Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

Journal of Chemical Physics

Volumn 134, Issue 21, 2011, Pages

  Send, Robert ^a   Kaila, Ville R I ^b,c   Sundholm, Dage ^b  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF HELSINKI   (Finland)

^c NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO; BASIS SETS; COMMON MODELS; COUPLED CLUSTERS; DIFFERENT SIZES; ENERGY THRESHOLDS; GASPHASE; GREEN FLUORESCENT PROTEIN; PHOTOACTIVE YELLOW PROTEINS; PROTONATED SCHIFF BASE; QUANTUM-MECHANICAL TREATMENTS; VIRTUAL ORBITALS; VIRTUAL SPACES;

CALCULATIONS; CHROMOPHORES; EMBEDDED SYSTEMS; ERRORS; FUNCTIONAL GROUPS; MOLECULAR MODELING; NUMERICAL METHODS; PROTEINS; QUANTUM THEORY;

EXCITATION ENERGY;

BACTERIAL PROTEIN; BENZYL DERIVATIVE; COUMARIC ACID; GREEN FLUORESCENT PROTEIN; IMIDAZOLINE DERIVATIVE; P HYDROXYBENZYLIDENEIMIDAZOLINONE; P-HYDROXYBENZYLIDENEIMIDAZOLINONE; PHOTOACTIVE YELLOW PROTEIN, BACTERIA; RETINAL; RHODOPSIN; VISUAL PROTEINS AND PIGMENTS;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; CLUSTER ANALYSIS; ENERGY TRANSFER; MOLECULAR DYNAMICS; QUANTUM THEORY;

BACTERIAL PROTEINS; BENZYL COMPOUNDS; CLUSTER ANALYSIS; COUMARIC ACIDS; ENERGY TRANSFER; GREEN FLUORESCENT PROTEINS; IMIDAZOLINES; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; PHOTORECEPTORS, MICROBIAL; QUANTUM THEORY; RETINALDEHYDE; RHODOPSIN;

EID: 79958818426     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3596729     Document Type: Article

References (55)

1. A. Hellweg, S. A. Grn, and C. Httig, Phys. Chem. Chem. Phys. 10, 4119 (2008). 10.1039/b803727b
2. O. Lehtonen, D. Sundholm, and T. Vnsk, Phys. Chem. Chem. Phys. 10, 4535 (2008). 10.1039/b804212h
3. O. Lehtonen and D. Sundholm, J. Chem. Phys. 125, 144314 (2006). 10.1063/1.2354496 (Pubitemid 44570791)
4. R. Send and D. Sundholm, Phys. Chem. Chem. Phys. 9, 2862 (2007). 10.1039/b616137e
5. O. Lehtonen, D. Sundholm, R. Send, and M. P. Johansson, J. Chem. Phys. 131, 024301 (2009). 10.1063/1.3158990
6. M. Kallay and J. Gauss, J. Chem. Phys. 121, 9257 (2004). 10.1063/1.1805494 (Pubitemid 40001690)
7. O. Christiansen, H. Koch, and P. Jrgensen, Chem. Phys. Lett. 243, 409 (1995). 10.1016/0009-2614(95)00841-Q
8. C. Httig and F. Weigend, J. Chem. Phys. 113, 5154 (2000). 10.1063/1.1290013
9. A. Khn and C. Httig, J. Chem. Phys. 119, 5021 (2003). 10.1063/1.1597635
10. C. Httig, Adv. Quantum Chem. 50, 37 (2005). 10.1016/S0065-3276(05)50003-0 (Pubitemid 43574811)
11. A. Castro, M. A. L. Marques, D. Varsano, F. Sottile, and A. Rubio, C. R. Phys. 10, 469 (2009). 10.1016/j.crhy.2008.09.001
12. F. Furche and D. Rappoport, in Computational Photochemistry, Computational and Theoretical Chemistry Vol. 16, edited by, M. Olivucci, (Elsevier, Amsterdam, 2005), Chap. III.
13. D. Rappoport and F. Furche, in Time-Dependent Density Functional Theory, Lecture Notes in Physics Vol. 706, edited by, M. A. L. Marques, C. A. Ullrich, F. Nogueira, A. Rubio, K. Burke, and, E. K. U. Gross, (Springer-Verlag, Berlin, 2006), pp. 337-354.
14. M. R. Silva-Junior, M. Schreiber, S. P. A. Sauer, and W. Thiel, J. Chem. Phys. 129, 104103 (2008). 10.1063/1.2973541
15. M. Caricato, G. W. Trucks, M. J. Frisch, and K. B. Wiberg, J. Chem. Theory Comput. 6, 370 (2010). 10.1021/ct9005129
16. J. Fabian, Dyes Pigm. 84, 36 (2010). 10.1016/j.dyepig.2009.06.008
17. R. Send, O. Valsson, and C. Filippi, J. Chem. Theory Comput. 7, 444 (2011). 10.1021/ct1006295
18. R. Send, D. Sundholm, M. P. Johansson, and F. Pawowski, J. Chem. Theory Comput. 5, 2401 (2009). 10.1021/ct900240s
19. M. Hada, H. Yokono, and H. Nakatsuji, Chem. Phys. Lett. 141, 339 (1987). 10.1016/0009-2614(87)85035-2
20. L. Adamowicz and R. J. Bartlett, J. Chem. Phys. 86, 6314 (1987). 10.1063/1.452468
21. C. Sosa, J. Geertsen, G. W. Trucks, and R. J. Bartlett, Chem. Phys. Lett. 159, 148 (1989). 10.1016/0009-2614(89)87399-3
22. A. G. Taube and R. J. Bartlett, Collect. Czech. Chem. Commun. 70, 837 (2005). 10.1135/cccc20050837 (Pubitemid 41215262)
23. P. Neogrady, M. Pitonak, and M. Urban, Mol. Phys. 103, 2141 (2005). 10.1080/00268970500096251 (Pubitemid 41647951)
24. A. Khn and J. Olsen, J. Chem. Phys. 125, 174110 (2006). 10.1063/1.2364491 (Pubitemid 44707822)
25. M. Piacenza, F. Della Sala, E. Fabiano, T. Maiolo, and G. Gigli, J. Comput. Chem. 29, 451 (2007). 10.1002/jcc.20804
26. A. Landau, K. Khistyaev, S. Dolgikh, and A. I. Krylov, J. Chem. Phys. 132, 014109 (2010). 10.1063/1.3276630
27. R. Send, M. Khn, and F. Furche, Assessing Excited State Methods by Adiabatic Excitation Energies., J. Chem. Theory Comput. (submitted).
28. F. Aquilante, T. K. Todorova, L. Gagliardi, T. B. Pedersen, and B. O. Roos, J. Chem. Phys. 131, 034113 (2009). 10.1063/1.3157463
29. H. M. Senn and W. Thiel, Angew. Chem., Int. Ed. 48, 1198 (2009). 10.1002/anie.200802019
30. F. Weigend, F. Furche, and R. Ahlrichs, J. Chem. Phys. 119, 12753 (2003). 10.1063/1.1627293
31. F. Weigend and M. Hser, Theor. Chem. Acc. 97, 331 (1997). 10.1007/s002140050269 (Pubitemid 127136416)
32. F. Weigend, M. Hser, H. Patzelt, and R. Ahlrichs, Chem. Phys. Lett. 294, 143 (1998). 10.1016/S0009-2614(98)00862-8
33. F. Weigend and R. Ahlrichs, Phys. Chem. Chem. Phys. 7, 3297 (2005). 10.1039/b508541a (Pubitemid 41412231)
34. A. Schfer, H. Horn, and R. Ahlrichs, J. Chem. Phys. 97, 2571 (1992). 10.1063/1.463096
35. T. H. Dunning, Jr., J. Chem. Phys. 90, 1007 (1989). 10.1063/1.456153
36. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988). 10.1103/PhysRevB.37.785
37. A. D. Becke, J. Chem. Phys. 98, 5648 (1993). 10.1063/1.464913
38. TURBOMOLE 6.2, TURBOMOLE GmbH, Karlsruhe, 2010; see http://www.turbomole. com.
39. G. Wald, Nature (London) 219, 800 (1968). 10.1038/219800a0
40. G. Wald, Science 162, 230 (1968). 10.1126/science.162.3850.230
41. K. J. Hellingwerf, J. Hendriks, and T. Gensch, J. Phys. Chem. A 107, 1082 (2003). 10.1021/jp027005y
42. R. Y. Tsien, Annu. Rev. Biochem. 67, 509 (1998). 10.1146/annurev.biochem. 67.1.509 (Pubitemid 28411137)
43. S. B. Nielsen, A. Lapierre, J. U. Andersen, U. V. Pedersen, S. Tomita, and L. H. Andersen, Phys. Rev. Lett. 87, 228102 (2001). 10.1103/PhysRevLett.87. 228102
44. R. Send, V. R. I. Kaila, and D. Sundholm, Benchmarking the approximate second-order coupled-cluster method on biochromophores., J. Chem. Theory Comput. (submitted).
45. See supplementary material at http://dx.doi.org/10.1063/1.3596729 E-JCPSA6-134-014122 for oscillator strengths calculated with and without RVS approach, basis-set dependence of excitation energies, excitation energies of the RVS calculation in the protein, and the basis-set dependence of computation times.
46. V. R. I. Kaila, R. Send, and D. Sundholm, The effect of protein environment on photoexcitation properties of retinal., J. Phys. Chem. B (submitted).
47. E. S. Sachs, J. Hinze, and N. H. Sabelli, J. Chem. Phys. 62, 3393 (1975). 10.1063/1.430993
48. K. K. Baeck, J. Chem. Phys. 112, 1 (2000). 10.1063/1.480555
49. C. B. Nielsen, O. Christiansen, K. V. Mikkelsen, and J. Kongsted, J. Chem. Phys. 126, 154112 (2007). 10.1063/1.2711182 (Pubitemid 46644914)
50. M. Ziolkowski, B. Jansik, P. Jrgensen, and J. Olsen, J. Chem. Phys. 131, 124112 (2009). 10.1063/1.3230604
51. Y. M. Rhee and M. Head-Gordon, J. Phys. Chem. A 111, 5314 (2007). 10.1021/jp068409j (Pubitemid 47152464)
52. J. Schirmer, Phys. Rev. A 26, 2395 (1982). 10.1103/PhysRevA.26.2395
53. Y. Shi, B. Radlwimmer, and S. Yokoyama, Proc. Natl. Acad. Sci. U.S.A. 98, 11731 (2001). 10.1073/pnas.201257398 (Pubitemid 32928797)
54. A. Altun, S. Yokoyama, and K. Morokuma, J. Phys. Chem. A 113, 11685 (2009). 10.1021/jp902754p
55. I. B. Nielsen, L. Lammich, and L. H. Andersen, Phys. Rev. Lett. 96, 018304 (2006). 10.1103/PhysRevLett.96.018304 (Pubitemid 43248417)