Large-ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26-derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

International Journal of Quantum Chemistry

Volumn 107, Issue 8, 2007, Pages 1657-1672

  Gotsev, Martin G ^a   Ivanov, Petko M ^a  

^a INSTITUTE OF ORGANIC CHEMISTRY   (Bulgaria)

Author keywords

AMBER; Conformational analysis; Cyclodextrins; Molecular dynamics

Indexed keywords

CARBOHYDRATES; CONFORMATIONS; MACROMOLECULES; MOLECULAR DYNAMICS; PARAMETERIZATION; POLYMERIZATION; STRUCTURAL DYNAMICS;

DEGREE OF POLYMERIZATION (DP); ENERGETICS; STRUCTURES GEOMETRIES; WATER SOLUTIONS;

CYCLODEXTRINS;

EID: 34248211261     PISSN: 00207608     EISSN: 1097461X     Source Type: Journal    
DOI: 10.1002/qua.21216     Document Type: Conference Paper

References (60)

1. (a) Saenger, W.; Jacob, J.; Gessler, K.; Steiner, T.; Hoffmann, D.; Sanbe, H.; Koizumi, K.; Smith, S. M.; Takaha, T. Chem Rev 1998, 98, 1787;
2. (b) Larsen, K. L. J Ind Phenom Macrocycl Chem 2002, 43, 1.
3. (a) Ueda, H. J Incl Phenom Macrocycl Chem 2002, 44, 53;
4. (b) Motohama, S.; Ishii, E.; Endo, T.; Nagase, H.; Ueda, H.; Takaha, T.; Okada, S. Biol Zh Arm 2001, 53, 27;
5. (c) Ueda, H.; Wakisaka, M.; Nagase, H.; Takaha, T.; Okada, S. J Ind Phenom Macrocycl Chem 2002, 44, 403.
6. Zheng, M.; Endo, T.; Zimmermann, W. J Incl Phenom Macrocycl Chem 2002, 44, 387.
7. Endo, T.; Zheng, M.; Zimmermann, W. Aust J Chem 2002, 55, 39.
8. Qi, Q.; She, X.; Endo, T.; Zimmermann, W. Tetrahedron 2004, 60, 799.
9. Endo, T.; Ueda, H.; Kobayashi, S.; Nagai, T. Carbohydr Res 1995, 269, 369.
10. Ueda, H.; Endo, T.; Nagase, H.; Kobayashi, S.; Nagai, T. J Inc Phenom 1996, 25, 17.
11. Larsen, K. L.; Mathiesen, F.; Zimmermann, W. Carbohydr Res 1997, 298, 59.
12. French, D.; Pulley, A. O.; Effenberger, J. A.; Rougvie, M. A.; Abdullah, M. Arch Biochem Biophys 1965, 111, 153.
13. Fujiwara, T.; Tanaka, N.; Kobayashi, S. Chem Lett 1990, 739.
14. (a) Jacob, J.; Gessler, K.; Hoffmann, D.; Sanbe, H.; Koizumi, K.; Smith, S. M.; Takaha, T.; Saenger, W. Angew Chem Int Ed Eng 1998, 37, 606;
15. (b) Jacob, J.; Gessler, K.; Hoffmann, D.; Sanbe, H.; Koizumi, K.; Smith, S. M.; Takaha, T.; Saenger, W. Carbohydr Res 1999, 322, 228.
16. (a) Gessler, K.; Usón, I.; Takaha, T.; Krauss, N.; Smith, S. M.; Okada, S.; Sheldrick, G. M.; Saenger, W. Proc Natl Acad Sci USA 1999, 96, 4246;
17. (b) Nimz, O.; Gessler, K.; Usón, I.; Saenger, W. Carbohydr Res 2001, 336, 141.
18. Bettinetti, G.; Sorrenti, M. Thermochim Acta 2002, 385, 63.
19. Terada, Y.; Yanase, M.; Takata, H.; Takaha, T.; Okada, S. J Biol Chem 1997, 272, 15729.
20. Takaha, T.; Yanase, M.; Takata, H.; Okada, S.; Smith, S. M. J Biol Chem 1996, 271, 2902.
21. Larsen, K. L.; Endo, T.; Ueda, H.; Zimmermann, W. Carbohydr Res 1998, 309, 153.
22. Kitamura, S.; Nakatani, K.; Takaha, T.; Okada, S. Macromol Rapid Commun 1999, 20, 612.
23. Furuishi, T.; Endo, T.; Nagase, H.; Ueda, H.; Nagai, T. Chem Pharm Bull 1998, 46, 1658.
24. Dodziuk, H.; Ejchart, A.; Anczewski, W.; Ueda, H.; Krinichnaya, E.; Dolgonos, G.; Kutner, W. Chem Commun 2003, 986.
25. Koehler, J. E. H.; Saenger, W.; van Gunsteren, W. F. Eur Biophys J 1987, 15, 211.
26. Koehler, J. E. H.; Saenger, W.; van Gunsteren, W. F. Eur Biophys J 1988, 16, 153.
27. Kitamura, S.; Isuda, H.; Shimada, J.; Takada, T.; Takaha, T.; Okada, S.; Mimura, M.; Kajiwara, K. Carbohydr Res 1997, 304, 303.
28. Lipkowitz, K. B. Chem Rev 1998, 98, 1829.
29. (a) Shimada, J.; Handa, S.; Kaneko, H.; Takada, T. Macromolecules 1996, 29, 6408;
30. (b) Shimada, J.; Kaneko, H.; Takada, T.; Kitamura, S.; Kajiwara, K. J Phys Chem B 2000, 104, 2136.
31. Momany, F. A.; Willett, J. L. Carbohydr Res 2000, 326, 194.
32. Momany, F. A.; Willett, J. L. Carbohydr Res 2000, 326, 210.
33. (a) Ivanov, P. M.; Jaime, C. J Phys Chem B 2004, 108, 6261;
34. (b) Ivanov, P. M.; Gotsev, M. G.; Jaime, C. Bulg Chem Commun 2005, 37, 380.
35. Gotsev, M. G.; Ivanov, P. M.; Jaime, C. Chirality (submitted).
36. Maestre, I.; Bea, I.; Ivanov, P. M.; Jaime, C. Theor Chem Acc 2006.
37. Allinger, N. L.; Yuh, Y. H.; Lii, J.-H. J Am Chem Soc 1989, 111, 8551.
38. (a) 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;
39. (b) MacroModel/BatchMin, Version 5; Columbia University: New York, 1995.
40. Cornell, W. D.; Cieplack, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
41. Wang, J.; Cieplack, P.; Kollman, P. A. J Comput Chem 2000, 21, 1049.
42. Woods, R. J.; Dwek, R. A.; Edge, C. J.; Fraser-Reid, B. J Phys Chem 1995, 99, 3832.
43. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, 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, CA, 2002.
44. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, F.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A. AMBER 8; University of California: San Francisco, CA, 2004.
45. (a) Kirschner, K. N.; Woods, R. J. Proc Natl Acad Sci USA 2001, 98, 10541;
46. (b) Basma, M.; Sundara, S.; Calgan, D.; Venali, T.; Woods, R. J. J Comput Chem 2001, 22, 1125;
47. (c) Kirschner, K. N.; Woods, R. J. J Phys Chem A 2001, 105, 4150.
48. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
49. (a) Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089;
50. (b) Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J Chem Phys 1995, 103, 8577;
51. (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; p 104;
52. (d) Toukmaji, A.; Sagui, C.; Board, J.; Darden, T. J Chem Phys 2000, 113, 10913.
53. Tsui, V.; Case, D. A. Biopolymers. Nucleic Acid Sci 2001, 56, 275.
54. Weiser, J.; Shenkin, P. S.; Still, W. C. J Comput Chem 1999, 20, 217.
55. Burkert, U.; Allinger, N. L. Molecular Mechanics, ACS Monograph 177; American Chemical Society: Washington, DC, 1982; p 107.
56. Dale, J. Acta Chem Scand 1973, 27, 1115.
57. Arteca, G. A. In Reviews in Comput Chem, Lipkowitz, K. B.; Boyd, D. B., Eds.; VCH: New York, 1996; Vol 9; Chapter 5; p 191.
58. Todeschini, R.; Consonni, V.; Mauri, A.; Pavan, M. http://www.disat. unimib.it/chm/.
59. Ivanov, P. M.; Jaime, C. An Quim Int Ed 1996, 92, 13.
60. Sato, H.; Sakaki, S. J Phys Chem B 2006, 110, 12714.