Insights into the structure of large-ring cyclodextrins through molecular dynamics simulations in solution

Journal of Physical Chemistry B

Volumn 108, Issue 20, 2004, Pages 6261-6274

  Ivanov, Petko M ^a,b   Jaime, Carlos ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b BULGARIAN ACADEMY OF SCIENCES   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

BENDING (DEFORMATION); COMPUTATIONAL METHODS; COMPUTER SIMULATION; CONFORMATIONS; CRYSTAL STRUCTURE; CRYSTALLINE MATERIALS; NUCLEAR MAGNETIC RESONANCE; PARAMETER ESTIMATION; POLYMERIZATION;

CAVITY-LIKE REGIONS; HELICAL STRANDS; SPIRAL PORTIONS; STRUCTURAL DEFORMATIONS;

MOLECULAR DYNAMICS;

EID: 2642583376     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp037527t     Document Type: Article

References (45)

1. (a) Chem. Rev. 1998, 98(5), all pages.
2. (b) Connors, K. A. Chem. Rev. 1997, 97, 1325-1357.
3. Larsen, K. L. J. Inclusion Phenom. Macrocycl. Chem. 2002, 43, 1-13.
4. Saenger, W.; Jacob, J.; Gessler, K.; Steiner, T.; Hoffmann, D.; Sanbe, H.; Koizumi, K.; Smith, S. M.; Takaha, T. Chem. Rev. 1998, 98, 1787-1802.
5. Koehler, J. E. H.; Saenger, W.; van Gunsteren, W. F. Eur. Biophys. J. 1987, 15, 211-224.
6. Koehler, J. E. H.; Saenger, W.; van Gunsteren, W. F. Eur. Biophys. J. 1988, 16, 153-168.
7. Kitamura, S.; Isuda, H.; Shimada, J.; Takada, T.; Takaha, T.; Okada, S.; Mimura, M.; Kajiwara, K. Carbohydr. Res. 1997, 304, 303-314.
8. Jacob, J.; Gessler, K.; Hoffmann, D.; Sanbe, H.; Koizumi, K.; Smith, S. M.; Takaha, T.; Saenger, W. Angew. Chem., Int. Ed. Engl. 1998, 37, 606-609.
9. Lipkowitz, K. B. Chem. Rev. 1998, 98, 1829-1873.
10. (a) Shimada, J.; Handa, S.; Kaneko, H.; Takada, T. Macromolecules 1996, 29, 6408-6421.
11. (b) Shimada, J.; Kaneko, H.; Takada, T.; Kitamura, S.; Kajiwara, K. J. Phys. Chem. B 2000, 104, 2136-2147.
12. Momany, F. A.; Willett, J. L. Carbohydr. Res. 2000, 326, 210-226.
13. (a) Beà, I. Ph.D. Thesis, Universitat Autònoma de Barcelona, Barcelona, 2001.
14. (b) Maestre, I.; Beà, I.; Ivanov, P. M.; Jaime, C. J. Mol. Struct., submitted for publication.
15. Fujiwara, T.; Tanaka, N.; Kobayashi, S. Chem. Lett. 1990, 739-742.
16. Ueda, H.; Endo, T.; Nagase, H.; Kobayashi, S.; Nagai, T. J. Inclusion Phenom. Mol. Recognit. Chem. 1996, 25, 17-20.
17. Jacob, J.; Gessler, K.; Hoffmann, D.; Sanbe, H.; Koizumi, K.; Smith, S. M.; Takaha, T.; Saenger, W. Carbohydr. Res. 1999, 522, 228-246.
18. (a) Gessler, K.; Usón, I.; Takaha, T.; Krauss, N.; Smith, S. M.; Okada, S.; Sheldrick, G. M.; Saenger, W. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 4246-4251.
19. (b) Nimz, O.; Gebier, K.; Usón, L; Saenger, W. Carbohydr. Res. 2001, 336, 141-153.
20. Koizumi, K.; Sanbe, H.; Kubota, Y.; Terada, Y.; Takaha, T. J. Chromatogr. A 1999, 852, 407-416.
21. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheathan, T. E., III; Wang, J.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Gohlke, H.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 7, University of California: San Francisco, 2002.
22. Wang, J.; Cieplack, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
23. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
24. (a) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
25. (b) Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593.
26. (c) Sagui, C.; Darden, T. A. In Simulation and Theory of Electrostatic Interactions in Solution; Pratt, L. R., Hummer, G., Eds.; American Institute of Physics: Melville, NY, 1999; pp 104-113.
27. (d) Toukmaji, A.; Sagui, C.; Board, J.; Darden, T. J. Chem. Phys. 2000, 113, 10913-10927.
28. (a) Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440-467.
29. (b) MacroModel/BatchMin, v. 5; Department of Chemistry, Columbia University, New York, 1995. The AMBER* force field is a well-documented version of AMBER force field, implemented in MacroModel/BatchMin, v.5 (see pp 81-82 of the BatchMin Reference Manual).
30. Melani, F.; Mura, P.; Adamo, M.; Maestrelli, F.; Gratteri, P.; Bonaccini, C. Chem. Phys. Lett. 2003, 370, 280-292.
31. (a) Kuttel, M.; Brady, J. W.; Naidoo, K. J. J. Comput. Chem. 2003, 23, 1236-1243.
32. (b) Chen, J. Y.; Naidoo, K. J. J. Phys. Chem. B 2003, 107, 9558-9566.
33. Tsui, V.; Case, D. A. Biopolymers (Nucl. Acid. Sci.) 2001, 56, 275-291.
34. Weiser, J.; Shenkin, P. S.; Still, W. C. J. Comput. Chem. 1999, 20, 217-230.
35. Arteca, G. A. in Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers: New York, 1996; Vol. 9, Chapter 5, pp 191-253.
36. Todeschini, R.; Consonni, V.; Mauri, A.; Pavan, M. DRAGON, version 3.0, 2003.
37. (a) Ivanov, P. M.; Jaime, C. Anal. Quím. Int. Ed. 1996, 92, 13-16.
38. (b) Ivanov, P. M.; Jaime, C. J. Mol. Struct. 1997, 377, 137-147.
39. (c) Ivanov, P. M.; Salvatierra, D.; Jaime, C. J. Org. Chem. 1996, 61, 7012-7017.
40. Harata, K.; Endo, T.; Ueda, H.; Nagai, T. Supramol. Chem. 1998, 9, 143-150.
41. Whidock, B. J.; Whitlock, H. W. J. Am. Chem. Soc. 1994, 116, 2301-2311.
42. Nimz, O.; Gessler, K.; Usón, I.; Laettig, S.; Welfle, H.; Sheldrick, G. M.; Saenger, W. Carbohydr. Res. 2003, 338, 977-986.
43. J. Inclusion Phenom. Macromol. Chem. 2002, 44, 1-4, all pages.
44. Machida, S.; Ogawa, S.; Xiaohua, S.; Takaha, T.; Fijii, K.; Hayashi, K. FEBS Lett. 2000, 486, 131-135.
45. Dodziuk, H.; Ejchart, A.; Anczewski, W.; Ueda, H.; Krinichnaya, E.; Dolgonos, G.; Kutner, W. Chem. Commun. 2003, 985-987.