1
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Zhang J, Singh P, Engel D, Fingerhut BP, Broser M, Hegemann P, Elsaesser T. Ultrafast terahertz Stark spectroscopy reveals the excited-state dipole moments of retinal in bacteriorhodopsin. Proc Natl Acad Sci U S A 2024; 121:e2319676121. [PMID: 38900801 PMCID: PMC11214056 DOI: 10.1073/pnas.2319676121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
The photoinduced all-trans to 13-cis isomerization of the retinal Schiff base represents the ultrafast first step in the reaction cycle of bacteriorhodopsin (BR). Extensive experimental and theoretical work has addressed excited-state dynamics and isomerization via a conical intersection with the ground state. In conflicting molecular pictures, the excited state potential energy surface has been modeled as a pure S[Formula: see text] state that intersects with the ground state, or in a 3-state picture involving the S[Formula: see text] and S[Formula: see text] states. Here, the photoexcited system passes two crossing regions to return to the ground state. The electric dipole moment of the Schiff base in the S[Formula: see text] and S[Formula: see text] state differs strongly and, thus, its measurement allows for assessing the character of the excited-state potential. We apply the method of ultrafast terahertz (THz) Stark spectroscopy to measure electric dipole changes of wild-type BR and a BR D85T mutant upon electronic excitation. A fully reversible transient broadening and spectral shift of electronic absorption is induced by a picosecond THz field of several megavolts/cm and mapped by a 120-fs optical probe pulse. For both BR variants, we derive a moderate electric dipole change of 5 [Formula: see text] 1 Debye, which is markedly smaller than predicted for a neat S[Formula: see text]-character of the excited state. In contrast, S[Formula: see text]-admixture and temporal averaging of excited-state dynamics over the probe pulse duration gives a dipole change in line with experiment. Our results support a picture of electronic and nuclear dynamics governed by the interaction of S[Formula: see text] and S[Formula: see text] states in a 3-state model.
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Affiliation(s)
- Jia Zhang
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489Berlin, Germany
| | - Poonam Singh
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489Berlin, Germany
| | - Dieter Engel
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489Berlin, Germany
| | - Benjamin P. Fingerhut
- Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-Universität München, 81377München, Germany
| | - Matthias Broser
- Institut für Biologie, Humboldt Universität zu Berlin, 10115Berlin, Germany
| | - Peter Hegemann
- Institut für Biologie, Humboldt Universität zu Berlin, 10115Berlin, Germany
| | - Thomas Elsaesser
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489Berlin, Germany
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2
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Lee C, Sekharan S, Mertz B. Theoretical Insights into the Mechanism of Wavelength Regulation in Blue-Absorbing Proteorhodopsin. J Phys Chem B 2019; 123:10631-10641. [PMID: 31757123 DOI: 10.1021/acs.jpcb.9b08189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Choongkeun Lee
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Sivakumar Sekharan
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- XtalPi Inc, 245 Main Street, 12th Floor, Cambridge, Massachusetts 01242, United States
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
- WVU Cancer Institute, West Virginia University, Morgantown, West Virginia 26506, United States
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3
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Gholami S, Pedraza-González L, Yang X, Granovsky AA, Ioffe IN, Olivucci M. Multistate Multiconfiguration Quantum Chemical Computation of the Two-Photon Absorption Spectra of Bovine Rhodopsin. J Phys Chem Lett 2019; 10:6293-6300. [PMID: 31545053 PMCID: PMC7141604 DOI: 10.1021/acs.jpclett.9b02291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recently, progress in IR sources has led to the discovery that humans can detect infrared (IR) light. This is hypothesized to be due to the two-photon absorption (TPA) events promoting the retina dim-light rod photoreceptor rhodopsin to the same excited state populated via one-photon absorption (OPA). Here, we combine quantum mechanics/molecular mechanics and extended multiconfiguration quasi-degenerate perturbation theory calculations to simulate the TPA spectrum of bovine rhodopsin (Rh) as a model for the human photoreceptor. The results show that the TPA spectrum of Rh has an intense S0 → S1 band but shows also S0 → S2 and S0 → S3 transitions whose intensities, relative to the S0 → S1 band, are significantly increased when compared to the corresponding bands of the OPA spectrum. In conclusion, we show that IR light in the 950 nm region can be perceived by rod photoreceptors, thus supporting the two-photon origin of the IR perception. We also found that the same photoreceptor can perceive red (i.e., close to 680 nm) light provided that TPA induces population of S2.
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Affiliation(s)
- Samira Gholami
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy , Università di Siena , via A. Moro 2 , I-53100 Siena , Siena , Italy
| | - Xuchun Yang
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | | | - Ilya N Ioffe
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | - Massimo Olivucci
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
- Department of Biotechnology, Chemistry and Pharmacy , Università di Siena , via A. Moro 2 , I-53100 Siena , Siena , Italy
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4
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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5
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Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Northwestern University , Evanston, IL, USA
| | - Toru Shiozaki
- Department of Chemistry, Northwestern University , Evanston, IL, USA
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6
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Xie P, Zhou P, Alsaedi A, Zhang Y. pH-dependent absorption spectra of rhodopsin mutant E113Q: On the role of counterions and protein. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:25-31. [PMID: 27865136 DOI: 10.1016/j.saa.2016.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/08/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
The absorption spectra of bovine rhodopsin mutant E113Q in solutions were investigated at the molecular level by using a hybrid quantum mechanics/molecular mechanics (QM/MM) method. The calculations suggest the mechanism of the absorption variations of E113Q at different pH values. The results indicate that the polarizations of the counterions in the vicinity of Schiff base under protonation and unprotonation states of the mutant E113Q would be a crucial factor to change the energy gap of the retinal to tune the absorption spectra. Glu-181 residue, which is close to the chromophore, cannot serve as the counterion of the protonated Schiff base of E113Q in dark state. Moreover, the results of the absorption maximum in mutant E113Q with the various anions (Cl-, Br-, I- and NO3-) manifested that the mutant E113Q could have the potential for use as a template of anion biosensors at visible wavelength.
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Affiliation(s)
- Peng Xie
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Ahmed Alsaedi
- Nonlinear Analysis and Applied Mathematics (NAAM) Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Yan Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China.
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7
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Varsano D, Caprasecca S, Coccia E. Theoretical description of protein field effects on electronic excitations of biological chromophores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:013002. [PMID: 27830666 DOI: 10.1088/0953-8984/29/1/013002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.
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Affiliation(s)
- Daniele Varsano
- S3 Center, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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8
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Maza JR, Jenkins S, Kirk SR. 11-cis retinal torsion: A QTAIM and stress tensor analysis of the S1 excited state. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Varsano D, Coccia E, Pulci O, Conte AM, Guidoni L. Ground state structures and electronic excitations of biological chromophores at Quantum Monte Carlo/Many Body Green’s Function Theory level. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Álvarez R, Vaz B, Gronemeyer H, de Lera ÁR. Functions, therapeutic applications, and synthesis of retinoids and carotenoids. Chem Rev 2013; 114:1-125. [PMID: 24266866 DOI: 10.1021/cr400126u] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rosana Álvarez
- Departamento de Química Orgánica, Centro de Investigación Biomédica (CINBIO), and Instituto de Investigación Biomédica de Vigo (IBIV), Universidade de Vigo , 36310 Vigo, Spain
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11
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Zhou P, Liu J, Han K, He G. The photoisomerization of 11-cis-retinal protonated schiff base in gas phase: Insight from spin-flip density functional theory. J Comput Chem 2013; 35:109-20. [DOI: 10.1002/jcc.23463] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/12/2013] [Accepted: 09/24/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Jianyong Liu
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
| | - Guozhong He
- State Key Laboratory of Molecular Reaction Dynamics; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 Liaoning People's Republic of China
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12
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Coccia E, Varsano D, Guidoni L. Protein Field Effect on the Dark State of 11- cis Retinal in Rhodopsin by Quantum Monte Carlo/Molecular Mechanics. J Chem Theory Comput 2013; 9:8-12. [PMID: 24611033 PMCID: PMC3943175 DOI: 10.1021/ct3007502] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accurate determination of the geometrical details of the dark state of 11-cis retinal in rhodopsin represents a fundamental step for the rationalization of the protein role in the optical spectral tuning in the vision mechanism. We have calculated geometries of the full retinal protonated Schiff base chromophore in the gas phase and in the protein environment using the correlated variational Monte Carlo method. The bond length alternation of the conjugated carbon chain of the chromophore in the gas phase shows a significant reduction when moving from the β-ionone ring to the nitrogen, whereas, as expected, the protein environment reduces the electronic conjugation. The proposed dark state structure is fully compatible with solid-state NMR data reported by Carravetta et al. [J. Am. Chem. Soc. 2004, 126, 3948-3953]. TDDFT/B3LYP calculations on such geometries show a blue opsin shift of 0.28 and 0.24 eV induced by the protein for S1 and S2 states, consistently with literature spectroscopic data. The effect of the geometrical distortion alone is a red shift of 0.21 and 0.16 eV with respect to the optimized gas phase chromophore. Our results open new perspectives for the study of the properties of chromophores in their biological environment using correlated methods.
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Affiliation(s)
- Emanuele Coccia
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’Aquila, via Vetoio, 67100, L’Aquila, Italy
| | - Daniele Varsano
- Dipartimento di Fisica, “Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’Aquila, via Vetoio, 67100, L’Aquila, Italy
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13
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Weingart O, Garavelli M. Modelling vibrational coherence in the primary rhodopsin photoproduct. J Chem Phys 2012; 137:22A523. [DOI: 10.1063/1.4742814] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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14
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Sekharan S, Wei JN, Batista VS. The Active Site of Melanopsin: The Biological Clock Photoreceptor. J Am Chem Soc 2012; 134:19536-9. [DOI: 10.1021/ja308763b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Sivakumar Sekharan
- Department
of Chemistry, Yale University, New Haven,
Connecticut 06520-8107, United States
| | - Jennifer N. Wei
- Department
of Chemistry, Yale University, New Haven,
Connecticut 06520-8107, United States
| | - Victor S. Batista
- Department
of Chemistry, Yale University, New Haven,
Connecticut 06520-8107, United States
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15
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Comparative study of spectroscopic properties of the low-lying electronic states of 2,4-pentadien-1-iminium cation and its N-substituted analogues. J CHEM SCI 2012. [DOI: 10.1007/s12039-012-0311-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Coccia E, Guidoni L. Quantum monte carlo study of the retinal minimal model C5H6NH2+. J Comput Chem 2012; 33:2332-9. [DOI: 10.1002/jcc.23071] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 06/22/2012] [Accepted: 06/26/2012] [Indexed: 12/22/2022]
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17
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Valsson O, Filippi C. Gas-Phase Retinal Spectroscopy: Temperature Effects Are But a Mirage. J Phys Chem Lett 2012; 3:908-912. [PMID: 26286419 DOI: 10.1021/jz300183g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We employ state-of-the-art first-principle approaches to investigate whether temperature effects are responsible for the unusually broad and flat spectrum of protonated Schiff base retinal observed in photodissociation spectroscopy, as has recently been proposed. We first carefully calibrate how to construct a realistic geometrical model of retinal and show that the exchange-correlation M06-2X functional yields an accurate description while the commonly used complete active space self-consistent field method (CASSCF) is not adequate. Using modern multiconfigurational perturbative methods (NEVPT2) to compute the excitations, we then demonstrate that conformations with different orientations of the β-ionone ring are characterized by similar excitations. Moreover, other degrees of freedom identified as active in room-temperature molecular dynamics simulations do not yield the shift required to explain the anomalous spectral shape. Our findings indicate that photodissociation experiments are not representative of the optical spectrum of retinal in the gas phase and call for further experimental characterization of the dissociation spectra.
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Affiliation(s)
- Omar Valsson
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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18
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Orekhov PS, Shaytan AK, Shaitan KV. Calculation of spectral shifts of the mutants of bacteriorhodopsin by QM/MM methods. Biophysics (Nagoya-shi) 2012. [DOI: 10.1134/s0006350912020170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Kaila VRI, Send R, Sundholm D. The effect of protein environment on photoexcitation properties of retinal. J Phys Chem B 2012; 116:2249-58. [PMID: 22166007 DOI: 10.1021/jp205918m] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Retinal is the photon absorbing chromophore of rhodopsin and other visual pigments, enabling the vertebrate vision process. The effects of the protein environment on the primary photoexcitation process of retinal were studied by time-dependent density functional theory (TDDFT) and the algebraic diagrammatic construction through second order (ADC(2)) combined with our recently introduced reduction of virtual space (RVS) approximation method. The calculations were performed on large full quantum chemical cluster models of the bluecone (BC) and rhodopsin (Rh) pigments with 165-171 atoms. Absorption wavelengths of 441 and 491 nm were obtained at the B3LYP level of theory for the respective models, which agree well with the experimental values of 414 and 498 nm. Electrostatic rather than structural strain effects were shown to dominate the spectral tuning properties of the surrounding protein. The Schiff base retinal and a neighboring Glu-113 residue were found to have comparable proton affinities in the ground state of the BC model, whereas in the excited state, the proton affinity of the Schiff base is 5.9 kcal/mol (0.26 eV) higher. For the ground and excited states of the Rh model, the proton affinity of the Schiff base is 3.2 kcal/mol (0.14 eV) and 7.9 kcal/mol (0.34 eV) higher than for Glu-113, respectively. The protein environment was found to enhance the bond length alternation (BLA) of the retinyl chain and blueshift the first absorption maxima of the protonated Schiff base in the BC and Rh models relative to the chromophore in the gas phase. The protein environment was also found to decrease the intensity of the second excited state, thus improving the quantum yield of the photoexcitation process. Relaxation of the BC model on the excited state potential energy surface led to a vanishing BLA around the isomerization center of the conjugated retinyl chain, rendering the retinal accessible for cis-trans isomerization. The energy of the relaxed excited state was found to be 30 kcal/mol (1.3 eV) above the minimum ground state energy, and might be related to the transition state of the thermal activation process.
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Affiliation(s)
- Ville R I Kaila
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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20
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Hernández-Rodríguez EW, Sánchez-García E, Crespo-Otero R, Montero-Alejo AL, Montero LA, Thiel W. Understanding Rhodopsin Mutations Linked to the Retinitis pigmentosa Disease: a QM/MM and DFT/MRCI Study. J Phys Chem B 2012; 116:1060-76. [DOI: 10.1021/jp2037334] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Erix Wiliam Hernández-Rodríguez
- Departamento de Bioquímica, Instituto de Ciencias Básicas y Preclínicas “Victoria de Girón”, 11600 Havana City, Cuba, and Charité Centrum für Innere Medizin und Dermatologie, Biomedizinisches Forschungszentrum, Campus Virchow, Charité-Universitätsmedizin, 13353 Berlin, Germany
| | | | | | - Ana Lilian Montero-Alejo
- Laboratorio de Química Computacional y Teórica, Departamento de Química Física, Universidad de La Habana, 10400 Havana City, Cuba
| | - Luis Alberto Montero
- Laboratorio de Química Computacional y Teórica, Departamento de Química Física, Universidad de La Habana, 10400 Havana City, Cuba
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, 45470 Germany
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21
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Valsson O, Angeli C, Filippi C. Excitation energies of retinal chromophores: critical role of the structural model. Phys Chem Chem Phys 2012; 14:11015-20. [DOI: 10.1039/c2cp41387f] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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22
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Sekharan S, Yokoyama S, Morokuma K. Quantum mechanical/molecular mechanical structure, enantioselectivity, and spectroscopy of hydroxyretinals and insights into the evolution of color vision in small white butterflies. J Phys Chem B 2011; 115:15380-8. [PMID: 22087641 DOI: 10.1021/jp208107r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since Vogt's discovery of A(3)-retinal or 3-hydroxyretinal in insects in 1983 and Matsui's discovery of A(4)-retinal or 4-hydroxyretinal in firefly squid in 1988, hydroxyretinal-protein interactions mediating vision have remained largely unexplored. In the present study, A(3)- and A(4)-retinals are theoretically incorporated into squid and bovine visual pigments by use of the hybrid quantum mechanics/molecular mechanics [SORCI+Q//B3LYP/6-31G(d):Amber96] method, and insights into structure, enantioselectivity, and spectroscopy are gathered and presented for the first time. Contrary to general perception, our findings rule out the formation of a hydrogen bond between the hydroxyl-bearing β-ionone ring portion of retinal and opsin. Compared to A(1)-pigments, A(3)- and A(4)-pigments exhibit slightly blue-shifted absorption maxima due to increase in bond-length alternation of the hydroxyretinal. We suggest that (i) the binding site of firefly squid (Watasenia scintillans) opsin is very similar to that of the Japanese common squid (Todarodes pacificus) opsin; (ii) the molecular mechanism of spectral tuning in small white butterflies involve sites S116 and T185 and breaking of a hydrogen bond between sites E180 and T185; and finally (iii) A(3)-retinal may have occurred during the conversion of A(1)- to A(2)-retinal and insects may have acquired them, in order to absorb light in the blue-green wavelength region and to speed up the G-protein signaling cascade.
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Affiliation(s)
- Sivakumar Sekharan
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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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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Rajamani R, Lin YL, Gao J. The opsin shift and mechanism of spectral tuning in rhodopsin. J Comput Chem 2011; 32:854-65. [PMID: 20941732 PMCID: PMC3021771 DOI: 10.1002/jcc.21663] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 08/07/2010] [Indexed: 01/12/2023]
Abstract
Molecular dynamics simulations and combined quantum mechanical and molecular mechanical calculations have been performed to investigate the mechanism of the opsin shift and spectral tuning in rhodopsin. A red shift of -980 cm(-1) was estimated in the transfer of the chromophore from methanol solution environment to the protonated Schiff base (PSB)-binding site of the opsin. The conformational change from a 6-s-cis-all-trans configuration in solution to the 6-s-cis-11-cis conformer contributes additional -200 cm(-1), and the remaining effects were attributed to dispersion interactions with the aromatic residues in the binding site. An opsin shift of 2100 cm(-1) was obtained, in reasonable accord with experiment (2730 cm(-1)). Dynamics simulations revealed that the 6-s-cis bond can occupy two main conformations for the β-ionone ring, resulting in a weighted average dihedral angle of about -50°, which may be compared with the experimental estimate of -28° from solid-state NMR and Raman data. We investigated a series of four single mutations, including E113D, A292S, T118A, and A269T, which are located near the PSB, along the polyene chain of retinal and close to the ionone ring. The computational results on absorption energy shift provided insights into the mechanism of spectral tuning, which involves all means of electronic structural effects, including the stabilization or destabilization of either the ground or the electronically excited state of the retinal PSB.
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Affiliation(s)
| | - Yen-lin Lin
- Department of Chemistry, Digital Technology Center, and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Jiali Gao
- Department of Chemistry, Digital Technology Center, and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
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25
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Sekharan S, Morokuma K. QM/MM study of the structure, energy storage, and origin of the bathochromic shift in vertebrate and invertebrate bathorhodopsins. J Am Chem Soc 2011; 133:4734-7. [PMID: 21391708 PMCID: PMC3075117 DOI: 10.1021/ja200322w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By comparing the results from a hybrid quantum mechanics/molecular mechanics method (SORCI+Q//B3LYP/6-31G*:Amber) between vertebrate (bovine) and invertebrate (squid) visual pigments, the mechanism of molecular rearrangements, energy storage, and origin of the bathochromic shift accompanying the transformation of rhodopsin to bathorhodopsin have been evaluated. The analysis reveals that, in the presence of an unrelaxed binding site, bathorhodopsin was found to carry almost 27 kcal/mol energy in both visual pigments and absorb (λ(max)) at 528 nm in bovine and 554 nm in squid. However, when the residues within 4.0 Å radius of the retinal are relaxed during the isomerization event, almost ∼16 kcal/mol energy is lost in squid compared to only ∼8 kcal/mol in bovine. Loss of a larger amount of energy in squid is attributed to the presence of a flexible binding site compared to a rigid binding site in bovine. Structure of the squid bathorhodopsin is characterized by formation of a direct H-bond between the Schiff base and Asn87.
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26
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Rostov IV, Amos RD, Kobayashi R, Scalmani G, Frisch MJ. Studies of the ground and excited-state surfaces of the retinal chromophore using CAM-B3LYP. J Phys Chem B 2010; 114:5547-55. [PMID: 20369810 DOI: 10.1021/jp911329g] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer (PSBT) is examined. Optimized structures on both the ground state and the excited state are calculated, and the dependence on torsional angles in the carbon chain is investigated. Time-dependent density functional theory is used to produce excitation energies and the excited-state surface. To avoid problems with the description of excited states that can arise with standard DFT methods, the CAM-B3LYP functional was used. Comparing CAM-B3LYP with B3LYP results indicates that the former is significantly more accurate, as a consequence of which detailed cross sections of the retinal excited-state surface are obtained.
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Affiliation(s)
- Ivan V Rostov
- Australian National University Supercomputer Facility, Mills Road, Canberra, ACT 0200, Australia
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27
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Sekharan S, Altun A, Morokuma K. Photochemistry of visual pigment in a G(q) protein-coupled receptor (GPCR)--insights from structural and spectral tuning studies on squid rhodopsin. Chemistry 2010; 16:1744-9. [PMID: 20066712 DOI: 10.1002/chem.200903194] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sivakumar Sekharan
- Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
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28
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Rajput J, Rahbek D, Andersen L, Hirshfeld A, Sheves M, Altoè P, Orlandi G, Garavelli M. Probing and Modeling the Absorption of Retinal Protein Chromophores in Vacuo. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Rajput J, Rahbek D, Andersen L, Hirshfeld A, Sheves M, Altoè P, Orlandi G, Garavelli M. Probing and Modeling the Absorption of Retinal Protein Chromophores in Vacuo. Angew Chem Int Ed Engl 2010; 49:1790-3. [DOI: 10.1002/anie.200905061] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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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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31
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Ma Y, Rohlfing M, Molteni C. Modeling the Excited States of Biological Chromophores within Many-Body Green's Function Theory. J Chem Theory Comput 2009; 6:257-65. [PMID: 26614336 DOI: 10.1021/ct900528h] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
First-principle many-body Green's function theory (MBGFT) has been successfully used to describe electronic excitations in many materials, from bulk crystals to nanoparticles. Here we assess its performance for the calculations of the excited states of biological chromophores. MBGFT is based on a set of Green's function equations, whose key ingredients are the electron's self-energy Σ, which is obtained by Hedin's GW approach, and the electron-hole interaction, which is described by the Bethe-Salpeter equation (BSE). The GW approach and the BSE predict orbital energies and excitation energies with high accuracy, respectively. We have calculated the low-lying excited states of a series of model biological chromophores, related to the photoactive yellow protein (PYP), rhodopsin, and the green fluorescent protein (GFP), obtaining a very good agreement with the available experimental and accurate theoretical data; the order of the excited states is also correctly predicted. MBGFT bridges the gap between time-dependent density functional theory and high-level quantum chemistry methods, combining the efficiency of the former with the accuracy of the latter: this makes MBGFT a promising method for studying excitations in complex biological systems.
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Affiliation(s)
- Yuchen Ma
- Fachbereich Physik, Universität Osnabrück, D-49069 Osnabrück, Germany, and Physics Department, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Michael Rohlfing
- Fachbereich Physik, Universität Osnabrück, D-49069 Osnabrück, Germany, and Physics Department, King's College London, Strand, London WC2R 2LS, United Kingdom
| | - Carla Molteni
- Fachbereich Physik, Universität Osnabrück, D-49069 Osnabrück, Germany, and Physics Department, King's College London, Strand, London WC2R 2LS, United Kingdom
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32
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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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33
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Photoexcitation of 11-Z-cis-7,8-dihydro retinal and 11-Z-cis retinal: A comparative computational study. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2008.12.089] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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34
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Abstract
The role of water molecules in spectral tuning of proteins has been left largely unexplored. This topic is important because changing hydrogen bond patterns during the activation process may lead to spectral shifts which can be of diagnostic value for the underlying structures. Arguments put forward in this article are based on spectral shift calculations of the rhodopsin and bathorhodopsin chromophore due to wat2a and 2b in the presence and absence of the counterion and of the amino acids lining the rhodopsin binding pocket. They show, among others, that a single water molecule can shift the absorbance by up to 0.1 eV or 34 nm depending on the environment of the chromophore.
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35
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Nielsen MB. Model systems for understanding absorption tuning by opsin proteins. Chem Soc Rev 2009; 38:913-24. [DOI: 10.1039/b802068j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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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; 112:16883-90. [DOI: 10.1021/jp807172h] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, and Department of Biology, Rollins Research Center, Emory University, Atlanta, Georgia 30322, USA and Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Shozo Yokoyama
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, and Department of Biology, Rollins Research Center, Emory University, Atlanta, Georgia 30322, USA and Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Keiji Morokuma
- Cherry L. Emerson Center for Scientific Computation, Department of Chemistry, and Department of Biology, Rollins Research Center, Emory University, Atlanta, Georgia 30322, USA and Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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37
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Altun A, Yokoyama S, Morokuma K. Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants. J Phys Chem B 2008; 112:6814-27. [PMID: 18473437 DOI: 10.1021/jp709730b] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11- cis-retinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants.
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Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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38
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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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39
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Röhrig UF, Sebastiani D. NMR Chemical Shifts of the Rhodopsin Chromophore in the Dark State and in Bathorhodopsin: A Hybrid QM/MM Molecular Dynamics Study. J Phys Chem B 2008; 112:1267-74. [DOI: 10.1021/jp075662q] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ute F. Röhrig
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Sebastiani
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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40
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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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41
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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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42
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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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43
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Lammich L, Nielsen IB, Sand H, Svendsen A, Andersen LH. Probing the Sub-microsecond Photodissociation Dynamics in Gas-Phase Retinal Chromophores. J Phys Chem A 2007; 111:4567-72. [PMID: 17477513 DOI: 10.1021/jp070331z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The photoinduced fragmentation of a retinal model chromophore (all-trans-n-butyl protonated Schiff-base retinal) was studied in vacuo using a new experimental technique. The apparatus is able to record the photodissociation yield of gas-phase biomolecular ions in the first microseconds after absorption. Together with the existing ion storage ring ELISA, which operates on the millisecond to second time scale, the complete decay dynamics of such molecules can now be followed. In the case of retinal, the time-dependent fragmentation yield observed after irradiation with a 410 nm laser pulse exhibits contributions from one- and two-photon absorption, which decay non-exponentially with lifetimes on the order of 1 ms and 1 micros, respectively. The decay can be simulated using a statistical model, yielding good agreement with the experimental findings on both the millisecond and the microsecond time scales. No indication for nonstatistical processes is found for this molecule, the upper limit for a possible direct rate being a factor of 10(4) below the observed statistical dissociation rate.
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Affiliation(s)
- Lutz Lammich
- Department of Physics and Astronomy, University of Aarhus, DK-8000 Aarhus C, Denmark
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44
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Weingart O, Schapiro I, Buss V. Photochemistry of Visual Pigment Chromophore Models by Ab Initio Molecular Dynamics. J Phys Chem B 2007; 111:3782-8. [PMID: 17388554 DOI: 10.1021/jp0683216] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ab initio excited-state molecular dynamics calculations have been performed to study the effect of methyl substitution and chromophore distortion on the photoreaction of different four-double-bond retinal model chromophores. Randomly distributed starting geometries were generated by zero-point energy sampling; after Franck-Condon excitation the reaction was followed on the S1 surface. For determining the photoproduct and its configuration, a simplified approach--torsion angle following--is discussed and applied. We find that chromophore distortion significantly affects the outcome of the photoreaction: with dihedral angles taken from the rhodopsin-embedded 11-cis-retinal chromophore, the reaction rate of the model chromophore is increased by a factor of 3 compared to that of the relaxed chromophore. Also, the reaction proceeds in a completely stereoselective manner involving only the cis double bond and with a minimum quantum yield of 72%. Bond torsion is more effective than methyl substitution for fast and selective photochemistry, which is in agreement with photophysical measurements on rhodopsin analogues. We conclude that apart from the geometric distortions caused by the protein pocket it is not necessary to postulate other specific interactions between the protein and the chromophore to effect the selective and ultrafast photoreaction in rhodopsin.
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Affiliation(s)
- Oliver Weingart
- Department of Chemistry, University of Duisburg-Essen, 47048 Duisburg, Germany
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45
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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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46
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Sekharan S, Sugihara M, Buss V. Origin of Spectral Tuning in Rhodopsin—It Is Not the Binding Pocket. Angew Chem Int Ed Engl 2007; 46:269-71. [PMID: 17120281 DOI: 10.1002/anie.200603306] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sivakumar Sekharan
- Departments of Chemistry and Physics, University of Duisburg-Essen, Campus Duisburg, 47048 Duisburg, Germany
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47
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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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Sekharan S, Sugihara M, Buss V. Ursprung der spektralen Verschiebung von Rhodopsin – es ist nicht die Bindungstasche. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603306] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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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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