A smooth solvation potential based on the conductor-like screening model

Journal of Physical Chemistry A

Volumn 103, Issue 50, 1999, Pages 11060-11079

  York, Darrin M ^a,b   Karplus, Martin ^a,c  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b HARVARD UNIVERSITY   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001355552     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp992097l     Document Type: Article

References (62)

1. Gilson, M. K. Curr. Opin. Struct. Biol. 1995, 5, 216-223.
2. Honig, B.; Nicholls, A. Science 1995, 268, 1144-1149.
3. Schaefer, M.; Karplus, M. J. Phys. Chem. 1995, 100, 1578-1599.
4. Smith, P. E.; Pettitt, B. M. J. Phys. Chem. 1994, 98, 9700-9711.
5. Perkyns, J.; Pettitt, B. M. Biophys. Chem. 1994, 51, 129-146.
6. Tomasi, J.; Persico, M. Chem. Rev. 1994, 94, 2027-2094.
7. Cramer, C. J.; Truhlar, D. G. Reviews in Computational Chemistry; VCH Publishers, Inc.: New York, 1995; Vol. VI Continuum Solvation Models: Classical and Quantum Mechanical Implementations, Chapter 1, pp 1-73.
8. Tomasi, J.; Mennucci, B.; Cammi, R.; Cossi, M. Computational Approaches to Biochemical Reactivity; Kluwer Academic Publishers: Dordrecht, 1997; Chapter 1, pp 1-102.
9. Bashford, D.; Karplus, M. Biochemistry 1990, 29, 10219.
10. van Vlijmen, H. W. T.; Curry, S.; Schaefer, M.; Karplus, M. J. Mol. Biol. 1998, 275, 295-30S.
11. Basilevsky, M. V.; Rostov, I. V.; Newton, M. D. Chem. Phys. 1998, 232, 189.
12. Lazaridis, T.; Karplus, M. Science 1997, 278, 1928-1931.
13. Schaefer, M.; Bartels, C.; Karplus, M. J. Mol. Biol. 1998, 284, 835-848.
14. Cossi, M.; Mennucci, B.; Cammi, R. J. Comput. Chem. 1996, 17, 57-73.
15. Klamt, A.; Schtiiirmann, G. J. Chem. Soc., Perkin. Trans. 2 1993, 799-805.
16. Truong, T. N.; Stefanovich, E. V. J. Chem. Phys. 1995, 103, 3709-3717.
17. Pomelli, C. S.; Tomasi, J. Theor. Chem. Ace. 1997, 96, 39-43.
18. Barone, V.; Cossi, M.; Tomasi, J. J. Comput. Chem. 1998, 19, 404417.
19. Jackson, J. D. Classical Electrodynamics; 2nd ed.; John Wiley & Sons: New York, 1975.
20. Gelfand, I. M.; Fomin, S. V. Calculus of Variations; Prentice-Hall;Inc.: Englewood Cliffs; New Jersey, 1963.
21. Zhou, Z.; Payne, P.; Vasquez, M.; KUhn, N.; Levitt, M. J. Comput. Chem. 1996, 77, 1344-1351.
22. Truong, T. N.; Stefanovich, E. V. Chem. Phys. Lett. 1995, 240, 253-260.
23. Stefanovich, E. V.; Truong, T. N. Chem. Phys. Lett. 1995, 244, 65-74.
24. Truong, T. N.; Nguyen, U. N.; Stefanovich, E. V. Int. J. Quantum Chem.: Quantum Chem. Sympos. 30 1996, 403-410.
25. Stefanovich, E. V.; Truong, T. N. J. Phys. Chem. B 1998, 102, 3018-3022.
26. York, D. M.; Lee, T.-S.; Yang, W. Chem. Phys. Lett. 1996, 263, 297-304.
27. York, D. M.; Lee, T.-S.; Yang, W. J. Am. Chem. Soc. 1996, 118, 10940-10941.
28. Baldridge, K.; Klamt, A. J. Chem. Phys. 1997, 106, 6622-6633.
29. Klamt, A.; Jonas, V.; Burger, T.; Lohrenz, J. C. W. J. Phys. Chem. A 1998, 102, 5074-5085.
30. Andzelm, J.; Komel, C.; Klamt, A. J. Chem. Phys. 1995, 103, 9312-9320.
31. Barone, V.; Cossi, M. J. Phys. Chem. A 1998, 102, 1995-2001.
32. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes in Fortran: The Art of Scientific Computing, 2nd ed.; Cambidge University Press: New York, 1992.
33. York, D. M.; Lee, T.-S.; Yang, W. Phys. Rev. Lett. 1998, 80, 5011-5014.
34. York, D. M.; Yang, W. J. Chem. Phys. 1996, 104, 159-172.
35. Chipman, D. M. J. Chem. Phys. 1997, 106, 10194-10206.
36. Zhan, C.; Bentley, J.; Chipman, D. M. J. Chem. Phys. 1998, 108, 177-192.
37. Im, W.; Beglov, D.; Roux, B. Comput. Phys. Commun. 1998, 111, 59-75.
38. Cammi, R.; Tomasi, J. J. Chem. Phys. 1994, 100, 7495-7502.
39. Cammi, R.; Tomasi, J. J. Chem. Phys. 1994, 101, 3888-3897.
40. Cances, E.; Mennucci, B. J. Chem. Phys. 1998, 109, 250-259.
41. Cances, E.; Mennucci, B.; Tomasi, J. J. Chem. Phys. 1998, 109, 260-266.
42. Pulay, P. Calculation of forces by non-Hellmann-Feynman methods. The Force Concept in Chemistry; Van Nostrand Reinhold Co.: New York, 1981; Chapter 9, pp 444-480.
43. Delley, B. J. Comput. Cliem. 1996, 17, 1152-1155.
44. Becke, A. D.; Dickson, R. M. J. Chem. Phys. 1988, 89, 2993.
45. Delley, B. J. Chem. Phys. 1990, 92, 508.
46. St-Amant, A. Reviews in Computational Chemistry', VCH Publishers, Inc: New York, 1996; Vol. VII (Density Functional Methods in Biomolecular Modeling), Chapter 5, pp 217-259.
47. Dunlap, B. I.; Connolly, J. W. D.; Sabin, J. R. J. Chem. Phys. 1979, 71, 3396.
48. Lee, T.-S.; York, D. M.; Yana, W. J. Cliem. Phys. 1995, 102, 7549-7556.
49. Luty, B. A.; Davis, E.; McCammon, J. A. J. Comput. Chem. 1992, 13, 1114.
50. Lopez, X.; Dejaegere, A.; Karplus, M. J. Am. Chem. Soc. 1999, 121, 5548-5558.
51. Sridharan, S.; Nicholls, A.; Sharp, K. A. J. Comput. Chem. 1995, 16, 1038-1044.
52. Pomelli, C. S.; Tomasi, J. Theor. Chem. Ace. 1998, 99, 34-43.
53. Cramer, C. J.; Truhlar, D. G. Science 1992, 256, 213-217.
54. Stavrev, K. K.; Tamm, T.; Zerner, M. C. Int. J. Quantum Chem.: Quantum Chem. Sympos. 30 1996, 373-382.
55. Beglov, D.; Roux, B. J. Chem. Phys. 1994, 100, 9050-9063.
56. A function is said to be "smooth" with respect to a variable if the corresponding first derivative is continuous.
57. 1)).
58. r} = 0.
59. The solvation energy is minimized with respect to variations in the surface charge density that is expanded in the basis of surface elements. Appearance of new surface elements causes a discontinuous increase in the variational basis space that can only decrease (or have no effect on) the solvation energy.
60. r = 0. A ratio greater than 1 indicates preferential solvent stabilization of the transition state, a ratio less than 1 indicates the reverse.
61. The solvent accessible surface is equivalent to the van der Waals surface with radii increased by the probe radius, and the van der Waals surface is identical to the solvent accessible surface with zero probe radius.
62. In the case of the conductor-like screening model, the number of surface elements representing the polarization surface charge determines the dimensions of the vectors and matrices in eqs 39-43. The situation is directly analogous in all boundary element methods.