Coherent two dimensional infrared spectroscopy of a cyclic decapeptide antamanide. A simulation study of the amide-I and A bands

Journal of Physical Chemistry B

Volumn 112, Issue 39, 2008, Pages 12479-12490

  Falvo, Cyril ^a   Hayashi, Tomoyuki ^a   Zhuang, Wei ^a   Mukamel, Shaul ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION; AMIDES; DENSITY FUNCTIONAL THEORY; DYNAMICS; HYDROGEN; HYDROGEN BONDS; MOLECULAR DYNAMICS; NETWORK PROTOCOLS; ORGANIC SOLVENTS; PHOTONS; QUANTUM CHEMISTRY; SENSOR NETWORKS; SPECTROSCOPIC ANALYSIS; TWO DIMENSIONAL;

EXPLICIT SOLVENTS; INFRARED PHOTONS; INTRAMOLECULAR COUPLINGS; INTRAMOLECULAR HYDROGEN BONDINGS; LOCAL STRUCTURES; MULTIDIMENSIONAL SPECTROSCOPIES; SIMULATION STUDIES; VIBRATIONAL HAMILTONIANS;

INFRARED SPECTROSCOPY;

EID: 54249088989     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp801493y     Document Type: Article

References (52)

1. Ernst, R. R.; Bodenhausen, G.; Wokaun, A. Principles of nuclear magnetic resonance in one and two dimensions; Oxford Univesity Press: New York, 1995.
2. Wuthrich, K. NMR of Proteins and Nucleic Acids; Wiley-Interscience: New York, 1986.
3. Zanni, M. T.; Hochstrasser, R. M. Curr. Opin. Struct. Biol. 2001, 11, 516.
4. Ge, N.-H.; Hochstrasser, R. M. Phys. Chem. Commun. 2002, 5, 17.
5. Fang, C.; Wang, J.; Kim, Y. S.; Charnley, A. K.; Barber-Armstrong, W.; A. B.; Smith, I.; Decatur, S. M.; Hochstrasser, R. M. J. Phys. Chem. B 2004, 108, 10415.
6. Brixner, T.; Stenger, J.; Vaswani, H. M.; Cho, M.; Blankenship, R. E.; Fleming, G. R. Nature 2005, 434, 625.
7. Zigmantas, D.; Read, E. L.; Mancal, T.; Brixner, T.; Gardiner, A. T.; Cogdell, R. J.; Fleming, G. R. Proc. Natl. Acad. Sci. USA 2006, 103, 12672.
8. Parkinson, D. Y.; Lee, H.; Fleming, G. R. J. Phys. Chem. B 2007, 111, 7449.
9. Chergui, M., private communication.
10. Mukamel, S. Annu. Rev. Phys. Chem. 2000, 51, 691.
11. Mukamel, S.; Abramavicius, D. Chem. Rev. 2004, 104, 2073.
12. Krimm, S.; Bandekar, J. J. Adv. Protein Chem. 1986, 38, 181.
13. Torii, H.; Tasumi, M. J. Chem. Phys. 1992, 96, 3379.
14. Torii, H.; Tasumi, M. J. Raman Spectrosc. 1998, 29, 81.
15. Decius, W. E. B.; Cross, J. C. Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectra; McGraw-Hill: New York, 1955.
16. Cheatum, C. M.; Tokmakoff, A.; Knoester, J. J. Chem. Phys. 2004, 120, 8201.
17. Cha, S.; Ham, S.; Cho, M. J. Chem Phys. 2002, 117, 740.
18. Hayashi, T.; Zhuang, W.; Mukamel, S. J. Phys. Chem. A 2005, 109, 9141.
19. Zhuang, W.; Abramavicius, D.; Hayashi, T.: Mukamel, S. J. Phys. Chem. B 2006, 110, 3362.
20. Hayashi, T.; Mukamel, S. J. Phys. Chem. 2007, 11, 11032.
21. Zhuang, W.; Hayashi, T.; Mukamel, S. Angew. Chem, in press.
22. Ham, S.; Cho, M. J. Chem. Phys. 2003, 118, 6915.
23. la Cour Jansen, T.; Knoester, J. J. Chem. Phys. 2006, 124, 044502.
24. Fecko, C. J.; Eaves, J. D.; Loparo, J. J.; Tokmakoff, A.; Geissler, P. L. Science 2003, 301, 1698.
25. Torii, H.; Tatsumi, T.; Kanazawa, T.; Tasumi, M. J. Phys. Chem. B 1998, 102 (1), 309.
26. Moran, A. M.; Park, S.-M.; Mukamel, S. J. Chem. Phys. 2003, 118, 9971.
27. la Cour Jansen, T.; Hayashi, T.; Zhuang, W.; Mukamel, S. J. Chem. Phys. 2005, 123, 114504.
28. Brüschweiler, R.; Roux, B.; Blackledge, M.; Griesinger, C.; Karplus, M.; Ernst, R. R. Biochemistry 1993, 32, 10960.
29. Schmidt, J. M.; Brüschweiler, R.; Ernst, R. R.; R. L.; Dunbrack, J.; Joseph, D.; Karplus, M. J. Am. Chem. Soc. 1993, 115, 8747.
30. Brunne, R. M.; van Gunsteren, W. F.; Brüschweiler, R.; Ernst, R. R. J. Am. Chem. Soc. 1993, 115, 8747.
31. Bremi, T.; Brüschweiler, R.; Ernst, R. R. J. Am. Chem. Soc. 1997, 119, 4272.
32. Wieland, T. Angew. Chem., Int. Ed. 1968, 7, 204.
33. Wieland, T.; Faulstich, H. Crit. Rev. Biochem. 1978, 5, 185.
34. Ivanov, V. T.; Miroshnikov, A. I.; Abdullaev, N. D.; Senyavina, L. B.; Arkhipova, S. F.; Uvarova, N. N.; Khalilulina, K. K.; Bystrov, V. F.; Ovchinnikov, Y. A. Biochem. Biophys. Res. Commun. 1971, 42, 654.
35. Ivanov, V. T.; Miroshnikov, A. I.; Koz'min, S. A.; Meshcheryakova, E. N.; Senyavina, L. B.; Uvarova, N. N.; Khalilulina, K. K.; Zabrodin, V. A.; Bystrov, V. F.; Ovchinnikov, Y. A. Chem. Nat. Compd. 1975, 9, 353.
36. Patel, D. J. Biochemstry 1973, 12, 667.
37. Kessler, H.; Bats, J. W.; Lautz, J.; Müller, A. Liebigs Ann. Chem. 1989, 913.
38. Brüschweiler, R.; Blackledge, M. J.; Ernst, R. R. J. Biomol. NMR 1991, 1, 3.
39. Bteckledge, M. J.; Brüschweiler, R.; Griesinger, C.; Schmidt, J. M.; Xu, P.; Ernst, R. R. Biochemistry 1993, 32, 10960.
40. Karle, I. L.; Wieland, T.; Schermer, D.; Ottenheym, H. C. J. Proc. Natl. Acad. Sci. USA 1979, 76, 1532.
41. Kalé, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comp. Phys. 1999, 151, 283.
42. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586.
43. Fox, T.; Kollman, P. A. J. Phys. Chem B 1998, 102, 8070.
44. Darden, T.; York, D.; Pedersen, L. J. Chem Phys. 1993, 98, 10089.
45. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Pedersen, L. G. J. Chem Phys. 1995, 103, 8577.
46. Tu, K.; Tobias, D. J.; Klein, M. L. Biophys. J. 1995, 69, 2558.
47. Feller, S. E.; Zhang, Y.; Pastor, R. W.; Brooks, B. R. J. Chem. Phys. 1995, 103, 4613.
48. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577.
49. Mukamel, S. Principles of Nonlinear Optical Spectroscopy, Oxford University Press: New York, 1995.
50. Tanimura, Y. J. Phys. Soc. Jpn. 2006, 75, 082001.
51. Hamm, P.; Lim, M.; Hochstrasser, R. M. J. Phys. Chem. B 1998, 102, 6123.
52. Wang, J.; Hochstrasser, R. M. J. Phys. Chem. B 2006, 110, 3798.