Benzene dimer: A good model for π-π interactions in proteins? A comparison between the benzene and the toluene dimers in the gas phase and in an aqueous solution

Journal of the American Chemical Society

Volumn 118, Issue 45, 1996, Pages 11217-11224

  Chipot, Christophe ^a,b,c   Jaffe, Richard ^b   Maigret, Bernard ^c   Pearlman, David A ^d   Kollman, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NASA AMES RESEARCH CENTER   (United States)

^c UNIVERSITÉ DE LORRAINE   (France)

^d VERTEX PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENZENE; TOLUENE;

ARTICLE; DIMERIZATION; DRUG STRUCTURE; MODEL; PROTEIN STRUCTURE;

EID: 0030001537     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja961379l     Document Type: Article

References (74)

1. Hunter, C. A.; Sanders, J. K. M. J. Am. Chem. Soc. 1990, 112, 5525.
2. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
3. Warne, P. K.; Morgan, R. S. Biochemistry 1978, 118, 273.
4. Burley, S. K.; Petsko, G. A. Science 1985, 229, 23.
5. Singh, J.; Thornton, J. M. FEBS Lett. 1985, 191, 1.
6. Blundell, T.; Singh, J.; Thornton, J.; Burley, S. K.; Petsko, G. A. Science 1986, 234, 1005.
7. Burley, S. K.; Petsko, G. A. Adv. Protein Chem. 1988, 39, 125.
8. Hunter, C. A.; Singh, J.; Thornton, J. M. J. Mol. Biol. 1991, 218, 837.
9. Serrano, L.; Bycroft, A. R. J. Mol. Biol. 1991, 218, 465.
10. Lehn, J. M.; Schmidt, F.; Vigneron, J. P. Tetrahedron Lett. 1988, 29, 5255.
11. Muehldorf, A. V.; Van Engen, D.; Warner, J. C.; Hamilton, A. D. J. Am. Chem. Soc. 1988, 110, 6561.
12. Smithrud, D. B.; Diederich, F. J. Am. Chem. Soc. 1990, 112, 339.
13. Ferguson, S. B.; Sanford, E. M.; Seward, E. M.; Diederich, F. J. Am. Chem. Soc. 1991, 113, 5410.
14. Lowe, M. J.; Schellman, J. A. J. Mol. Biol. 1972, 65, 91.
15. Ts'O, P. O. P. In Basic Principles of Nucleic Acid Chemistry; Ts'O, P., Ed.; Academic Press: New York, 1974; Vol. 1, Chapter 6.
16. Janda, K. C.; Hemminger, J. C.; Winn, J. S.; Novick, S. E.; Harris, S. J.; Klemperer, W. J. Chem. Phys. 1975, 63, 1419.
17. Steed, J. M.; Dixon, T. A.; Klemperer, W. J. Chem. Phys. 1979, 70, 4940.
18. Börnsen, K. O.; Selzle, H. L.; Schlag, E. W. J. Chem. Phys. 1986. 85, 1726.
19. Pawliszyn, J.; Szczȩśniak, M. M.; Scheiner, S. J. Phys. Chem. 1984, 88, 1726.
20. Cox, E. G.; Cruickshank, D. W.; Smith, J. A. S. Proc. R. Soc. London, Ser. A 1958, 247, 1.
21. Henson, B. F.; Hartland, G. V.; Venturo, V. A.; Felker, P. M. J. Chem. Phys. 1992, 97, 2189.
22. Arunan, E.; Gutowsky, H. S. J. Chem. Phys. 1993, 98, 4294.
23. Law, K. S.; Schauer, M.; Bernstein, E. R. J. Chem. Phys. 1984, 81, 4871.
24. Karlström, G.; Linse, P.; Wallqvist, A.; Jönsson, B. J. Am. Chem. Soc. 1983, 105, 3777.
25. Hobza, P.; Selzle, H. L.; Schlag, E. W. J. Chem. Phys. 1990, 93, 5893.
26. Hobza, P.; Selzle, H. L.; Schlag, E. W. J. Phys. Chem. 1993, 97, 3937.
27. Hobza, P.; Selzle, H. L.; Schlag, E. W. J. Am. Chem. Soc. 1994, 116, 3500.
28. Hobza, P.; Selzle, H. L.; Schlag, E. W. Chem. Rev. 1994, 94, 1767.
29. Linse, P. J. Am. Chem. Soc. 1992, 114, 4366.
30. Jorgensen, W. L.; Severance, D. L. J. Am. Chem. Soc. 1990, 112, 4768.
31. Linse, P. J. Am. Chem. Soc. 1993, 115, 8793.
32. Linse, P. J. Am. Chem. Soc. 1990, 112, 1744.
33. Cozzi, F.; Cinquina, M.; Annuziata, R.; Dwyer, T.; Siegel, J. S. J. Am. Chem. Soc. 1992, 114, 5729.
34. Cozzi, F.; Cinquina, M.; Annuziata, R.; Siegel, J. S. J. Am. Chem. Soc. 1993, 115, 5330.
35. Hunter, C. A. Angew. Chem., Int. Ed. Engl. 1993, 32, 1584.
36. Hunter, C. A. Chem. Soc. Rev. 1994, 23, 101.
37. Neusser, H. J.; Krause, H. Chem. Rev. 1994, 94, 1829.
38. Mezei, M.; Beveridge, D. L. Ann. N.Y. Acad. Sci. 1986, 482, 1.
39. Beveridge, D. L.; DiCapua, F. M. Anna. Rev. Biophys. Biophys. Chem. 1989, 18, 431.
40. Mruzik, M. R.; Abraham, F. F.; Schreiber, D. E.; Pound, G. M. J. Chem. Phys. 1976, 64, 481.
41. Mezei, M.; Swaminathan, S.; Beveridge, D. L. J. Am. Chem. Soc. 1978, 100, 3255.
42. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765.
43. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. J. Comput. Chem. 1986, 7, 230.
44. Pearlman, D. A. J. Chem. Phys. 1993, 98, 8946.
45. Chipot, C.; Kollman, P. A.; Pearlman, D. A. J. Comput. Chem. 1996, 17, 1112.
46. Tobias, D. J.; Brooks, C. L., III J. Chem. Phys. 1988, 89, 5115.
47. Pearlman, D. A.; Case, D. A.; Caldwell, J. C.; Ross, W. S.; Cheatham, T. C.; Seibel, G.; Singh, U. C.; Weiner, P.; Kollman, P. A. AMBER 4.1; University of California, San Francisco (UCSF), San Francisco, 1994.
48. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. C.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
49. Cox, S. R.; Williams, D. E. J. Comput. Chem. 1981, 2, 304.
50. Chipot, C.; Ángyán, J. G. GRID Version 3.0: Point Multipoles Derived From Molecular Electrostatic Properties; QCPE No. 655, 1994; Version 3.1 currently available.
51. Hariharan, P. C.; Pople, J. A. Chem. Phys. Lett. 1972, 16, 217.
52. Jorgensen, W. L.; Chandrsekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
53. Ben-Naim, A.; Marcus, Y. J. Chem. Phys. 1984, 81, 2016.
54. Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
55. Ryckaert, J.; Cicotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
56. Van Gunsteren, W. F.; Berendsen, H. J. C. Mol. Phys. 1977, 34, 1311.
57. In the case of the benzene dimer, use was made of 100 windows involving 2.5 ps of equilibration followed by 7.5 ps of data collection for the T-shaped motif (δR = 0.055 Å), and 50 windows involving 5.0 ps of equilibration followed by 15.0 ps of data collection for both the stacked (δR = 0.110 Å) and the orientationally-averaged (δR = 0.130 Å) motifs. Identical protocols were employed for the three different motifs of the toluene dimer, at the exception of the T-shaped conformation, for which δR - 0.065 Å.
58. Karplus, M.; McCammon, J. A. Annu. Rev. Biochem. 1983, 52, 263.
59. Nagy, J.; Smith, V. H., Jr.; Weaver, D. F. J. Phys. Chem. 1995, 99, 13868.
60. Jaffe, R. L.; Smith, G. D. J. Chem. Phys. 1996, 105, 2780.
61. Smith, G. D.; Jaffe, R. L. J. Phys. Chem. 1996, 100, 9624.
62. Jaffe, R. L. Work in progress, 1996.
63. Shoup, D.; Szabo, A. Biophys. J. 1982, 40, 33.
64. McMillan, W.; Mayer, J. J. Chem. Phys. 1945, 13, 276.
65. _V. J. Solution Chem. 1973, 2, 119.
66. a and B, ΔG(r) represents an effective - i.e. solvent-averaged and orientation-averaged-potential of mean force between the two aromatic moities, at a separation "r". Estimates of these quantities for the constrained geometries have clearly a different reference, and are, as a result, not directly comparable.
67. Tucker, E. E.; Christian, S. D. J. Phys. Chem. 1979, 83, 246.
68. Rossky, P. J.; Friedman, H. L. J. Phys. Chem. 1980, 84, 587.
69. Abola, E. E.; Bernstein, F. C.; Bryant, S. H.; Koetzle, T. F.; Weng, J. In Crystallographic Databases - Information Content, Software Systems, Scientific Application; Allen, F., Sievers, R., Eds.; Data Commission of the International Union of Crystallography: Bonn/Cambridge/Chester, 1978; p 107.
70. Maigret, B.; Chipot, C. Unpublished results, 1996.
71. Battaglia, M. R.; Buckingham, A. D.; Williams, J. H. Chem. Phys. Lett. 1981, 78, 421.
72. Lindley, P. F.; Bajaj, M.; Evans, R. W. Acta Crystallogr., Sect. D, Biological 1993, 49, 292.
73. Holmes, M. A.; Stenkamp, R. E. J. Mol. Biol. 1991, 220, 723.
74. Matouschek, A.; Kellis, J.; Serrano, L.; Fersht, A. R. Nature 1989, 340, 122.