Electronic and vibrational second-order nonlinear optical properties of protein secondary structural motifs

Journal of Physical Chemistry B

Volumn 109, Issue 42, 2005, Pages 20009-20026

  Perry, John M ^a   Moad, Andrew J ^a   Begue, Nathan J ^a   Wampler, Ronald D ^a   Simpson, Garth J ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE BACKBONES; QUANTUM CHEMICAL CALCULATIONS; VIBRATIONAL TRANSITIONS;

AMINO ACIDS; CHROMOPHORES; ELECTRONIC STRUCTURE; MACROMOLECULES; MOLECULAR DYNAMICS; NONLINEAR OPTICS; PERTURBATION TECHNIQUES; POLARIZATION;

PROTEINS;

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHEMICAL MODEL; CHEMISTRY; ELECTRON; ISOMERISM; MOLECULAR GENETICS; NONLINEAR SYSTEM; PROTEIN SECONDARY STRUCTURE;

ALGORITHMS; AMINO ACID SEQUENCE; ELECTRONS; ISOMERISM; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; NONLINEAR DYNAMICS; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 27744593567     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0506888     Document Type: Article

References (97)

1. Gannaway, J. N.; Sheppard, C. J. R. Opt. Quantum Electron. 1978, 10, 435.
2. Freund, L; Deutsch, M.; Sprecher, A. Biophys. J. 1986, 50, 693.
3. Zipfel, W. R.; Williams, R. M.; Christie, R.; Nikitin, A. Y.; Hyman, B.; Webb, W. W. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7075.
4. Moreaux, L.; Sandre, O.; Mertz, J. J. Opt. Soc. Am. B 2000, 17, 1685.
5. Campagnola, P. J.; Millard, A. C.; Terasaki, M.; Hoppe, P. E.; Malone, C. J.; Mohler, W. A. Biophys. J. 2002, 81, 493.
6. Cox, G.; Kable, E.; Jones, A.; Fraser, L; Manconi, F.; Gorrell, M. D. J. Structural Biol. 2003, 141, 53.
7. Stoller, P.; Kim, B.-M; Rubenchik, A. M.; Reiser, K. M.; Da Silva, L. B. J. Biamed. Opt. 2002, 7, 205.
8. Yasui, T.; Tohno, Y.; Araki, T. Appl. Opt. 2004, 43, 2861.
9. Stoller, P.; Celliers, P. M.; Reiser, K. M.; Rubenchik, A. M. Appl. Opt. 2003, 42, 5209.
10. Kriech, M. A.; Conboy, J. C. J. Am. Chem. Soc. 2005, 127, 2834.
11. Simpson, G. J. ChemPhysChem 2004, 5, 1301.
12. Petralli-Mallow, T.; Wong, T. M.; Byers, J. D.; Yee, H. I.; Hicks, J. M. J. Phys. Chem. 1993, 97, 1383.
13. Kauranen, M.; Verbiest, T.; Maki, J. J.; Persoons, A. J. Chem. Phys. 1994, 101, 8193.
14. Maki, J. J.; Kauranen, M.; Persoons, A. Phys. Rev. B 1995, 51, 1425.
15. Byers, J. D.; Hicks, J. M. Chem. Phys. Lett. 1994, 257, 216.
16. Byers, J. D.; Yee, H. I.; Petralli-Mallow, T.; Hicks, J. M. Phys. Rev. B 1994, 49, 14643.
17. Verbiest, T.; Kauranen, M.; Persoons, A.; Ikonen, M.; Kurkela, J.; Lemmetyinen, H. J. Am. Chem. Soc. 1994, 116, 9203.
18. Ji, N.; Shen, Y. R. J. Am. Chem. Soc. 2004, 126, 15008.
19. Polizzi, M. A.; Plocinik, R. M.; Simpson, G. J. J. Am. Chem. Soc. 2004, 126, 5001.
20. Kriech, M. A.; Conboy, J. C. J. Am. Chem. Soc. 2003, 125, 1148.
21. Conboy, J. C.; Kriech, M. A. Anal. Chim. Acta 2003, 496, 143.
22. Chen, X.; Clarke, M. L.; Wang, J.; Chen, Z. Int. J. Mod. Phys. B 2005, 19, 691.
23. Pászti, Z.; Wang, J.; Clarke, M. L.; Chen, Z. J. Phys. Chem. B 2004, 108, 7779.
24. Koffas, T. S.; Kim, J.; Lawrence, C. C.; Somorjai, G. A. Langmuir 2003, 19, 3564.
25. Wang, J.; Even, M. A.; Chen, X.; Schmaier, A. H.; Waite, J. H.; Chen, Z. J. Am. Chem. Soc. 2003, 125, 9914.
26. Wang, J.; Clarke, M. L.; Zhang, Y.; Chen, X.; Chen, Z. Langmuir 2003, 19, 7862.
27. Jung, S.-Y.; Lim, S.-M.; Albertorio, F.; Kim, G.; Gurau, M. C.; Yang, R. D.; Holden, M. A.; Cremer, P. S. J. Am. Chem. Soc. 2003, 125, 12782.
28. Dreesen, L.; Humbert, C.; Sartenaer, H.; Caudano, Y.; Volcke, C.; Mani, A. A.; Peremans, A.; Thiry, P. A.; Hanique, S.; Frère, J.-M. Langmuir 2004, 20, 7201.
29. Kim, G.; Gurau, M. C.; Lim, S.-M.; Cremer, P. S. J. Phys. Chem. B 2003, 107, 1403.
30. Wang, J.; Pászti, Z.; Even, M. A.; Chen, Z. J. Phys. Chem. B 2004, 108, 3625.
31. Wang, J.; Buck, S. M.; Chen, Z. J. Phys. Chem. B 2002, 106, 11666.
32. Wang, J.; Buck, S. M.; Even, M. A.; Chen, Z. J. Am. Chem. Soc. 2002, 124, 13302.
33. Hayashi, M.; Lin, S. H.; Raschke, M. B.; Shen, Y. R. J Phys. Chem. A 2002, 106, 2271.
34. Belkin, M. A.; Han, S. H.; Wei, X.; Shen, Y. R. Phys. Rev. Lett. 2001, 87, 113001.
35. Fischer, P.; Wise, F. W.; Albrecht, A. C. J. Phys. Chem. A 2003, 107, 8232.
36. Fischer, P.; Buckingham, A. D.; Albrecht, A. C. Phys. Rev. A 2001, 64, 053816.
37. Boyd, R. W.; Sipe, J. E.; Milonni, P. W. J. Opt. A 2004, 6, S14.
38. Fischer, P.; Beckwitt, K.; Wise, F. W.; Albrecht, A. C. Chem. Phys. Lett. 2002, 352, 463.
39. Belkin, M. A.; Shen, Y. R.; Harris, R. A. J. Chem. Phys. 2004, 120, 10118.
40. Champagne, B.; Fischer, P.; Buckingham, A. D. Chem. Phys. Lett. 2000, 331, 83.
41. Kim, J.; Somorjai, G. A. J. Am. Chem. Soc. 2003, 125, 3150.
42. Belkin, M. A.; Shen, Y. R.; Flytzanis, C. Chem. Phys. Lett. 2002, 363, 479.
43. Woody, R. W. Theory of Circular Dichroism of Proteins; Plenum Press: New York, 1996.
44. Woody, R. W.; Koslowski, A. Biophys. Chem. 2002, 101, 535.
45. Charney, E. The Molecular Basis of Optical Activity; John Wiley & Sons: New York, 1979.
46. Moffitt, W.; Yang, J. T. Proc. Natl. Acad. Sci. U.S.A. 1956, 42, 596.
47. Moffitt, W. J. Chem. Phys. 1956, 25, 467.
48. Moffitt, W. Proc. Natl. Acad. Sci. U.S.A. 1956, 42, 736.
49. Keller, D. Theories of circular dichroism for nucleic acids. In Circular Dichroism and the Conformational Analysis of Biomolecules; Fasman, G., Ed.; Plenum Press: New York, 1996.
50. Simpson, G. J.; Perry, J. M.; Moad, A. J.; Wampler, R. D. Chem. Phys. Lett. 2004, 399, 26.
51. Burke, B. J.; Moad, A. J.; Polizzi, M. A.; Simpson, G. J. J. Am. Chem. Soc. 2003, 125, 9111.
52. Ostroverkhov, V.; Singer, K. D.; Petschek, R. G. J. Opt. Soc. Am. B 2001, 18, 1858.
53. Ostroverkhov, V.; Petschek, R. G.; Singer, K. D.; Twieg, R. J. Chem. Phys. Lett. 2001, 340, 109.
54. Ostroverkhov, V.; Ostroverkhov, O.; Petschek, R. G.; Singer, K. D.; Sukhomlinova, L.; Tweig, R. J. IEEE. J. Sel. Top. Quantum Electron. 2001. 7, 781.
55. Simpson, G. J. J. Chem. Phys. 2002, 117, 3398.
56. Simpson, G. J.; Perry, J. M.; Ashmore-Good, C. L. Phys. Rev. B 2002, 66, 165437.
57. Moad, A. J.; Simpson, G. J. J. Phys. Chem. B 2004, 108, 3548.
58. Moad, A. J.; Simpson, G. J. J. Phys. Chem. A 2005, 1709, 1316.
59. Hirose, C.; Akamatsu, N.; Domen, K. J. Chem. Phys. 1992, 96, 997.
60. Wang, J.; Chen, X.; Clarke, M. L.; Chen, Z. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 4978.
61. Dick, B. Chem. Phys. 1985, 96, 199.
62. Giordmaine, J. A. Phys. Rev. 1965, 138, A1599.
63. Fischer, P.; Albrecht, A. C. Bull. Chem. Soc. Jpn. 2002, 75, 1119.
64. Joffre, M.; Yaron, D.; Silbey, R. J.; Zyss, J. J. Chem. Phys. 1992, 97, 5607.
65. Zyss, J.; Ledoux, I. Chem. Rev. 1994, 94, 77.
66. Long, D. A. The Roman effect. A unified treatment of the theory of Raman scattering by molecules; John Wiley and Sons: New York, 2002.
67. Belkin, M. A.; Shen, Y. R. Phys. Rev. Lett. 2003, 97, 213907.
68. Arfken, G. B.; Weber, H. J. Mathematical methods for physicists, 4th ed.; Academic Press: San Diego, CA, 1995.
69. Venyaminov, S. Y.; Yang, J. T. Determination of protein secondary structure. In Circular dichroism and the Conformational Analysis of Biomolecules; Fasman, G., Ed.; Plenum Press: New York, 1996.
70. Woody, R. W.; Dunker, A. K. Aromatic and cystine side-chain CD in proteins. In Circular Dichroism and the Conformational Analysis of Biomolecules; Fasman, G., Ed.; Plenum Press: New York, 1996.
71. Mukamel, S. Principles of nonlinear optical spectroscopy; Oxford University Press: New York, 1995.
72. Jonas, D. M. Annu. Rev. Phys. Chem. 2003, 54, 425.
73. Wright, C. J. Int. Rev. Phys. Chem. 2002, 21, 185.
74. Fayer, M. D. Annu. Rev. Phys. Chem. 2001, 52, 315.
75. Tokmakoff, A.; Fayer, M. D. Acc. Chem. Res. 1995, 28, 437.
76. Shen, Y. R. The Principles of Nonlinear Optics; John Wiley & Sons: New York, 1984.
77. Boyd, R. W. Nonlinear Optics, 2nd ed.; Academic Press: Amsterdam, 2003.
78. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, M. A.; Zakrzewski, V. G.; Montgomery, J. A.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Varone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. T.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Oritz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Koraromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Dieith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayaddara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98; Gaussian Inc.: Pittsburgh, PA, 1998.
79. Kanis, D. R.; Ratner, M. A.; Marks, T. J. J. Am. Chem. Soc. 1992, 114, 10338.
80. Hohlneicher, G.; Dick, B. J. Chem. Phys. 1979, 70, 5427.
81. Serrano-Andrés, L.; Fülscher, M. P. J. Am. Chem. Soc. 1996, 115, 12190.
82. Hayashi, M.; Lin, S. H.; Shen, Y. R. J. Phys. Chem. A 2004, 105, 8058.
83. Kanis, D. R.; Ratner, M. A.; Marks, T. J. Chem. Rev. 1994, 94, 195.
84. Cha, S.; Ham, S.; Cho, M. J. Chem. Phys. 2002, 117, 740.
85. Bernath, P. F. Chapter 7. In Spectra of atoms and molecules; Oxford University Press: New York, 1995.
86. Barlow, D. J.; Thornton, M. J. J. Mol. Biol. 1988, 201, 601.
87. Voet, D.; Voet, J. G. Biochemistry; John Wiley and Sons: Ney York, 1995.
88. Ramachandran, G. N.; Sasisekharan. Conformation of polypeptides and proteins. In Advances in Protein Chemistry; Anfinsen, J. C. B., Anson, M. L., Edsall, J. T., Richards, F. M., Eds.; Academic Press: New York, 1968; Vol. 23.
89. Mitchell, S. A.; McAloney, R. A.; Moffatt, D.; Mora-Diez, N.; Zgierski, M. Z. J. Chem. Phys. 2005, 122, 114707.
90. Mortensen, O. S.; Svendsen, E. N. J. Chem. Phys. 1981, 74, 3185.
91. Yen, C.-C; Araoka, F.; Tokita, M.; Dawauchi, S.; Park, B.; Takezoe, H.; Watanabe, T. Jpn. J. Appl. Phys. 2004, 43, 7026.
92. Park, B.; Kinoshita, Y.; Takezoe, H.; Watanabe, T. Jpn. J. Appl. Phys. 1988, 37, L136.
93. Simpson, G. J. Molecular orientation at surfaces and interfaces. Ph.D. Thesis, University of Colorado, 2000.
94. Plocinik, R. M.; Simpson, G. J. Anal. Chim. Acta 2003, 496, 133.
95. Botek, E.; André, J.-M.; Champagne, B.; Verbiest, T.; Persoons, A. J. Chem. Phys. 2005, 122, 234713.
96. Oh-e, M.; Yokoyama, H.; Yorozuya, S.; Akagi, K.; Belkin, M. A.; Shen, Y. R. Phys. Rev. Lett. 2004, 93, 267402.
97. Belkin, M. A.; Kulakov, T. A.; Enrst, K.-H.; Yan, L.; Shen, Y. R. Phys. Rev. Lett. 2000, 85, 4474.