An analytic potential energy function for the amide-amide and amide-water intermolecular hydrogen bonds in peptides

Journal of Computational Chemistry

Volumn 30, Issue 15, 2009, Pages 2567-2575

  Sun, Chang Liang ^a   Jiang, Xiao Nan ^a   Wang, Chang Sheng ^a  

^a LIAONING NORMAL UNIVERSITY   (China)

Author keywords

Analytic potential energy function; Hydrogen bonded dimers; Potential energy curves

Indexed keywords

ALANINE DIPEPTIDES; ANALYTIC FUNCTIONS; ANALYTIC POTENTIAL ENERGY FUNCTION; DIPEPTIDE; HYDROGEN BONDING INTERACTIONS; HYDROGEN BONDINGS; HYDROGEN-BONDED DIMERS; INTERMOLECULAR HYDROGEN BONDS; N-METHYLACETAMIDE; N-METHYLFORMAMIDE; POTENTIAL ENERGY CURVES; WATER DIMERS; WATER MOLECULE;

AMIDES; AMINES; BINDING ENERGY; BINDING SITES; CURVE FITTING; DIMERS; FUNCTIONAL ANALYSIS; HYDROGEN; PEPTIDES; POTENTIAL ENERGY FUNCTIONS; REACTION KINETICS;

HYDROGEN BONDS;

AMIDE; PEPTIDE; WATER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; HYDROGEN BOND; THERMODYNAMICS;

AMIDES; COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, CHEMICAL; PEPTIDES; THERMODYNAMICS; WATER;

EID: 70349898420     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21266     Document Type: Article

References (57)

1. Jeffrey, G. A.; Saenger, W. Hydrogen Bonding in Biological Structures; Springer-Verlag: Berlin, 1991.
2. Jeffrey, G. A. An Introduction to Hydrogen Bonding; Oxford Uni- versity Press: New York, 1997.
3. Desiraju, G. R.; Steiner, T. The Weak Hydrogen Bond in Structural Chemistry and Biology; Oxford University Press: New York, 1999.
4. MacDonald, J. C.; Whitesides, G. M. Chem Rev 1994, 94, 2383.
5. Etter, M. C. J Phys Chem 1991, 95, 4601.
6. Bernstein, J.; David, R. E.; Shimoni, L.; Chang, N.-L. Angew Chem Int Ed Engl 1995, 34, 1555.
7. Desiraju, G. R. Angew Chem Int Ed Engl 1995, 34, 2311.
8. Tan, H.; Qu, W.; Chen, G.; Liu, R. J Phys Chem A 2005, 109, 6303.
9. Giese, T. J.; Sherer, E. C.; Cramer, C. J.; York, D. M. J Chem Theory Comput 2005, 1, 1275.
10. Scheiner, S. J Phys Chem B 2005, 109, 16132.
11. Singh, S. K.; Babu, M. M.; Balaram, P. Proteins: Struct Funct Genet 2003, 51, 167.
12. Sense, A.; Ubarretxena-Belandia, Engelman, M. Proc Natl Acad Sci U.S.A. 2001, 98, 9056.
13. Babu, M. M.; Singh, S. K.; Balaram, P. J Mol Biol 2002, 322, 871.
14. Moller, C.; Plesset, M. S. Phys Rev 1934, 46, 618.
15. Pople, J. A.; Seeger, R.; Krishnan, R. Int J Quantum Chem Symp 1977, 11, 149.
16. Bartlett, R. Annu Rev Phys Chem 1981, 32, 359.
17. Dunning, T. H., Jr. J Phys Chem A 2000, 104, 9062.
18. Vargas, R.; Garza, J.; Friesner, R. A.; Stern H.; Hay, B. P.; Dixon, D. A. J Phys Chem A 2001, 105, 4963.
19. Scheiner, S. J Phys Chem B 2006, 110, 18670.
20. Chin, W.; Piuzzi, F.; Dimicoli, I.; Mons, M. Phys Chem Chem Phys 2006, 8, 1033.
21. Mei, Y.; Wu, E. L.; Han, K. L.; Zhang, J.-Z. H. Int J Quantum Chem 2006, 106, 1267.
22. Chen, X. H.; Zhang, D. W.; Zhang, J.-Z. H. J Chem Phys 2004, 120, 839.
23. Deshmukh, M. M.; Gadre, S. R.; Bartolotti, L. J. J Phys Chem A 2006, 110, 12519;
24. Deshmukh, M. M.; Suresh, C. H.; Gadre, S. R. J Phys Chem A 2007, 111, 6472.
25. Deshmukh, M. M.; Bartolotti, L. J.; Gadre, S. R. J Phys Chem A 2008, 112, 312.
26. Ishimoto, T.; Tokiwa, H.; Teramae, H.; Nagashima, U. J Chem Phys 2005,122, 094905.
27. Buckingham, A. D. Quar Rev Chem Soc 1959, 13, 183.
28. Grabowski, S. J.; Sokalski, W. A.; Leszczynski, J. J Phys Chem A. 2006,110, 4772.
29. Kang, Y. K. J Phys Chem B 2000, 104, 8321.
30. Tschumper, G. S.; Leininger, M. L.; Hoffman, B. C.; Valeev, E. F.; Schaefer, H. F. III; Quack, M. J Chem Phys 2002, 116, 690.
31. Klopper, W.; van Duijneveldt-van de Rijdt, J. G. C. M.; van Duijne-veldt, F. B. Phys Chem Chem Phys 2000, 2, 2227.
32. Klopper, W.; Luthi, H. P. Mol Phys 1999, 96, 559.
33. Feyereisen, M. W.; Feller, D.; Dixon, D. A. J Phys Chem 1996, 100, 2993.
34. Boys, S. F.; Bernardi, F. Mol Phys 1970, 19, 553.
35. Simon, S.; Duran, M.; Dannenberg, J. J. J Chem Phys 1996, 105, 11024.
36. 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.; Raghava- chari, K.; Foresman, J. B; Cioslowski, J.; Ortiz, J. V.; Baboul, A. D.; 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.; Chem, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 03; Gaussian Inc.: Pittsburgh, PA, 2003.
37. Hamzaoui, F.; Baert, F. Acta Crystallogr 1994, C50, 757.
38. Dixon, D. A.; Dobbs, K. D.; Valentini, J. J. J Phys Chem 1994, 98, 13435.
39. Torii, H.; Tatsumi, T.; Kanazawa, T.; Tasumi, M. J Phys Chem B 1998, 102, 309.
40. Steiner, T. Angew Chem Int Ed 2002, 41, 48.
41. Perrin, C. L.; Nielson, J. B. Annu Rev Phys Chem 1997, 48, 511.
42. Novoa, J. J.; Fuenta, P.; Mota, F. Chem Phys Lett 1998, 290, 519.
43. Lehninger, A. L.; Nelson, D. L.; Cox, M. M. Principles of Biochem- istry, 2nd ed.; Worth: New York, 1993.
44. Koh, E.; Kim, T. Proteins 2005, 61, 559.
45. Parisien, M.; Major, F. Proteins 2005, 61, 545.
46. Petkova, T. A.; Ishii, Y.; Balbach, J. J.; Antzutkin, O. N.; Leapman, R. D.; Delaglio, F.; Tycko, R. Proc Natl Acad Sic USA 2002, 99, 16742.
47. Lührs, T.; Ritter, C.; Adrian, M. Riek-Loher, D. Bohrmann, B.; Döbeli, H.; Schubert, D.; Riek, R. Proc Natl Acad Sic U.S.A. 2005, 102, 17342.
48. Nelson, R.; Sawaya, M. R.; Balbirnie, M.; Madsen, A. Ø Riekel, C.; Grothe, R.; Eisenberg. D. Nature 2005, 435, 773.
49. Sawaya, M. R.; Sambashivan, S.; Nelson, R.; Ivanova, M. I.; Sievers, S. A.; Apostol, M. I.; Thompson, M. J.; Balbirnie, M.; Wilt- zius, J. J.; Macfarlane, H. T.; Madsen, A. 0.; Riekel, C.; Eisenberg. D. Nature 2007, 447, 453.
50. Zhao, Y.-L.; Wu, Y.-D. J Am Chem Soc 2002, 124, 1570.
51. Viswanathan, R.; Asensio, A.; Dannenberg, J. J. J Chem Phys A 2004, 108, 9205.
52. Viswanathan, R.; Dannenberg, J. J. J Phys Chem B 2008, 112, 5199.
53. Perczel, A.; Gáspári, Z. Csizmadia, G. J Comput Chem 2005, 26, 1155.
54. Levin, S.; Nowick, J. S. J Am Chem Soc 2007, 129, 13043.
55. Jorgensen, W. L.; Pranata, J. J Am Chem Soc 2008, 1990, 112.
56. Cornell, W. D.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Koll- man, P. A. J Am Chem Soc 1995, 117, 5179.
57. Zhang, Y.; Wang, C.-S. J Comput Chem 2009, 30, 1251.