QM/MM-based fitting of atomic polarizabilities for use in condensed-phase biomolecular simulation

Journal of Chemical Theory and Computation

Volumn 8, Issue 10, 2012, Pages 3839-3853

  Vosmeer, C Ruben ^a   Rustenburg, Ariën S ^a   Rice, Julia E ^b   Horn, Hans W ^b   Swope, William C ^b   Geerke, Daan P ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b IBM ALMADEN RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84867364314     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300085z     Document Type: Article

References (95)

1. Frenkel, D.; Smit, B. Understanding Molecular Simulation; Elsevier: San Diego, CA, 2002.
2. van Gunsteren, W. F.; Bakowies, D.; Baron, R.; Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P.; Geerke, D. P.; Glaettli, A.; Huenenberger, P. H.; Kastenholz, M. A.; Ostenbrink, C.; Schenk, M.; Trzesniak, D.; van der Vegt, N. F. A.; Yu, H. B. Biomolecular modeling: Goals, problems, perspectives Angew. Chem., Int. Ed. 2006, 45, 4064-4092
3. Dror, R. O.; Jensen, M.; Borhani, D. W.; Shaw, D. E. Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations J. Gen. Physiol. 2010, 135, 555-562
4. Voelz, V. A.; Bowman, G. R.; Beauchamp, K.; Pande, V. S. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39) J. Am. Chem. Soc. 2010, 132, 1526-1528
5. Miao, L.; Schulten, K. Probing a structural model of the nuclear pore complex channel through molecular dynamics Biophys. J. 2010, 98, 1658-1667
6. Dror, R. O.; Arlow, D. H.; Maragakis, P.; Mildorf, T. J.; Pan, A. C.; Xu, H.; Borhani, D. W.; Shaw, D. E. Activation mechanism of the beta(2)-adrenergic receptor Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 18684-18689
7. Hünenberger, P. H.; van Gunsteren, W. F. Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications; Kluwer Academic Publisher: Dordrecht, the Netherlands, 1997; Vol. 3.
8. MacKerell, A. D. Empirical force fields for biological macromolecules: Overview and issues J. Comput. Chem. 2004, 25, 1584-1604
9. Yu, H. B.; van Gunsteren, W. F. Accounting for polarization in molecular simulation Comput. Phys. Commun. 2005, 172, 69-85
10. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 1995, 117, 5179-5197
11. Wang, J.; Wolf, R.; Caldwell, J.; Kollman, P.; Case, D. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174
12. Yang, L.; Tan, C.; Hsieh, M.; Wang, J.; Duan, Y.; Cieplak, P.; Caldwell, J.; Kollman, P.; Luo, R. New-generation amber united-atom force field J. Phys. Chem. B 2006, 110, 13166-13176
13. 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.; 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, 3586-3616
14. MacKerell, A. D.; Banavali, N.; Foloppe, N. Development and current status of the CHARMM force field for nucleic acids Biopolymers 2000, 56, 257-265
15. Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields J. Comput. Chem. 2010, 31, 671-690
16. Jorgensen, W. L.; Tirado-Rives, J. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 1988, 110, 1657-1666
17. 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
18. 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, 6474-6487
19. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf Hochschulverlag, ETH: Zurich, Switzerland, 1996.
20. Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1676
21. Schmid, N.; Eichenberger, A. P.; Choutko, A.; Riniker, S.; Winger, M.; Mark, A. E.; van Gunsteren, W. F. Definition and testing of the GROMOS force-field versions 54A7 and 54B7 Eur. Biophys. J. 2011, 40, 843-856
22. Geerke, D. P.; van Gunsteren, W. F. Calculation of the free energy of polarization: Quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters J. Phys. Chem. B 2007, 111, 6425-6436
23. van Maaren, P. J.; van der Spoel, D. Molecular dynamics simulations of water with novel shell-model potentials J. Phys. Chem. B 2001, 105, 2618-2626
24. Harder, E.; Anisimov, V. M.; Whitfield, T. W.; MacKerell, A. D.; Roux, B. Understanding the dielectric properties of liquid amides from a polarizable force field J. Phys. Chem. B 2008, 112, 3509-3521
25. Warshel, A.; Levitt, M. Theoretical studies of enzymic reactions-dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme J. Mol. Biol. 1976, 103, 227-249
26. Vesely, F. N-particle dynamics of polarizable stockmayer-type molecules J. Comput. Phys. 1977, 24, 361-371
27. van Belle, D.; Couplet, I.; Prevost, M.; Wodak, S. J. Calculations of electrostatic properties in proteins-Analysis of contributions from induced protein dipoles J. Mol. Biol. 1987, 198, 721-735
28. Drude, P. The Theory of Optics; Longmans, Green and Co.: New York, 1902.
29. Straatsma, T. P.; McCammon, J. A. Molecular dynamics simulations with interaction potentials including polarization development of a noniterative method and application to water Mol. Simul. 1990, 5, 181-192
30. Rappe, A. K.; Goddard, W. A. Charge equilibration for molecular-dynamics simulations J. Phys. Chem. 1991, 95, 3358-3363
31. Rick, S. W.; Stuart, S. J.; Berne, B. J. Dynamical fluctuating charge force-fields-application to liquid water J. Chem. Phys. 1994, 101, 6141-6156
32. Rick, S.; Stuart, S. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Boyd, D., Eds.; John Wiley Sons, Inc.: New Jersey, 2002; Vol. 18.
33. Caldwell, J. W.; Dang, L. X.; Kollman, P. A. Implementation of nonadditive intermolecular potentials by use of molecular-dynamics-development of a water water potential and water ion cluster interactions J. Am. Chem. Soc. 1990, 112, 9144-9147
34. Yu, H. B.; Hansson, T.; van Gunsteren, W. F. Development of a simple, self-consistent polarizable model for liquid water J. Chem. Phys. 2003, 118, 221-234
35. Sprik, M. Hydrogen-bonding and the static dielectric-constant in liquid water J. Chem. Phys. 1991, 95, 6762-6769
36. van Belle, D.; Froeyen, M.; Lippens, G.; Wodak, S. Molecular-dynamics simulation of polarizable water by extended Lagrangian method Mol. Phys. 1992, 77, 239-255
37. van Belle, D.; Wodak, S. J. Extended Lagrangian-formalism applied to temperature control and electronic polarization effects in molecular-dynamics simulations Comput. Phys. Commun. 1995, 91, 253-262
38. Lamoureux, G.; Roux, B. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm J. Chem. Phys. 2003, 119, 3025-3039
39. Miller, K. Calculation of the molecular polarizability tensor J. Am. Chem. Soc. 1990, 112, 8543-8551
40. Applequist, J.; Carl, J. R.; Fung, K. K. Atom dipole interaction-model for molecular polarizability-application to polyatomic molecules-and determination of atom polarizabilities J. Am. Chem. Soc. 1972, 94, 2952-2960
41. Anisimov, V. M.; Lamoureux, G.; Vorobyov, I. V.; Huang, N.; Roux, B.; MacKerell, A. D. Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator J. Chem. Theory Comput. 2005, 1, 153-168
42. Lamoureux, G.; MacKerell, A. D.; Roux, B. A simple polarizable model of water based on classical Drude oscillators J. Chem. Phys. 2003, 119, 5185-5197
43. Geerke, D. P.; Van Gunsteren, W. F. The performance of non-polarizable and polarizable force-field parameter sets for ethylene glycol in molecular dynamics simulations of the pure liquid and its aqueous mixtures Mol. Phys. 2007, 105, 1861-1881
44. Anisimov, V. M.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D. Polarizable empirical force field for the primary and secondary alcohol series based on the classical drude model J. Chem. Theory Comput. 2007, 3, 1927-1946
45. Caldwell, J. W.; Kollman, P. A. Structure and properties of neat liquids using nonadditive molecular-dynamics-water, methanol, and n-methylacetamide J. Phys. Chem. 1995, 99, 6208-6219
46. Gao, J. L.; Habibollazadeh, D.; Shao, L. A polarizable intermolecular potential function for simulation of liquid alcohols J. Phys. Chem. 1995, 99, 16460-16467
47. Dang, L. X.; Chang, T. M. Many-body interactions in liquid methanol and its liquid/vapor interface: A molecular dynamics study J. Chem. Phys. 2003, 119, 9851-9857
48. Patel, S.; Brooks, C. L. A nonadditive methanol force field: Bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model J. Chem. Phys. 2005, 122, 024508
49. Schropp, B.; Tavan, P. The polarizability of point-polarizable water models: Density functional theory molecular mechanics results J. Phys. Chem. B 2008, 112, 6233-6240
50. Kunz, A.-P. E.; van Gunsteren, W. F. Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D J. Phys. Chem. A 2009, 113, 11570-11579
51. Ren, P. Y.; Ponder, J. W. Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations J. Comput. Chem. 2002, 23, 1497-1506
52. Ren, P. Y.; Wu, C.; Ponder, J. W. Polarizable atomic multipole-based molecular mechanics for organic molecules J. Chem. Theory Comput. 2011, 7, 3143-3161
53. Thole, B. Molecular polarizabilities calculated with a modified dipole interaction Chem. Phys. 1981, 59, 341-350
54. Baker, C. M.; MacKerell, A. D. Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers J. Mol. Model. 2010, 16, 567-576
55. Yu, H. B.; Geerke, D. P.; Liu, H. Y.; van Gunsteren, W. F. Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models J. Comput. Chem. 2006, 27, 1494-1504
56. Becke, A. D. Density-functional thermochemistry. 3. The role of exact exchange J. Chem. Phys. 1993, 98, 5648-5652
57. Stephens, P. J.; Devlin, F. J.; Cabalowski, 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
58. Hertwig, R. H.; Koch, W. On the parameterization of the local correlation functional. What is Becke-3-LYP? Chem. Phys. Lett. 1997, 268, 345-351
59. Kendall, R. A.; Dunning, T. H.; Harrison, R. J. Electron-affinities of the 1s-row atoms revisited-systematic basis-sets and wave-functions J. Chem. Phys. 1992, 96, 6796-680
60. 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.; Montgomery, J. A. General atomic and molecular electronic-structure system J. Comput. Chem. 1993, 14, 1347-1363
61. Gordon, M.; Schmidt, M. In Theory and Applications of Computational Chemistry: The First Forty Years; Dykstra, C.; Frenking, G.; Kim, K.; Scuseria, G., Eds.; Elsevier: Amsterdam, 2005.
62. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Reidel: Dordrecht, The Netherlands, 1981; pp 331-338.
63. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The missing term in effective pair potentials J. Phys. Chem. 1987, 91, 6269-6271
64. Walser, R.; Mark, A. E.; van Gunsteren, W. F.; Lauterbach, M.; Wipff, G. The effect of force-field parameters on properties of liquids: Parametrization of a simple three-site model for methanol J. Chem. Phys. 2000, 112, 10450-10459
65. Weerasinghe, S.; Smith, P. E. A Kirkwood-Buff derived force field for methanol and aqueous methanol solutions J. Phys. Chem. B 2005, 109, 15080-15086
66. Tironi, I. G.; van Gunsteren, W. F. A molecular-dynamics simulation study of chloroform Mol. Phys. 1994, 83, 381-403
67. Hockney, R. W. The potential calculation and some applications Methods Comput. Phys. 1970, 9, 136-211
68. Berendsen, H. J. C.; Postma, J. P. M; van Gunsteren, W. F.; Di Nola, A.; Haak, J. R. Molecular-dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684-3690
69. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
70. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. A generalized reaction field method for molecular dynamics simulations J. Chem. Phys. 1995, 102, 5451-5495
71. Heinz, T. N.; van Gunsteren, W. F.; Hunenberger, P. H. Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations J. Chem. Phys. 2001, 115, 1125-1136
72. Singh, U.; Kollman, P. An approach to computing electrostatic charges for molecules J. Comput. Chem. 1984, 5, 129-145
73. de Proft, F.; Tielens, F.; Geerlings, P. Performance and basis set dependence of density functional theory dipole and quadrupole moments THEOCHEM 2000, 506, 1-8
74. Johnson, R. D., III. NIST Standard Reference Database, number 101, release 15b; National Institute of Standards and Technology: Gaithersburg, MD, August 2011.
75. Geerke, D. P.; van Gunsteren, W. F. On the calculation of atomic forces in classical simulation using the charge-on-spring method to explicitly treat electronic polarization J. Chem. Theory Comput. 2007, 3, 2128-2137
76. Lide, D. R. CRC Handbook of Chemistry and Physics; CRC Press: Boca Raton, FL, 2007.
77. Scott, W. R. P.; Hunenberger, P. H.; Tironi, I. G.; Mark, A. E.; Billeter, S. R.; Fennen, J.; Torda, A. E.; Huber, T.; Kruger, P.; van Gunsteren, W. F. The GROMOS biomolecular simulation program package J. Phys. Chem. A 1999, 103, 3596-3607
78. Lin, Z.; Kunz, A.; van Gunsteren, W. F. A one-site polarizable model for liquid chloroform: COS/C Mol. Phys. 2010, 108, 1749-1757
79. Yu, H. B.; van Gunsteren, W. F. Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice J. Chem. Phys. 2004, 121, 9549-9564
80. Glättli, A.; Daura, X.; van Gunsteren, W. F. Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/L J. Chem. Phys. 2002, 116, 9811-9828
81. Yamaguchi, T.; Hidaka, K.; Soper, A. The structure of liquid methanol revisited: A neutron diffraction experiment at -80 degrees C and +25 degrees C Mol. Phys. 1999, 96, 1159-1168
82. Yamaguchi, T.; Hidaka, K.; Soper, A. The structure of liquid methanol revisited: a neutron diffraction experiment at -80 degrees C and +25 degrees C Mol. Phys. 1999, 97, 603-605
83. Lama, R. F.; Lu, C. Y. Excess thermodynamic properties of aqueous alcohol solutions J. Chem. Eng. Data 1965, 10, 216-219
84. Guillot, B. A reappraisal of what we have learnt during three decades of computer simulations on water J. Mol. Liq. 2002, 101, 219-260
85. Fernández, D. P.; Mulev, Y.; Goodwin, A. R. H.; Levelt Sengers, J. M. H. A database for the static dielectric constant of water and steam J. Phys. Chem. 1995, 24, 33-70
86. Dang, L. The nonadditive intermolecular potential for water revised J. Chem. Phys. 1992, 97, 2659-2660
87. Smith, D.; Dang, L. Computer simulations of NaCl association in polarizable water J. Chem. Phys. 1994, 100, 3757-3766
88. Stern, H.; Rittner, F.; Berne, B.; Friesner, R. Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function J. Chem. Phys. 2001, 115, 2237-2251
89. Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D. A polarizable model of water for molecular dynamics simulations of biomolecules Chem. Phys. Lett. 2006, 418, 245-249
90. Vorobyov, I. V.; Anisimov, V. M.; MacKerell, A. D. Polarizable empirical force field for alkanes based on the classical drude oscillator model J. Phys. Chem. B 2005, 109, 18988-18999
91. Foloppe, N.; MacKerell, A. D. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 2000, 21, 86-104
92. Mikhail, S. Z.; Kimel, W. R. Densities and viscosities of methanol-water mixtures J. Chem. Eng. Data 1961, 6, 533-537
93. McClellan, A. L. L. Tables of Experimental Dipole Moments; Rahara Enterprise: El Cerrito, CA, 1989.
94. Hurle, R. L.; Easteal, A. J.; Woolf, L. A. Self-diffusion in monohydric alcohols under pressure. Methanol, methan(2H)ol and ethanol J. Chem. Soc., Faraday Trans. 1 1985, 81, 769-779
95. Katritzky, A. R.; Oliferenko, A. A.; Oliferenko, P. V.; Petrukhin, R.; Tatham, D. B.; Maran, U.; Lomaka, A.; Acree, W. E. A general treatment of solubility. 1. The QSPR correlation of solvation free energies of single solutes in series of solvents J. Chem. Inf. Comput. Sci. 2003, 43, 1794-1805