Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes

Journal of Physical Chemistry B

Volumn 117, Issue 27, 2013, Pages 8232-8244

  Huggins, David J ^a,b   Payne, Mike C ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; FORECASTING; HYDRATION; MOLECULES; PERTURBATION TECHNIQUES; PROBABILITY DISTRIBUTIONS; SOLVATION;

COEFFICIENT OF DETERMINATION; FREE ENERGY PERTURBATION; HYDRATION FREE ENERGIES; INHOMOGENEOUS FLUID SOLVATION THEORIES; INTERACTION ENERGIES; SOLVATION FREE ENERGIES; SOLVATION THERMODYNAMICS; STATISTICAL MECHANICAL METHODS;

FREE ENERGY;

EID: 84880154439     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp4042233     Document Type: Article

References (54)

1. Lazaridis, T. Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory J. Phys. Chem. B 1998, 102 (18) 3531-3541
2. Lazaridis, T. Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to simple fluids J. Phys. Chem. B 1998, 102 (18) 3542-3550
3. Li, Z.; Lazaridis, T. Thermodynamics of Buried Water Clusters at a Protein-Ligand Binding Interface J. Phys. Chem. B 2006, 110 (3) 1464-1475
4. Czapiewski, D.; Zielkiewicz, J. Structural Properties of Hydration Shell Around Various Conformations of Simple Polypeptides J. Phys. Chem. B 2010, 114 (13) 4536-4550
5. Lazaridis, T. Solvent Reorganization Energy and Entropy in Hydrophobic Hydration J. Phys. Chem. B 2000, 104 (20) 4964-4979
6. Esposito, R.; Saija, F.; Saitta, A. M.; Giaquinta, P. V. Entropy-Based Measure of Structural Order in Water Phys. Rev. E 2006, 73 (4) 040502
7. Young, T.; Abel, R.; Kim, B.; Berne, B. J.; Friesner, R. A. Motifs for Molecular Recognition Exploiting Hydrophobic Enclosure in Protein-Ligand Binding Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (3) 808-813
8. Li, Z.; Lazaridis, T. Computing the Thermodynamic Contributions of Interfacial Water Methods Mol. Biol. 2012, 819, 393-404
9. Nguyen, C. N.; Young, T. K.; Gilson, M. K. Grid Inhomogeneous Solvation Theory: Hydration Structure and Thermodynamics of the Miniature Receptor Cucurbit[7]uril J. Chem. Phys. 2012, 137 (4) 044101
10. Beuming, T.; Farid, R.; Sherman, W. High-Energy Water Sites Determine Peptide Binding Affinity and Specificity of PDZ Domains Protein Sci. 2009, 18 (8) 1609-1619
11. Abel, R.; Salam, N. K.; Shelley, J.; Farid, R.; Friesner, R. A.; Sherman, W. Contribution of Explicit Solvent Effects to the Binding Affinity of Small-Molecule Inhibitors in Blood Coagulation Factor Serine Proteases Chemmedchem 2011, 6 (6) 1049-1066
12. Huggins, D. J.; Marsh, M.; Payne, M. C. Thermodynamic Properties of Water Molecules at a Protein Protein Interaction Surface J. Chem. Theory Comput. 2011, 7 (11) 3514-3522
13. Huggins, D. J. Benchmarking the Thermodynamic Analysis of Water Molecules Around a Model Beta Sheet J. Comput. Chem. 2012, 33 (15) 1383-1392
14. Hess, B.; van der Vegt, N. F. Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models J. Phys. Chem. B 2006, 110 (35) 17616-17626
15. Zwanzig, R. W. High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases J. Chem. Phys. 1954, 22, 1420
16. Abascal, J. L. F.; Vega, C. A General Purpose Model for the Condensed Phases of Water: TIP4P/2005 J. Chem. Phys. 2005, 123 (23) 234505
17. Klauda, J. B.; Venable, R. M.; Freites, J. A.; O'Connor, J. W.; Tobias, D. J.; Mondragon-Ramirez, C.; Vorobyov, I.; MacKerell, A. D., Jr.; Pastor, R. W. Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types J. Phys. Chem. B 2010, 114 (23) 7830-7843
18. Grubmüller, H. Solvate: A Program to Create Atomic Solvent Models, 1996.
19. Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant-Pressure Molecular-Dynamics Algorithms J. Chem. Phys. 1994, 101 (5) 4177-4189
20. Feller, S. E.; Zhang, Y. H.; Pastor, R. W.; Brooks, B. R. Constant-Pressure Molecular-Dynamics Simulation-the Langevin Piston Method J. Chem. Phys. 1995, 103 (11) 4613-4621
21. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G.; Smooth, A. Particle Mesh Ewald Method J. Chem. Phys. 1995, 103 (19) 8577-8593
22. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26 (16) 1781-1802
23. Huggins, D. J. Application of Inhomogeneous Fluid Solvation Theory to Model the Distribution and Thermodynamics of Water Molecules around Biomolecules Phys. Chem. Chem. Phys. 2012, 14 (43) 15106-15117
24. Kirkwood, J. G. Statistical Mechanics of Fluid Mixtures J. Chem. Phys. 1935, 3 (5) 300-313
25. Zielkiewicz, J. Structural Properties of Water: Comparison of the SPC, SPCE, TIP4P, and TIP5P Models of Water J. Chem. Phys. 2005, 123 (10) 104501
26. Huggins, D. J. Correlations in Liquid Water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP Models J. Chem. Phys. 2012, 136 (6) 064518
27. Beutler, T. C.; Mark, A. E.; Vanschaik, R. C.; Gerber, P. R.; Vangunsteren, W. F. Avoiding Singularities and Numerical Instabilities in Free-Energy Calculations Based on Molecular Simulations Chem. Phys. Lett. 1994, 222 (6) 529-539
28. Zacharias, M.; Straatsma, T. P.; Mccammon, J. A. Separation-Shifted Scaling, a New Scaling Method for Lennard-Jones Interactions in Thermodynamic Integration J. Chem. Phys. 1994, 100 (12) 9025-9031
29. Pohorille, A.; Jarzynski, C.; Chipot, C. Good Practices in Free-Energy Calculations J. Phys. Chem. B 2010, 114 (32) 10235-10253
30. Bennett, C. H. Efficient Estimation of Free-Energy Differences from Monte-Carlo Data J. Comput. Phys. 1976, 22 (2) 245-268
31. Liu, P.; Dehez, F.; Cai, W. S.; Chipot, C. A Toolkit for the Analysis of Free-Energy Perturbation Calculations J. Chem. Theory Comput. 2012, 8 (8) 2606-2616
32. 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 (26) 6271-6285
33. Sharp, K. A.; Nicholls, A.; Friedman, R.; Honig, B. Extracting Hydrophobic Free-Energies from Experimental-Data-Relationship to Protein Folding and Theoretical-Models Biochemistry 1991, 30 (40) 9686-9697
34. Ben-Naim, A. Standard Thermodynamics of Transfer. Uses and Misuses J. Chem. Phys. 1978, 82 (7) 792-803
35. Ben-Naim, A.; Marcus, Y. Solvation Thermodynamics of Nonionic Solutes J. Chem. Phys. 1984, 81 (4) 2016-2027
36. Wolfenden, R. Interaction of the Peptide Bond with Solvent Water: A Vapor Phase Analysis Biochemistry 1978, 17 (1) 201-204
37. Ding, Y. B.; Bernardo, D. N.; Kroghjespersen, K.; Levy, R. M. Solvation Free-Energies of Small Amides and Amines from Molecular-Dynamics Free-Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials J. Phys. Chem. 1995, 99 (29) 11575-11583
38. Dellagatta, G.; Barone, G.; Elia, V. Enthalpies of Solvation for N-Alkylamides in Water and in Carbon-Tetrachloride at 25-Degrees-C J. Solution Chem. 1986, 15 (2) 157-167
39. 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 (49) 10527-10534
40. Lazaridis, T.; Karplus, M. Orientational Correlations and Entropy in Liquid Water J. Chem. Phys. 1996, 105 (10) 4294-4316
41. Giuffre, E.; Prestipino, S.; Saija, F.; Saitta, A. M.; Giaquinta, P. V. Entropy from Correlations in TIP4P Water J. Chem. Theory Comput. 2010, 6 (3) 625-636
42. Wang, L.; Abel, R.; Friesner, R. A.; Berne, B. J. Thermodynamic Properties of Liquid Aater: An Application of a Nonparametric Approach to Computing the Entropy of a Neat Fluid J. Chem. Theory Comput. 2009, 5 (6) 1462-1473
43. Sharma, R.; Chakraborty, S. N.; Chakravarty, C. Entropy, Diffusivity, and Structural Order in Liquids with Waterlike Anomalies J. Chem. Phys. 2006, 125 (20) 204501
44. Agarwal, M.; Kushwaha, H. R.; Chakravarty, C. Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides J. Phys. Chem. B 2010, 114 (1) 651-659
45. Singh, H.; Misra, N.; Hnizdo, V.; Fedorowicz, A.; Demchuk, E. Nearest Neighbor Estimates of Entropy Am. J. Math. Manage. Sci. 2003, 23 (3-4) 301-322
46. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14 (1) 33-38
47. Beuming, T.; Che, Y.; Abel, R.; Kim, B.; Shanmugasundaram, V.; Sherman, W. Thermodynamic Analysis of Water Molecules at the Surface of Proteins and Applications to Binding Site Prediction and Characterization Proteins 2012, 80 (3) 871-83
48. Fernández, A.; Scott, R. Dehydron: A Structurally Encoded Signal for Protein Interaction Biophys. J. 2003, 85 (3) 1914-1928
49. Peter, C.; Oostenbrink, C.; van Dorp, A.; van Gunsteren, W. F. Estimating Entropies from Molecular Dynamics Simulations J. Chem. Phys. 2004, 120 (6) 2652-2661
50. Yamazaki, T.; Kovalenko, A. Spatial Decomposition of Solvation Free Energy Based on the 3D Integral Equation Theory of Molecular Liquid: Application to Miniproteins J. Phys. Chem. B 2011, 115 (2) 310-318
51. Kovalenko, A.; Hirata, F. Three-Dimensional Density Profiles of Water in Contact with a Solute of Arbitrary Shape: A RISM Approach Chem. Phys. Lett. 1998, 290 (1-3) 237-244
52. Henchman, R. H. Free Energy of Liquid Water from a Computer Simulation via Cell Theory J. Chem. Phys. 2007, 126 (6) 064504
53. Irudayam, S. J.; Henchman, R. H. Solvation Theory to Provide a Molecular Interpretation of the Hydrophobic Entropy Loss of Noble-Gas Hydration J. Phys.: Condens. Matter 2010, 22 (28) 284108
54. Abel, R.; Wang, L.; Friesner, R. A.; Berne, B. J.; Displaced-Solvent, A. Functional Analysis of Model Hydrophobic Enclosures J. Chem. Theory Comput. 2010, 6 (9) 2924-2934