SORCI for photochemical and thermal reaction paths: A benchmark study

Computational and Theoretical Chemistry

Volumn 1040-1041, Issue , 2014, Pages 84-98

  Schapiro, Igor ^a   Neese, Frank ^a  

^a MAX PLANCK INSTITUTE FOR CHEMICAL ENERGY CONVERSION   (Germany)

Author keywords

Conical intersection; Dynamic electron correlation; Excited state; Photoisomerization; Retinal model; SORCI

Indexed keywords

EID: 84903815693     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2014.04.002     Document Type: Article

References (66)

1. Dugave C. Cis-trans Isomerization in Biochemistry 2006, Wiley-VCH, Weinheim.
2. Structures and functions of retinal proteins, John Libbey & Co. Ltd. London, 1992.
3. Spudich J.L., Yang C.-S., Jung K.-H., Spudich E.N. Retinylidene proteins: structures and Functions from Archaea to humans. Annu. Rev. Cell Dev. Biol. 2000, 16:365-392.
4. Spudich J.L., Jung K.-H. Microbial rhodopsins: phylogenetic and functional diversity. Handbook of Photosensory Receptors 2005, 1-23. Wiley-VCH Verlag GmbH & Co. KGaA.
5. Kukura P., McCamant D.W., Yoon S., Wandschneider D.B., Mathies R.A. Structural observation of the primary isomerization in vision with femtosecond-stimulated Raman. Science 2005, 310:1006-1009.
6. Polli D., Altoe P., Weingart O., Spillane K.M., Manzoni C., Brida D., Tomasello G., Orlandi G., Kukura P., Mathies R.A., Garavelli M., Cerullo G. Conical intersection dynamics of the primary photoisomerization event in vision. Nature 2010, 467:U440-U488.
7. Schoenlein R.W., Peteanu L.A., Mathies R.A., Shank C.V. The first step in vision: femtosecond isomerization of Rhodopsin. Science 1991, 254:412-415.
8. Frutos L.M., Andruniow T., Santoro F., Ferre N., Olivucci M. Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry. Proc. Nat. Acad. Sci. USA 2007, 104:7764-7769.
9. Schapiro I., Ryazantsev M.N., Frutos L.M., Ferre N., Lindh R., Olivucci M. The ultrafast photoisomerizations of rhodopsin and bathorhodopsin are modulated by bond length alternation and HOOP driven electronic effects. J. Am. Chem. Soc. 2011, 133:3354-3364.
10. Hayashi S., Tajkhorshid E., Schulten K. Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation. Biophys. J. 2009, 96:403-416.
11. Weingart O., Altoe P., Stenta M., Bottoni A., Orlandi G., Garavelli M. Product formation in rhodopsin by fast hydrogen motions. Phys. Chem. Chem. Phys. 2011, 13:3645-3648.
12. Gozem S., Schapiro I., Ferré N., Olivucci M. The molecular mechanism of thermal noise in rod photoreceptors. Science 2012, 337:1225-1228.
13. Neese F. A spectroscopy oriented configuration interaction procedure. J. Chem. Phys. 2003, 119:9428-9443.
14. Neese F. The ORCA program system. Wiley Interdiscipl. Rev.: Comput. Mol. Sci. 2012, 2:73-78.
15. Wanko M., Hoffmann M., Strodel P., Koslowski A., Thiel W., Neese F., Frauenheim T., Elstner M. Calculating absorption shifts for retinal proteins: computational challenges. J. Phys. Chem. B 2005, 109:3606-3615.
16. 2-. Chem. Phys. Lett. 1992, 198:555-562.
17. Miralles J., Castell O., Caballol R., Malrieu J.-P. Specific CI calculation of energy differences: transition energies and bond energies. Chem. Phys. 1993, 172:33-43.
18. García V.M., Castell O., Caballol R., Malrieu J.P. An iterative difference-dedicated configuration interaction. Proposal Test Stud., Chem. Phys. Lett. 1995, 238:222-229.
19. Langhoff S.R., Davidson E.R. Configuration interaction calculations on the nitrogen molecule. Int. J. Quantum Chem. 1974, 8:61-72.
20. Hoffmann M., Wanko M., Strodel P., König P.H., Frauenheim T., Schulten K., Thiel W., Tajkhorshid E., Elstner M. Color tuning in Rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory Rhodopsin II. J. Am. Chem. Soc. 2006, 128:10808-10818.
21. Altun A., Yokoyama S., Morokuma K. Mechanism of spectral tuning going from retinal in Vacuo to Bovine Rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies. J. Phys. Chem. B 2008, 112:16883-16890.
22. Schöneboom J.C., Neese F., Thiel W. Toward identification of the compound i reactive intermediate in Cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters. J. Am. Chem. Soc. 2005, 127:5840-5853.
23. Neese F., Petrenko T., Ganyushin D., Olbrich G. Advanced aspects of ab initio theoretical optical spectroscopy of transition metal complexes: multiplets, spin-orbit coupling and resonance Raman intensities. Coord. Chem. Rev. 2007, 251:288-327.
24. 2+ complexes in their lowest triplet and quintet states using multireference ab initio and density functional theory methods. J. Inorg. Biochem. 2006, 100:716-726.
25. Sinnecker S., Svensen N., Barr E.W., Ye S., Bollinger J.M., Neese F., Krebs C. Spectroscopic and computational evaluation of the structure of the high-spin Fe(IV)-Oxo intermediates in Taurine: α-ketoglutarate dioxygenase from escherichia coli and its His99Ala ligand variant. J. Am. Chem. Soc. 2007, 129:6168-6179.
26. Liakos D.G., Ganyushin D., Neese F. A multiconfigurational ab initio study of the zero-field splitting in the di- and trivalent hexaquo-chromium complexes. Inorg. Chem. 2009, 48:10572-10580.
27. Maganas D., Sottini S., Kyritsis P., Groenen E.J.J., Neese F. Theoretical analysis of the spin Hamiltonian parameters in Co(II)S4 complexes, using density functional theory and correlated ab initio methods. Inorg. Chem. 2011, 50:8741-8754.
28. Maganas D., Grigoropoulos A., Staniland S.S., Chatziefthimiou S.D., Harrison A., Robertson N., Kyritsis P., Neese F. Tetrahedral and square planar Ni[(SPR2)2N]2 complexes, R = Ph & iPr revisited: experimental and theoretical analysis of interconversion pathways, structural preferences, and spin delocalization. Inorg. Chem. 2010, 49:5079-5093.
29. Gozem S., Huntress M., Schapiro I., Lindh R., Granovsky A.A., Angeli C., Olivucci M. Dynamic electron correlation effects on the ground state potential energy surface of a retinal chromophore model. J. Chem. Theory Comput. 2012, 8:4069-4080.
30. Gozem S., Krylov A.I., Olivucci M. Conical intersection and potential energy surface features of a model retinal chromophore: comparison of EOM-CC and multireference methods. J. Chem. Theory Comput. 2012, 9:284-292.
31. Xu X., Gozem S., Olivucci M., Truhlar D.G. Combined self-consistent-field and spin-flip Tamm-Dancoff Density functional approach to potential energy surfaces for photochemistry. J. Phys. Chem. Lett. 2012, 4:253-258.
32. Huix-Rotllant M., Filatov M., Gozem S., Schapiro I., Olivucci M., Ferré N. Assessment of density functional theory for describing the correlation effects on the ground and excited state potential energy surfaces of a retinal chromophore model. J. Chem. Theory Comput. 2013, 9:3917-3932.
33. Gozem S., Melaccio F., Lindh R., Krylov A.I., Granovsky A.A., Angeli C., Olivucci M. Mapping the excited state potential energy surface of a retinal chromophore model with multireference and equation-of-motion coupled-cluster methods. J. Chem. Theory Comput. 2013, 9:4495-4506.
34. De Vico L., Page C.S., Garavelli M., Bernardi F., Basosi R., Olivucci M. Reaction path analysis of the "tunable" photoisomerization selectivity of free and locked retinal chromophores. J. Am. Chem. Soc. 2002, 124:4124-4134.
35. De Vico L., Garavelli M., Bernardi F., Olivucci M. Photoisomerization mechanism of 11-cis-locked artificial retinal chromophores: acceleration and primary photoproduct assignment. J. Am. Chem. Soc. 2005, 127:2433-2442.
36. Garavelli M., Bernardi F., Robb M.A., Olivucci M. The short-chain acroleiniminium and pentadieniminium cations: towards a model for retinal photoisomerization. A CASSCF/PT2 study. J. Mol. Struct. (Thoechem) 1999, 463:59-64.
37. Tomasello G., Olaso-González G., Altoeỳ P., Stenta M., Serrano-Andrés L., Merchán M., Orlandi G., Bottoni A., Garavelli M. Electrostatic control of the photoisomerization efficiency and optical properties in visual pigments: on the role of counterion quenching. J. Am. Chem. Soc. 2009, 131:5172-5186.
38. Laricheva E.N., Gozem S., Rinaldi S., Melaccio F., Valentini A., Olivucci M. Origin of fluorescence in 11-cis locked bovine Rhodopsin. J. Chem. Theory Comput. 2012, 8:2559-2563.
39. Garavelli M., Celani P., Bernardi F., Robb M.A., Olivucci M. The C5H6NH2+ protonated shiff base: an ab initio minimal model for retinal photoisomerization. J. Am. Chem. Soc. 1997, 119:6891-6901.
40. Strambi A., Coto P., Ferré N., Olivucci M. Effects of water re-location and cavity trimming on the CASPT2//CASSCF/AMBER excitation energy of Rhodopsin. Theoret. Chem. Acc. 2007, 118:185-191.
41. Barlow H.B. The thermal limit to seeing. Nature 1988, 334:296-297.
42. Aho A.C., Donner K., Hyden C., Larsen L.O., Reuter T. Low retinal noise in animals with low body temperature allows high visual sensitivity. Nature 1988, 334:348-350.
43. Kefalov V., Fu Y., Marsh-Armstrong N., Yau K.-W. Role of visual pigment properties in rod and cone phototransduction. Nature 2003, 425:526-531.
44. Mori T., Nakano K., Kato S. Conical intersections of free energy surfaces in solution: effect of electron correlation on a protonated Schiff base in methanol solution. J. Chem. Phys. 2010, 133.
45. Valsson O., Filippi C. Photoisomerization of model retinal chromophores: insight from quantum monte carlo and multiconfigurational perturbation theory. J. Chem. Theory Comput. 2010, 6:1275-1292.
46. Levine B.G., Ko C., Quenneville J., Martinez T.J. Conical intersections and double excitations in time-dependent density functional theory. Mol. Phys. 2006, 104:1039-1051.
47. Barbatti M., Lan Z., Crespo-Otero R., Szymczak J.J., Lischka H., Thiel W. Critical appraisal of excited state nonadiabatic dynamics simulations of 9H-adeninea. J. Chem. Phys. 2012, 137.
48. McGuire M.J., Piecuch P. Balancing dynamic and nondynamic correlation for diradical and aromatic transition states: a renormalized coupled-cluster study of the cope rearrangement of 1,5-hexadiene. J. Am. Chem. Soc. 2005, 127:2608-2614.
49. Kinal A., Piecuch P. Computational investigation of the conrotatory and disrotatory isomerization channels of bicyclo[1.1.0]butane to buta-1,3-diene: a completely renormalized coupled-cluster study. J. Phys. Chem. A 2007, 111:734-742.
50. Sand A.M., Schwerdtfeger C.A., Mazziotti D.A. Strongly correlated barriers to rotation from parametric two-electron reduced-density-matrix methods in application to the isomerization of diazene. J. Chem. Phys. 2012, 136.
51. Werner H.J., Knowles P.J., Knizia G., Manby F.R., Schütz M., Celani P., Korona T., Lindh R., Mitrushenkov A., Rauhut G., Shamasundar K.R., Adler T.B., Amos R.D., Bernhardsson A., Berning A., Cooper D.L., Deegan M.J.O., Dobbyn A.J., Eckert F., Goll E., Hampel C., Hesselmann A., Hetzer G., Hrenar T., Jansen G., Köppl C., Liu Y., Lloyd A.W., Mata R.A., May A.J., McNicholas S.J., Meyer W., Mura M.E., Nicklass A., O'Neill D.P., Palmieri P., Pflüger K., Pitzer R., Reiher M., Shiozaki T., Stoll H., Stone A.J., Tarroni R., Thorsteinsson T., Wang M., Wolf A. MOLPRO 2010, University of Cardiff; Universität Stuttgart, UK; Germany.
52. Werner H.-J., Kállay M., Gauss J. The barrier height of the F+H2 reaction revisited: coupled-cluster and multireference configuration-interaction benchmark calculations. J. Chem. Phys. 2008, 128.
53. Andersson K., Malmqvist P.Å., Roos B.O. Second-order perturbation theory with a complete active space self-consistent field reference function. J. Chem. Phys. 1992, 96:1218-1226.
54. Angeli C., Cimiraglia R., Evangelisti S., Leininger T., Malrieu J.P. Introduction of n-electron valence states for multireference perturbation theory. J. Chem. Phys. 2001, 114:10252.
55. Angeli C., Pastore M., Cimiraglia R. New perspectives in multireference perturbation theory: the n-electron valence state approach. Theoret. Chem. Acc. 2007, 117:743-754.
56. Granovsky A.A. Extended multi-configuration quasi-degenerate perturbation theory: the new approach to multi-state multi-reference perturbation theory. J. Chem. Phys. 2011, 134.
57. Finley J., Malmqvist P.-Å., Roos B.O., Serrano-Andrés L. The multi-state CASPT2 method. Chem. Phys. Lett. 1998, 288:299-306.
58. Ghigo G., Roos B.O., Malmqvist P.-Å. A modified definition of the zeroth-order Hamiltonian in multiconfigurational perturbation theory (CASPT2). Chem. Phys. Lett. 2004, 396:142-149.
59. Aquilante F., De Vico L., Ferré N., Ghigo G., Malmqvist P.-Å., Neogrády P., Pedersen T.B., Pitoňák M., Reiher M., Roos B.O., Serrano-Andrés L., Urban M., Veryazov V., Lindh R. MOLCAS 7: the next generation. J. Comput. Chem. 2010, 31:224-247.
60. Angeli C., Borini S., Cestari M., Cimiraglia R. A quasidegenerate formulation of the second order n-electron valence state perturbation theory approach. J. Chem. Phys. 2004, 121:4043-4049.
61. Krylov A.I. Size-consistent wave functions for bond-breaking: the equation-of-motion spin-flip model. Chem. Phys. Lett. 2001, 338:375-384.
62. Slipchenko L.V., Krylov A.I. Singlet-triplet gaps in diradicals by the spin-flip approach: a benchmark study. J. Chem. Phys. 2002, 117:4694-4708.
63. Levchenko S.V., Krylov A.I. Equation-of-motion spin-flip coupled-cluster model with single and double substitutions: theory and application to cyclobutadiene. J. Chem. Phys. 2004, 120:175-185.
64. Manohar P.U., Krylov A.I. A noniterative perturbative triples correction for the spin-flipping and spin-conserving equation-of-motion coupled-cluster methods with single and double substitutions. J. Chem. Phys. 2008, 129.
65. Mulliken R.S. Electronic population analysis on LCAO-MO molecular wave functions. I. J. Chem. Phys. 1955, 23:1833-1840.
66. Huntress M.M., Gozem S., Malley K.R., Jailaubekov A.E., Vasileiou C., Vengris M., Geiger J.H., Borhan B., Schapiro I., Larsen D.S., Olivucci M. Toward an understanding of the retinal chromophore in Rhodopsin mimics. J. Phys. Chem. B 2013, 117:10053-10070.