A simple and realistic model system for studying hydrogen bonds in β-sheets

Journal of Chemical Physics

Volumn 118, Issue 21, 2003, Pages 9783-9794

  Rossmeisl, Jan ^a   Hinnemann, Berit ^a   Jacobsen, Karsten W ^a   Nørskov, Jens K ^a   Olsen, Ole H ^b   Pedersen, Jan T ^c  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b NOVO NORDISK A S   (Denmark)

^c H LUNDBECK A S   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRON ENERGY LEVELS; HYDROGEN BONDS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; NUMERICAL METHODS; PROBABILITY DENSITY FUNCTION; STRUCTURE (COMPOSITION);

AB INITIO DENSITY FUNCTIONAL THEORY; PEPTIDE CHAINS; STRUCTURAL PROPERTIES;

POLYPEPTIDES;

EID: 0038679482     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1570395     Document Type: Article

References (42)

1. L. C. Pauling and R. B. Corey, Proc. R. Soc. London, Ser. B 141, 21 (1953).
2. G. E. Schulz and R. H. Schirmer, Principles of Protein Structure (Springer, New York, 1979).
3. E. N. Baker and R. E. Hubbard, Prog. Biophys. Mol. Biol. 44, 97 (1984).
4. R. Taylor and O. Kennard, J. Am. Chem. Soc. 104, 3063 (1982).
5. Z. S. Derewenda, L. Lee, and U. Derewenda, J. Mol. Biol. 252, 248 (1995).
6. G. F. Fabiola, S. Krishnaswamy, V. Nagarajan, and V. Pattabhi, Acta Crystallogr., Sect. D: Biol. Crystallogr. 53, 316 (1997).
7. M. D. Beachy, D. Chasman, R. B. Murphy, T. A. Halgren, and R. A. Friesner, J. Am. Chem. Soc. 119, 5908 (1997).
8. N. Gresh, H. Guo, D. R. Salahub, B. P. Roques, and S. A. Kafafi, J. Am. Chem. Soc. 121, 7885 (1999).
9. J. K. Kang, J. Mol. Struct.: Theochem 546, 183 (2001).
10. I. L. Shamovsky, G. M. Ross, and R. J. Riopelle, J. Phys. Chem. B 104, 11296 (2000).
11. S. Scheiner, T. Karr, and Y. Gu, J. Biol. Chem. 276, 9832 (2001).
12. R. Vargas, J. Garza, D. A. Dixon, and B. P. Hay, J. Am. Chem. Soc. 122, 4750 (2000).
13. R. Vargas, J. Garza, R. A. Friesner, H. Stern, B. P. Hay, and D. A. Dixon, J. Phys. Chem. A 105, 4963 (2001).
14. R. Vargas, J. Garza, B. P. Hay, and D. A. Dixon, J. Phys. Chem. A 106, 3213 (2002).
15. A. Yang and B. Honig, J. Mol. Biol. 252, 366 (1995).
16. W. D. Cornell, P. Cieplak, C. I. Bayly et al., J. Am. Chem. Soc. 117, 5179 (1995).
17. P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991).
18. E. A. Merrit and D. J. Bacon, Methods Enzymol. 277, 505 (1997).
19. R. Improta, W. Barone, K. N. Kudin, and G. E. Scuseria, J. Chem. Phys. 114, 2541 (2001).
20. R. Improta, W. Barone, K. N. Kudin, and G. E. Scuseria, J. Am. Chem. Soc. 123, 3311 (2001).
21. P. Hohenberg and W. Kohn, Phys. Rev. 136, B864 (1964).
22. W. Kohn and L. J. Sham, Phys. Rev. 140, A1133 (1965).
23. R. G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules (Oxford University Press, New York, 1989).
24. The DFT calculations were performed with the DACAPO pseudopotential code, which is available at http://www.fysik.dtu.dk/campos
25. J. P. Perdew, J. A. Chevary, S. H. Vosko, K. A. Jackson, M. R. Pederson, D. J. Singh, and C. Fiolhais, Phys. Rev. B 46, 6671 (1992).
26. S. Tsuzuki and H. P. Lü Thi, J. Chem. Phys. 114, 3949 (2000).
27. D. R. Hamann, Phys. Rev. B 55, 10157 (1997).
28. D. Vanderbilt, Phys. Rev. B 41, 7892 (1990).
29. G. Kresse and J. Furthmüller, J. Comput. Mater. Sci. 6, 15 (1996).
30. K. Hinsen, J. Comput. Chem. 21, 79 (2000).
31. P. Y. Chou and G. D. Fasman, Biochemistry 13, 222 (1974).
32. G. A. Jeffrey and W. Saenger, Hydrogen Bonding in Biological Structures (Springer, Berlin, 1991).
33. S. Scheiner, Hydrogen Bonding: A Theoretical Perspective (Oxford University Press, New York, 1997).
34. G. A. Jeffrey, J. Mol. Struct. 485, 293 (1999).
35. Y. Gu, T. Karr, and S. Scheiner, J. Am. Chem. Soc. 121, 9411 (1999).
36. Y.-L. Zhao and Y.-D. Wu, J. Am. Chem. Soc. 124, 1570 (2002).
37. M. Buck and M. Karplus, J. Phys. Chem. B 105, 11000 (2001).
38. D. A. Dixon, K. B. Dobbs, and J. J. Valentini, J. Phys. Chem. 98, 13435 (1994).
39. C. I. Bayly, P. Cieplak, W. D. Cornell, and P. A. Kollman, J. Phys. Chem. 97, 10269 (1993).
40. P. K. C. Paul and C. Ramakrishnan, J. Biomol. Struct. Dyn. 2, 879 (1985).
41. J. R. Damewood, Jr., R. A. Kumpf, W. C. F. Mühlbauer, R. J. Urban, and J. E. Eksterowicz, J. Phys. Chem. 94, 6619 (1990).
42. C. Clothia, J. Mol. Biol. 75, 295 (1973).