Free energy of amide hydrogen bond formation in vacuum, in water, and in liquid alkane solution

Journal of Physical Chemistry B

Volumn 101, Issue 3, 1997, Pages 450-457

  Ben Tal, Nir ^a   Sitkoff, Doree ^c   Topol, Igor A ^b   Yang, An Suei ^a   Burt, Stanley K ^b   Honig, Barry ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; MOLECULES; PARAFFINS; PROBABILITY DENSITY FUNCTION; PROTEINS; SOLUTIONS; VACUUM; WATER;

AMIDES; CONTINUUM SOLVENT MODEL; DENSITY FUNCTIONAL THEORY (DFT); DIMERIZATION ENERGY; LIQUID ALKANE SOLUTIONS; NORMAL METHYLACETAMIDE (NMA);

HYDROGEN BONDS;

EID: 0030736114     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp961825r     Document Type: Article

References (75)

1. Baker, E. N.; Hubbard, R. E. Prog. Biophys. Mol. Biol. 1984, 44, 97-179.
2. Dill, K. A. Biochemistry 1990, 29, 7133.
3. Popot, J.-L.; Engelman, D. M. Biochemistry 1990, 29, 4031-4036.
4. Jeffrey, G. A.; Saenger, W. Hydrogen bonding in biological structures; Springer-Verlag; Berlin, 1991.
5. Stickle, D. F.; Presta, L. G.; Dill, K. A.; Rose, G. D. J. Mol. Biol. 1992, 226, 1143-1159.
6. Schellman, J. A. Trav. Lab. Carlsberg, Ser. Chim. 1955, 29, 230-259.
7. Schellman, J. A. Trav. Lab. Carlsberg, Ser. Chim. 1955, 29, 223-229.
8. Lord, R. C.; Porro, T. J. Z. Elektrochem. 1960, 64, 672-676.
9. Klotz, I. M.; Franzen, J. S. J. Am. Chem. Soc. 1962, 84, 3461-3466.
10. Franzen, J. S.; Stevens, R. E. Biochemistry 1963, 2, 1321.
11. Affsprung, H. E.; Christian, S. D.; Worley, J. D. Spectrochem. Acta, Part A 1964, 20, 1451-1420.
12. Susi, H.; Timasheff, S. N.; Ard, J. S.; Koput, J. J. Biol. Chem. 1964, 239, 3051-3054.
13. Kreshek, G. C.; Klotz, I. M. Biochemistry 1969, 8, 8-12.
14. Gill, S. J.; Noll, L. J. Phys. Chem. 1972, 76, 3065-3068.
15. Hopmann, R. F. W. J. Phys. Chem. 1974, 78, 2341-2348.
16. Josefiak, C.; Schneider, G. M. J. Phys. Chem. 1979, 83, 2126-2128.
17. Spencer, J. N.; Garrett, R. C.; Mayer, F. J.; Markle, J. E.; Powell, C. R.; Tran, M. T.; Berger, S. K. Can. J. Chem. 1980, 58, 1372-1375.
18. Krikorian, S. E. J. Phys. Chem. 1982, 86, 1975-1981.
19. Eberhardt, E. S.; Raines, R. T. J. Am. Chem. Soc. 1994, 116, 2149-2150.
20. Wimley, W. C.; Creamer, T. P.; White, S. H. Biochemistry 1996, 35, 5109-5124.
21. Ben-Naim, A. J. Phys. Chem. 1991, 95, 1437-1444.
22. Doig, A. J.; Williams, D. H. J. Am. Chem. Soc. 1992, 114, 338-343.
23. Fersht, A. R.; Shi, J.-P.; Knill-Jones, J.; Lowe, D. M.; Wilkinson, A. J.; Blow, D. M.; Brick, P.; Carter, P.; Waye, M. M. Y.; Winter, G. Nature 1985, 314, 235-238.
24. Fersht, A. R. TIBS 1987, 12, 301-304.
25. Shirley, B. A.; Stanssens, P.; Hahn, U.; Pace, C. N. Biochemistry 1992, 31, 725-732.
26. Roseman, M. J. Mol. Biol. 1988, 201, 621-623.
27. Klotz, I. M.; Farnham, S. B. Biochemistry 1968, 7, 3879-3832.
28. Jorgensen, W. L. J. Am. Chem. Soc. 1989, 111, 3770-3771.
29. Sneddon, S. F.; Tobias, D. J.; Brooks, C. L., III. J. Mol. Biol. 1989, 209, 817-820.
30. Simonson, T.; Brunger, A. T. J. Phys. Chem. 1994, 98, 4683-4694.
31. Ösapay, K.; Young, W. S.; Bashford, D.; Brooks, C. L.; Case, D. C. J. Phys. Chem. 1996, 100, 2698-2705.
32. Baldwin, R. L. TIBS 1989, 14, 291-294.
33. Alber, T. Annu. Rev. Biochem. 1989, 58, 765-798.
34. Privalov, P. L.; Makhatadze, G. I. J. Mol. Biol. 1993, 232, 660-679.
35. Honig, B.; Yang, A.-S. Adv. Protein Chem. 1995, 46, 27-58.
36. Brunger, A. T. X-PLOR Manual. Version 3.0; Yale University: New Haven, CT, 1992.
37. Warshel, A. Computer modeling of chemical reactions in enzymes and solutions.; John-Wiley & Sons, Inc.: New York, 1991.
38. Hagler, A. T.; Huler, E.; Lifson, S. J. Am. Chem. Soc. 1973, 96. 5319-5327.
39. Mitchell, J. B. O.; Price, S. L. J. Comput. Chem. 1990, 11, 1217-1233.
40. Godbout, N.; Salahub, D. R.; Andzelm, J.; Wimmer, E. Can. J. Chem. 1992, 70, 560-571.
41. Sule, P.; A. Nagy. J. Chem. Phys. 1996, 104, 8524-8534.
42. Sim, F.; St. Amant, A.; Papai, I.; Salahub, D. R. J. Am. Chem. Soc. 1992, 114, 4391-4400.
43. Kieninger, M.; Suhai, S. Int. J. Quantum Chem. 1994, 52, 465-478.
44. Topol, I. A.; Burt, S. K.; Rashin, A. A. Chem. Phys. Lett. 1995, 247, 112-119.
45. Del Bene, J. E.; Person, W. B.; Szczepaniak, K. J. Phys. Chem. 1995, 99, 10705-10707.
46. Novoa, J. J.; Sosa, C. J. Phys. Chem. 1995, 99, 15837-15845.
47. Han, W.-G.; Suhai, S. J. Phys. Chem. 1996, 100, 3942-3949.
48. Dykstra, C. E. Chem. Rev. 1993, 93, 2339.
49. Frisch, M.; Trucks, G.; Head-Gordon, M.; Gill, P.; Wong, P.; Foresman, M.; Johnson, J.; Schelgel. H.; Robb, M.; Reploge, E.; Gormperts, R.; Andrew, J.; Ragavachari, K.; Binkley, S.; Gonzales. C.; Martin, R.; Fox, D.; Defrees, D.; Baker, J.; Stewart, J.; Pople, J. Gaussian, Inc., Pittsburgh, PA, 1992.
50. Reed, A. E.; Curtiss, L. A.; Weinhold, F. Chem. Rev. 1988, 88, 899-926.
51. Weinhold, F., Carpenter, J. E., Eds. The structure of small molecules and ions. Plenum: New York, 1988.
52. Ringnalda, M. N.; Langlois, J.-M.; Greeley, B. H.; Russo, T. V.; Muller, R. P.; Marten, B.; Won, Y.; Donnelly, R. E., Jr.; Pollard, W. T.; Miller, G. H.; Goddard, W. A. I.; Friesner, R. A. Schroedinger, Inc., Pasadena, CA, 1993.
53. Friesner, R. Annu. Rev. Phys. Chem. 1991, 42, 341-362.
54. Dunning, T. J. Chem. Phys. 1989, 90, 1007-1023.
55. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988.
56. Sitkoff, D.; Ben-Tal, N.; Honig, B. J. Phys. Chem. 1996, 100, 2744-2752.
57. Lide, D. R., Ed. CRC Handhook of Chemistry and Physics; CRC Press: Boca Raton, FL, 1992.
58. Sharp, K.; Jean-Charles, J.; Honig, B. J. Phys. Chem. 1992, 96, 3822-3828.
59. Warwicker, J.; Watson, H. C. J. Mol. Biol. 1982, 157, 671.
60. Nicholls, A.; Honig, B. J. Comput. Chem. 1991, 12, 435-445.
61. Nicholls, A.; Sharp, K. A.; Honig, B. DelPhi; Department of Biochemistry and Molecular Biophysics: Columbia University. NY, 1990.
62. Jackson, J. D. Classical Electrodynamics; John Wiley and Sons: New York, 1962.
63. Chothia, C. J. Mol. Biol. 1976, 105, 1-14.
64. Hermann, R. B. J. Phys. Chem. 1972, 76, 2754-2759.
65. Nozaki, Y.; Tanford, C. H. J. Biol. Chem. 1971, 246, 2211.
66. Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. 1995, 99, 7137-7146.
67. Sridharan, S.; Nicholls, A.; Honig, B. Biophys. J. 1992, 61, A174.
68. Shrake, A.; Rupley, J. A. J. Mol. Biol. 1973, 79, 351-371.
69. Guo, H.; Karplus, M. J. Phys. Chem. 1994, 98, 7104-7105.
70. Dixon, D. A.; Dobbs, K. D.; Valentini, J. J. J Phys Chem. 1994, 98, 13435-13439.
71. Yang, A.-S.; Honig, B. J. Mol. Biol. 1995, 252, 351-365.
72. Ben-Tal, N.; Ben-Shaul, A.; Nicholls, A.; Honig, B. Biophys. J. 1996, 70, 1803-1812.
73. Engelman, D. M.; Steitz, T. A.; Goldman, A. Annu. Rev. Biophys. Biophys. Chem. 1986, 15, 321-353.
74. Fasman, G. D.; Gilbert, W. A. TIBS 1990, 15, 89-92.
75. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.