QM/MM calculation of solvent effects on absorption spectra of guanine

Journal of Computational Chemistry

Volumn 31, Issue 1, 2010, Pages 90-106

  Parac, Maja ^a   Doerr, Markus ^a   Marian, Christel M ^b   Thiel, Walter ^a  

^a MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

^b HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Density functional theory; Excitation energy; Guanine; Multireference configuration interaction; QM MM; Solvent effect

Indexed keywords

ABSORPTION MAXIMA; BASIS SETS; DENSITY FUNCTIONAL TIGHT BINDINGS; ELECTRONIC SPECTRUM; FORCE FIELDS; GASPHASE; LOW-ENERGY SPECTRA; MOLECULAR DYNAMICS SIMULATIONS; MULTI REFERENCE CONFIGURATION INTERACTIONS; MULTIREFERENCE CONFIGURATION INTERACTION; NUCLEAR MOTIONS; OSCILLATOR STRENGTHS; QM/MM CALCULATIONS; QUANTUM MECHANICAL/MOLECULAR MECHANICAL; RED SHIFT; SELF CONSISTENT CHARGES; SOLUTE-SOLVENT INTERACTION; SOLVENT EFFECTS; STRUCTURAL CHANGE; THEORETICAL ABSORPTION SPECTRA; TIME DEPENDENT DENSITY FUNCTIONAL THEORY; VERTICAL EXCITATION ENERGY; WATER ENVIRONMENTS;

ASTROPHYSICS; BAND STRUCTURE; CHARGE DENSITY; DOPPLER EFFECT; EXCITATION ENERGY; EXCITED STATES; GAS ABSORPTION; GASES; GEOMETRY; GROUND STATE; LIGHT ABSORPTION; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; POSITIVE IONS; PROBABILITY DENSITY FUNCTION; SOLVENTS; SPECTROSCOPY; SULFUR COMPOUNDS;

DENSITY FUNCTIONAL THEORY;

GUANINE; SOLVENT;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; CONFORMATION; MOLECULAR DYNAMICS; QUANTUM THEORY;

GUANINE; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; QUANTUM THEORY; SOLVENTS;

EID: 72449121493     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21233     Document Type: Article

References (79)

1. Cramer, C. J.; Truhlar, D. G. Chem Rev 1999, 99, 2161.
2. Tomasi, J.; Mennucci, B.; Cammi, R. Chem Rev 2005, 105, 2999.
3. Tomasi, J.; Persico, M. Chem Rev 1994, 94, 2027.
4. Tomasi, J. Theor Chem Acc 2004, 112, 184.
5. Klamt, A.; Jonas, V.; Bürger, T.; Lohrenz, J. C. W. J Phys Chem A1998, 102, 5074.
6. Warshel, A.; Levitt, M. J Mol. Biol 1976, 103, 227.
7. Field, M. J.; Bash, P. A.; Karplus, M. J Comp Chem 1990, 11, 700.
8. Gao, J. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Boyd, D. B., Eds.; Wiley: New York, 1995; Vol.7, pp. 119-185.
9. Senn, H. M.; Thiel, W. In Atomistic Approaches in Modern Biology; Reiner, M., Ed.; 2007; Vol.268 of Topics Current Chemistry; pp. 173-290.
10. Frenkel, D.; Smit, B. Understanding Molecular Simulation; 2nd ed.; Academic Press: New York, 2000.
11. Car, R.; Parrinello, M. Phys Rev Lett 1985, 55, 2471.
12. Röhrig, U. F.; Frank, I.; Hutter, J.; Laio, A.; VandeVondele, J.; Röthlisberger, U. Chem Phys Chem 2003, 4, 1177.
13. Sulpizi, M.; Carloni, P.; Hutter, J.; Röthlisberger, U. Phys Chem Chem Phys 2003, 5, 4798.
14. Hoffmann, M.; Wanko, M.; Strodel, P.; König, P. H.; Frauenheim, T.; Schulten, K.; Thiel, W.; Tajkhorshid, E.; Elstner, M. J Am Chem Soc 2006, 128, 10808.
15. Shukla, M. K.; Mishra, S. K.; Kumar, A.; Mishra, P. C. J Comput Chem 2000, 21, 826.
16. Broo, A.; Holmén, A. J Phys Chem A 1997, 101, 3589.
17. Mennucci, B.; Toniolo, A.; Tomasi, J. J Phys Chem A 2001, 105, 7126.
18. Fälscher, M.; Serrano-Andrés, L.; Roos, B. O. J Am Chem Soc 1997, 119, 6168.
19. Langer, H.; Doltsinis, N. L. J Chem Phys 2003, 118, 5400.
20. Shukla, M. K.; Leszczynski, J. J Comput Chem 2004, 25, 768.
21. Shukla, M. K.; Leszczynski, J. J Phys Chem A 2005, 109, 7775.
22. Shukla, M. K.; Leszczynski, J. J Phys Chem B 2005, 109, 17333.
23. Tsolakidis, A.; Kaxiras, E. J Phys Chem A 2005, 109, 2373.
24. Chen, H.; Li, S. J Phys Chem A 2006, 110, 12360.
25. Marian, C. M. J Phys Chem A 2007, 111, 1545.
26. Serrano-Andrés, L.; Merchán, M.; Borin, A. C. J Am Chem Soc 2008, 130, 2473.
27. Yamazaki, S.; Domcke, W. J Phys Chem A 2008, 112, 7090.
28. Pugliesi, L; Müller-Dethlefs, K. J Phys Chem A 2006, 110, 13045.
29. Lan, Z.; Fabiano, E.; Thiel, W. ChemPhysChem 2009, in press.
30. Nir, E.; Grace, L.; Brauer, B.; de Vries, M. S. J Am Chem Soc 1999, 121, 4896.
31. Nir, E.; Janzen, C.; Imhof, R; Kleinermanns, K.; de Vries, M. S. J Chem Phys 2001, 115, 4604.
32. Nir, E.; Kleinermanns, K.; de Vries, M. S. Nature (London) 2000, 408, 949.
33. Nir, E.; Janzen, C.; Imhof, P.; Kleinermanns, K.; de Vries, M. S. Phys Chem Chem Phys 2002, 4, 732.
34. Piuzzi, F.; Mons, M.; Dimicoli, L.; Tardivel, B.; Zhao, Q. Chem Phys 2001, 270, 205.
35. Mons, M.; Dimicoli, L.; Piuzzi, F.; Tardivel, B.; Elhanine, M. J Phys Chem A 2002, 106, 5088.
36. Chin, W; Mons, M.; Piuzzi, F.; Tardivel, B.; Dimicoli, I.; Gorb, L.; Leszczynski, J. J Phys Chem A 2004, 108, 8237.
37. Choi, M. Y.; Miller, R. E. J Am Chem Soc 2006, 128, 7320.
38. Mons, M.; Piuzzi, F.; Dimicoli, I.; Gorb, L.;Leszczynski, J. J Phys Chem A 2006, 110, 10921.
39. Fujiwara, T.; Kamoshida, Y.; Morita, R.; Yamashita, M. J Photochem Photobiol B: Biol 1997, 41, 114.
40. Callis, P. R. Annu Rev Phys Chem 1983, 34, 329.
41. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W; Klein, M. L. J Chem Phys 1983, 79, 926.
42. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comp Chem 1983, 4, 187.
43. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J Am Chem Soc 1985, 107, 3902.
44. Kolb, M.; Thiel, W. J Comput Chem 1993, 14, 775.
45. Weber, W; Thiel, W. Theor Chem Acc 2000, 103, 495.
46. Schölten, M. Semiempirische Verfahren mit Orthogonalisierungskorrekturen: Die OM3 Methode, PhD Dissertation, Universität Düsseldorf, 2003.
47. Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Phys Rev B 1998, 58, 7260.
48. Sherwood, P.; de Vries, A. H.; Guest, M. F.; Schreckenbach, G.; Catlow, C. R. A.; French, S. A.; Sokol, A. A.; Bromley, S. T.; Thiel, W.; Turner, A. J.; Billeter, S.; Terstegen, F.; Thiel, S.; Kendrick, J.; Rogers, S. C.; Casei, J.; Watson, M.; King, F.; Karlsen, E.; Sjøvoll, M.; Fahmi, A.; Schäfer, A.; Lennartz, C. J Mol Struct (THEOCHEM) 2003, 632, 1.
49. Smith, W.; Forester, T. R. J Mol Graph 1996, 14, 136.
50. Bauernschmitt, R.; Häser, M.; Treutier, O.; Ahlrichs, R. Chem Phys Lett 1997, 264, 573.
51. van Gisbergen, S. J. A.; Snijders, J.; Baerends, E. J. J Chem Phys 1995, 103, 9347.
52. Jamorski, C.; Casida, M. E.; Salahub, D. R. J Chem Phys 1996, 104, 5134.
53. Petersilka, M.; Gossmann, U. J.; Gross, E. K. U. Phys Rev Lett 1996, 76, 1212.
54. Grimme, S.; Waletzke, M. J Chem Phys 1999, 111, 5645.
55. Billeter, S. R.; Turner, A. J.; Thiel, W. Phys Chem Chem Phys 2000, 2, 2177.
56. Becke, A. D. J Chem Phys 1993, 98, 5648.
57. Lee, C.; Yang, W.; Parr, R. G. Phys Rev B 1988, 37, 785.
58. Bauernschmitt, R.; Ahlrichs, R. Chem Phys Lett 1996, 256, 454.
59. Silva-Junior, M. R.; Schreiber, M.; Sauer, S. P. A.; Thiel, W. J Chem Phys 2008, 129, 104103.
60. Becke, A. D. J Chem Phys 1993, 98, 1372.
61. Gerenkamp, M., Entwicklung und Anwendung quantenchemischer Methoden zur Berechnung komplexer chemischer Systeme, PhD Dissertation, Universität Münster, 2005.
62. Schäfer, A.; Huber, C.; Ahlrichs, R. J Chem Phys 1994, 100, 5829.
63. Marian, C. M. J Chem Phys 2005, 122, 104314.
64. Mordasini, T. Z.; Hanser, C.; Thiel, W. Chem Phys Lett 1998, 288, 183.
65. Bernhardt, E.; Willner, H.; Kornath, A.; Breidung, J.; Bühl, M.; Jonas, V.; Thiel, W. J Phys Chem A 2003, 107, 859.
66. Bühl, M.; Grigoleit, S. Organometallics 2005, 24, 1516.
67. Klamt, A.; Schüürmann, G. J Chem Soc Perkin Trans 2 1993, 799.
68. Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Chem Phys Lett 1989, 162, 165.
69. Schäfer, A.; Klamt, A.; Sattel, D.; Lohrenz, J. C. W; Eckert, F. Phys Chem Chem Phys 2000, 2, 2187.
70. Polewski, K.; Zinger, D.; Trank, J.; Monteleone, D. C.; Sutherland, J. S. J Photochem Photobiol B 1994, 24, 169.
71. Hanus, M.; Ryjáček, F.; Kabeláč, M.; Kubař, T.; .Bogdan, T. V.; Trygubenko, S. A.; Hobza, P. J Am Chem Soc 2003, 125, 7678.
72. Dreuw, A.; Weisman, J. L.; Head-Gordon, M. J Chem Phys 2003, 119, 2943.
73. Sobolewski, A. L.; Domcke, W. Chem Phys 2003, 294, 73.
74. Dreuw, A.; Fleming, G. R.; Head-Gordon, M. J Phys Chem B 2003, 107, 6500.
75. Tozer, D. J. J Chem Phys 2003, 119, 12697.
76. Dreuw, A.; Head-Gordon, M. J Am Chem Soc 2004, 126, 4007.
77. Gritsenko, O.; Baerends, E. J. J Chem Phys 2004, 121, 655.
78. Maitra, N. T. J Chem Phys 2005, 122, 234104.
79. Hieringer, W.; Görling, A. Chem Phys Lett 2005, 419, 557.