Evaluation of the molecular configuration integral in all degrees of freedom for the direct calculation of conformational free energies: Prediction of the anomeric free energy of monosaccharides

Journal of Physical Chemistry A

Volumn 101, Issue 51, 1997, Pages 9900-9905

  Kolossváry, István ^a,b  

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

^b BUDAPEST UNIVERSITY OF TECHNOLOGY AND ECONOMICS   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; CALCULATIONS; COMPUTER SIMULATION; CONFORMATIONS; DEGREES OF FREEDOM (MECHANICS); INTEGRAL EQUATIONS; INTEGRATION; MONTE CARLO METHODS; SUGARS;

COMPUTATIONAL ALCHEMY; CONFORMATIONAL FREE ENERGY; MOLECULAR CONFIGURATION INTEGRAL; MONOSACCHARIDES;

FREE ENERGY;

EID: 0031337279     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp972794i     Document Type: Review

References (57)

1. Kollman, P. A. Chem. Rev. (Washington, D.C.) 1993, 93, 2395-2417.
2. Senderowitz, H.; Guarnieri, F.; Still, W. C. J. Am. Chem. Soc. 1995, 117, 8211-8219.
3. Head, M. S.; Given, J. A.; Gilson, M. K. J. Phys. Chem. A 1997, 101, 1609-1618.
4. (a) Stroud, A. H. Approximate Calculation of Multiple Integrals; Prentice Hall: Englewood Cliffs, New Jersey, 1971; Chapter 6.
5. (b) Lepage, G. P. J. Comput. Phys. 1978, 27, 192-203.
6. (c) Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes in C Second Edition; Cambridge University Press: New York, 1992; pp 316-328.
7. Kolossváry, I.; Guida, W. C. J. Am. Chem. Soc. 1996, 118, 5011-5019.
8. (a) Karplus, M.; Kushick, J. N. Macromolecules 1981, 14, 325-332.
9. (b) Levy, R. M.; Karplus, M.; Kushick, J.; Perahia, D. Macromolecules 1984, 17, 1370-1374.
10. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440.
11. Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127-8134.
12. Allinger, N. L.; Yuh, Y. H.; Lii, J.-H. J. Am. Chem. Soc. 1989, 111, 8551-8566.
13. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ohio, C.; Alagona, G.; Profeta Jr., S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765-784.
14. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, G. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
15. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657-1666.
16. Halgren, T. A. J. Comput. Chem. 1996, 17, 490-519.
17. (a) Roitberg, A.; Gerber, R. B.; Elber, R.; Ratner, M. A. Science 1995, 268, 1319-1322.
18. (b) Roitberg, A. E.; Gerber, R. B.; Ratner, M. A. J. Phys. Chem. B 1997, 101, 1700-1706.
19. Go, N.; Noguti, T.; Nishikawa, T. Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 3696.
20. Kolossváry, I.; Guida, W. C. J. Am. Chem. Soc. 1993, 115, 2107-2119.
21. Eliel, L. E.; Wilen, S. H. Stereochemistry of Organic Compounds; Wiley-Interscience: New York, 1994; pp 696-702.
22. Straatsma, T. P.; McCammon, J. A. Annu. Rev. Phys. Chem. 1992, 43, 407.
23. (a) Melberg, S.; Rasmussen, K. J. Mol. Struct. 1979, 57, 215.
24. (b) Melberg, S.; Rasmussen, K. Carbohyd. Res. 1979, 76, 23.
25. (c) Melberg, S.; Rasmussen, K. Carbohyd. Res. 1980, 78, 215.
26. (d) Jeffrey, G. A.; Taylor, R. J. Comput. Chem. 1980, 1, 99.
27. (e) Rasmussen, K. Acta Chem. Scand. 1982, A36, 323.
28. (f) Ha, S. N.; Giammona, A.; Field, M.; Brady, J. W. Carbohyd. Res. 1988, 180, 207.
29. (g) Mardsen, A.; Robson, B.; Thompson, J. S. J. Chem. Soc., Faraday Trans. 1 1988, 84, 2519.
30. (h) Homans, S. W. Biochemistry 1990, 29, 9110.
31. (i) Grootenhuis, P. D. J.; Haasnoot, C. A. G. Mol. Simul. 1993, 10, 75.
32. (j) Glennon, T. M.; Zheng, Y. J.; Le Grand, S. M.; Shutzberg, B. A.; Merz, K. M. J. Comput. Chem. 1994, 15, 1019.
33. (k) Woods, R. J.; Dwek, R. A.; Edge, C. J.; Fraser-Reid, B. J. Phys. Chem. 1995, 99, 3832.
34. (l) Asensio, J. L.; Jimenez-Barbero, J. Biopolymers 1995, 35, 55.
35. (m) Reiling, S.; Schlenkrich, M.; Brickmann, J. J. Comput. Chem. 1996, 17, 450.
36. (n) Csonka, G. I.; Éliás, K.; Csizmadia; I. G. J. Comput. Chem. 1997, 18, 330-342.
37. (o) Csonka, G. I.; Éliás, K.; Kolossváry, I.; Sosa, C. P.; Csizmadia; I. G. J. Phys. Chem. A, in press.
38. (a) Ha, S.; Gao, J.; Tidor J.; B.; Brady, J. W.; Karplus, M. J. Am. Chem. Soc. 1991, 113, 1553.
39. (b) Zheng, Y.-J.; Le Grand, S. M.; Merz, K. M.; J. Comput. Chem. 1992, 13, 772.
40. (c) van Eijck, B. P.; Hooft, R. W. W.; Kroon, J. J. Phys. Chem. 1993, 97, 12093.
41. (d) Schmidt, R. K.; Karplus, M.; Brady, J. W. J. Am. Chem. Soc. 1996, 118, 541.
42. (e) Senderowitz, H.; Parish, C.; Still, W. C. J. Am. Chem. Soc. 1996, 118, 2078-2086.
43. (f) Senderowitz, H.; Still, W. C. J. Phys. Chem. B 1997, 101, 1409-1412.
44. (a) Eisenberg, D.; McLachlan, A. D. Nature 1986, 319, 199.
45. (b) Ooi, T.; Oobatake, M.; Némethy, G.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 3086.
46. (c) Kang, Y. K.; Némethy, G.; Scheraga, H. A. J. Phys. Chem. 1987, 91, 4105, 4109, 4118.
47. (d) Warshel, A.; Russel, S. T. Rev. Biophys. 1984, 17, 283.
48. (e) Gilson, M.; Honig, B. Proteins 1988, 4, 7.
49. (f) Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129.
50. (g) Cramer, C. J.; Truhlar, D. G. J. Am. Chem. Soc. 1991, 113, 8305.
51. (a) Rossky, P. J.; Karplus, M. J. Am. Chem. Soc. 1979, 101, 1913.
52. (b) Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
53. (c) Jorgensen, W. L.; Ravimohan, C. J. J. Chem. Phys. 1985, 83, 3050.
54. Marten, B.; Kim, K.; Cortis, C.; Friesner, R. A.; Murphy, R. B.; Ringnalda, M. N.; Sitkoff, D.; Honig, B. J. Phys. Chem. 1996, 100, 11775-11788.
55. (a) Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005-3014.
56. (b) Edinger, S. R.; Cortis, C.; Shenkin, P. S.; Friesner, R. A. J. Phys. Chem. B 1997, 101, 1190-1197.
57. Kolossváry, I. J. Am. Chem. Soc. 1997, 119, 10233-10234.