Accounting for polarization cost when using fixed charge force fields. II. Method and application for computing effect of polarization cost on free energy of hydration

Journal of Physical Chemistry B

Volumn 114, Issue 26, 2010, Pages 8631-8645

  Swope, William C ^a   Horn, Hans W ^a   Rice, Julia E ^a  

^a IBM ALMADEN RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COST ACCOUNTING; COSTS; FREE ENERGY; HYDRATION; ORGANIC ACIDS; POLARIZATION; SOLVENTS;

AQUEOUS SOLVENTS; CHARGE MODELS; COMPUTING EFFECTS; CONDENSED PHASE; DIPOLE POLARIZATION; EXPERIMENTAL DATA; EXPLICIT SOLVENTS; FIXED CHARGES; FORCE FIELDS; FREE ENERGY OF HYDRATION; GASPHASE; HIGHER ORDER; HYBRID DENSITY FUNCTIONAL CALCULATIONS; HYDRATION FREE ENERGIES; IMPLICIT MODEL; IMPLICIT SOLVENTS; MATHEMATICAL EXPRESSIONS; MOLECULAR POLARIZATION; MULTIPOLES; ON-ELECTRON DENSITY; POINT CHARGE; RESPONSE TO ENVIRONMENT; SIDE-CHAIN ANALOGUES; SOLVATED STATE; STANDARD PRACTICES; WATER INTERACTIONS;

COST BENEFIT ANALYSIS;

EID: 77954345621     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp911701h     Document Type: Article

References (44)

1. Swope, W. C.; Horn, H. W.; Rice, J. E. Accounting for Polarization Energy When Using Fixed Charge Force Fields I. Method Energy. J. Phys. Chem. B 2009, DOI: 10.1021/jp911699p.
2. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The missing term in effective pair potentials J. Phys. Chem. 1987, 91, 6269-6271
3. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an improved four-site model for biomolecular simulations: TIP4P-Ew J. Chem. Phys. 2004, 120, 9665
4. Abascal, J. L. F.; Vega, C. A General Purpose Model for the Condensed Phases of Water TIP4P/2005 J. Chem. Phys. 2005, 123, 234505
5. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926
6. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction Models for Water in Relation to Protein Hydration. In Intermolecular Forces; Pullmann, B., Ed.; D. Reidel Publishing: Dordrecht, 1981; p 331.
7. Rukes, B., Ed. Guideline on the Use of Fundamental Physical Constants and Basic Constants of Water, 2001 ed.; The International Association for the Properties of Water and Steam, Rukes, B., president: Gaithersburg, Maryland, USA, 2001.
8. See http://www.iapws.org (accessed December 9, 2009).
9. Hess, B.; van der Vegt, N. F. A. Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models J. Phys. Chem. B 2006, 110, 17616
10. 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 and private communications
11. Mobley, D. L. Erratum in reference to
12. 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 2010, submitted.
13. We wish to emphasize that the polarization energy correction that is computed using our procedure is different from that reported by Mobley (9) and co-workers for the point charge model that they produced based on their fit to the electrostatic potentials generated by their B3LYP/cc-pVTZ/c-PCM charge densities. Our polarization energies are based on the point charges themselves or, more precisely, on the multipole moments generated by them. Mobley and co-workers determined their polarization energies from the charge density from which these charges were derived. As discussed in the companion paper, (1) these two approaches will only give the same result if the fitted charge model is capable of reproducing not only the molecule's dipole moment but the higher-order multipole moments as well. Since, in general, this is not the case, we chose to calculate the polarization energy based on the fixed charge model in a manner consistent for all the force fields.
14. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation J. Am. Chem. Soc. 1993, 115, 9620-9631
15. One may use either classical or quantum mechanical expressions for the vibrational partition functions. Since the point of these process steps is to relate a classical molecular dynamics simulation with an experimental measurement, one should in principle include a step in the thermodynamic cycle to account for the switch from quantum dynamics to classical dynamics. These issues are outside the scope of this work, and classical dynamics and classical statistical mechanics are assumed. However, earlier work (3, 14) provide examples of an approach to address this.
16. Horn, H. W.; Swope, W. C.; Pitera, J. W. Pitera Characterization of the TIP4P-Ew water model vapor pressure and boiling point J. Chem. Phys. 2005, 123, 194504
17. Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Atomistic Simulations J. Chem. Theory Comput. 2009, 5, 350-358
18. Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations J. Mol. Graphics Modell. 2006, 25, 247-260
19. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General Amber Force Field J. Comput. Chem. 2004, 25, 1157-1174
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
21. Rizzo, R. C.; Jorgensen, W. L. OPLS All-Atom Model for Amines: Resolution of the Amine Hydration Problem J. Am. Chem. Soc. 1999, 121, 4827-4836
22. Price, M. L. P.; Ostrovsky, D.; Jorgensen, W. L. Gas-Phase and Liquid-State Properties of Esters, Nitriles, and Nitro Compounds with the OPLS-AA Force Field J. Comput. Chem. 2001, 22, 1340-1352
23. 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, 5740
24. Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields J. Phys. Chem. 1994, 98, 11623-11627
25. Barone, V.; Cossi, M. Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model J. Phys. Chem. A 1998, 102, 1995-2001
26. Cossi, M.; Rega, N.; Scalmani, G.; Barone, V. Energies, structures, and electronic properties of molecules in solution with the c-PCM solvation model J. Comput. Chem. 2003, 24, 669-681
27. Cossi, M.; Scalmani, G.; Rega, N.; Barone, V. New Developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution J. Chem. Phys. 2002, 117, 43
28. Dunning, T. H., Jr. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen J. Chem. Phys. 1989, 90, 1007
29. Kendall, R. A.; Dunning, T. H., Jr.; Harrison, R. J. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions J. Chem. Phys. 1992, 96, 6796
30. Woon, D. E.; Dunning, T. H., Jr. The atoms aluminum through argon. III J. Chem. Phys. 1993, 98, 1358
31. Dunning, T. H., Jr.; Peterson, K. A.; Wilson, A. K. Gaussian basis sets for use in correlated molecular calculations. X. The atoms aluminum through argon revisited J. Chem. Phys. 2001, 114, 9244
32. These properties were computed relative to a reference frame coincident with the center of nuclear charge. The multipole moments were obtained from the charge density, and the polarizabilities were computed by finite difference of energies and multipole moments each with different directions of small finite perturbing electrostatic potentials (0.001 au) or potential gradients (0.001 au).
33. Voisin, C.; Cartier, A.; Rivail, J.-L. Computation of accurate electronic molecular polarizabilities J. Phys. Chem. 1992, 96, 7966-7971
34. Bak, K. L.; Gauss, J.; Helgaker, T.; Jorgensen, P.; Olsen, J. The accuracy of molecular dipole moments in standard electronic structure calculations Chem. Phys. Lett. 2000, 319, 563-568
35. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. J.; Windus, T. L.; Dupuis, M. M.; Montgomery, J. A. General atomic and molecular electronic structure system J. Comput. Chem. 1993, 14, 1347-1363
36. (http://www.msg.ameslab.gov/GAMESS/GAMESS.html (R5)). Modifications were made to support calculation of DFT energies and multipole moments in the presence of a field gradient.
37. Wolfenden, R.; Andersson, L.; Cullis, P. M.; Southgate, C. C. B. Affinities of Amino Acid Side Chains for Solvent Water Biochemistry 1981, 20, 849-855
38. Wolfenden, R. Interaction of Peptide Bond with Solvent Water: A Vapor Phase Analysis Biochemistry 1978, 17, 201
39. -8 for acetamide correspond to hydration free energies of- 10.1(± 0.2) and-9.7(± 0.3) kcal/mol, respectively.
40. Abraham, M. H.; Whiting, G. S.; Fuchs, R.; Chambers, E. J. Thermodynamics of Solute Transfer from Water to Hexadecane J. Chem. Soc., Perkin Trans. 1990, 2, 291-300
41. Values reported are offset by 4.27 kcal/mol from ours due to use of a different reference state. This paper reports hydration free energies of 2.07 kcal/mol for n -butane;-5.00 for ethanol; 2.32 for isobutane;-5.10 for methanol;-1.36 for methanethiol; 2.00 for methane;-6.13 for p -cresol; 1.96 for propane; and-0.79 for toluene, with expected errors of approximately 0.2 kcal/mol, making them consistent with the Wolfenden data.
42. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. A Computer Simulation Method of the Calculation of Equilibrium Constants for the Formation of Physical Clusters of Molecules: Application to Small Water Clusters J. Chem. Phys. 1982, 76, 637
43. Andersen, H. C. RATTLE: A "Velocity" Version of the SHAKE Algorithm for Molecular Dynamics Calculations J. Comput. Phys. 1983, 52, 24-34
44. Andersen, H. C. Molecular Dynamics Simulations At Constant Pressure and/or Temperature J. Chem. Phys. 1980, 72, 2384-2393