First-principles simulation of amide and aromatic side chain ultraviolet spectroscopy of a cyclic dipeptide

Journal of Physical Chemistry A

Volumn 111, Issue 45, 2007, Pages 11579-11583

  Li, Zhenyu ^a   Mukamel, Shaul ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIPEPTIDE; MOLECULAR DYNAMICS SIMULATIONS; TYROSINE;

AROMATIC COMPOUNDS; CHROMOPHORES; DENSITY FUNCTIONAL THEORY; DICHROISM; MOLECULAR DYNAMICS; MOLECULAR MODELING; PEPTIDES; ULTRAVIOLET SPECTROSCOPY;

AMIDES;

AMIDE; CYCLOPEPTIDE; DIPEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CIRCULAR DICHROISM; METHODOLOGY; ULTRAVIOLET SPECTROPHOTOMETRY;

AMIDES; CIRCULAR DICHROISM; DIPEPTIDES; MODELS, MOLECULAR; PEPTIDES, CYCLIC; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 36649038938     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp075515s     Document Type: Article

References (65)

1. Hammes, G. G. Spectroscopy for the Biological Sciences; Wiley: New York, 2005.
2. Platt, J. R. J. Chem. Phys. 1949, 17, 484.
3. Lednev, I. K.; Karnoup, A. S.; Sparrow, M. C.; Asher, S. A. J. Am. Chem. Soc. 1999, 121, 8074.
4. Lednev, I. K.; Karnoup, A. S.; Sparrow, M. C.; Asher, S. A. J. Am. Chem. Soc. 1001, 123, 2388.
5. Asher, S. A.; Mikhonin, A.; Bykov, S. J. Am. Chem. Soc. 2004, 126, 8433.
6. Ahmed, Z.; Beta, I. A.; Mikhonin, A. V.; Asher, S. A. J. Am. Chem. Soc. 2004, 127, 10943.
7. Mikhonin, A. V.; Asher, S. A. J. Am. Chem. Soc. 2006, 128, 13879.
8. Bayley, P. M.; Nielsen, E. B.; Schellman, J. A. J. Phys. Chem. 1969, 73, 228.
9. Woody, R. W. J. Chem. Phys. 1968, 49, 4797.
10. Besley, N. A.; Hirst, J. D. J. Am. Chem. Soc. 1999, 121, 9636.
11. Balasubramanian, D.; Wetlaufer, W. B. J. Am. Chem. Soc. 1966, 88, 3449.
12. Urry, D. W. Annu. Rev. Phys. Chem. 1968, 19, 477.
13. Kopple, K. D.; Ohnishi, M. J. Am. Chem. Soc. 1969, 91, 962.
14. Sletten, E. J. Am. Chem. Soc. 1970, 92, 172.
15. Strickland, E. H.; Wilchek, M.; Horwitz, J.; Billups, C. J. Biol. Chem. 1970, 245, 4168.
16. Karle, I. L. J. Am. Chem. Soc. 1972, 94, 81.
17. Karle, I. L.; Ottenheym, H. C. J. Am. Chem. Soc. 1974, 96, 539.
18. Snow, J. W.; Hooker, T. M., Jr. J. Am. Chem. Soc. 1975, 97, 3506.
19. Madison, V.; Young, P. E.; Blout, E. R. J. Am. Chem. Soc. 1976, 98, 5358.
20. Young, P. E.; Madison, V.; Blout, E. R. J. Am. Chem. Soc. 1976, 98, 5365.
21. Sammes, P. G.; Weedon, A. C. J. Chem. Soc., Perkin Trans. 1979, I., 3048.
22. Bowman, R. L.; Kellerman, M.; Hohnson, W. C., Jr. Biopolymers 1983, 22, 1045.
23. Fleischhauer, J.; Grotzinger, J.; Kramer, B.; Kruger, P.; Wollmer, A.; Woody, R. W.; Zobel, E. Biophys. Chem. 1994, 49, 141.
24. Besley, N. A.; Brienne, M.-J.; Hirst, J. D. J. Phys. Chem. B 2000, 104, 12371.
25. Kaya, K.; Nagakura, S. Theor. Chim. Acta 1967, 7, 124.
26. Nielsen, E. B.; Schellman, J. A. J. Phys. Chem. 1967, 71, 2297.
27. Kaya, K.; Nagakuru, S. J. Mol. Spectrosc. 1972, 44, 279.
28. Song, S.; Asher, S.; Krimm, S.; Shaw, K. D. J. Am. Chem. Soc. 1991, 113, 1155.
29. Hirst, J. D.; Persson, B. J. J. Phys. Chem. A 1998, 102, 7519.
30. Nakanishi, K.; Berova, N.; Woody, R. W. Circular Dichroism Principles and Applications; VCH: New York, 1994.
31. Fasman, G. D. Circular Dichroism and the Conformational Analysis of Biomolecules; Plenum: New York, 1996.
32. Creighton, T. E. Proteins, structures and Molecular Properties, 2nd ed.; W. H. Freeman: New York, 1993.
33. Woody, R. W. Private communication.
34. Frelek, J.; Kowalska, P.; Masnyk. M.; Kazimierski, A.; Korda, A.; Woznica, M.; Chmielewski, M.; Furche, F. Chem. Eur. J. 2007, 13, 6732.
35. Mukamel, S. Principles of Nonlinear Optical Spectroscopy; Oxford University Press: New York, 1995.
36. Mukamel, S. Ann. Rev. Phys. Chem. 2000, 51, 691.
37. Asplund, M. C.; Zanni, M. T.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 8219.
38. Brixner, T.; Stenger, J.; Vaswani, H. M.; Cho, M.; Blankenship, R. E.; Fleming, G. R. Nature 2005, 434, 625.
39. Li, Z.; Abramavicius, D.; Zhuang, W.; Mukamel, S. Chem. Phys. 2007, in press. DOI:10.1016/j.chemphys.2007.03.029.
40. Verlet, L. Phys. Rev. 1967, 159, 98.
41. Elliott, S. D.; Ahlrichs, R.; Hampe, O.; Kappes, M. M. Phys. Chem. Chem. Phys. 2000, 2, 3415.
42. Ahlrichs, R.; Bar, M.; Haser, M.; Horn, H.; Kolmel, C. Chem. Phys. Lett. 1989, 162, 165.
43. Schafer, A.; Horn, H.; Ahlrichs, R. J. Chem. Phys. 1992, 97, 2571.
44. Becke, A. D. Phys. Rev. A 1988, 38, 3098.
45. Perdew, J. P. Phys. Rev. B 1986, 33, 8822.
46. Eichkorn, K.; Treutier, O.; Ohm, H.; Haser, M.; Ahlrichs, R. Chem. Phys. Lett. 1995, 242, 652.
47. Eichkorn, K.; Weigend, F.; Treutier, O.; Ahlrichs, R. Theor. Chem. Acc. 1997, 97, 119.
48. Treutler, O.; Ahlrichs, R. J. Chem. Phys. 1995, 102, 346.
49. Klamt, A.; Schurmann, G. J. Chem. Soc. Perkin Trans. 1993, 5, 799.
50. Hoover, W. G. Phys. Rev. A 1985, 31, 1695.
51. Perdew, J. P.; Ernzerhof, M.; Burke, K. J. Chem. Phys. 1996, 105, 9982.
52. Adamo, C.; Scuseria, G. E.; Barone, V. J. Chem. Phys. 1999, 111, 2889.
53. Zhuang, W.; Abramavicius, D.; Hayashi, T.; Mukamel, S. J. Phys. Chem. B 2006, 110, 3362.
54. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, 1987.
55. Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to applications, 2nd ed.; Academic Press: San Diego, CA, 2001.
56. Maitra, N. T.; Zhang, F.; Cave, R. J.; Burke, K. J. Chem. Phys. 2004, 120, 5932.
57. Casida, M. J. Chem. Phys. 2005, 122, 54111.
58. IUPAC Biochemistry 1970, 9, 3471.
59. Dreuw, A.; Head-Gordon, M. Chem. Rev. 2005, 105, 4009.
60. Oakley, M. T.; Hirst, J. D. J. Am. Chem. Soc. 2006, 128, 12414.
61. Abramavicius, D.; Mukamel, S. Chem. Rev. 2004, 104, 2073.
62. Abramavicius, D.; Mukamel, S. J. Chem. Phys. 2006, 124, 34113.
63. Abramavicius, D.; Zhuang, W.; Mukamel, S. J. Phys. B: At. Mol. Opt. Phys. 2006, 39, 5051.
64. Cave, R. J.; Zhang, R.; Maitra, N. T.; Burke, K. Chem. Phys. Lett. 2004, 389, 39.
65. Yang, L.; Mukamel, S. Phys. Rev. Lett. 2007, submitted.