An improved OPLS-AA force field for carbohydrates

Journal of Computational Chemistry

Volumn 23, Issue 15, 2002, Pages 1416-1429

  Kony, D ^a   Damm, W ^b   Stoll, S ^a   Van Gunsteren, W F ^b  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b ETH ZURICH   (Switzerland)

Author keywords

1,2 ethanediol; Carbohydrates; Conformational analysis; Force field; Hexopyranoses; Molecular dynamics

Indexed keywords

CALCULATIONS; COMPUTER SIMULATION; CONFORMATIONS; ELECTRON ENERGY LEVELS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE;

CONFORMATIONAL ANALYSIS; ELECTROSTATIC INTERACTION; ETHANEDIOL; HEXAPYRANOSES;

CARBOHYDRATES;

CARBOHYDRATE; ETHYLENE GLYCOL DERIVATIVE;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION;

CARBOHYDRATE CONFORMATION; CARBOHYDRATES; ETHYLENE GLYCOLS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE;

EID: 0037202434     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10139     Document Type: Article

References (50)

1. Lii, J.-H.; Ma, B.; Allinger, N. L. J Comput Chem 1999, 20, 1593.
2. van Gunsteren, W. F.; Berendsen, H. J. C. Angew Chem Int Ed Engl 1990, 102, 1020.
3. (a) Jorgensen, W. L. Org Chem 1991, 4, 91;
4. (b) Damm, W.; van Gunsteren, W. F. J Comput Chem 2000, 21, 774.
5. For a brief introduction to Force Field concept, see, for example: Connolly, M. L.; von Ragué Schleyer, P.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, H. F., Schreiner, P. R., Eds.; Encyclopedia of Computational Chemistry; Wiley: New York, 1998; vol. 3, p 1698.
6. (a) Carlson, H. A.; Nguyen, T. B.; Orozco, M.; Jorgensen, W. L. J Comput Chem 1993, 14, 1240;
7. (b) Jorgensen, W. L. In von Ragué Schleyer, P.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, H. F., Schreiner, P. R., Eds.; Encyclopedia of Computational Chemistry: Wiley: New York, 1998, p. 1061, vol. 2;
8. (c) Jorgensen, W. L.; von Ragué Schleyer, P.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, H. F., Schreiner, P. R., Eds.; Encyclopedia of Computational Chemistry; Wiley: New York, 1998; vol 3, p 1986.
9. Ott, K.-H.; Meyer, B. J Comput Chem 1996, 17, 1068.
10. Kouwijzer, M. L. C. E.; van Eijck, B. P.; Kooijman, H.; Kroon, J. Acta Crystallogr B 1995, 51, 209.
11. van Eijck, B. P.; Kroon, J. J Comput Chem 1999, 20, 799.
12. Damm, W.; Frontera, A.; Tirado-Rives, J.; Jorgensen, W. L J Comput Chem 1997, 18, 1955.
13. (a) Glennon, T. M.; Merz, K. M. J Mol Struct (Theochem) 1997, 395, 157;
14. (b) Glennon, T. M.; Zheng, Y.-J.; Le Grand, S. M.; Shutzberg, B. A.; Merz, K. M., Jr. J Comput Chem 1994, 15, 1019.
15. Senderowitz, H.; Parish, C.; Still, W. C. J Am Chem Soc 1996, 118, 2078.
16. Woods, R. J.; Dwek, R. A.; Edge, C. J.; Fraser-Reid, B. J Phys Chem 1995, 99, 3832.
17. Simmerling, C.; Fox, T.; Kollman, P. A. J Am Chem Soc 1998, 120, 5771.
18. Reiling, S.; Schlenkrich, M.; Brickmann, J. J Comp Chem 1996, 17, 450.
19. Ha, S. N.; Giammona, A.; Field, M.; Brady, J Carbohydr Res 1988, 180, 207.
20. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. J Am Chem Soc 1993, 115, 9620.
21. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J Am Chem Soc 1996, 118, 11225.
22. Jorgensen, W. L.; Damm, W.; Frontera, A.; Lamb, M. L. NATO ASI Ser C, 1996, 485, 115.
23. Jorgensen, W. L. unpublished results. Available from the parameter file in BOSS, Version 3.5, Yale University: New Haven, CT, 1994.
24. Damm, W.; Jorgensen, W. L. unpublished results.
25. Vishnyakov, A.; Widmalm, G.; Kowaleski, J.; Laaksonen, A. J Am Chem Soc 1999, 121, 5403.
26. (a) Daura, X.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. J Mol Biol 1998, 280, 925;
27. (b) Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Angew Chem Int Ed 1999, 38, 236.
28. (a) Duan, Y.; Kollman, P. A. Science 1998, 282, 740;
29. (b) Duan, Y.; Wang, L.; Kollman, P. A. Proc Natl Acad Sci USA 1998, 95, 9897.
30. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Ciolowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. Gaussian 94, Revision B.2; Gaussian Inc.: Pittsburgh, PA, 1995.
31. Csonka, G. I.; Csizmadia, I. G. Chem Phys Lett 1995, 243, 419.
32. For B3LYP performance, see, for example: Bauschlicher, C. W. Chem Phys Lett 1995, 246, 40.
33. Cramer, C. J.; Truhlar, D. G. J Am Chem Soc 1994, 116, 3892.
34. (a) Barrows, S. E.; Storer, J. W.; Cramer, C. J.; French, A. D.; Truhlar, D. G. J Comput Chem. 1998, 19, 1111;
35. (b) Cramer, C. J.; Truhlar, D. G.; French, A. D. Carbohydr Res 1997, 298, 1;
36. (c) Barrows, S. E.; Dulles, F. J.; Cramer, C. J.; Truhlar, D. G.; French, A. D. Carbohydr Res 1995, 276, 219.
37. Maxwell, D. S.; Tirado-Rives, J.; Jorgensen, W. L. J Comput Chem 1995, 16, 984.
38. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A. Huenenberger, P. H.; Krueger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: the GROMOS96 Manual and User Guide; Hochschulverlag AG/ETH Zurich: Zurich, 1996.
39. Maxwell, D. S.; Tirado-Rives, J. Potent, Yale University: New Haven, CT.
40. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
41. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
42. Haasnoot, C. A. G.; De Leeuw, F. A. A. M.; Altona, C. Tetrahedron 1980, 36, 2783.
43. Maxwell, D. S.; Tirado-Rives, J. Fitpar, Version 1.1.1, Yale University, New Haven, CT, 1994.
44. (a) Wladkowski, B. D.; Chenoweth, S. A.; Jones, K. E.; Brown, J. W. J Phys Chem A 1998, 102, 5086,
45. (b) Brown, J. W.; Wladkowski, B. D. J Am Chem Soc 1996, 118, 1190.
46. Nishida, Y.; Ohrui, H.; Meguro, H. Tetrahedron Lett 1984, 25, 1575.
47. Ohrui, H.; Nishida, Y.; Higuchi, H.; Hori, H.; Meguro, H. Can J Chem 1987, 65, 1145.
48. Nishida, Y.; Hori, H.; Ohrui, H.; Meguro, H. J Carbohydr Chem 1988, 7, 239.
49. Astley, T.; Birch, G. G.; Drew, M. G. B.; Rodger, P. M. J Phys Chem A, 1999, 103, 5080.
50. Bernardo, D. N.; Ding, Y.; Krogh-Jespersen, K.; Levy, R. M. J Phys Chem 1994, 98, 4180.