Quantum-classical description of the amide I vibrational spectrum of trialanine

Journal of Chemical Physics

Volumn 126, Issue 5, 2007, Pages

  Gorbunov, Roman D ^a   Nguyen, Phuong H ^a   Kobus, Maja ^a   Stock, Gerhard ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; APPROXIMATION THEORY; CONFORMATIONS; MOLECULAR DYNAMICS; MOLECULAR VIBRATIONS; PROBABILITY DENSITY FUNCTION;

CUMULANT APPROXIMATIONS; TRIALANINE; VIBRATIONAL EIGENSTATES; VIBRATIONAL LINE SHAPES;

QUANTUM THEORY;

ALANYL ALANYL ALANINE; ALANYL-ALANYL-ALANINE; AMIDE; OLIGOPEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; QUANTUM THEORY; SPECTROSCOPY;

AMIDES; COMPUTER SIMULATION; OLIGOPEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; QUANTUM THEORY; SPECTRUM ANALYSIS;

EID: 33846982601     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2431803     Document Type: Article

References (69)

1. S. Mukamel and R. M. Hochstrasser, Chem. Phys. 0301-0104 10.1016/S0301-0104(01)00335-4 266, 135 (2001).
2. S. Woutersen and P. Hamm, J. Phys.: Condens. Matter 14, R 1035 (2002).
3. S. Krimm and J. Bandekar, Adv. Protein Chem. 38, 181 (1986).
4. H. Torii and M. Tatsumi, in Infrared Spectroscopy of Biomolecules, edited by, H. H. Mantsch, and, D. Chapman, (Wiley-Liss, New York, 1996), p. 1.
5. P. Hamm, M. Lim, and R. M. Hochstrasser, J. Phys. Chem. B 1089-5647 10.1021/jp9813286 102, 6123 (1998).
6. M. T. Zanni, N. -H. Ge, Y. S. Kim, and R. M. Hochstrasser, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.201412998 98, 11265 (2001).
7. H. S. Chung, M. Khalil, A. W. Smith, Z. Ganim, and A. Tokmakoff, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.0408646102 102, 612 (2005).
8. D. Marx and J. Hutter, in Ab Initio Molecular Dynamics: Theory and Implementation, edited by, J. Grotendorst, (NIC, FZ Jülich, 2000), p. 301, www.fz-juelich.de/nic-series/Volume1/.
9. P. Carloni, U. Röthlisberger, and M. Parrinello, Acc. Chem. Res. 0001-4842 10.1021/ar010018u 35, 455 (2002).
10. R. Rousseau, V. Kleinschmidt, U. W. Schmidt, and D. Marx, Angew. Chem. Int. Ed. 43, 4804 (2004). 1433-7851
11. S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, J. Chem. Phys. 0021-9606 10.1063/1.1683072 120, 8107 (2004).
12. T. Jansen, W. Zhuang, and S. Mukamel, J. Chem. Phys. 0021-9606 10.1063/1.1807824 121, 10577 (2004).
13. S. Gnanakaran, R. M. Hochstrasser, and A. E. Garcia, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.0402933101 101, 9229 (2004).
14. M. Schmitz and P. Tavan, J. Chem. Phys. 0021-9606 10.1063/1.1822914 121, 12233 (2004).
15. S. Hahn, S. Ham, and M. Cho, J. Phys. Chem. B 1089-5647 10.1021/jp050450j 109, 11789 (2005).
16. P. Bour and T. A. Keiderling, J. Phys. Chem. B 1089-5647 10.1021/jp054107q 109, 23687 (2005).
17. W. Zhuang, D. Abramavicius, T. Hayashi, and S. Mukamel, J. Phys. Chem. B 1089-5647 10.1021/jp055813u 110, 3362 (2006).
18. Z. Ganim and A. Tokmakoff, Biophys. J. 0006-3495 10.1529/biophysj.106. 088070 91, 2636 (2006).
19. R. J. Kubo, J. Phys. Soc. Jpn. 12, 570 (1943).
20. S. Mukamel, Principles of Nonlinear Optical Spectroscopy (University Press, Oxford, 1995).
21. H. Hu, M. Elstner, and J. Hermans, Proteins 0887-3585 10.1002/prot.10279 50, 451 (2003).
22. Y. Mu, D. S. Kosov, and G. Stock, J. Phys. Chem. B 1089-5647 10.1021/jp022445a 107, 5064 (2003).
23. S. Gnanakaran and A. E. Garcia, J. Phys. Chem. B 1089-5647 10.1021/jp0359079 107, 12555 (2003).
24. S. Ham and M. Cho, J. Chem. Phys. 0021-9606 10.1063/1.1559681 118, 6915 (2003).
25. K. Kwac and M. Cho, J. Chem. Phys. 0021-9606 10.1063/1.1580807 119, 2247 (2003).
26. J. Choi, S. Ham, and M. Cho, J. Phys. Chem. B 1089-5647 10.1021/jp034835i 107, 9132 (2003).
27. P. Bour and T. A. Keiderling, J. Chem. Phys. 0021-9606 10.1063/1.1622384 119, 11253 (2003).
28. H. Torii, J. Phys. Chem. A 1089-5639 10.1021/jp048320i 108, 7272 (2004).
29. J. R. Schmidt, S. A. Corcelli, and J. L. Skinner, J. Chem. Phys. 0021-9606 10.1063/1.1791632 121, 8887 (2004).
30. N. A. Besley, J. Phys. Chem. A 1089-5639 10.1021/jp046073c 108, 10794 (2004).
31. T. Hayashi, T. la Cour Jansen, W. Zhuang, and S. Mukamel, J. Phys. Chem. A 1089-5639 10.1021/jp046685x 109, 64 (2005).
32. T. la Cour Jansen and J. Knoester, J. Chem. Phys. 0021-9606 10.1063/1.2148409 124, 044502 (2006).
33. S. Li, J. R. Schmidt, S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, J. Chem. Phys. 0021-9606 10.1063/1.2200690 124, 204110 (2006).
34. J. R. Schmidt, S. A. Corcelli, and J. L. Skinner, J. Chem. Phys. 0021-9606 10.1063/1.1961472 123, 044513 (2005).
35. K. Kwac, H. Lee, and M. Cho, J. Chem. Phys. 0021-9606 10.1063/1.1633549 120, 1477 (2004).
36. A. Piryatinski, C. P. Lawrence, and J. L. Skinner, J. Chem. Phys. 0021-9606 10.1063/1.1566434 118, 9664 (2003).
37. J. Antony, B. Schmidt, and C. Schütte, J. Chem. Phys. 0021-9606 10.1063/1.1829057 122, 014309 (2005).
38. K. Giese, M. Petkovic, H. Naundorf, and O. Kühn, Phys. Rep. 430, 211 (2006). 0370-1573
39. S. Woutersen and P. Hamm, J. Phys. Chem. B 1089-5647 10.1021/jp001546a 104, 11316 (2000).
40. S. Woutersen and P. Hamm, J. Chem. Phys. 0021-9606 10.1063/1.1336807 114, 2727 (2001).
41. S. Woutersen, Y. Mu, G. Stock, and P. Hamm, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.201169498 98, 11254 (2001).
42. S. Woutersen, R. Pfister, P. Hamm, Y. Mu, D. Kosov, and G. Stock, J. Chem. Phys. 0021-9606 10.1063/1.1506151 117, 6833 (2002).
43. R. Schweitzer-Stenner, F. Eker, Q. Huang, and K. Griebenow, J. Am. Chem. Soc. 0002-7863 10.1021/ja016202s 123, 9628 (2001).
44. R. Schweitzer-Stenner, Biophys. J. 83, 523 (2002). 0006-3495
45. J. Graf, P. H. Nguyen, G. Stock, and H. Schwalbe, J. Am. Chem. Soc. 129, 1179 (2007).
46. Y. Mu and G. Stock, J. Phys. Chem. B 1089-5647 106, 5294 (2002).
47. R. D. Gorbunov, D. S. Kosov, and G. Stock, J. Chem. Phys. 0021-9606 10.1063/1.1898215 122, 224904 (2005).
48. H. Torii and M. Tasumi, J. Raman Spectrosc. 0377-0486 10.1002/(SICI)1097-4555(199801)29:1<81::AID-JRS214>3.0.CO;2-H 29, 81 (1998).
49. P. Hamm and S. Woutersen, Bull. Chem. Soc. Jpn. 0009-2673 10.1246/bcsj.75.985 75, 985 (2002).
50. S. Cha, S. Ham, and M. Cho, J. Chem. Phys. 0021-9606 10.1063/1.1483257 117, 740 (2002).
51. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. 0192-8651 26, 1701 (2005).
52. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide (Vdf Hochschulverlag AG an der ETH Zürich, Zürich, 1996).
53. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans, in Intermolecular Forces, edited by, B. Pullman, (Reidel, Dordrecht, 1981), pp. 331-342.
54. T. Darden, D. York, and L. Petersen, J. Chem. Phys. 0021-9606 10.1063/1.464397 98, 10089 (1993).
55. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, and J. R. Haak, J. Chem. Phys. 0021-9606 10.1063/1.448118 81, 3684 (1984).
56. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 0002-7863 10.1021/ja00124a002 117, 5179 (1995).
57. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, J. Phys. Chem. B 1089-5647 10.1021/jp973084f 102, 3586 (1998).
58. W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 0002-7863 10.1021/ja9621760 118, 11225 (1996).
59. A. D. Becke, J. Chem. Phys. 0021-9606 10.1063/1.464913 98, 5648 (1993).
60. M. J. Frisch, G. W. Trucks, H. B. Schlegel, Gaussian 03, Revision B.03 (Gaussian, Inc., Pittsburgh, PA, 2003).
61. Employing techniques from the nonperturbative calculation of time-resolved spectra (Ref.), the time-dependent Schrödinger equation for the Hamiltonian H (x (t)) in Eq. is solved in the local-mode basis ( n〉 ) along the MD trajectory x (t), thus giving the matrix elements Unm (t) = 〈n U (t) m〉 of the time evolution operator. In a second step, a classical average over the equilibrium trajectory is performed according to 〈 Unm (t) 〉 = 1 T 0T Unm (t+τ) dτ, which gives the desired correlation functions used in Eq..
62. L. Seidner, G. Stock, and W. Domcke, J. Chem. Phys. 0021-9606 10.1063/1.469586 103, 3998 (1995).
63. D. J. Adams and G. S. Dubey, J. Comput. Phys. 0021-9991 10.1016/0021-9991(87)90076-3 72, 156 (1987).
64. H. Köppel, W. Domcke, and L. S. Cederbaum, Adv. Chem. Phys. 57, 59 (1984). 0065-2385
65. J. C. Light and Z. Bacic, J. Chem. Phys. 0021-9606 10.1063/1.452904 87, 4008 (1987).
66. N. Makri, Chem. Phys. Lett. 0009-2614 10.1016/0009-2614(92)85654-S 193, 435 (1992).
67. S. Hammes-Schiffer, J. Chem. Phys. 0021-9606 10.1063/1.472093 105, 2236 (1996).
68. V. May and O. Kühn, Charge and Energy Transfer Dynamics in Molecular Systems (Wiley-VCH, Berlin, 2004).
69. C. Kolano, J. Helbig, M. Kozinski, W. Sander, and P. Hamm, Nature 0028-0836 10.1038/nature05352 444, 469 (2006).