A Multifrequency Virtual Spectrometer for Complex Bio-Organic Systems: Vibronic and Environmental Effects on the UV/Vis Spectrum of Chlorophyll a

ChemPhysChem

Volumn 15, Issue 15, 2014, Pages 3355-3364

  Barone, Vincenzo ^a   Biczysko, Malgorzata ^a,b   Borkowska Panek, Monika ^a,c   Bloino, Julien ^a,b  

^a SCUOLA NORMALE SUPERIORE   (Italy)

^b CNR   (Italy)

^c KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

Author keywords

chlorophyll; environmental effects; line shapes; UV Vis spectra; vibronic effects

Indexed keywords

CHLOROPHYLL; CHLOROPHYLL A; GAS; METHANOL;

CHEMISTRY; CONFORMATION; ELECTRON; GAS; QUANTUM THEORY; ULTRAVIOLET SPECTROPHOTOMETRY;

CHLOROPHYLL; ELECTRONS; GASES; METHANOL; MOLECULAR CONFORMATION; QUANTUM THEORY; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 84907985505     PISSN: 14394235     EISSN: 14397641     Source Type: Journal    
DOI: 10.1002/cphc.201402300     Document Type: Article

References (97)

1. S. Vassiliev, D. Bruce, Photosynth. Res. 2008, 97, 75-89.
2. T. Renger, E. Schlodder, ChemPhysChem 2010, 11, 1141-1153.
3. C. König, J. Neugebauer, ChemPhysChem 2012, 13, 386-425.
4. T. Renger, F. Muh, Phys. Chem. Chem. Phys. 2013, 15, 3348-3371.
5. T. Vreven, K. Morokuma, Theor. Chem. Acc. 2003, 109, 125-132.
6. S. Grimme, in Reviews in Computational Chemistry (Eds.:, K. B. Lipkowitz, R. Larta, T. R. Cundari,), John Wiley and Sons, Hoboken, 2004, Chapter 3, pp. 153-218.
7. N. A. Murugan, J. Kongsted, Z. Rinkevicius, K. Aidas, H. Ågren, J. Phys. Chem. B 2010, 114, 13349-13357.
8. J. Neugebauer, Phys. Rep. 2010, 489, 1-87.
9. A. Pedone, G. Prampolini, S. Monti, V. Barone, Chem. Mater. 2011, 23, 5016-5023.
10. C. Curutchet, J. Kongsted, A. Munoz-Losa, H. Hossein-Nejad, G. D. Scholes, B. Mennucci, J. Am. Chem. Soc. 2011, 133, 3078-3084.
11. F. Labat, T. Le Bahers, I. Ciofini, C. Adamo, Acc. Chem. Res. 2012, 45, 1268-1277.
12. G. Prampolini, F. Bellina, M. Biczysko, C. Cappelli, L. Carta, M. Lessi, A. Pucci, G. Rugger, V. Barone, Chem. Eur. J. 2013, 19, 1996-2004.
13. A. Pedone, E. Gambuzzi, V. Barone, S. Bonacchi, D. Genovese, E. Rampazzo, L. Prodi, M. Montalti, Phys. Chem. Chem. Phys. 2013, 15, 12360-12372.
14. A. Dreuw, S. Faraji, Phys. Chem. Chem. Phys. 2013, 15, 19957-19969.
15. V. Barone, A. Baiardi, M. Biczysko, J. Bloino, C. Cappelli, F. Lipparini, Phys. Chem. Chem. Phys. 2012, 14, 12404-12422.
16. K. Burke, J. Werschnik, E. K. U. Gross, J. Chem. Phys. 2005, 123, 062206.
17. M. E. Casida, J. Mol. Struct.: THEOCHEM 2009, 914, 3-18.
18. D. Jacquemin, V. Wathelet, E. A. Perpete, C. Adamo, J. Chem. Theory Comput. 2009, 5, 2420-2435.
19. M. Isegawa, R. Peverati, D. G. Truhlar, J. Chem. Phys. 2012, 137, 244104.
20. J. Neugebauer, J. Chem. Phys. 2007, 126, 134116.
21. F. Furche, R. Ahlrichs, J. Chem. Phys. 2004, 121, 12772.
22. G. Scalmani, M. J. Frisch, B. Mennucci, J. Tomasi, R. Cammi, V. Barone, J. Chem. Phys. 2006, 124, 094107.
23. J. Liu, W. Liang, J. Chem. Phys. 2011, 135, 184111.
24. J. Liu, W. Liang, J. Chem. Phys. 2013, 138, 024101.
25. J. Linnanto, J. Korppi-Tommola, Phys. Chem. Chem. Phys. 2006, 8, 663-687.
26. C. König, J. Neugebauer, J. Chem. Theory Comput. 2013, 9, 1808-1820.
27. Computational Strategies for Spectroscopy, from Small Molecules to Nano Systems (Ed.:, V. Barone,), Wiley, Hoboken, 2011.
28. Computational Spectroscopy (Ed.:, J. Grunenberg,), Wiley-VCH, Weinheim, 2010.
29. Handbook of High-Resolution Spectroscopy (Eds.:, M. Quack, F. Merkt,), Wiley, Chichester, 2011, p. 2182.
30. V. Barone, Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, Elsevier, 2013, DOI:.
31. M. Biczysko, J. Bloino, G. Brancato, I. Cacelli, C. Cappelli, A. Ferretti, A. Lami, S. Monti, A. Pedone, G. Prampolini, C. Puzzarini, F. Santoro, F. Trani, G. Villani, Theor. Chem. Acc. 2012, 131, 1201.
32. J. Pieper, M. Ratsep, I. Trostmann, H. Paulsen, G. Renger, A. Freiberg, J. Phys. Chem. B 2011, 115, 4042-4052.
33. J. Pieper, M. Ratsep, I. Trostmann, F.-J. Schmitt, C. Theiss, H. Paulsen, H. Eichler, A. Freiberg, G. Renger, J. Phys. Chem. B 2011, 115, 4053-4065.
34. A. Chenu, N. Christensson, H. F. Kauffmann, T. Mancal, Sci. Rep. 2013, 3, 2029.
35. J. R. Reimers, Z.-L. Cai, R. Kobayashi, M. Ratsep, A. Freiberg, E. Krausz, Sci. Rep. 2013, 3, 2761.
36. A. Kolli, E. J. O'Reilly, G. D. Scholes, A. Olaya-Castro, J. Chem. Phys. 2012, 137, 174109.
37. M. Biczysko, J. Bloino, F. Santoro, V. Barone, in Computational Strategies for Spectroscopy, from Small Molecules to Nano Systems (Ed.:, V. Barone,), Wiley, Chichester, 2011, pp. 361-443.
38. J. Bloino, M. Biczysko, F. Santoro, V. Barone, J. Chem. Theory Comput. 2010, 6, 1256-1274.
39. V. Barone, J. Bloino, M. Biczysko, F. Santoro, J. Chem. Theory Comput. 2009, 5, 540-554.
40. A. Lami, F. Santoro, in Computational Strategies for Spectroscopy, from Small Molecules to Nano Systems (Ed.:, V. Barone,), Wiley, Chichester, 2011, pp. 475-516.
41. A. Baiardi, J. Bloino, V. Barone, J. Chem. Theory Comput. 2013, 9, 4097-4115.
42. J. Bloino, M. Biczysko, O. Crescenzi, V. Barone, J. Chem. Phys. 2008, 128, 244105.
43. F. Egidi, J. Bloino, C. Cappelli, V. Barone, J. Chem. Theory Comput. 2014, 10, 346-363.
44. A. Warshel, M. Karplus, J. Am. Chem. Soc. 1974, 96, 5677-5689.
45. J. Gao, Acc. Chem. Res. 1996, 29, 298-305.
46. D. G. Truhlar, J. Am. Chem. Soc. 2008, 130, 16824-16827.
47. Q. Cui, M. Karplus, J. Chem. Phys. 2000, 112, 1133-1149.
48. S. Canuto, K. Coutinho, D. Trzesniak, in Advances in Quantum Chemistry, Vol. 41 (Eds.:, J. R. Sabin, E. Brandas,), Academic Press, Waltham, 2002, pp. 161-183.
49. J. Gao, D. G. Truhlar, Annu. Rev. Phys. Chem. 2002, 53, 467-505.
50. K. Aidas, K. V. Mikkelsen, J. Kongsted, J. Comput. Methods Sci. Eng. 2007, 7, 135-158.
51. V. Barone, A. Polimeno, Chem. Soc. Rev. 2007, 36, 1724-1731.
52. Computational Proteomics (Ed.:, M. J. Ramos,), Transworld Research Network, Kerala, 2008.
53. Multiscale Simulation Methods in Molecular Sciences. Lecture Notes, Vol. 42 (Eds.:, J. Grotendorst, N. Attig, S. Blügel, D. Marx,), Forschungszentrum Jülich, Jülich, 2009.
54. H. M. Senn, W. Thiel, Angew. Chem. 2009, 121, 1220-1254;
55. Angew. Chem. Int. Ed. 2009, 48, 1198-1229.
56. Advances in Quantum Chemistry, Vol. 59 (Ed.:, S. Canuto,), Academic Press, Waltham, 2010.
57. L. Visscher, P. Bolhuis, F. M. Bickelhaupt, Phys. Chem. Chem. Phys. 2011, 13, 10399-10400.
58. S. C. L. Kamerlin, A. Warshel, Phys. Chem. Chem. Phys. 2011, 13, 10401-10411.
59. B. Mennucci, Phys. Chem. Chem. Phys. 2013, 15, 6583-6594.
60. F. Lipparini, F. Egidi, C. Cappelli, V. Barone, J. Chem. Theory Comput. 2013, 9, 1880-1884.
61. G.-J. Zhao, K.-L. Han, Biophys. J. 2008, 94, 38-46.
62. L. Fiedor, A. Kania, B. Mys̈liwa-Kurdziel, L. Orzel, G. Stochel, Biochim. Biophys. Acta, Bioenerg. 2008, 1777, 1491-1500.
63. P. Jaramillo, K. Coutinho, B. J. Cabral, S. Canuto, Chem. Phys. Lett. 2011, 516, 250-253.
64. B. J. C. Cabral, K. Coutinho, S. Canuto, J. Chem. Phys. 2013, 138, 225102.
65. G. Zucchelli, R. C. Jennings, F. M. Garlaschi, G. Cinque, R. Bassi, O. Cremonesi, Biophys. J. 2002, 82, 378-390.
66. M. Rätsep, J. Linnanto, A. Freiberg, J. Chem. Phys. 2009, 130, 194501.
67. G. Zucchelli, S. Santabarbara, R. C. Jennings, Biochemistry 2012, 51, 2717-2736.
68. L. O. Björn, G. C. Papageorgiou, R. E. Blankenship, Govindjee, Photosynth. Res. 2009, 99, 85-98.
69. H. Du, R-C. A. Fuh, J. Li, L. A. Corkan, J. S. Lindsey, Photochem. Photobiol. 1998, 68, 141-142.
70. H. H. Strain, M. R. Thomas, J. J. Katz, Biochim. Biophys. Acta 1963, 75, 306-311.
71. J. M. Dixon, M. Taniguchi, J. S. Lindsey, Photochem. Photobiol. 2005, 81, 212-213.
72. Continuum Solvation Models in Chemical Physics: Theory and Applications, (Eds.:, B. Mennucci, R. Cammi,), Wiley, Chichester, 2007, pp.
73. J. Tomasi, B. Mennucci, R. Cammi, Chem. Rev. 2005, 105, 2999-3094.
74. J. Tomasi, WIREs Comput. Mol. Sci. 2011, 1, 855-867.
75. B. Mennucci, WIREs Comput. Mol. Sci. 2012, 2, 386-404.
76. M. Cossi, G. Scalmani, N. Rega, V. Barone, J. Comput. Chem. 2003, 24, 669.
77. F. J. A. Ferrer, F. Santoro, Phys. Chem. Chem. Phys. 2012, 14, 13549-13563.
78. V. Barone, M. Biczysko, J. Bloino, L. Carta, A. Pedone, Comput. Theor. Chem. 2014, 1037, 35-48.
79. F. Duschinsky, Acta Physicochim. URSS 1937, 7, 551.
80. J. Franck, Trans. Faraday Soc. 1926, 21, 536-542.
81. E. U. Condon, Phys. Rev. 1928, 32, 858-872.
82. G. Herzberg, E. Teller, Z. Phys. Chem. Abt. B 1933, 21, 410-446.
83. V. Barone, J. Chem. Phys. 2005, 122, 014108.
84. V. Barone, M. Biczysko, J. Bloino, Phys. Chem. Chem. Phys. 2014, 16, 1759-1787.
85. P. Macak, Y. Luo, H. Ågren, Chem. Phys. Lett. 2000, 330, 447-456.
86. D. C. Blazej, W. L. Peticolas, J. Chem. Phys. 1980, 72, 3134-3142.
87. M. J. G. Peach, T. Helgaker, P. Salek, T. W. Keal, O. B. Lutnaes, D. J. Tozer, N. C. Handy, Phys. Chem. Chem. Phys. 2006, 8, 558-562.
88. J. L. Hughes, B. Conlon, T. Wydrzynski, E. Krausz, Phys. Procedia 2010, 3, 1591-1599.
89. T. Yanai, D. P. Tew, N. C. Handy, Chem. Phys. Lett. 2004, 393, 51.
90. Double- and triple-ξ basis sets of SNS and N07 families are available for download at http://compchem.sns.it (accessed February 1, 2014).
91. V. Barone, J. Bloino, M. Biczysko, Phys. Chem. Chem. Phys. 2010, 12, 1092-1101.
92. B. Mennucci, R. Cammi, J. Tomasi, J. Chem. Phys. 1998, 109, 2798-2807.
93. M. Cossi, V. Barone, J. Phys. Chem. A 2000, 104, 10614-10622.
94. A. V. Marenich, C. J. Cramer, D. G. Truhlar, C. A. Guido, B. Mennucci, G. Scalmani, M. J. Frisch, Chem. Sci. 2011, 2, 2143-2161.
95. R. Improta, in Computational Strategies for Spectroscopy, from Small Molecules to Nano Systems (Ed.:, V. Barone,), Wiley, Chichester, 2011, pp. 37-75.
96. M. Cossi, V. Barone, J. Chem. Phys. 2001, 115, 4708-4717.
97. Gaussian 09 (Revision D.01), M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.