Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

Journal of Chemical Physics

Volumn 125, Issue 5, 2006, Pages

  Piquemal, Jean Philip ^a,c   Perera, Lalith ^a   Cisneros, G Andrés ^a   Ren, Pengyu ^b   Pedersen, Lee G ^a   Darden, Thomas A ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^b The University of Texas at Austin   (United States)

^c SORBONNE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMOEBA FORCE FIELD; CALCIUM CATIONS; GAS PHASE AB INITIA CALCULATIONS; POLARIZATION DAMPING;

COMPUTER SIMULATION; DECOMPOSITION; HYDRATION; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; PARAMETER ESTIMATION; SOLVENTS;

POSITIVE IONS;

CALCIUM; CATION; ION; MAGNESIUM; SOLVENT; WATER;

AMOEBA; ANIMAL; ARTICLE; BIOPHYSICS; CHEMICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; METABOLISM; METHODOLOGY; PHYSICAL CHEMISTRY; REPRODUCIBILITY; THERMODYNAMICS;

AMOEBA; ANIMALS; BIOPHYSICS; CALCIUM; CATIONS; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; IONS; MAGNESIUM; MODELS, CHEMICAL; REPRODUCIBILITY OF RESULTS; SOFTWARE; SOLVENTS; THERMODYNAMICS; WATER;

EID: 33746907422     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2234774     Document Type: Article

References (52)

1. F. G. Prendergast and K. Mann, J. Biol. Chem. 252. 840 (1977).
2. S. X. Wang, E. Hur, C. A. Sousa, L. Brinen, E. J. Slivka, and R. J. Fietterick, Biochemistry 42, 7959 (2003).
3. F. C. Lightstone, E. Schwegler, R. Q. Hood, F. Gygi, and G. Galli, Chem. Phys. Lett. 343, 549 (2001).
4. M. M. Naor, K. Van Nostrand, and C. Dellago, Chem. Phys. Lett. 369, 159 (2003).
5. I. Bako, J. Hutter, and G. Palinkas, J. Chem. Phys. 117, 9838 (2002).
6. F. C. Lightstone, E. Schwegler, M. Allesch, F. Gygi, and G. Galli, ChemPhysChem 6, 1745 (2005).
7. N. Gresh and D. R. Garmer, J. Comput. Chem. 17, 1481 (1996).
8. J. W. Ponder and D. A. Case, Adv. Protein Chem. 66, 27 (2003).
9. T. A. Halgren and W. Damm, Curr. Opin. Struct. Biol. 11, 236 (2001).
10. J.-P. Piquemal, B. Williams-Hubbard, N. Fey, R. J. Deeth, N. Gresh, and C. Giesner-Prettre, J. Comput. Chem. 24, 1963 (2003).
11. J. Anthony, J.-P. Piquemal, and N. Gresh, J. Comput. Chem. 26, 1131 (2005).
12. N. Gresh, J.-P. Piquemal, and M. Krauss, J. Comput. Chem. 26, 1113 (2005).
13. D. Hagberg, G. Karlstrom, B. O. Roos, and L. Gagliardi, J. Am. Chem. Soc. 127, 14250 (2005).
14. P. Ren and J. W. Ponder, J. Phys. Chem. B 107, 5933 (2003).
15. A. Grossfield, P. Ren, and J. W. Ponder, J. Am. Chem. Soc. 125, 15671 (2003).
16. P. Ren and J. W. Ponder (unpublished).
17. D. A. Case, T. A. Darden, T. E. Cheatham III et al., AMBER 9.0.
18. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103, 8577 (1995).
19. A. Toumkmaji, C. Sagui, J. Board, and T. Darden, J. Chem. Phys. 113, 10913 (2000).
20. C. Sagui, L. G. Pedersen, and T. Darden, J. Chem. Phys. 120, 73 (2004).
21. P. S. Bagus and F. Illas. J. Chem. Phys. 96, 8962 (1992).
22. B. T. Tholé, Chem. Phys. 59, 341 (1981).
23. M. Frish, G. W. Trucks, H. B. Schlegel, et al., GAUSSIAN 03, Revision C.02, Gaussian, Inc., Wallingford, CT, 2004.
24. T. H. Dunning, Jr., J. Chem. Phys. 90, 1007 (1989).
25. M. Dupuis, A. Marquez, and E. R. Davidson, HONDO 95.3, QCPE, Indiana University, Bloomington, IN, 1995.
26. A. D. Becke, Phys. Rev. A 38, 3098 (1988).
27. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988).
28. I. E. McMurchie and E. R. Davidson, J. Comput. Phys. 26, 21 (1978).
29. D. M. Young, Iterative Solution of Large Linear Systems (Academic, New York, 1971).
30. Since the induction rules in which nearby permanent moment contributions to permanent fields at an atom are not the same rules that govern the polarization energy, extra complications arise in the computation of amoeba's polarization gradients. In general, the gradients can be calculated correctly using two sets of induced dipoles (Ref. 16). For the specific case of an ion in a water bath, this complication does not arise.
31. M. Masia, M. Probst, and R. Rey, J. Chem. Phys. 123, 164505 (2005).
32. J.-P. Piquemal, A. Marquez, O. Parisel, and C. Giessner-Prettre, J. Comput. Chem. 26, 1052 (2005).
33. T. A. Halgren, J. Am. Chem. Soc. 114, 7827 (1992).
34. M. P. Alien and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987), Sec. 2.8.
35. R. W. Impey, P. A. Madden, and I. R. McDonald, J. Phys. Chem. 87, 5071 (1983).
36. J.-P. Piquemal, G. A. Cisneros, P. Reinhardt, N. Gresh, and T. Darden, J. Chem. Phys. 124, 104101 (2006).
37. A. Tongraar and B. M. Rode, Chem. Phys. Lett. 409, 304 (2005).
38. J. Neely and R. Connick, J. Am. Chem. Soc. 92, 3476 (1970).
39. Y. S. Badyal, A. C. Barnes, G. J. Cuello, and J. M. Simonson, J. Phys. Chem. A 108, 11819 (2004).
40. F. Jalilehvand, D. Spangberg, P. Linvquist-Reis, K. Hermansson, I. Persson, and M. Sandström, J. Am. Chem. Soc. 123, 431 (2001).
41. R. Car and M. Parrinello. Phys. Rev. Lett. 55, 2471 (1985).
42. J. P. Perdew, K. Burke, and M. Emzerhof, Phys. Rev. Lett. 77, 3865 (1996).
43. I.-F. W. Kuo, C. J. Mundy, M. J. McGrath et al., J. Phys. Chem. B 108, 12990 (2004).
44. J. Burgess, in Ions in Solution; Basis Principles of Chemical Interactions, Department of Chemistry, Ellis Hoi-wood Series in Inorganic Chemistry, edited by U. o. L. J. Burgess (Leicester, U.K., 1988).
45. S. F. Lincoln and A. Merbach, Advances in Inorganic Chemistry (Academic, San Diego, 1995), Vol. 42, pp. 1-88.
46. H. Ohtaki and T. Radnai, Chem. Rev. (Washington, D.C.) 93, 1157 (1993).
47. L. Helm and A. E. Merbach, Coord. Chem. Rev. 187, 151 (2001).
48. C. F. Schwenk and B. R. Rode, Pure Appl. Chem. 76, 37 (2004).
49. L. Perera and M. L. Berkowitz, J. Chem. Phys. 95, 3 (1991).
50. G. A. Cisneros, J.-P. Piquemal, and T. A. Darden (unpublished).
51. C. S. Babu and C. Lim, J. Phys. Chem. A 110, 691 (2006).
52. N. A. Hewish, G. W. Neilson, and J. E. Enderby, Nature (London) 297, 138 (1982).