The challenge of predicting optical properties of biomolecules: What can we learn from time-dependent density-functional theory?

Comptes Rendus Physique

Volumn 10, Issue 6, 2009, Pages 469-490

  Castro, Alberto ^a,b   Marques, Miguel A L ^b,c,d   Varsano, Daniele ^b,e   Sottile, Francesco ^b,f   Rubio, Angel ^b,g  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b European Theoretical Spectroscopy Facility (ETSF)   (Spain)

^c UNIVERSITÉ LYON 1   (France)

^d UNIVERSITY OF COIMBRA   (Portugal)

^e INFM   (Italy)

^f LABORATOIRE DES SOLIDES IRRADIÉS   (France)

^g UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

Author keywords

Biomolecules; Excitations; TDDFT

Indexed keywords

EID: 70349176716     PISSN: 16310705     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.crhy.2008.09.001     Document Type: Short Survey

References (118)

1. Prasad P.N. Introduction to Biophotonics (2003), John Wiley & Sons, Hoboken
2. Bacon K. Photosynthesis. Photobiochemistry and Photobiophysics (1999), Springer, Berlin
3. In: Musio C. (Ed). Vision: The Approach of Biophysics and Neurosciences (2001), World Scientific, Singapore
4. Shimomura O. Biolumnescence: Chemical Principles and Methods (2006), World Scientific, Singapore
5. In: Shoseyov O., and Levy I. (Eds). NanoBioTechnology: BioInspired Devices and Materials of the Future (2007), Humana Press
6. In: Marques M.A.L., Ullrich C., Nogueira F., Rubio A., and Gross E.K.U. (Eds). Time-Dependent Density-Functional Theory. Lecture Notes in Physics vol. 706 (2006), Springer-Verlag, Berlin
7. Marques M.A.L., Castro A., Bertsch G.F., and Rubio A. Comput. Phys. Commun. 151 (2003) 60
8. Castro A., Appel H., Oliveira M., Rozzi C.A., Andrade X., Lorenzen F., Gross E.K.U., Marques M.A.L., and Rubio A. Phys. Status Solidi B 243 (2006) 2465
9. Runge E., and Gross E.K.U. Phys. Rev. Lett. 52 (1984) 997
10. Gross E.K.U., and Kohn W. Adv. Quantum. Chem. 21 (1990) 255
11. Marques M.A.L., and Gross E.K.U. Annu. Rev. Phys. Chem. 55 (2004) 427
12. Onida G., Reinig L., and Rubio A. Rev. Mod. Phys. 74 (2002) 601
13. See, for example. Livet J., et al. Nature 450 (2007) 56
14. Takeda S., Kamiya N., and Nagamune T. Biotechnology Lett. 26 (2004) 121
15. Creemers T.M.H., Lock A.J., Subramaniam V., Jovin T.M., and Völker S. Proc. Natl. Acad. Sci. USA 97 (2000) 2974
16. Creemers T.M.H., Lock A.J., Subramaniam V., Jovin T.M., and Völker S. Nature Struct. Biol. 6 (1999) 557
17. Nielsen S.B., Lapierre A., Andersen J.U., Pedersen U.V., Tomita S., and Andersen L.H. Phys. Rev. Lett. 87 (2001) 228102
18. Marques M.A.L., López X., Varsano D., Castro A., and Rubio A. Phys. Rev. Lett. 90 (2003) 258101
19. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. J. Comput. Chem. 2 (1983) 187
20. Field M.J., Bash P.A., and Karplus M. J. Comput. Chem. 11 (1990) 700
21. Gao J. In: Lipkowitz K.B., and Boyd D.B. (Eds). Reviews in Computational Chemistry, vol. 7 (1995), Wiley VCH, New York 119
22. Dewar M.J.S., Zoebisch E., Healy E.F., and Stewart J.J.P. J. Am. Chem. Soc. 107 (1995) 3902
23. Wachter R., King B., Heim R., Kallio K., Tsien R., Boxer S., and Remington S. Biochemistry 36 (1997) 36
24. Bublitz B.G., King B., and Boxer S. J. Am. Chem. Soc. 120 (1998) 9370
25. Zimmer M. Chem. Rev. 102 (2002) 759 and references therein
26. Chattoraj M., King B., Bublitz G., and Boxer S. Proc. Natl. Acad. Sci. USA 93 (1996) 8362
27. López X., Marques M.A.L., Castro A., and Rubio A. J. Am. Chem. Soc. 127 (2005) 12329
28. M.A.L. Marques, X. Löpez, A. Castro, A. Rubio, in press
29. In: Kadish K., Smith K.M., and Guilard R. (Eds). The Porphyrin Handbook (1999), Academic Press, London
30. Gouterman M. In: Dolphin D. (Ed). The Porphyrins, vol. 3 (1973), Academic Press, New York
31. F. Sottile, C. Hogan, M. Palummo, A. Rubio, in preparation
32. Varsano D., Di Felice R., Marques M.A.L., and Rubio A. J. Phys. Chem. B 110 (2006) 7129
33. Daniels M. In: Yang S.Y. (Ed). Photochemistry and Photobiology of Nucleic Acids (1976), Academic Press, New York 23
34. Hernández C.E.C., Cohen B., Hare P.M., and Kohler B. Chem. Rev. 104 (2004) 1977
35. Porath D., Cuniberti G., and Felice R.D. In: Schuster G. (Ed). Topics in Current Chemistry (2004), Springer-Verlag, Heidelberg 183
36. Di Ventra M., and Zwolak M. In: Nalwa H.S. (Ed). Encyclopedia of Nanoscience and Nanotechnology and Handbook of Nanostructured Biomaterials and their Application in Nanotechnology (2004), APS, College Park, MD 475
37. Endres R.G., Cox D., and Singh R. Rev. Mod. Phys. 76 (2004) 195
38. Coehn H., Nogues C., Naaman R., and Porath D. Proc. Natl. Acad. Sci. USA 102 (2005) 11589
39. Di Felice R., Calzolari A., Molinari E., and Garbesi A. Phys. Rev. B 65 (2002) 045104
40. Di Felice R., and Calzolari A. In: Starikov E.B., Tanaka S., and Lewis J.P. (Eds). Modern Methods for Theoretical Physical Chemistry of Biopolymers (2005), Elsevier, Amsterdam
41. Nägele T., Hoche R., Zinth W., and Wachtveitl J. Chem. Phys. Lett. 272 (1997) 489
42. Simmons J.M., Campbell V.E., Mark T.J., Léonard F., Gopalan P., and Eriksson M.A. Phys. Rev. Lett. 98 (2007) 086802
43. García-Lastra J.M., Thygesen K., and Rubio A. Phys. Rev. Lett. 101 (2008) 13302
44. Spörlein S., Carstens H., Satzger H., Renner C., Behrendt R., Moroder L., Tavan P., Zinth W., and Wachtveitl J. Proc. Natl. Acad. Sci. USA 99 (2002) 7998
45. Watson J.H., and Crick F.H. Nature 171 (1953) 737
46. Henry A.A., and Romesbergi F.E. Curr. Opin. Chem. Biol. 7 (2003) 727
47. Krueger A.T., Lu H., Lee A.H., and Kool E.T. Acc. Chem. Res. 40 (2007) 141
48. Hirao I. Curr. Opin. Chem. Biol. 10 (2006) 622
49. Gao J., Liu H., and Kool E.T. Angew. Chem. Int. Ed. 44 (2005) 3118
50. Liu H., Gao J., Lynch S.R., and Kool E.T. Science 302 (2003) 868
51. Varsano D., Garbesi A., and Di Felice R. J. Phys. Chem. B 111 (2007) 14012
52. Liu H., Gao J., Maynard L., Saito Y.D., and Kool E.T. J. Am. Chem. Soc. 126 (2004) 1102
53. Liu H., Gao J., and Kool E.T. J. Org. Chem. 70 (2005) 639
54. Yabana K., and Bertsch G.F. Phys. Rev. A 60 (1999) 1271
55. D. Varsano, A. Castro, M.A.L. Marques, R. Di Felice, A. Rubio, in preparation
56. Kadhane U., Holm A.I.S., Hoffmann S.V., and Nielsen S.B. Phys. Rev. E 77 (2008) 021901
57. Kreibich T., and Gross E.K.U. Phys. Rev. Lett. 86 (2001) 2984
58. Bonačić-Koutecký V., and Persico M. J. Am. Chem. Soc. 105 (1983) 3388
59. Bonačić-Koutecký V., Köhler J., and Michl J. Chem. Phys. Lett. 104 (1984) 440
60. Casida M.E. In: Chong D.P. (Ed). Recent Advances in Density Functional Methods, Part I (1995), World Scientific, Singapore 155
61. Casida M. In: Seminario J. (Ed). Recent Developments and Applications in Density Functional Theory (1996), Elsevier, Amsterdam 391
62. Yabana K., and Bertsch G.F. Phys. Rev. B 54 (1996) 4484
63. Yabana K., and Bertsch G.F. Z. Phys. D 42 (1997) 219
64. Yabana K., and Bertsch G.F. Phys. Rev. A 58 (1999) 2604
65. Yabana K., and Bertsch G.F. Phys. Rev. A 60 (1999) 3809
66. Marques M.A.L., Castro A., and Rubio A. J. Chem. Phys. 115 (2001) 3006
67. Bonačić-Koutecký V., and Michl J. Theor. Chim. Acta 68 (1985) 45
68. Bonačić-Koutecký V., Schöffel K., and Michl J. Theor. Chim. Acta 72 (1987) 459
69. Frank I., Hütter J., Marx D., and Parrinello M. J. Chem. Phys. 108 (1998) 4060
70. Doltsinis N.L., and Marx D. Phys. Rev. Lett. 88 (2002) 166402
71. Tully J.C., and Preston R.K. J. Chem. Phys. 55 (1971) 562
72. Tully J.C. J. Chem. Phys. 93 (1990) 1061
73. Ziegler T., Rauk A., and Baerends E.J. Theor. Chim. Acta 43 (1977) 261
74. Castro A., Marques M.A.L., Alonso J.A., Bertsch G.F., and Rubio A. Eur. Phys. J. D 28 (2004) 211
75. Castro A. A first-principles time-dependent density functional theory scheme for the computation of the electromagnetic response of nanostructures. PhD. Thesis, University of Valladolid, 2004. The thesis can be downloaded from. http://nano-bio.ehu.es/files/acastro_phd.pdf
76. Horsfield A.P., Bowler D.R., Fisher A.J., Todorov T.N., and Sanchez C.G. J. Phys. Cond. Matt. 16 (2004) 8521
77. Lewis G.N. J. Am. Chem. Soc. 38 (1916) 762
78. Becke A.D., and Edgecombe K.E. J. Chem. Phys. 92 (1990) 5397
79. Burnus T., Marques M.A.L., and Gross E.K.U. Phys. Rev. A 71 (2005) 010501
80. Bader R.F.W., Johnson S., Tang T.-H., and Popelier P.L.A. J. Phys. Chem. 100 (1996) 15398
81. Dobson J.F. J. Chem. Phys. 98 (1993) 8870
82. Silvi B., and Savin A. Nature 371 (1994) 683
83. Savin A., Nesper R., Wengert S., and Fässler T.F. Angew. Chem. Int. Ed. Engl. 36 (1997) 1808
84. van Leeuwen R., and Baerends E.J. Phys. Rev. B 49 (1994) 2421
85. Della Sala F., and Grling A. Int. J. Quantum Chem. 91 (2003) 131
86. Perdew J.P., and Zunger A. Phys. Rev. B 23 (1981) 5408
87. Hult E., Andersson Y., and Lundqvist B.I. Phys. Rev. Lett. 77 (1996) 202
88. Rydberg H., Dion M., Jacobson N., Schröder E., Hyldgaard P., Simak S.I., Langreth D.C., and Lundqvist B.I. Phys. Rev. Lett. 91 (2003) 126402
89. Kohn W., Meir Y., and Makarov D.E. Phys. Rev. Lett. 80 (1998) 4153
90. Dobson J.F., White A., and Rubio A. Phys. Rev. Lett. 96 (2006) 073201
91. Orestes E., and Capelle K. J. Chem. Phys. 127 (2007) 124101
92. Vignale G., and Kohn W. Phys. Rev. Lett. 77 (1996) 2037
93. Bünner M.J., and Gross E.K.U. Phys. Rev. Lett. 79 (1997) 1905
94. Vignale G., Ullrich C.A., and Conti S. Phys. Rev. Lett. 79 (1997) 4878
95. Ullrich C.A., and Vignale G. Phys. Rev. B 65 (2002) 245102
96. Ullrich C.A., and Vignale G. Phys. Rev. B 70 (2004) 239903E
97. Kurzweil Y., and Baer R. J. Chem. Phys. 121 (2004) 8731
98. Tokatly I.V. Phys. Rev. B 71 (2005) 165104
99. Tokatly I.V. Phys. Rev. B 71 (2005) 165105
100. Maitra N., Zhang F., and Cave R. J. Chem. Phys. 120 (2004) 5932
101. Casida M. J. Chem. Phys. 122 (2004) 054111
102. Dreuw A., Weisman J.L., and Head-Gordon M. J. Chem. Phys. 119 (2003) 2943
103. Tozer D.J. J. Chem. Phys. 119 (2003) 12697
104. Tozer D.J., and Head-Gordon M. J. Am. Chem. Soc. 126 (2004) 4007
105. Botti S., Schindlmayr A., Del Sole R., and Reining L. Rep. Prog. Phys. 70 (2007) 357
106. Gross E.K.U., Dobson J., and Petersilka M. In: Nalewajski R.F. (Ed). Density Functional Theory II. Topics in Current Chemistry vol. 18 (1996), Springer, Berlin
107. Görling A. Phys. Rev. A 55 (1997) 2630
108. Görling A. Phys. Rev. A 57 (1998) 3433
109. Görling A. Int. J. Quantum Chem. 69 (1998) 265
110. Kim Y.H., and Görling A. Phys. Rev. B 66 (2002) 035114
111. Botti S., Fourreau A., Nguyen F., Renault Y.-O., Sottile F., and Reining L. Phys. Rev. B 72 (2005) 125203
112. Botti S., Sottile F., Vast N., Olevano V., Reining L., Weissker H.-C., Rubio A., Onida G., Del Sole R., and Godby R.W. Phys. Rev. B 69 (2004) 155112
113. Reining L., Olevano V., Rubio A., and Onida G. Phys. Rev. Lett. 88 (2002) 066404
114. Bastida A., Cruz C., Zúñiga J., Requena A., and Miguel B. J. Chem. Phys. 126 (2007) 014503
115. Takatsuka K. J. Phys. Chem. A 111 (2007) 10196
116. Horsfield A.P., Bowler D.R., Ness H., Sánchez C.G., Todorov T.N., and Fisher A.J. Rep. Prog. Phys. 69 (2006) 1195
117. Furche F., and Ahlrichs R. J. Chem. Phys. 117 (2002) 7433
118. Tavernelli I., Röhrig U.F., and Rothlisberger U. Mol. Phys. 103 (2005) 963