Computational studies of the arabinofuranose ring: Conformational preferences of fully relaxed methyl α-D-arabinofuranoside

Journal of Physical Chemistry A

Volumn 105, Issue 24, 2001, Pages 5911-5922

  McCarren, Patrick R ^a   Gordon, Matthew T ^a   Lowary, Todd L ^a   Hadad, Christopher M ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABINOFURANOSE RINGS;

COMPUTATIONAL METHODS; CONFORMATIONS; HYDROGEN BONDS; MONTE CARLO METHODS; OPTIMIZATION;

AROMATIC COMPOUNDS;

EID: 0035928166     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp004611p     Document Type: Article

References (59)

1. Gordon, M. T.; Lowary, T. L.; Hadad, C. M. J. Am. Chem. Soc. 1999, 121, 9682.
2. Gordon, M. T.; Lowary, T. L.; Hadad, C. M. J. Org. Chem. 2000, 65, 4954.
3. D'Souza, F. W.; Ayers, J. D.; McCarren, P. R.; Lowary, T. L. J. Am. Chem. Soc. 2000, 122, 1251.
4. Brennan, P. J.; Nikaido, H. Annu. Rev. Biochem. 1995, 64, 29.
5. (a) Garrett, E. C.; Serianni, A. S. In Computer Modeling of Carbohydrate Molecules; French, A. D., Brady, J. W., Eds; ACS Symposium Series 430. American Chemical Society: Washington, DC, 1990, pp 91-119.
6. (b) Serianni, A. S.; Chipman, D. M. J. Am. Chem. Soc. 1987, 109, 5297.
7. (c) Church, T. J.; Carmichael, I.; Serianni, A. S. J. Am. Chem. Soc. 1997, 119, 8946.
8. Altona, C.; Sundaralingam, M. J. Am. Chem. Soc. 1972, 94, 8205.
9. Hehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. Ab Initio Molecular Orbital Theory; John Wiley & Sons: New York, 1986.
10. (a) Labanowski, J. W.; Andzelm, J. Density Functional Methods in Chemistry; Springer. New York, 1991.
11. (b) Parr, R. G.; Yang, W. Density Functional Theory in Atoms and Molecules; Oxford University Press: New York, 1989.
12. (c) Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
13. (d) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
14. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B ; Scuseria, G. E.; Robb, M A ; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, Revision A.7, Gaussian, Inc.; Pittsburgh, PA, 1998.
15. (a) Lii, J. H.; Ma, B.; Allinger, N. L. J. Comput. Chem. 1999, 15, 1593.
16. (b) Csonka, G ; Éliás, K.; Csizmadia, I. G. J. Comput. Chem. 1996, 18, 330.
17. (c) Csonka, G. I.; Éliás, K.; Kolossváry, I ; Sosa, C. P.; Csizmadia, I. G. J. Phys Chem. A 1998, 102, 1219.
18. (d) Csonka, G. I.; Kolossváry, I.; Császár, P.; Éliás, K.; Csizmadia, I. G. J. Phys. Chem. A 1998, 102, 1219.
19. (e) Del Bene, J. E.; Person, W. B.; Szczepaniak, K. J. Phys. Chem. 1995, 99, 10 705.
20. Scott, A. P.; Radom, L. J. Phys. Chem. 1996, 100, 16 502.
21. (a) MacroModel V6.5: Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caulfield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440.
22. (b) Goodman, J.; Still, W. C. J. Comput. Chem. 1991, 12, 1110.
23. Homans, S. W. Biochemistry 1990, 29, 9112.
24. 2 = ± 0.005 Å, and E = ± 0.1 kcal/mol. A similar comparison of the AMBER conformations decreased the number of unique conformations to 159.
25. ConforMole, P. R. McCarren, The Ohio State University. This program is available upon request.
26. Houseknecht, J. B ; McCarren, P. R.; Lowary, T. L.; Hadad, C. M. J. Am. Chem. Soc., submitted.
27. Jeffrey, G. A. An Introduction to Hydrogen Bonding; Oxford Press: New York, 1997; pp 11-32.
28. Cremer, D.; Pople, J. A. J. Am. Chem. Soc. 1975, 97, 1354.
29. (a) Jebber, K. A.; Zhang, K.; Cassady, C. J.; Chung-Phillips, A J. Am. Chem. Soc. 1996, 118, 10 515.
30. (b) Brown, J. W.; Wladkowski, B. D. J. Am. Chem. Soc. 1996, 118, 1190.
31. (c) Barrows, S. E.; Dulles, F. J.; Cramer, C. J.; French, A. D.; Truhlar, D. G. Carbohydr. Res. 1995, 276, 219.
32. (d) Cramer, C. J.; Truhlar, D. G. J. Am. Chem. Soc. 1993, 115, 5745.
33. (e) Polavarapu, P. L.; Ewig, C. S. J. Comput. Chem. 1992, 13, 1255.
34. (f) Barrows, S. E.; Storer, J. W.; Cramer, C. J.; French, A. D.; Truhlar, D. G. J. Comput. Chem. 1998, 19, 1111.
35. (g) Csonka, G. I.; Csizmadia, I. G. Chem. Phys. Lett. 1995, 243, 419.
36. (g) Ma, B.; Schaefer, H. F., III.; Allinger, N. L. J. Am. Chem. Soc. 1998, 120, 3411.
37. 4 gg-1-h On the potential energy surface obtained from the hydrogen-bonded envelopes, this conformer has an energy that is 2.2 kcal/mol above the global minimum.
38. Evdokimov, A. G.; Kalb (Gilboa), A. J.; Koetzle, T. F.; Klooster, W. T.; Martin, J. M. L. J. Phys. Chem. A 1999, 103, 744.
39. Callam, C. S.; Singer, S. J.; Lowary, T. L.; Hadad, C. M , manuscript in preparation.
40. (a) Xidos, J.D.; Li, J.; Hawkins, G. D.; Liotard, D. A ; Cramer, C. J.; Truhlar, D. G.; Frisch, M. J. MN-GSM, version 99.2, University of Minnesota, Minneapolis, MN 55455.
41. (b) Li, J.; Zhu, T.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. A 1998, 102, 1820.
42. (c) Li, J.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Chem. Phys. Lett. 1998, 288, 293.
43. (d) Zhu, T.; Li, J.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Chem. Phys 1998, 109, 9117.
44. (e) Li, J.; Zhu, T.; Hawkins, G. D.; Winget, P.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G. Theor. Chem. Acc. 1999, 103, 9.
45. Cramer, C. J.; Truhlar, D. G. J. Am. Chem Soc. 1994, 116, 3892.
46. (a) Evdokimov, A. G.; Martin, J. M. L.; Kalb (Gilboa), A. J. J. Phys. Chem. A 2000, 104, 5291.
47. (b) French, A. D ; Dowd, M. K. J. Comput. Chem. 1994, 15, 561.
48. (c) French, A. D ; Dowd, M. K.; Reilly, P. J. J. Mol. Struct. (Theochem.) 1997, 395-396, 271.
49. (d) Cassett, F.; Imberty, A ; Hérve du Penhoat, C.; Koca, J ; Perez, S. J. Mol. Struct. (THEOCHEM) 1997, 395-396, 211.
50. (e) Cros, S.; Hérve du Penhoat, C. H.; Pérez, S.; Imberty, A Carbohydr. Res 1993, 248, 81.
51. (f) French, A. D.; Tran, V. Biopolymers 1990, 29, 1599.
52. (f) Mazeau, K.; Perez, S. Carbohydr. Res. 1998, 311, 203.
53. Saunders, M.; Houk, K. N.; Wu, Y. D.; Still, W. C.; Lipton, M.; Chang, G.; Guida, W. C. J. Am. Chem. Soc. 1990, 112, 1419.
54. (d) Csonka, G. I.; Sosa, C. P. J. Phys. Chem. A 2000, 104, 7113.
55. (e) Csonka, G. I.; Sosa, C. P.; Csizmadia, I. G. J Phys. Chem. A 2000, 104, 3381.
56. (a) Gohlke, H ; Immel, S.; Lichtenthaler, F. W. Carbohydr. Res. 1999, 321, 96.
57. (b) Immel, S.; Schmitt, G. E.; Lichtenthaler, F. W. Carbohydr. Res. 1998, 313, 91.
58. (c) Gruza, J.; Koca, J.; Perez, S.; Imberty, A. J. Mol. Struct. (THEOCHEM) 1998, 424, 269.
59. Pérez, S.; Imberty, A.; Engelsen, S. B.; Gruza, J.; Mazeau, K.; Jimenez-Barbero, J.; Poveda, A.; Espinosa, J.-F.; van Eyck, B. P.; Johnson, G.; French, A. D.; Kouwijzer, M. L. C. E.; Grootenuis, P. D. J.; Bernardi, A.; Raimondi, L.; Senderowitz, H.; Durier, V.; Vergoten, G ; Rasmussen, K. Carbohydr. Res. 1998, 314, 141.