Quantum mechanics studies of the intrinsic conformation of trehalose

Journal of Physical Chemistry A

Volumn 106, Issue 19, 2002, Pages 4988-4997

  French, Alfred D ^a   Johnson, Glenn P ^a   Kelterer, Anne Marie ^b   Dowd, Michael K ^a   Cramer, Christopher J ^c  

^a SOUTHERN REGIONAL RESEARCH CENTER   (United States)

^b GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DENSITY FUNCTIONAL THEORY; DISACCHARIDE TREHALOSE; ENERGY SURFACE; GAUCHE LINKAGE CONFORMATION; LINKAGE TORSION ANGLES; MOLECULAR ORBITAL; MOLECULE CRYSTAL STRUCTURE; SOLVATION;

BINDING ENERGY; BOND STRENGTH (CHEMICAL); COMPOSITION EFFECTS; CRYSTAL STRUCTURE; MOLECULAR STRUCTURE; ORGANIC SOLVENTS; QUANTUM THEORY;

ISOMERS;

EID: 0037118414     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp020126d     Document Type: Article

References (64)

1. Elbein, A. D. Adv. Carbohydrate Chem. Biochem. 1974, 30, 227-256.
2. Asahina, E.; Tanno, K. Nature 1964, 204, 1222.
3. Franks, F. In Biophysics and Biochemistry at Low Temperatures, Cambridge University Press: Cambridge, 1985, ch. 6, pp 112-124.
4. Lee, C.-K.; Koh, L. L. I. Carbohydr. Res. 1994, 254, 281-287.
5. Tvaroška, I.; Váklavík, L. Carbohydr. Res. 1987, 160, 137-149.
6. Cramer, C. J.; Kelterer, A.-M.; French, A. D. J. Comput. Chem. 2001, 22, 1194-1204.
7. Ollis, J. V.; James, J.; Angyal, S. J.; Pojer, P. M. Carbohydr. Res. 1978, 60, 219-228.
8. Luger, P.; Paulsen, H. Acta Crystallogr., Sect. B 1981, 37, 1693-1698
9. Williams, G.; Lavallee, P.; Hanessian, S.; Brisse, F. Acta Crystallogr., Sect. B 1979, 35, 2574-2579.
10. Jeffrey, G. A.; Nanni, R. Carbohydr. Res. 1985, 137, 21-30.
11. Brown, J. M.; Cook, S. J.; Jones, R. H.; Khan, R. Tetrahedron 1986, 42, 5089-5096.
12. Lee, C.-K.; Linden, A. J. Carbohydr. Chem. 1995, 14, 9-16.
13. Saviano, M.; Iacovino, R.; Benedetti, E.; Cucinotta, V.; Grasso, G.; Sciotto, D. Z. Kristallogr.-New Crystal Structures 214 (1999) 297-299.
14. Linden, A.; Lee, C.-K. Acta Crystallogr., Sect. C (Cr. Str. Comm.) 1994, 50, 1108-1112.
15. Linden, A.; Lee, C.-K. Acta Crystallogr., Sect. C (Cr. Str. Comm.) 1995, 51, 747-751.
16. Linden, A.; Lee, C.-K. Acta Crystallogr., Sect. C (Cr. Str. Comm.) 1995, 51, 751-754.
17. Cook, W. J.; Bugg, C. E. Carbohydr. Res. 1973, 31, 265-275.
18. Brown, G. M.; Rohrer, D. C.; Berking, B.; Beevers, C. A.; Gould, R. O.; Simpson, R. Acta Crystallogr., Sect. B 1972, 28, 3145-3158.
19. Lee, C.-K.; Koh, L. L.; Xu, Y.; Linden, A. Acta Crystallogr., Sect. C (Cr. Str. Comm.) 1994, 50, 915-919.
20. Lee, C.-K.; Linden, A. Carbohydr. Res. 1994, 264, 319-325.
21. Linden, A.; Lee, C.-K. Acta Crystallogr., Sect. C (Cr. Str. Comm.) 1995, 51, 1007-1012.
22. Linden, A.; Lee, C.-K. Acta Crystallogr., Sect. C (Cr. Str. Comm.) 1995, 51, 1012-1016.
23. Baddeley, T. C.; Clow, S. M.; Cox, P. J.; McLaughlin, A. M.; Wardell, J. L. Acta Crystallogr. 2001, E57, 456-457.
24. Färnbäck, M.; Erikson, L.; Widmalm, G. Acta Crystallogr. C, in press
25. Wang, Y. F.; Dutzler, R.; Rizkallah, P. J.; Rosenbusch, J. P.; Schirmer, T. J. Mol. Biol. 1997, 272, 56-63.
26. Batta, G. J.; Kövér, K. E.; Gervay, J.; Hornyäk, M.; Roberts, G. M. J. Am. Chem. Soc. 1997, 119, 1336-1345.
27. Duda, C. A.; Stevens, E. S. J. Am. Chem. Soc. 1990, 112, 7406-7407.
28. Donnamaria, M. C.; Howard, E. I.; Grigera, J. R. J. Chem. Soc., Faraday Trans. 1994, 90, 2731-2735.
29. Liu, Q.; Schmidt, R. K.; Teo, B.; Karplus, P. A. J. Am. Chem. Soc. 1997, 119, 7851-7862.
30. Engelsen, S. B.; Pérez, S. J. Phys. Chem. B 2000, 104, 9301-9311.
31. Dowd, M. K.; Reilly, P. J.; French, A. D. J. Comput. Chem. 1992, 13, 102-114.
32. Allinger, N. L.; Rahman, M.; Lii, J.-H. J. Am. Chem. Soc. 1990, 112, 8293-8307.
33. French, A. D.; Kelterer, A.-M.; Johnson, G. P.; Dowd, M. K.; Cramer, C. J. J. Mol. Graphics Mol. Modelling 2000, 18, 95-107. The trehalose surfaces were not published in this work, but the average energies of the crystalline conformations were tabulated.
34. Marchessault, R. H.; Perez, S. Biopolymers 1979, 18, 2369-2374.
35. Ha, S. N.; Giammons, A.; Field, M.; Brady, J. W. Carbohydr. Res. 1988, 180, 207-221.
36. van Gunsteren, W. F. GROMOS, Groningen Molecular Simulation Package; University of Groningen, The Netherlands, 1987.
37. French, A. D.; Kelterer, A.-M.; Johnson, G. P.; Dowd, M. K.; Cramer, C. J. J. Comput. Chem. 2001, 22, 65-78.
38. Adv. Carbohydr. Chem. Biochem. 1997, 52. 43-177;
39. Carbohydr. Res., 1997, 297, 1-90;
40. J. Carbohydr. Chem. 1997, 16, 1191-1280;
41. Pure Appl. Chem. 1996, 68, 1919-2008.
42. Barrows, S. E.; Dulles, F. J.; Cramer, C. J.; French, A. D.; Truhlar, D. G. Carbohydr. Res. 1995, 276, 219-251.
43. Lii, J.-H.; Ma, B.; Allinger, N. L. J. Comput. Chem. 1999, 20, 1593-1603.
44. The importance of diffuse functions, represented by the + signs in the 6-311++G** basis set designation, to the correct calculation of the energy when correlation is included was stated in, Csonka, G. I.; Elias, K.; Csizmadia, I. G. Chem. Phys. Letts. 1996, 257 49-60. Our work in ref 39 also reported over-estimation of hydrogen bonding strength with the 6-31G * basis set when the MP2 level of theory was used. In his comments on a draft of our manuscript, Prof. Csonka suggested that less CPU time would be required with the 6-31+G* basis set and the accuracy would be similar. In the present case, the bulk of the computer time was spent on the energy minimizations with the B3LYP/6-31G* level of theory. The succeeding single point calculations with the 6-311++G** basis set added little to the total time required.
45. Momany, F. A.; Willett, J. L. J. Comput. Chem. 2000, 21, 1204-1219.
46. Jaguar 4.0, Schrodinger, Inc., Portland, Oregon, U.S.A.
47. SURFER is available from Golden Software, Golden Colorado, U.S.A.
48. Ha, S. N.; Madsen, L. J.; Brady, J. W. Biopolymers 1988, 27, 1927-1952.
49. French, A. D.; Tran, V. H.; Pérez, S. ACS Symp. Ser. 1990, 430, 191-212.
50. Barrows, S. E.; Storer, J. W.; Cramer, C. J.; French, A. D.; Truhlar, D. G. J. Comput. Chem. 1998, 19, 1111-1129.
51. The calculations that were redundant because of symmetry were used to test the robustness of the minimizer for these complex systems.
52. Senderowitz, H.; Still, W. C. J. Org. Chem. 1997, 62, 1427-1438.
53. MacroModel is available from Schrodinger, Inc., Portland, Oregon, U.S.A.
54. Sanford, M.; Johnson, G. P.; French, A. D.; Laine, R. A. J. Phys. Chem. A. 2002, 106, 4115-4124.
55. McCarren, P. R.; Gordon, M. T.; Lowary, T. L.; Hadad, C. M. J. Phys. Chem. A 2001, 105, 5911-5922.
56. Csonka, G. I.; Sosa, C. P. J. Phys. Chem. A 2000, 104, 7113-7122.
57. Chem-X is no longer available.
58. Li, J.; Zhu, T.; Hawkins, G. D.; Winget, P.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G. Theor. Chem. Acc. 1999, 103, 63.
59. Easton, R. E.; Giesen, D. J.; Welch, A.; Cramer, C. J.; Truhlar, D. G. Theor. Chim. Acta 1996, 93, 281.
60. Peralta-Inga, Z.; Johnson, G. P.; Kelterer, A.-M.; Dowd, M. K.; Stevens, E. D.; French, A. D. Carbohydr. Res., in press.
61. Gridding is a preliminary step in the preparation of contour plots with the SURFER software. A final grid of energy data is prepared by mathematical fitting. Although it would be better if less interpolation were used, our experiences with various grid sizes and isolation of minima shows that the procedure works reasonably well.
62. The pragmatism of reducing hydrogen bond strength so the surface can best rationalize the crystal structures should be taken in context. Although the calculated relative potential energies of an isolated molecule are being used to predict the molecular shapes in crystals, the crystalline shapes be actually governed by the total free energy of the system and kinetics effects. If the modeling method explicitly provides an opportunity to determine the free energy, then the reduced hydrogen bonding strength may not be appropriate. Furthermore, if neighboring molecules, such as solve are explicitly part of the model, then intramolecular hydrogen bonds may not predominate. There again, reduced hydrogen bonding strength may not be appropriate. Other explanations for the utility of reduced hydrogen bonding strength have been given in ref 33.
63. Tvaroška, I.; Carver, J. J. Phys. Chem. 1995, 99, 6234-6241.
64. French, A. D.; Johnson, G. P.; Kelterer, A.-M.; Dowd, M. K.; Cramer, C. J. Int. J. Quantum Chem. 2001, 84, 416-425.