Empirical solvent correction for multiple amide group vibrational modes

Journal of Chemical Physics

Volumn 122, Issue 14, 2005, Pages

  Bour̂, Petr ^a   Michalík, David ^a,b   Kapitán, Josef ^a  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b INSTITUTE OF CHEMICAL TECHNOLOGY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE GROUP; HYDRATED BIOPOLYMERS; SOLVENT CORRECTION; VIBRATIONAL CIRCULAR DICHROISM (VCD);

BANDWIDTH; CHROMOPHORES; ELECTROSTATICS; LAGRANGE MULTIPLIERS; MATHEMATICAL MODELS; MATRIX ALGEBRA;

VIBRATIONS (MECHANICAL);

EID: 20844436194     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1877272     Document Type: Article

References (64)

1. J. Noell and K. Morokuma, Chem. Phys. Lett. 36, 465 (1975).
2. U. C. Singh and P. A. Kollman, J. Comput. Chem. 7, 718 (1986).
3. M. A. Thomson, J. Phys. Chem. 100, 14492 (1996).
4. J. Florián and A. Warshel, J. Phys. Chem. B 101 5583 (1997).
5. P. Bouř, Chem. Phys. Lett. 365, 82 (2002).
6. S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, J. Chem. Phys. 120, 8107 (2004).
7. K. Kwac and M. Cho, J. Chem. Phys. 119, 2247 (2003).
8. P. Bouř and T. A. Keiderling, J. Chem. Phys. 119, 11253 (2003).
9. S. Izvekov, M. Parrinello, C. J. Burnham, and G. A. Voth, J. Chem. Phys. 120, 10896 (2004).
10. C. H. Langley and N. L. Allinger, J. Phys. Chem. A 107, 5208 (2003).
11. J. Kongsted, A. Osted, K. Mikkelsen, and O. Christiansen, J. Phys. Chem. A 107, 2578 (2003).
12. S. Y. Ham, S. Hahn, C. Lee, T. K. Kim, K. Kwak, and M. Cho, J. Phys. Chem. B 108, 9333 (2004).
13. J. H. Choi, S. Y. Ham, and M. Cho, J. Phys. Chem. B 107, 9132 (2003).
14. H. Huang, S. Malkov, M. Coleman, and P. Painter, J. Phys. Chem. A 107, 7697 (2003).
15. S. Krimm and J. Bandekar, Adv. Protein Chem. 38, 181 (1986).
16. V. Andrushchenko, H. Wieser, and P. Bouř, J. Phys. Chem. B 106, 12623 (2002).
17. V. Andrushchenko, H. Wieser, and P. Bouř, J. Phys. Chem. B 108, 3899 (2004).
18. T. A. Kedierling, in Circular Dichroism: Principles and Applications, edited by, N. Berova, K. Nakanishi, and, R. W. Woody, (Wiley, New York, 2000), pp. 621-666.
19. Spectroscopic Methods for Determining Protein Structure in Solution, edited by, H. Havel, (VCH, New York, 1995).
20. P. L. Polavarapu, Vib. Spectrosc. 17B, 319 (1989).
21. T. A. Keiderling, R. A. G. D. Silva, G. Yoder, and R. K. Dukor, Bioorg Med. Chem. 7, 133 (1999).
22. R. A. G. D. Silva, J. Kubelka, P. Bouř, S. M. Decatur, and T. A. Keiderling, Proc. Natl. Acad. Sci. U.S.A. 97, 8318 (2000).
23. P. Bouř and T. A Keiderling, J. Am. Chem. Soc. 15, 9602 (1993).
24. P. Bouř, J. Sopková, L. Bednárová, P. Maloň, and T. A. Keiderling, J. Comput. Chem. 18, 646 (1997).
25. P. Bouř and T. A. Keiderling, J. Mol. Struct.: THEOCHEM 675, 95 (2004).
26. J. Kubelka and T. A. Keiderling, J. Am. Chem. Soc. 123, 12048 (2001).
27. J. Hilario, J. Kubelka, F. A. Syud, S. H. Gellman, and T. A. Keiderling, Biopolymers 67, 233 (2002).
28. A. G. Cochran, N. J. Skelton, and M. A. Starovasnik, Proc. Natl. Acad. Sci. U.S.A. 98, 5578 (2001).
29. S. H. Gellman, Curr. Opin. Struct. Biol. 2, 717 (1998).
30. L. Onsager, J. Am. Chem. Soc. 58, 1486 (1936).
31. M. W. Wong, M. J. Frisch, and K. B. Wiberg, J. Am. Chem. Soc. 113, 4776 (1991).
32. V. Barone, M. Cossi, and J. Tomasi, J. Comput. Chem. 19, 404 (1998).
33. F. Eckert and A. Klamt, AIChE J. 48, 369 (2002).
34. H. Sato and S. Sakaki, J. Phys. Chem. A 108, 1629 (2004).
35. S. Tenno, F. Hirata, and S. Kato, J. Chem. Phys. 100, 7443 (1994).
36. J. R. Schmidt, S. A. Corcelli, and J. L. Skinner, J. Chem. Phys. 121, 8887 (2004).
37. J. Choi and M. Cho, J. Chem. Phys. 120, 4383 (2004).
38. T. Hayashi, T. la C. Jansen, W. Zhuang, and S. Mukamel, J. Phys. Chem. A 109, 64 (2005).
39. H. Torii, J. Phys. Chem. A 108, 7272 (2004).
40. S. Ham, J. H. Kim, H. Kochan, and M. Cho, J. Chem. Phys. 118, 3491 (2003).
41. M. Cho, J. Chem. Phys. 118, 3480 (2003).
42. N. A. Besley, J. Phys. Chem. A 108, 10794 (2004).
43. P. Bouř, J. Chem. Phys. 121, 7545 (2004).
44. D. Papoušek and M. R. Aliev, Molecular Vibrational Rotational Spectra (Academia, Prague, 1982).
45. A. D. Becke, J. Chem. Phys. 98, 5648 (1993).
46. A. D. Becke, in Modern Electronic Structure Theory, edited by, D. R. Yarkony, (World Scientific, Singapore, 1995), Vol. 2, pp. 1022-1046.
47. A. D. Becke, Phys. Rev. A 38, 3098 (1988).
48. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, GAUSSIAN 03, Revision A.1, Gaussian, Inc., Pittsburgh PA, 2003.
49. P. Bouř and T. A. Keiderling, J. Chem. Phys. 117, 4126 (2002).
50. SPECTRACALC (Galactic Industries Corp., 1990).
51. H. Torii, T. Tatsumi, and M. Tasumi, J. Raman Spectrosc. 29, 537 (1998).
52. H. Guo and M. Karplus, J. Phys. Chem. 96, 7273 (1992).
53. J. Kubelka and T. A. Kedierling, J. Am. Chem. Soc. 105, 10922 (2001).
54. R. V. Pappu, R. K. Hart, and J. W. Ponder, J. Phys. Chem. B 102, 9725 (1998).
55. R. Zhang, H. Li, Y. Lei, and S. Han, J. Mol. Struct. 693, 17 (2004).
56. S. K. Gregurick, G. M. Chaban, and R. B. Gerber, J. Phys. Chem. 106, 8696 (2002).
57. M. T. Zanni, M. C. Asplund, and R. M. Hochstrasser, J. Chem. Phys. 114, 4579 (2001).
58. G. D. Fasman, Prediction of Protein Structure and the Principles of Protein Conformation (Plenum, New York, 1989).
59. P. Bouř, J. Kubelka, and T. A. Keiderling, Biopolymers 65, 45 (2002).
60. J. Kubelka, R. A. G. D. Silva, P. Bouř, S. M. Decatur, and T. A. Keiderling, Chirality: Physical Chemistry, ACS Symp. Ser. 810, edited by, J. M. Hicks, (American Chemical Society, Washington DC, 2002), Vol. 810, pp. 50-64.
61. P. Maloň, R. Kobrinskaya, and T. A. Keiderling, Biopolymers 23, 733 (1988).
62. V. Baumruk and T. A. Keiderling, J. Am. Chem. Soc. 115, 6939 (1993).
63. H. Yu, T. Hansson, and W. F. van Gunsteren, J. Chem. Phys. 118, 221 (2003).
64. D. Marx and J. Hutter, Modern Methods and Algorithms of Quantum Chemistry (Forschungszentrum Juelich, NIC Series, 2000), Vol. 1, pp. 301-449.