New estimators for calculating solvation entropy and enthalpy and comparative assessments of their accuracy and precision

Journal of Physical Chemistry B

Volumn 114, Issue 24, 2010, Pages 8166-8180

  Wyczalkowski, Matthew A ^a   Vitalis, Andreas ^a   Pappu, Rohit V ^a  

^a WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DECOMPOSITION; ENTHALPY; ENTROPY; SOLVATION;

ACCURACY AND PRECISION; BENNETT ACCEPTANCE RATIO; COMPARATIVE ASSESSMENT; ENTROPY AND ENTHALPIES; FREE-ENERGY CALCULATIONS; ONE-DIMENSIONAL MODEL; OPLS-AA FORCE FIELD; TEMPERATURE DERIVATIVES;

FREE ENERGY;

EID: 77953782222     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp103050u     Document Type: Article

References (58)

1. Ben-Naim. A. Solvation Thermodynamics; Plenum Press: New York, 1987.
2. Smith, D. E.; Haymet, A. D. J. Free energy, entropy and internal energy of hydrophobic interactions: Computer simulations J. Chem. Phys. 1993, 98 (8) 6445-6454
3. Durell, S. R.; Wallqvist, A. Atomic-scale analysis of the solvation thermodynamics of hydrophobic hydration Biophys. J. 1996, 71 (4) 1695-706
4. Mobley, D. L.; Dill, K. A. Binding of small molecule ligands to proteins: "what you see" is not always "what you get" Structure 2009, 17 (4) 489-498
5. Kubo, M. M.; Gallicchio, E.; Levy, R. M. Thermodynamic decomposition of hydration free energies by computer simulation: Application to amines, oxides and sulfides J. Phys. Chem. B 1997, 101, 10527-10534
6. Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins J. Chem. Phys. 2003, 119 (11) 5740-5761
7. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 1998, 102 (18) 3586-3616
8. Udier-Blagović, M.; De Tirado, P. M.; Pearlman, S. A.; Jorgensen, W. L. Accuracy of free energies of hydration using CM1 and CM3 atomic charges J. Comput. Chem. 2004, 25 (11) 1322-1332
9. Horinek, D.; Mamatkulov, S. I.; Netz, R. R. Rational design of ion force fields based on thermodynamic solvation properties J. Chem. Phys. 2009, 130 (12) 124507
10. Levy, R. M.; Gallicchio, E. Computer simulations with explicit solvent: Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects Annu. Rev. Phys. Chem. 1998, 49, 531-567
11. Fleischman, S. H.; Brooks, C. L., III Thermodynamics of aqueous solvation-solution properties of alcohols and alkanes J. Chem. Phys. 1987, 87 (5) 3029-3037
12. Makhatadze, G. I.; Lopez, M. M.; Privalov, P. L. Heat capacities of protein functional groups Biophys. Chem. 1997, 64 (1-3) 93-101
13. Graziano, G. Hydration thermodynamics of N-methylacetamide J. Phys. Soc. Jpn. 2000, 69 (11) 3720-3725
14. Wolfenden, R. Interaction of the peptide bond with solvent water: A vapor phase analysis Biochemistry 1978, 17 (1) 201-204
15. Mobley, D. L.; Dumont, E.; Chodera, J. D.; Dill, K. A. Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent J. Phys. Chem. B 2007, 111, 2242-2254
16. Gallicchio, E.; Kubo, M. M.; Levy, R. M. Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation J. Phys. Chem. B 2000, 104, 6271-6285
17. Lu, N.; Kofke, D. A.; Woolf, T. B. Staging is more important than perturbation method for computation of enthalpy and entropy changes in complex systems J. Phys. Chem. B 2003, 107 (23) 5598-5611
18. Bennett, H. Efficient estimation of free energy differences from Monte Carlo data J. Comput. Phys. 1976, 22) 245-268
19. Shirts, M. R.; Chodera, J. D. Statistically optimal analysis of samples from multiple equilibrium states J. Chem. Phys. 2008, 129 (12) 124105
20. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
21. Vitalis, A.; Pappu, R. V. Absinth: A new continuum solvation model for simulations of polypeptides in aqueous solutions J. Comput. Chem. 2009, 30 (5) 673-699
22. Kirkwood, J. Statistical mechanics of fluid mixtures J. Chem. Phys. 1935, 3 (5) 300-313
23. Mezei, M.; Beveridge, D. L. Free energy simulations Ann. N.Y. Acad. Sci. 1986, 482 (1) 1-23
24. Zwanzig, R. W. High-temperature equation of state by a perturbation method. I. Nonpolar gases J. Chem. Phys. 1954, 22 (8) 1420-1426
25. Sun, S. X. Equilibrium free energies from path sampling of nonequilibrium trajectories J. Chem. Phys. 2003, 118 (13) 5769-5775
26. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: New York, 1987.
27. Vitalis, A.; Pappu, R. V. Methods for Monte Carlo simulations of biomacromolecules Ann. Rep. Comput. Chem. 2009, 5, 49-76
28. Vitalis, A.; Steffen, A.; Lyle, N.; Mao, A.; Pappu, R. V. Campari: A software suite for modeling and computational analysis of macromolecular properties across resolutions and interfaces, in preparation.
29. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 2001, 105 (28) 6474-6487
30. Beutler, T. C.; Mark, A. E.; van Scheik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Avoiding singularities and numerical instabilities in free energy calculations based on molecular mechanics simulations Chem. Phys. Lett. 1994, 222, 529-539
31. Jorgensen, W.; Chandrasekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79 (2) 926-935
32. Shirts, M. R.; Pande, V. S. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models J. Chem. Phys. 2005, 122, 134508
33. Pauling, L. General Chemistry; W. H. Freeman Press: San Francisco, CA, 1970.
34. Skeel, R. D.; Izaguirre, J. A. An impulse integrator for Langevin dynamics Mol. Phys. 2002, 100 (24) 3885-3891
35. Onsager, L. Electric moments of molecules in liquids J. Am. Chem. Soc. 1936, 58, 1486-1493
36. Garde, S.; Hummer, G.; Paulaitis, M. E. Free energy of hydration of a molecular ionic solute: Tetramethylammonium ion J. Chem. Phys. 1998, 108 (4) 1552-1561
37. Hunenberger, P. Thermostat algorithms for molecular dynamics simulations Adv. Polym. Sci. 2005, 173, 105-147
38. Wyczalkowski, M. A.; Pappu, R. V. Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange Phys. Rev. E 2008, 77 (2) 026104
39. Shenfeld, K.; Xu, H.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations Phys. Rev. E 2009, 80 (4 046705
40. Crooks, G. E. Measuring thermodynamic length Phys. Rev. Lett. 2007, 99 (10) 100602
41. Ben-Naim, A.; Marcus, Y. Solvation thermodynamics of nonionic solutes J. Chem. Phys. 1984, 81 (4) 2016-2027
42. Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous-solution J. Solution Chem. 1981, 10 (8) 563-595
43. Jorgensen, W. L.; Jenson, C. Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density J. Comput. Chem. 1998, 19 (10) 1179-1186
44. Mahoney, M. W.; Jorgensen, W. L. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions J. Chem. Phys. 2000, 112, 8910-8922
45. Lu, N. D.; Kofke, D. A. Accuracy of free-energy perturbation calculations in molecular simulation. I. modeling J. Chem. Phys. 2001, 114 (17) 7303-7311
46. Zuckerman, M.; Woolf, T. B. Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities J. Stat. Phys. 2004, 114 (5-6) 1303-1323
47. Roux, B.; Simonson, T. Implicit solvent models Biophys. Chem. 1999, 78, 1-20
48. Wu, D.; Kofke, D. A. Asymmetric bias in free-energy perturbation measurements using two hamiltonian-based models Phys. Rev. E 2004, 70 (6 066702
49. Trzesniak, D.; van Gunsteren, W. F. Pathway dependence of the efficiency of calculating free energy and entropy of solute-solute association in water Chem. Phys. 2006, 330 (3) 410-416
50. Pratt, L. R.; Chandler, D. Theory of the hydrophobic effect J. Chem. Phys. 1977, 67, 3683
51. Oberhofer, H.; Dellago, C.; Geissler, P. L. Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods J. Phys. Chem. B 2005, 109 (14) 6902-15
52. Nummela, J.; Yassin, F.; Andricioaei, I. Entropy-energy decomposition from nonequilibrium work trajectories J. Chem. Phys. 2008, 128 (2 024104
53. Wolfram Research. Mathematica 7.0.; Wolfram Research Inc.: Champaign, IL, 2008.
54. Avbelj, F.; Luo, P.; Baldwin, R. L. Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities Proc. Natl. Acad. Sci. U.S.A. 2000, 97 (20) 10786-91
55. Moore, J. C.; Battino, R.; Rettich, T. R.; Handa, Y. P.; Wilhelm, E. Partial molar volumes of gases at infinite dilution in water at 298.15 K J. Chem. Eng. Data 1982, 27 (1) 22-24
56. Hnedkovsky, L.; Degrange, S.; Cibulka, I. Partial molar volumes of organic solutes in water. I. O-, m-, and p-cresol at temperatures 298 K to 573 K J. Chem. Thermodyn. 1998, 30 (5) 557-569
57. Wilhelm, E.; Battino, R.; Wilcock, R. Low-pressure solubility of gases in liquid water Chem. Rev. 1977, 77, 219
58. Humphrey, W.; Dalke, A.; Schulten, K. VMD-Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38