51
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Melaccio F, Ferré N, Olivucci M. Quantum chemical modeling of rhodopsin mutants displaying switchable colors. Phys Chem Chem Phys 2012; 14:12485-95. [DOI: 10.1039/c2cp40940b] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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52
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Kraack JP, Buckup T, Motzkus M. Evidence for the Two-State-Two-Mode model in retinal protonated Schiff-bases from pump degenerate four-wave-mixing experiments. Phys Chem Chem Phys 2012; 14:13979-88. [DOI: 10.1039/c2cp42248d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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53
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Muñoz-Losa A, Martín ME, Galván IF, Sánchez ML, Aguilar MA. Solvent Effects on the Radiative and Nonradiative Decay of a Model of the Rhodopsin Chromophore. J Chem Theory Comput 2011; 7:4050-9. [DOI: 10.1021/ct200295r] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aurora Muñoz-Losa
- Química Física, Universidad de Extremadura, Avda. de Elvas s/n 06071 Badajoz, Spain
| | - M. Elena Martín
- Química Física, Universidad de Extremadura, Avda. de Elvas s/n 06071 Badajoz, Spain
| | - Ignacio Fdez. Galván
- Química Física, Universidad de Extremadura, Avda. de Elvas s/n 06071 Badajoz, Spain
| | - M. Luz Sánchez
- Química Física, Universidad de Extremadura, Avda. de Elvas s/n 06071 Badajoz, Spain
| | - Manuel A. Aguilar
- Química Física, Universidad de Extremadura, Avda. de Elvas s/n 06071 Badajoz, Spain
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54
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Odinokov AV, Basilevsky MV, Nikitina EA. Association constants and distribution functions for ion pairs in binary solvent mixtures: Application to a cyanine dye system. J Chem Phys 2011; 135:144503. [DOI: 10.1063/1.3647955] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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55
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Conte AM, Guidoni L, Del Sole R, Pulci O. Many-body study of the photoisomerization of the minimal model of the retinal protonated Schiff base. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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56
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Send R, Kaila VRI, Sundholm D. Benchmarking the Approximate Second-Order Coupled-Cluster Method on Biochromophores. J Chem Theory Comput 2011; 7:2473-84. [DOI: 10.1021/ct200215d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Robert Send
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Ville R. I. Kaila
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland, United States
- Department of Chemistry, P.O. Box 55 (A. I. Virtanens plats 1), FIN-00014 University of Helsinki, Finland
- Helsinki Bioenergetics Group, Programme of Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014 Helsinki, Finland
| | - Dage Sundholm
- Department of Chemistry, P.O. Box 55 (A. I. Virtanens plats 1), FIN-00014 University of Helsinki, Finland
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57
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Kraack JP, Buckup T, Motzkus M. Vibrational analysis of excited and ground electronic states of all-trans retinal protonated Schiff-bases. Phys Chem Chem Phys 2011; 13:21402-10. [DOI: 10.1039/c1cp22245g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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58
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Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping. Proc Natl Acad Sci U S A 2010; 107:20172-7. [PMID: 21048087 DOI: 10.1073/pnas.1007000107] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantum mechanics/molecular mechanics calculations based on ab initio multiconfigurational second order perturbation theory are employed to construct a computer model of Bacteriorhodopsin that reproduces the observed static and transient electronic spectra, the dipole moment changes, and the energy stored in the photocycle intermediate K. The computed reaction coordinate indicates that the isomerization of the retinal chromophore occurs via a complex motion accounting for three distinct regimes: (i) production of the excited state intermediate I, (ii) evolution of I toward a conical intersection between the excited state and the ground state, and (iii) formation of K. We show that, during stage ii, a space-saving mechanism dominated by an asynchronous double bicycle-pedal deformation of the C10═C11─C12═C13─C14═N moiety of the chromophore dominates the isomerization. On this same stage a N─H/water hydrogen bond is weakened and initiates a breaking process that is completed during stage iii.
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59
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Malhado JP, Spezia R, Hynes JT. Dynamical Friction Effects on the Photoisomerization of a Model Protonated Schiff Base in Solution. J Phys Chem A 2010; 115:3720-35. [DOI: 10.1021/jp106096m] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- João Pedro Malhado
- Département de Chimie, CNRS UMR 8640 PASTEUR, École Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
| | - Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environement, CNRS UMR 8587, Université d’Evry Val d’Essonne, Bd. F. Mitterrand, 91025 Evry, France
| | - James T. Hynes
- Département de Chimie, CNRS UMR 8640 PASTEUR, École Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
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60
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Tsutsui K, Shichida Y. Multiple functions of Schiff base counterion in rhodopsins. Photochem Photobiol Sci 2010; 9:1426-34. [PMID: 20842311 DOI: 10.1039/c0pp00134a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In rhodopsins, visible-light absorption is achieved by the protonation of the chromophore Schiff base. The Schiff base proton is stabilized by the negative charge of an amino acid residue called the Schiff base counterion. Since E113 was identified as the counterion in bovine rhodopsin, there has been growing evidence that the counterion has multiple functions besides proton stabilization. Here, we first introduce generally accepted findings as well as some controversial theories about the identity of the Schiff base counterion in the dark and in intermediate states and then review multiple functions of the counterion in vertebrate visual pigments. Special focus is placed on the recently demonstrated role in photoisomerization efficiency. Finally, differences in the position of the counterion between vertebrate visual pigments and other opsins and its relevance to the molecular evolution of opsins are discussed.
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Affiliation(s)
- Kei Tsutsui
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
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61
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Odinokov AV, Bazilevskii MV, Petrov NK, Chibisov AK, Alfimov MV. Effect of counterions on photoprocesses of thiacarbocyanine in a binary solvent blend. HIGH ENERGY CHEMISTRY 2010. [DOI: 10.1134/s0018143910050048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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62
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Schapiro I, Ryazantsev MN, Ding WJ, Huntress MM, Melaccio F, Andruniow T, Olivucci M. Computational Photobiology and Beyond. Aust J Chem 2010. [DOI: 10.1071/ch09563] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.
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63
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Cotton FA, Li Z, Murillo CA. Evidence of disruption of conjugation involving delta bonds in intramolecular electronic coupling. Inorg Chem 2009; 48:11847-52. [PMID: 19911818 DOI: 10.1021/ic9018647] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A dimer of dimers containing two quadruply bonded [Mo(2)(DAniF)(3)](+) units (DAniF = N,N'-di(p-anisyl)formamidinate) linked by the S-donor linker, dimethyldithiooxamidate was synthesized, structurally characterized, and electronic communication was probed. The core of [Mo(2)(DAniF)(3)](2)(C(2)S(2)N(2)Me(2)), 1, formed by the Mo(2)NSC(2)SNMo(2) atoms shows two fused but non planar six-membered rings, which differs from that of the beta form of dimethyloxamidate analogue that has a heteronaphthalene-type structure (Cotton, F. A.; Liu, C. Y.; Murillo, C. A.; Villagran, D.; Wang, X. J. Am. Chem. Soc. 2004, 126, 14822). For these two analogous compounds electronic coupling between the two [Mo(2)] units, as determined by electrochemical measurements, diminishes considerably upon replacement of O-donor by S-donor atoms (DeltaE(1/2) = 531 mV and 440 mV, respectively). This suggests that the non planar conformation of the linker in 1 hampers a pathway leading to pi conjugation. Density functional theory (DFT) calculations show that the highest occupied molecular orbitals HOMO-HOMO-1 energy gap of 0.12 eV for 1 is much smaller than that of 0.61 eV for the O-donor analogue, which is consistent with the electrochemical data.
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Affiliation(s)
- F Albert Cotton
- Department of Chemistry, Laboratory for Molecular Structure and Bonding, P.O. Box 30012, Texas A&M University, College Station, Texas 77842-3012, USA
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64
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Bovee-Geurts PHM, Fernández Fernández I, Liu RSH, Mathies RA, Lugtenburg J, DeGrip WJ. Fluoro Derivatives of Retinal Illuminate the Decisive Role of the C12-H Element in Photoisomerization and Rhodopsin Activation. J Am Chem Soc 2009; 131:17933-42. [DOI: 10.1021/ja907577p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Petra H. M. Bovee-Geurts
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Isabelle Fernández Fernández
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Robert S. H. Liu
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Richard A. Mathies
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Johan Lugtenburg
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
| | - Willem J. DeGrip
- Department of Biochemistry, UMCN 286, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands, Department of BioOrganic Photochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Department of Chemistry, University of Hawaii at Manao, 2545 The Mall, Honolulu, Hawaii 96822, and Department of Chemistry, University of California, Berkeley, California 94720
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65
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Send R, Sundholm D, Johansson MP, Pawłowski F. Excited State Potential Energy Surfaces of Polyenes and Protonated Schiff Bases. J Chem Theory Comput 2009; 5:2401-14. [DOI: 10.1021/ct900240s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert Send
- Institut für Physikalische Chemie, Universität Karlsruhe, Kaiserstrasse 12, D-76128 Karlsruhe, Germany
| | - Dage Sundholm
- Department of Chemistry, P.O. Box 55 (A.I. Virtanens plats 1), University of Helsinki, FI-00014 Helsinki, Finland
| | - Mikael P. Johansson
- Lundbeck Foundation Centre for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Århus C, Denmark
| | - Filip Pawłowski
- Physics Institute, Kazimierz Wielki University, Plac Weyssenhoffa 11, PL-85-072 Bydgoszcz, Poland
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66
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Epifanovsky E, Polyakov I, Grigorenko B, Nemukhin A, Krylov AI. Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore. 1. Electronically Excited and Ionized States of the Anionic Chromophore in the Gas Phase. J Chem Theory Comput 2009; 5:1895-906. [DOI: 10.1021/ct900143j] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Evgeny Epifanovsky
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Igor Polyakov
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Bella Grigorenko
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alexander Nemukhin
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California,
Los Angeles, California 90089, Department of Chemistry, M.V. Lomonosov
Moscow State University, Moscow 119991, Russia, and Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow 119334, Russia
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67
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Tomasello G, Olaso-González G, Altoè 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; 131:5172-86. [PMID: 19309158 DOI: 10.1021/ja808424b] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hybrid QM(CASPT2//CASSCF/6-31G*)/MM(Amber) computations have been used to map the photoisomerization path of the retinal chromophore in Rhodopsin and explore the reasons behind the photoactivity efficiency and spectral control in the visual pigments. It is shown that while the electrostatic environment plays a central role in properly tuning the optical properties of the chromophore, it is also critical in biasing the ultrafast photochemical event: it controls the slope of the photoisomerization channel as well as the accessibility of the S(1)/S(0) crossing space triggering the ultrafast decay. The roles of the E113 counterion, the E181 residue, and the other amino acids of the protein pocket are explicitly analyzed: it appears that counterion quenching by the protein environment plays a key role in setting up the chromophore's optical properties and its photochemical efficiency. A unified scenario is presented that discloses the relationship between spectroscopic and mechanistic properties in rhodopsins and allows us to draw a solid mechanism for spectral tuning in color vision pigments: a tunable counterion shielding appears as the elective mechanism for L<-->M spectral modulation, while a retinal conformational control must dictate S absorption. Finally, it is suggested that this model may contribute to shed new light into mutations-related vision deficiencies that opens innovative perspectives for experimental biomolecular investigations in this field.
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Affiliation(s)
- Gaia Tomasello
- Dipartimento di Chimica G. Ciamician, Università di Bologna, via Selmi 2, Bologna I-40126, Italy
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68
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Sumita M, Ryazantsev MN, Saito K. Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane motion: theoretical study on a model system of retinal protonated Schiff base. Phys Chem Chem Phys 2009; 11:6406-14. [PMID: 19809672 DOI: 10.1039/b900882a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the result of comparison between two reaction coordinates [on the potential energy surface of the first excited state (S(1))] produced by CASSCF and these energies recalculated by MRMP2 in the Z to E photoisomerization of penta-2,4-dieniminium (PDI) as the minimal model of the retinal protonated Schiff base (RPSB). One coordinate is the S(1) state minimum-energy-path (MEP) in mass-weighted coordinates from the S(1) vertically excited point, where a strong hydrogen-out-of plane (HOOP) motion is not exhibited. The energy profile of the S(1) MEP at the MRMP2//CASSCF level shows a barrier for the rotation around the reactive C-C and hits the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by 65 degrees . The other coordinate is an S(1) coordinate obtained by the relaxed scan strategy. The relaxed coordinate along the central C-C-C-C dihedral angle, which we call the HOOP coordinate, shows strong HOOP motion. According to the MRMP2//CASSCF calculation, there is no barrier on the HOOP coordinate. Furthermore, the S(1) to S(0) transition may be possible without the large skeletal deformation by HOOP motion because the HOOP coordinate encounters the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by only 40 degrees . Consequently, if PDI is a suitable model molecule for the RPSB as often assumed, the 11-cis to all-trans photoisomerization is predicted to be accelerated by the HOOP motion.
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Affiliation(s)
- Masato Sumita
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, 305-8571, Japan
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69
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Rivado-Casas L, Sampedro D, Campos PJ, Fusi S, Zanirato V, Olivucci M. Fluorenylidene−Pyrroline Biomimetic Light-Driven Molecular Switches. J Org Chem 2009; 74:4666-74. [DOI: 10.1021/jo802792j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laura Rivado-Casas
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Diego Sampedro
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Pedro J. Campos
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Stefania Fusi
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Vinicio Zanirato
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
| | - Massimo Olivucci
- Departamento de Química, Universidad de La Rioja, Grupo de Síntesis Química de La Rioja, Unidad Asociada al C.S.I.C., Madre de Dios, 51, 26006 Logroño, Spain, Dipartimento di Scienze Farmaceutiche, Università di Ferrara, via Fossato di Mortara 17-19, I-44100 Ferrara, Italy, Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy, and Chemistry Department, Bowling Green State University, Bowling Green 43403, Ohio
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70
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Zgrablić G, Haacke S, Chergui M. Heterogeneity and Relaxation Dynamics of the Photoexcited Retinal Schiff Base Cation in Solution. J Phys Chem B 2009; 113:4384-93. [DOI: 10.1021/jp8077216] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Goran Zgrablić
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, BSP, CH-1015 Lausanne-Dorigny, Switzerland, Sincrotrone Trieste Elettra, S.S. 14 km 163.5 in Area Science Park, 34012 Basovizza, Trieste, Italy, and Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-ULP, 67034 Strasbourg Cédex, France
| | - Stefan Haacke
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, BSP, CH-1015 Lausanne-Dorigny, Switzerland, Sincrotrone Trieste Elettra, S.S. 14 km 163.5 in Area Science Park, 34012 Basovizza, Trieste, Italy, and Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-ULP, 67034 Strasbourg Cédex, France
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, BSP, CH-1015 Lausanne-Dorigny, Switzerland, Sincrotrone Trieste Elettra, S.S. 14 km 163.5 in Area Science Park, 34012 Basovizza, Trieste, Italy, and Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-ULP, 67034 Strasbourg Cédex, France
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71
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Excited state isomerization and effect of viscosity- and temperature-dependent torsional relaxation on TICT fluorescence of trans-2-[4-(dimethylamino)styryl]benzothiazole. J Photochem Photobiol A Chem 2008. [DOI: 10.1016/j.jphotochem.2008.05.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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72
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Bravaya KB, Bochenkova AV, Granovsky AA, Savitsky AP, Nemukhin AV. Modeling Photoabsorption of the asFP595 Chromophore. J Phys Chem A 2008; 112:8804-10. [DOI: 10.1021/jp804183w] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ksenia B. Bravaya
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
| | - Anastasia V. Bochenkova
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
| | - Alexander A. Granovsky
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
| | - Alexander P. Savitsky
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
| | - Alexander V. Nemukhin
- Department of Chemistry, M. V. Lomonosov Moscow State University, 1/3, Leninskie gory, Moscow, 119991, Russian Federation, A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, Moscow, 119071, Russian Federation, and N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, ul. Kosygina, Moscow, 119334, Russian Federation
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73
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The molecular structure of a curl-shaped retinal isomer. J Mol Model 2008; 14:717-26. [DOI: 10.1007/s00894-008-0284-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 02/05/2008] [Indexed: 10/22/2022]
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74
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Dietzek B, Brüggemann B, Pascher T, Yartsev A. Pump-shaped dump optimal control reveals the nuclear reaction pathway of isomerization of a photoexcited cyanine dye. J Am Chem Soc 2007; 129:13014-21. [PMID: 17924621 DOI: 10.1021/ja072639+] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using optimal control as a spectroscopic tool we decipher the details of the molecular dynamics of the essential multidimensional excited-state photoisomerization - a fundamental chemical reaction of key importance in biology. Two distinct nuclear motions are identified in addition to the overall bond-twisting motion: Initially, the reaction is dominated by motion perpendicular to the torsion coordinate. At later times, a second optically active vibration drives the system along the reaction path to the bottom of the excited-state potential. The time scales of the wavepacket motion on a different part of the excited-state potential are detailed by pump-shaped dump optimal control. This technique offers new means to control a chemical reaction far from the Franck-Condon point of absorption and to map details of excited-state reaction pathways revealing unique insights into the underlying reaction mechanism.
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Affiliation(s)
- Benjamin Dietzek
- Department of Chemical Physics, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.
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75
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Bravaya K, Bochenkova A, Granovsky A, Nemukhin A. An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase. J Am Chem Soc 2007; 129:13035-42. [PMID: 17924622 DOI: 10.1021/ja0732126] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We considered a series of model systems for treating the photoabsorption of the 11-cis retinal chromophore in the protonated Schiff-base form in vacuum, solutions, and the protein environment. A high computational level, including the quantum mechanical-molecular mechanical (QM/MM) approach for solution and protein was utilized in simulations. The S0-S1 excitation energies in quantum subsystems were evaluated by means of an augmented version of the multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) with the ground-state geometry parameters optimized in the density functional theory PBE0/cc-pVDZ approximation. The computed positions of absorption bands lambdamax, 599(g), 448(s), and 515(p) nm for the gas phase, solution, and protein, respectively, are in excellent agreement with the corresponding experimental data, 610(g), 445(s), and 500(p) nm. Such consistency provides a support for the formulated qualitative conclusions on the role of the chromophore geometry, environmental electrostatic field, and the counterion in different media. An essentially nonplanar geometry conformation of the chromophore group in the region of the C14-C15 bond was obtained for the protein, in particular, owing to the presence of the neighboring charged amino acid residue Glu181. Nonplanarity of the C14-C15 bond region along with the influence of the negatively charged counterions Glu181 and Glu113 are found to be important to reproduce the spectroscopic features of retinal chromophore inside the Rh cavity. Furthermore, the protein field is responsible for the largest bond-order decrease at the C11-C12 double bond upon excitation, which may be the reason for the 11-cis photoisomerization specificity.
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Affiliation(s)
- Ksenia Bravaya
- Department of Chemistry, M.V. Lomonosov Moscow State University, 1/3, Leninskie Gory, Moscow 119992, Russian Federation
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76
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Send R, Sundholm D. Stairway to the conical intersection: a computational study of the retinal isomerization. J Phys Chem A 2007; 111:8766-73. [PMID: 17713894 DOI: 10.1021/jp073908l] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The potential-energy surface of the first excited state of the 11-cis-retinal protonated Schiff base (PSB11) chromophore has been studied at the density functional theory (DFT) level using the time-dependent perturbation theory approach (TDDFT) in combination with Becke's three-parameter hybrid functional (B3LYP). The potential-energy curves for torsion motions around single and double bonds of the first excited state have also been studied at the coupled-cluster approximate singles and doubles (CC2) level. The corresponding potential-energy curves for the ground state have been calculated at the B3LYP DFT and second-order Møller-Plesset (MP2) levels. The TDDFT study suggests that the electronic excitation initiates a turn of the beta-ionone ring around the C6-C7 bond. The torsion is propagating along the retinyl chain toward the cis to trans isomerization center at the C11=C12 double bond. The torsion twist of the C10-C11 single bond leads to a significant reduction in the deexcitation energy indicating that a conical intersection is being reached by an almost barrierless rotation around the C10-C11 single bond. The energy released when passing the conical intersection can assist the subsequent cis to trans isomerization of the C11=C12 double bond. The CC2 calculations also show that the torsion barrier for the twist of the retinyl C10-C11 single bond adjacent to the isomerization center almost vanishes for the excited state. Because of the reduced torsion barriers of the single bonds, the retinyl chain can easily deform in the excited state. Thus, the CC2 and TDDFT calculations suggest similar reaction pathways on the potential-energy surface of the excited state leading toward the conical intersection and resulting in a cis to trans isomerization of the retinal chromophore. According to the CC2 calculations the cis to trans isomerization mechanism does not involve any significant torsion motion of the beta-ionone ring.
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Affiliation(s)
- Robert Send
- Institut für Physikalische Chemie, Universität Karlsruhe, Kaiserstrasse 12, D-76128 Karlsruhe, Germany
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77
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Substituent-controlled photoisomerization in retinal chromophore models: Fluorinated and methoxy-substituted protonated Schiff bases. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2006.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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78
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Garavelli M, Robb MA. Preface. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0325-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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79
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Abstract
The standard model for photoinduced cis-trans isomerization about carbon double bonds is framed in terms of two electronic states and a one-dimensional reaction coordinate. We review recent work that suggests that a minimal picture of the reaction mechanism requires the consideration of at least two molecular coordinates and three electronic states. In this chapter, we emphasize the role of conical intersections and charge transfer in the photoisomerization mechanism.
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Affiliation(s)
- Benjamin G Levine
- Department of Chemistry, Beckman Institute, Center for Biophysics and Computational Biology, and Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, IL 61801, USA.
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80
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Altoè P, Stenta M, Bottoni A, Garavelli M. A tunable QM/MM approach to chemical reactivity, structure and physico-chemical properties prediction. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0275-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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81
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Strambi A, Coto PB, Ferré N, Olivucci M. Effects of water re-location and cavity trimming on the CASPT2//CASSCF/AMBER excitation energy of Rhodopsin. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0273-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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82
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Sun M, Ding Y, Cui G, Liu Y. S1 and S2 Excited States of Gas-Phase Schiff-Base Retinal Chromophores: A Time-Dependent Density Functional Theoretical Investigation. J Phys Chem A 2007; 111:2946-50. [PMID: 17388381 DOI: 10.1021/jp0709757] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In concert with the recent photoabsorption experiments of gas-phase Schiff-base retinal chromophores (Nielsen et al. Phys. Rev. Lett. 2006, 96, 018304), quantum chemical calculations using time-dependent density functional theory coupled with different functionals and under the Tamm-Dancoff approximation were made on the first two excited states (S1 and S2) of two retinal chromophores: 11-cis and all-trans protonated Schiff bases. The calculated vertical excitation energies (Tv) and oscillator strengths (f) are consistent with the experimental absorption bands. The experimentally observed phenomenon that the transition dipole moment (mu) of S2 is much smaller that of S1 was interpreted by 3D representation of transition densities. The different optical behaviors (linear and nonlinear optical responds) of the excited states were investigated by considering different strengths of external electric fields.
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Affiliation(s)
- Mengtao Sun
- National Laboratory for Condensed State Matter Physics, Institute of Physics, Chinese Academy of Sciences, P. O. Box 603-146, Beijing 100080, China.
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83
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About the intrinsic photochemical properties of the 11-cis retinal chromophore: computational clues for a trap state and a lever effect in Rhodopsin catalysis. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0259-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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84
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Crozier PS, Stevens MJ, Woolf TB. How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations. Proteins 2007; 66:559-74. [PMID: 17109408 PMCID: PMC2848121 DOI: 10.1002/prot.21175] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Rhodopsin is the prototypical G-protein coupled receptor, coupling light activation with high efficiency to signaling molecules. The dark-state X-ray structures of the protein provide a starting point for consideration of the relaxation from initial light activation to conformational changes that may lead to signaling. In this study we create an energetically unstable retinal in the light activated state and then use molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis-trans light activation. The results suggest that changes occur throughout the protein, with changes in the orientation of Helices 5 and 6, a closer interaction between Ala 169 on Helix 4 and retinal, and a shift in the Schiff base counterion that also reflects changes in sidechain interactions with the retinal. Taken together, the simulation is suggestive of the types of changes that lead from local conformational change to light-activated signaling in this prototypical system.
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Affiliation(s)
- Paul S Crozier
- Sandia National Laboratories, MS 1322, Albuquerque, New Mexico 87185-1322, USA.
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85
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Bismuth O, Friedman N, Sheves M, Ruhman S. Photochemistry of a Retinal Protonated Schiff-Base Analogue Mimicking the Opsin Shift of Bacteriorhodopsin. J Phys Chem B 2007; 111:2327-34. [PMID: 17298090 DOI: 10.1021/jp0669308] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A retinal Schiff base analogue which artificially mimics the protein-induced red shifting of absorption in bacteriorhodopsin (BR) has been investigated with femtosecond multichannel pump probe spectroscopy. The objective is to determine if the catalysis of retinal internal conversion in the native protein BR, which absorbs at 570 nm, is directly correlated with the protein-induced Stokes shifting of this absorption band otherwise known as the "opsin shift". Results demonstrate that the red shift afforded in the model system does not hasten internal conversion relative to that taking place in a free retinal-protonated Schiff base (RPSB) in methanol solution, and stimulated emission takes place with biexponential kinetics and characteristic timescales of approximately 2 and 10.5 ps. This shows that interactions between the prosthetic group and the protein that lead to the opsin shift in BR are not directly involved in reducing the excited-state lifetime by nearly an order of magnitude. A sub-picosecond phase of spectral evolution, analogues of which are detected in photoexcited retinal proteins and RPSBs in solution, is observed after excitation anywhere within the intense visible absorption band. It consists of a large and discontinuous spectral shift in excited-state absorption and is assigned to electronic relaxation between excited states, a scenario which might also be relevant to those systems as well. Finally, a transient excess bleach component that tunes with the excitation wavelength is detected in the data and tentatively assigned to inhomogeneous broadening in the ground state absorption band. Possible sources of such inhomogeneity and its relevance to native RPSB photochemistry are discussed.
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Affiliation(s)
- Oshrat Bismuth
- Department of Physical Chemistry, Hebrew University, Jerusalem 91904, Israel
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86
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Send R, Sundholm D. Coupled-cluster studies of the lowest excited states of the 11-cis-retinal chromophore. Phys Chem Chem Phys 2007; 9:2862-7. [PMID: 17538731 DOI: 10.1039/b616137e] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first few excited states of the 11-cis-retinal (PSB11) chromophore have been studied at the coupled-cluster approximative singles and doubles (CC2) level using triple-zeta quality basis sets augmented with double sets of polarisation functions. The two lowest vertical excitation energies of 2.14 and 3.21 eV are in good agreement with recently reported experimental values of 2.03 and 3.18 eV obtained in molecular beam measurements. Calculations at the time-dependent density functional theory (TDDFT) level using the B3LYP hybrid functional yield vertical excitation energies of 2.34 and 3.10 eV for the two lowest states. Zero-point vibrational energy (ZPVE) corrections of -0.09 and -0.17 eV were deduced from the harmonic vibrational frequencies for the ground and excited states calculated at the density functional theory (DFT) and TDDFT level, respectively, using the B3LYP hybrid functional.
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Affiliation(s)
- Robert Send
- Institut für Physikalische Chemie, Universität Karlsruhe, Kaiserstrasse 12, 76128, Karlsruhe, Germany
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87
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Send R, Sundholm D. The Role of the β-Ionone Ring in the Photochemical Reaction of Rhodopsin. J Phys Chem A 2006; 111:27-33. [PMID: 17201384 DOI: 10.1021/jp065510f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Time-dependent density functional theory (TDDFT) calculations on the photoabsorption process of the 11-cis retinal protonated Schiff base (PSB) chromophore show that the Franck-Condon relaxation of the first excited state of the chromophore involves a torsional twist motion of the beta-ionone ring relative to the conjugated retinyl chain. For the ground state, the beta-ionone ring and the retinyl chain of the free retinal PSB chromophore form a -40 degrees dihedral angle as compared to -94 degrees for the first excited state. The double bonds of the retinal are shorter for the fully optimized structure of the excited state than for the ground state suggesting a higher cis-trans isomerization barrier for the excited state than for the ground state. According to the present TDDFT calculations, the excitation of the retinal PSB chromophore does not primarily lead to a reaction along the cis-trans torsional coordinate at the C11-C12 bond. The activation of the isomerization center seems to occur at a later stage of the photo reaction. The results obtained at the TDDFT level are supported by second-order Møller-Plesset (MP2) and approximate singles and doubles-coupled cluster (CC2) calculations on retinal chromophore models; the MP2 and CC2 calculations yield for them qualitatively the same ground state and excited-state structures as obtained in the density functional theory and TDDFT calculations.
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Affiliation(s)
- Robert Send
- Institut für Physikalische Chemie, Universität Karlsruhe, Kaiserstrasse 12, D-76128 Karlsruhe, Germany
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88
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Dreuw A. Quantum Chemical Methods for the Investigation of Photoinitiated Processes in Biological Systems: Theory and Applications. Chemphyschem 2006; 7:2259-74. [PMID: 17009357 DOI: 10.1002/cphc.200600064] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.
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Affiliation(s)
- Andreas Dreuw
- Institut für Physikalische und Theoretische Chemie, Johann Wolfgang Goethe-Universität, Max von Laue-Str. 7, 60438 Frankfurt am Main, Germany.
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89
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Wanko M, Hoffmann M, Frauenheim T, Elstner M. Computational photochemistry of retinal proteins. J Comput Aided Mol Des 2006; 20:511-8. [PMID: 17043908 DOI: 10.1007/s10822-006-9069-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Accepted: 08/18/2006] [Indexed: 10/24/2022]
Abstract
High spectral tunability and quantum yield are the striking features of rhodopsin photochemistry. They rely on a strong and complex interaction of their chromophore, the protonated Schiff base of retinal, with its protein environment. In this article, we review the progress in the computational modeling of these systems, focusing on the optical properties and the excited state dynamics. While the earlier success of atomistic theoretical models was based on the breakthrough in X-ray crystallography and combined quantum mechanical molecular mechanical (QM/MM) methodology, recent advances point out the importance of high-level QM methods and the incorporation of effects that are neglected in conventional QM/MM or ONIOM schemes, like polarization and charge transfer.
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Affiliation(s)
- Marius Wanko
- BCCMS, Universität Bremen, Bremen 28334, Germany
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90
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Oliveira CS, Bastos EL, Duarte EL, Itri R, Baptista MS. Ion pairs of crystal violet in sodium bis(2-ethylhexyl)sulfosuccinate reverse micelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:8718-26. [PMID: 17014109 DOI: 10.1021/la061117p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The interfacial localization and the ion pair formation of the positively charged dye crystal violet (CV) in sodium bis(2-ethylhexyl)sulfosuccinate reverse micelles (AOT RMs) were studied by several structural and spectroscopic techniques and by quantum chemical calculations. The size and shape of the AOT RMs in the presence of CV were investigated by small-angle X-ray scattering, showing that CV does not significantly change the RM structure. CV localization as a function of the water to surfactant molar ratio (w(0)) was characterized by H(1) and (13)C NMR, indicating the close proximity of CV to the sulfosuccinate group of AOT at small and large w(0) values. These results were confirmed by calculation of magnetic shielding constants using the gauge-independent atomic orbital method with the HF/6-31G(d) basis set. Two different types of ion pairs between AOT and CV, i.e., contact ion pair (CIPs) and solvent-separated ion pair (SSIPs), were characterized by UV-vis spectroscopy and quantum chemical calculations using the semiempirical ZINDO-CI method. In nonpolar isotropic solvents CIPs are formed with an association constant (K(ASSOC)) of 2 x 10(4) mol(-1) L in isooctane and 750 mol(-1) L in chloroform. In AOT RMs at low w(0), CV-AOT CIPs are also formed. By increasing w(0), there is a sharp decrease in the CIP association free energy, and SSIPs are formed. (CV(+))(H(2)O)(AOT(-)) SSIPs are stable in the AOT RM up to the largest w(0) tested (w(0) = 33).
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Affiliation(s)
- Carla S Oliveira
- Departamento de Bioquímica, IQ-USP, São Paulo-SP, C.P. 26077, 05599-970, Brazil
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91
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Verhoeven MA, Bovee-Geurts PHM, de Groot HJM, Lugtenburg J, DeGrip WJ. Methyl Substituents at the 11 or 12 Position of Retinal Profoundly and Differentially Affect Photochemistry and Signalling Activity of Rhodopsin. J Mol Biol 2006; 363:98-113. [PMID: 16962138 DOI: 10.1016/j.jmb.2006.07.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Revised: 07/12/2006] [Accepted: 07/19/2006] [Indexed: 11/18/2022]
Abstract
The C-11=C-12 double bond of the retinylidene chromophore of rhodopsin holds a central position in its light-induced photoisomerization and hence the photosensory function of this visual pigment. To probe the local environment of the HC-11=C-12H element we have prepared the 11-methyl and 12-methyl derivatives of 11-Z retinal and incorporated these into opsin to generate the rhodopsin analogs 11-methyl and 12-methyl rhodopsin. These analog pigments form with much slower kinetics and lower efficiency than the native pigment. The initial photochemistry and the signaling activity of the analog pigments were investigated by UV-vis and FTIR spectroscopy, and by a G protein activation assay. Our data indicate that the ultrafast formation of the first photointermediate is strongly perturbed by the presence of an 11-methyl substituent, but much less by a 12-methyl substituent. These results support the current concept of the mechanism of the primary photoisomerization event in rhodopsin. An important stronghold of this concept is an out-of-plane movement of the C-12H element, which is facilitated by torsion as well as extended positive charge delocalization into the C-10-C-13 segment of the chromophore. We argue that this mechanism is maintained principally with a methyl substituent at C-12. In addition, we show that both an 11-methyl and a 12-methyl substitutent perturb the photointermediate cascade and finally yield a low-activity state of the receptor. The 11-methyl pigment retains about 30% of the G protein activation rate of native rhodopsin, while the 12-methyl chromophore behaves like an inverse agonist up to at least 20 degrees C, trapping the protein in a perturbed Meta-I-like conformation. We conclude that the isomerization region of the chromophore and the spatial structure of the binding site are finely tuned, in order to achieve a high photosensory potential with an efficient pathway to a high-activity state.
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92
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Burghardt I, Hynes JT. Excited-State Charge Transfer at a Conical Intersection: Effects of an Environment. J Phys Chem A 2006; 110:11411-23. [PMID: 17020251 DOI: 10.1021/jp057569c] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influence of a polar and polarizable environment on charge transfer processes at a conical intersection (CI) can be described by a diabatic free energy model yielding coupled surfaces as a function of both molecular coordinates and a solvent coordinate. We extend and apply this model for the S1-S0 CI in protonated Schiff bases, representing a model for retinal isomerization (Faraday Discuss. 2004, 127, 395, 2004). A dielectric continuum description of the solvent is combined with a minimal, two-electron-two-orbital electronic structure model according to Bonacić-Koutecký, Koutecký, and Michl (Angew. Chem. 1987, 26, 170), which characterizes the charge translocation effects at the CI. The model predicts that the nonequilibrium solvent state resulting from the S0-->S1 Franck-Condon transition can entail the disappearance of the CI, such that solvent motion is necessary to reach the CI seam. The concerted evolution of the intramolecular coordinates and the solvent coordinate is illustrated by an excited-state minimum energy path.
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Affiliation(s)
- Irene Burghardt
- Département de Chimie, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France
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93
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Lenz MO, Huber R, Schmidt B, Gilch P, Kalmbach R, Engelhard M, Wachtveitl J. First steps of retinal photoisomerization in proteorhodopsin. Biophys J 2006; 91:255-62. [PMID: 16603495 PMCID: PMC1479053 DOI: 10.1529/biophysj.105.074690] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The early steps (<1 ns) in the photocycle of the detergent solubilized proton pump proteorhodopsin are analyzed by ultrafast spectroscopic techniques. A comparison to the first primary events in reconstituted proteorhodopsin as well as to the well known archaeal proton pump bacteriorhodopsin is given. A dynamic Stokes shift observed in fs-time-resolved fluorescence experiments allows a direct observation of early motions on the excited state potential energy surface. The initial dynamics is dominated by sequentially emerging stretching (<150 fs) and torsional (approximately 300 fs) modes of the retinal. The different protonation states of the primary proton acceptor Asp-97 drastically affect the reaction rate and the overall quantum efficiencies of the isomerization reactions, mainly evidenced for time scales above 1 ps. However, no major influence on the fast time scales (approximately 150 fs) could be seen, indicating that the movement out of the Franck-Condon region is fairly robust to electrostatic changes in the retinal binding pocket. Based on fs-time-resolved absorption and fluorescence spectra, ground and exited state contributions can be disentangled and allow to construct a reaction model that consistently explains pH-dependent effects in solubilized and reconstituted proteorhodopsin.
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Affiliation(s)
- Martin O Lenz
- Institut für Physikalische und Theoretische Chemie, Johann-Wolfgang-Goethe-Universität, Frankfurt, Germany
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Nielsen IB, Lammich L, Andersen LH. S1 and S2 excited States of gas-phase Schiff-base retinal chromophores. PHYSICAL REVIEW LETTERS 2006; 96:018304. [PMID: 16486529 DOI: 10.1103/physrevlett.96.018304] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Indexed: 05/06/2023]
Abstract
Photoabsorption studies of 11-cis and all-trans Schiff-base retinal chromophore cations in the gas phase have been performed at the electrostatic ion storage ring in Aarhus. A broad absorption band due to the optically allowed excitation to the first electronically excited singlet state (S1) is observed at around 600 nm. A second "dark" excited state (S2) just below 400 nm is reported for the first time. It is located approximately 1.2 eV above S1 for both chromophores. The S2 state was not visible in a solution measurement where only one highly blueshifted absorption band corresponding to the first excited state was visible. Knowledge of the position of the excited states in retinal is essential for the understanding of the fast photoisomerization in, for example, visual pigments.
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Affiliation(s)
- I B Nielsen
- Department of Physics and Astronomy, University of Aarhus, DK-8000 Aarhus C, Denmark
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