free energies: An informal blind test for computational chemistry., J. Med. Chem. 51 (4), 769-779 (2008). 10.1021/jm070549+ (Pubitemid 351304686)
56. W. E. Lorensen and H. E. Cline, Marching cubes: A high resolution 3D surface reconstruction algorithm., Comput. Graphics 21, 163-169 (1987). 10.1145/37402.37422
57. W. H. Geng and G. W. Wei, Multiscale molecular dynamics via the matched interface and boundary (mib) method., J. Comput. Phys. 230, 435-457 (2011). 10.1016/j.jcp.2010.09.031
58. S. Cabani, P. Gianni, V. Mollica, and L. Lepori, Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution., J. Solution Chem. 10 (8), 563-595 (1981). 10.1007/BF00646936
59. D. A. Perlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, S. Debolt, D. Ferguson, G. Seibel, and P. Kollman, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules., Comput. Phys. Commun. 91, 1-41 (1995). 10.1016/0010-4655(95)00041-D
60. D. Veenstra, D. Ferguson, and P. Kollman, How transferable are hydrogen parameters in molecular mechanics calculations?, J. Comput. Chem. 13 (8), 971-978 (1992). 10.1002/jcc.540130807
61. E. L. Ratkova, G. N. Chuev, V. P. Sergiievskyi, and M. V. Fedorov, An accurate prediction of hydration free energies by combination of molecular integral equations theory with structural descriptors., J. Phys. Chem. B 114 (37), 12068-12079 (2010). 10.1021/jp103955r