Excited state geometry of photoactive yellow protein chromophore: A combined conductorlike polarizable continuum model and time-dependent density functional study

Journal of Chemical Physics

Volumn 133, Issue 3, 2010, Pages

  Wang, Yali ^a   Li, Hui ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; CHROMOPHORES; CONTINUUM MECHANICS; DENSITY FUNCTIONAL THEORY; GAS ABSORPTION; GASES; PROTEINS; QUANTUM CHEMISTRY; SOLUTIONS;

ABSORPTION MAXIMA; AQUEOUS SOLUTIONS; B3LYP METHOD; DOUBLE BONDS; EMISSION MAXIMA; EXCITED-STATE GEOMETRIES; EXPERIMENTAL VALUES; FIXED POINTS; GASPHASE; ISOMERIZATION PATHWAYS; MINIMUM ENERGY; P-COUMARIC ACID; PHOTOACTIVE YELLOW PROTEIN CHROMOPHORES; POLARIZABLE CONTINUUM MODEL; SINGLE BOND; SOLVENT EFFECTS; TD-B3LYP; TIME DEPENDENT DENSITY FUNCTIONAL THEORY; TIME-DEPENDENT DENSITY; VARIABLE AREA; VERTICAL EXCITATION;

EXCITED STATES;

BACTERIAL PROTEIN; PHOTOACTIVE YELLOW PROTEIN, BACTERIA; VISUAL PROTEINS AND PIGMENTS;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; ISOMERISM; QUANTUM THEORY; THERMODYNAMICS; TIME;

BACTERIAL PROTEINS; ISOMERISM; MODELS, MOLECULAR; PHOTORECEPTORS, MICROBIAL; QUANTUM THEORY; THERMODYNAMICS; TIME FACTORS;

EID: 77956259339     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3462248     Document Type: Article

References (71)

1. M. E. Casida, in Recent Advances in Density Functional Methods, edited by, D. P. Chong, (World Scientific, Singapore, 1995), pp. 155; M. E. Casida, C. Jamorski, K. C. Casida, and D. R. Salahub, J. Chem. Phys. JCPSA6 0021-9606 108, 4439 (1998). 10.1063/1.475855
2. T. Ziegler, M. Seth, M. Krykunov, J. Autschbach, and F. Wang, J. Chem. Phys. JCPSA6 0021-9606 130, 154102 (2009). 10.1063/1.3114988
3. C. Van Caillie and R. D. Amos, Chem. Phys. Lett. CHPLBC 0009-2614 308, 249 (1999) 10.1016/S0009-2614(99)00646-6
4. C. Van Caillie and R. D. Amos, Chem. Phys. Lett. CHPLBC 0009-2614 317, 159 (2000). 10.1016/S0009-2614(99)01346-9
5. F. Furche and R. Ahlrichs, J. Chem. Phys. JCPSA6 0021-9606 117, 7433 (2002) 10.1063/1.1508368
6. F. Furche and R. Ahlrichs, J. Chem. Phys. JCPSA6 0021-9606 121, 12772 (2004). 10.1063/1.1824903
7. N. C. Handy and H. F. Schaefer III, J. Chem. Phys. JCPSA6 0021-9606 81, 5031 (1984). 10.1063/1.447489
8. A. Öhrn and G. Karlstrom, Mol. Phys. MOPHAM 0026-8976 104, 3087 (2006). 10.1080/00268970600965629
9. Y. Lin and J. Gao, J. Chem. Theory Comput. JCTCCE 1549-9618 3, 1484 (2007). 10.1021/ct700058c
10. J. Kongsted, A. Osted, K. V. Mikkelsen, and O. Christiansen, J. Chem. Phys. JCPSA6 0021-9606 118, 1620 (2003) 10.1063/1.1529680
11. J. Kongsted, A. Osted, K. V. Mikkelsen, P. -O. Astrand, and O. Christiansen, J. Chem. Phys. JCPSA6 0021-9606 121, 8435 (2004). 10.1063/1.1804957
12. L. Jensen, P. T. van Duijnen, and J. G. Snijders, J. Chem. Phys. JCPSA6 0021-9606 119, 3800 (2003) 10.1063/1.1590643
13. P. T. Van Duijnen and T. L. Netzel, J. Phys. Chem. A JPCAFH 1089-5639 110, 2204 (2006) 10.1021/jp0542221
14. C. R. Jacob, J. Neugebauer, L. Jensen, and L. Visscher, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 8, 2349 (2006). 10.1039/b601997h
15. S. Yoo, F. Zahariev, S. Sok, and M. S. Gordon, J. Chem. Phys. JCPSA6 0021-9606 129, 144112 (2008). 10.1063/1.2992049
16. M. Cossi and V. Barone, J. Chem. Phys. JCPSA6 0021-9606 115, 4708 (2001). 10.1063/1.1394921
17. G. Scalmani, M. J. Frisch, B. Mennucci, J. Tomasi, R. Cammi, and V. Barone, J. Chem. Phys. JCPSA6 0021-9606 124, 094107 (2006). 10.1063/1.2173258
18. S. Miertuš, E. Scrocco, and J. Tomasi, Chem. Phys. CMPHC2 0301-0104 55, 117 (1981). 10.1016/0301-0104(81)85090-2
19. E. Canc̀s, B. Mennucci, and J. Tomasi, J. Chem. Phys. JCPSA6 0021-9606 107, 3032 (1997). 10.1063/1.474659
20. B. Mennucci, E. Cances, and J. Tomasi, J. Phys. Chem. B JPCBFK 1089-5647 101, 10506 (1997). 10.1021/jp971959k
21. V. Barone and M. Cossi, J. Phys. Chem. A JPCAFH 1089-5639 102, 1995 (1998). 10.1021/jp9716997
22. H. Li and J. H. Jensen, J. Comput. Chem. JCCHDD 0192-8651 25, 1449 (2004). 10.1002/jcc.20072
23. A. Klamt and G. Schuurmann, J. Chem. Soc., Perkin Trans. 2 JCPKBH 0300-9580 2, 799 (1993). 10.1039/p29930000799
24. T. N. Truong and E. V. Stefanovich, Chem. Phys. Lett. CHPLBC 0009-2614 240, 253 (1995). 10.1016/0009-2614(95)00541-B
25. D. M. Chipman, Theor. Chem. Acc. TCACFW 1432-881X 107, 80 (2002) 10.1007/s00214-001-0302-1
26. D. M. Chipman and M. Dupuis, Theor. Chem. Acc. TCACFW 1432-881X 107, 90 (2002). 10.1007/s00214-001-0303-0
27. A. V. Marenich, R. M. Olson, C. P. Kelly, C. J. Cramer, and D. G. Truhlar, J. Chem. Theory Comput. JCTCCE 1549-9618 3, 2011 (2007). 10.1021/ct7001418
28. P. Su and H. Li, J. Chem. Phys. JCPSA6 0021-9606 130, 074109 (2009). 10.1063/1.3077917
29. A. W. Lange and J. M. Herbert, The Journal of Physical Chemistry Letters 1, 556 (2010). 10.1021/jz900282c
30. G. Scalmani and M. J. Frisch, J. Chem. Phys. JCPSA6 0021-9606 132, 114110 (2010). 10.1063/1.3359469
31. T. E. Meyer, Biochim. Biophys. Acta BBACAQ 0006-3002 806, 175 (1985). 10.1016/0005-2728(85)90094-5
32. J. J. Van Beeumen, B. V. Devreese, S. M. Van Bun, W. D. Hoff, K. J. Hellingwerf, T. E. Meyer, D. E. McRee, and M. A. Cusanovich, Protein Sci. PRCIEI 0961-8368 2, 1114 (1993) 10.1002/pro.5560020706
33. M. Baca, G. E. O. Borgstahl, M. Boissinot, P. M. Burke, D. R. Williams, K. A. Slater, and E. D. Getzoff, Biochemistry BICHAW 0006-2960 33, 14369 (1994). 10.1021/bi00252a001
34. U. K. Genick, S. M. Soltis, P. Kuhn, I. L. Canestrelli, and E. D. Getzoff, Nature (London) NATUAS 0028-0836 392, 206 (1998). 10.1038/32462
35. D. S. Larsen, M. Vengris, I. H. M. van Stokkum, M. A. van der Horst, R. A. Cordfunke, K. J. Hellingwerf, and R. van Grondelle, Chem. Phys. Lett. CHPLBC 0009-2614 369, 563 (2003). 10.1016/S0009-2614(03)00003-4
36. D. S. Larsen, M. Vengris, I. H. M. van Stokkum, M. A. van der Horst, F. L. de Weerd, K. J. Hellingwerf, and R. van Grondelle, Biophys. J. BIOJAU 0006-3495 86, 2538 (2004). 10.1016/S0006-3495(04)74309-X
37. M. Vengris, M. A. van der Horst, G. Zgrabli, I. H. M. van Stokkum, S. Haacke, M. Chergui, K. J. Hellingwerf, R. van Grondelle, and D. S. Larsen, Biophys. J. BIOJAU 0006-3495 87, 1848 (2004). 10.1529/biophysj.104.043224
38. M. Vengris, D. S. Larsen, M. A. van der Horst, O. F. A. Larsen, K. J. Hellingwerf, and R. van Grondelle, J. Phys. Chem. B JPCBFK 1089-5647 109, 4197 (2005) 10.1021/jp045763d
39. L. L. Premvardhan, F. Buda, M. A. van der Horst, D. C. Luhrs, K. J. Hellingwerf, and R. van Grondelle, J. Phys. Chem. B JPCBFK 1089-5647 108, 5138 (2004). 10.1021/jp037469b
40. I. B. Nielsen, S. Boye-Peronne, M. O. A. El Ghazaly, M. B. Kristensen, S. Brondsted Nielsen, and L. H. Andersen, Biophys. J. BIOJAU 0006-3495 89, 2597 (2005). 10.1529/biophysj.105.061192
41. W. L. Ryan, D. J. Gordon, and D. H. Levy, J. Am. Chem. Soc. JACSAT 0002-7863 124, 6194 (2002). 10.1021/ja017505p
42. P. Changenet-Barret, P. Plaza, and M. M. Martin, Chem. Phys. Lett. CHPLBC 0009-2614 336, 439 (2001) 10.1016/S0009-2614(01)00137-3
43. A. Espagne, P. Changenet-Barret, P. Plaza, and M. M. Martin, J. Phys. Chem. A JPCAFH 1089-5639 110, 3393 (2006). 10.1021/jp0563843
44. M. A. van der Horst, J. C. Arents, R. Kort, and K. J. Hellingwerf, Photochem. Photobiol. Sci. PPSHCB 1474-905X 6, 571 (2007). 10.1039/b701072a
45. I. R. Lee, W. Lee, and A. H. Zewail, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 103, 258 (2006). 10.1073/pnas.0510015103
46. G. Groenhof, M. Bouxin-Cademartory, B. Hess, S. P. de Visser, H. J. C. Berendsen, M. Olivucci, A. E. Mark, and M. A. Robb, J. Am. Chem. Soc. JACSAT 0002-7863 126, 4228 (2004). 10.1021/ja039557f
47. V. Molina and M. Merchan, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 98, 4299 (2001). 10.1073/pnas.071058098
48. C. Ko, B. Levine, A. Toniolo, L. Manohar, S. Olsen, H. -J. Werner, and T. J. Martinez, J. Am. Chem. Soc. JACSAT 0002-7863 125, 12710 (2003). 10.1021/ja0365025
49. E. V. Gromov, I. Burghardt, H. Koppel, and L. S. Cederbaum, J. Am. Chem. Soc. JACSAT 0002-7863 129, 6798 (2007). 10.1021/ja069185l
50. P. B. Coto, D. Roca-Sanjuan, L. Serrano-Andres, A. Martin-Pendas, S. Marti, and J. Andres, J. Chem. Theory Comput. JCTCCE 1549-9618 5, 3032 (2009). 10.1021/ct900401z
51. M. Boggio-Pasqua, M. A. Robb, and G. Groenhof, J. Am. Chem. Soc. JACSAT 0002-7863 131, 13580 (2009). 10.1021/ja904932x
52. A. Sergi, M. Gruning, M. Ferrario, and F. Buda, J. Phys. Chem. B JPCBFK 1089-5647 105, 4386 (2001). 10.1021/jp002270+
53. G. Groenhof, M. F. Lensink, H. J. C. Berendsen, J. G. Snijders, and A. E. Mark, Proteins 18PLAF 0887-3585 48, 202 (2002). 10.1002/prot.10136
54. M. J. Thompson, D. Bashford, L. Noodleman, and E. D. Getzoff, J. Am. Chem. Soc. JACSAT 0002-7863 125, 8186 (2003). 10.1021/ja0294461
55. B. G. Levine, C. Ko, J. Quenneville, and T. J. Martinez, Mol. Phys. MOPHAM 0026-8976 104, 1039 (2006). 10.1080/00268970500417762
56. M. Chiba, D. G. Fedorov, and K. Kitaura, J. Comput. Chem. JCCHDD 0192-8651 29, 2667 (2008). 10.1002/jcc.21000
57. B. Mennucci, R. Cammi, and J. Tomasi, J. Chem. Phys. JCPSA6 0021-9606 109, 2798 (1998) 10.1063/1.476878
58. M. Cossi and V. Barone, J. Chem. Phys. JCPSA6 0021-9606 112, 2427 (2000). 10.1063/1.480808
59. M. Cossi, N. Rega, G. Scalmani, and V. Barone, J. Comput. Chem. JCCHDD 0192-8651 24, 669 (2003). 10.1002/jcc.10189
60. M. W. Schmidt, K. K. Baldridge, J. A. Boatz, S. T. Elbert, M. S. Gordon, J. H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. J. Su, T. L. Windus, M. Dupuis, and J. A. Montgomery, J. Comput. Chem. JCCHDD 0192-8651 14, 1347 (1993) 10.1002/jcc.540141112
61. M. S. Gordon and M. W. Schmidt, in Theory and Applications of Computational Chemistry, edited by, C. E. Dykstra, G. Frenking, K. S. Kim, and, G. E. Scuseria, (Elsevier, New York, 2005).
62. M. Chiba, T. Tsuneda, and K. Hirao, J. Chem. Phys. JCPSA6 0021-9606 124, 144106 (2006) 10.1063/1.2186995
63. M. Chiba, T. Tsuneda, and K. Hirao, Chem. Phys. Lett. CHPLBC 0009-2614 420, 391 (2006). 10.1016/j.cplett.2006.01.015
64. J. Tomasi, B. Mennucci, and E. Cances, J. Mol. Struct.: THEOCHEM THEODJ 0166-1280 464, 211 (1999). 10.1016/S0166-1280(98)00553-3
65. H. Li, C. S. Pomelli, and J. H. Jensen, Theor. Chem. Acc. TCACFW 1432-881X 109, 71 (2003). 10.1007/s00214-002-0427-x
66. R. H. Hertwig and W. Koch, Chem. Phys. Lett. CHPLBC 0009-2614 268, 345 (1997). 10.1016/S0009-2614(97)00207-8
67. T. H. Dunning, J. Chem. Phys. JCPSA6 0021-9606 90, 1007 (1989). 10.1063/1.456153
68. C. S. Pomelli, J. Tomasi, and V. Barone, Theor. Chem. Acc. TCACFW 1432-881X 105, 446 (2001). 10.1007/s002140000239
69. E. M. González, L. Guidoni, and C. Molteni, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 11, 4556 (2009). 10.1039/b902615k
70. Y. Ma, M. Rohlfing, and C. Molteni, J. Chem. Theory Comput. JCTCCE 1549-9618 6, 257 (2010). 10.1021/ct900528h
71. M. Chiba, D. G. Fedorov, and K. Kitaura, Chem. Phys. Lett. CHPLBC 0009-2614 444, 346 (2007). 10.1016/j.cplett.2007.07.034