1
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Kochman MA, Palczewski K, Kubas A. Theoretical Study of the Photoisomerization Mechanism of All- Trans-Retinyl Acetate. J Phys Chem A 2021; 125:8358-8372. [PMID: 34546761 PMCID: PMC8488936 DOI: 10.1021/acs.jpca.1c05533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
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The compound 9-cis-retinyl acetate (9-cis-RAc) is a precursor
to 9-cis-retinal,
which has potential application in the treatment of some hereditary
diseases of the retina. An attractive synthetic route to 9-cis-RAc is based on the photoisomerization reaction of the
readily available all-trans-RAc. In the present study,
we examine the mechanism of the photoisomerization reaction with the
use of state-of-the-art electronic structure calculations for two
polyenic model compounds: tEtEt-octatetraene and tEtEtEc-2,6-dimethyl-1,3,5,7,9-decapentaene. The occurrence
of photoisomerization is attributed to a chain-kinking mechanism,
whereby a series of S1/S0 conical intersections
associated with kinking deformations at different positions along
the polyenic chain mediate internal conversion to the S0 state, and subsequent isomerization around one of the double bonds.
Two other possible photoisomerization mechanisms are taken into account,
but they are rejected as incompatible with simulation results and/or
the available spectroscopic data.
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Affiliation(s)
- Michał Andrzej Kochman
- Institute of Physical Chemistry, Polish Academy of Sciences, Ul. Marcina Kasprzaka 44/52, 01-224 Warszawa, Poland
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, California 92697, United States.,Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States.,Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Adam Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Ul. Marcina Kasprzaka 44/52, 01-224 Warszawa, Poland
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2
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Sinha B, Goswami T, Paul S, Misra A. Spectral tuning of 11-cis retinal in conjugation with Au14 cluster and concomitant effect on isomerization: A theoretical outlook. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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3
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Nikolaev DM, Manathunga M, Orozco-Gonzalez Y, Shtyrov AA, Guerrero Martínez YO, Gozem S, Ryazantsev MN, Coutinho K, Canuto S, Olivucci M. Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems. J Chem Theory Comput 2021; 17:5885-5895. [PMID: 34379429 DOI: 10.1021/acs.jctc.1c00221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel technique for computing the free energy differences between two chromophore "isomers" hosted in a molecular environment (a generalized solvent). Such an environment may range from a relatively rigid protein cavity to a flexible solvent environment. The technique is characterized by the application of the previously reported "average electrostatic solvent configuration" method, and it is based on the idea of using the free energy perturbation theory along with a chromophore annihilation procedure in thermodynamic cycle calculations. The method is benchmarked by computing the ground-state room-temperature relative stabilities between (i) the cis and trans isomers of prototypal animal and microbial rhodopsins and (ii) the analogue isomers of a rhodopsin-like light-driven molecular switch in methanol. Furthermore, we show that the same technology can be used to estimate the activation free energy for the thermal isomerization of systems i-ii by replacing one isomer with a transition state. The results show that the computed relative stability and isomerization barrier magnitudes for the selected systems are in line with the available experimental observation in spite of their widely diverse complexity.
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Affiliation(s)
- Dmitrii M Nikolaev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Madushanka Manathunga
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Andrey A Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | | | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Mikhail N Ryazantsev
- Saint Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg 199034, Russia.,Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy.,Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg-CNRS, UMR 7504, F-67034 Strasbourg, France
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4
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Iyer A, Reis RAG, Gannavaram S, Momin M, Spring-Connell AM, Orozco-Gonzalez Y, Agniswamy J, Hamelberg D, Weber IT, Gozem S, Wang S, Germann MW, Gadda G. A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity. Biochemistry 2021; 60:711-724. [PMID: 33630571 DOI: 10.1021/acs.biochem.1c00054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Proteins are inherently dynamic, and proper enzyme function relies on conformational flexibility. In this study, we demonstrated how an active site residue changes an enzyme's reactivity by modulating fluctuations between conformational states. Replacement of tyrosine 249 (Y249) with phenylalanine in the active site of the flavin-dependent d-arginine dehydrogenase yielded an enzyme with both an active yellow FAD (Y249F-y) and an inactive chemically modified green FAD, identified as 6-OH-FAD (Y249F-g) through various spectroscopic techniques. Structural investigation of Y249F-g and Y249F-y variants by comparison to the wild-type enzyme showed no differences in the overall protein structure and fold. A closer observation of the active site of the Y249F-y enzyme revealed an alternative conformation for some active site residues and the flavin cofactor. Molecular dynamics simulations probed the alternate conformations observed in the Y249F-y enzyme structure and showed that the enzyme variant with FAD samples a metastable conformational state, not available to the wild-type enzyme. Hybrid quantum/molecular mechanical calculations identified differences in flavin electronics between the wild type and the alternate conformation of the Y249F-y enzyme. The computational studies further indicated that the alternate conformation in the Y249F-y enzyme is responsible for the higher spin density at the C6 atom of flavin, which is consistent with the formation of 6-OH-FAD in the variant enzyme. The observations in this study are consistent with an alternate conformational space that results in fine-tuning the microenvironment around a versatile cofactor playing a critical role in enzyme function.
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Affiliation(s)
- Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Swathi Gannavaram
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Mohamed Momin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | | | | | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Irene T Weber
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
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5
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Ryazantsev MN, Nikolaev DM, Struts AV, Brown MF. Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. J Membr Biol 2019; 252:425-449. [PMID: 31570961 DOI: 10.1007/s00232-019-00095-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
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Affiliation(s)
- Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, Saint Petersburg, Russia, 198504
| | - Dmitrii M Nikolaev
- Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, Saint Petersburg, Russia, 194021
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, Saint Petersburg State University, Saint Petersburg, Russia, 199034
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
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6
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Valentini A, Nucci M, Frutos LM, Marazzi M. Photosensitized Retinal Isomerization in Rhodopsin Mediated by a Triplet State. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alessio Valentini
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Department of Biotechnology, Chemistry and PharmacyUniversity of Siena via A. Moro 2 53100 Siena Italy
- Theoretical Physical Chemistry, Research Unit MolSysUniversité de Liège Allée du 6 Aôut, 11 4000 Liège Belgium
| | - Martina Nucci
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
| | - Luis Manuel Frutos
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Unidad de Química FísicaUniversidad de Alcalá Ctra. Madrid-Barcelona Km. 33,600 E-28871 Alcalá de Henares, Madrid Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR)Universidad de Alcalá E-28871 Alcalá de Henares, Madrid Spain
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7
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Sala M, Egorova D. Quantum dynamics of multi-dimensional rhodopsin photoisomerization models: Approximate versus accurate treatment of the secondary modes. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Evidence for a vibrational phase-dependent isotope effect on the photochemistry of vision. Nat Chem 2018; 10:449-455. [DOI: 10.1038/s41557-018-0014-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 01/23/2018] [Indexed: 01/05/2023]
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9
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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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10
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Melaccio F, del Carmen Marín M, Valentini A, Montisci F, Rinaldi S, Cherubini M, Yang X, Kato Y, Stenrup M, Orozco-Gonzalez Y, Ferré N, Luk HL, Kandori H, Olivucci M. Toward Automatic Rhodopsin Modeling as a Tool for High-Throughput Computational Photobiology. J Chem Theory Comput 2016; 12:6020-6034. [DOI: 10.1021/acs.jctc.6b00367] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Federico Melaccio
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - María del Carmen Marín
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Alessio Valentini
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Fabio Montisci
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Silvia Rinaldi
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Marco Cherubini
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Xuchun Yang
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Yoshitaka Kato
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Japan
| | - Michael Stenrup
- Aix-Marseille Université, CNRS, ICR, 13284 Marseille, France
| | - Yoelvis Orozco-Gonzalez
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Institut
de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
- USIAS
Institut d’Études Avancées, Université de Strasbourg, 5 allée du Général Rouvillois, F-67083 Strasbourg, France
| | - Nicolas Ferré
- Aix-Marseille Université, CNRS, ICR, 13284 Marseille, France
| | - Hoi Ling Luk
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Hideki Kandori
- Department
of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Japan
| | - Massimo Olivucci
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Institut
de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
- USIAS
Institut d’Études Avancées, Université de Strasbourg, 5 allée du Général Rouvillois, F-67083 Strasbourg, France
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11
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Coupled HOOP signature correlates with quantum yield of isorhodopsin and analog pigments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1858:118-125. [PMID: 27836700 DOI: 10.1016/j.bbabio.2016.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 09/29/2016] [Accepted: 11/04/2016] [Indexed: 11/21/2022]
Abstract
With a quantum yield of 0.66±0.03 the photoisomerization efficiency of the visual pigment rhodopsin (11-cis⇒all-trans chromophore) is exceptionally high. This is currently explained by coherent coupling of the excited state electronic wavepacket with local vibrational nuclear modes, facilitating efficient cross-over at a conical intersection onto the photoproduct energy surface. The 9-cis counterpart of rhodopsin, dubbed isorhodopsin, has a much lower quantum yield (0.26±0.03), which, however, can be markedly enhanced by modification of the retinal chromophore (7,8-dihydro and 9-cyclopropyl derivatives). The coherent coupling in the excited state is promoted by torsional skeletal and coupled HOOP vibrational modes, in combination with a twisted conformation around the isomerization region. Since such torsion will strongly enhance the infrared intensity of coupled HOOP modes, we investigated FTIR difference spectra of rhodopsin, isorhodopsin and several analog pigments in the spectral range of isolated and coupled HCCH wags. As a result we propose that the coupled HOOP signature in these retinal pigments correlates with the distribution of torsion over counteracting segments in the retinylidene polyene chain. As such the HOOP signature can act as an indicator for the photoisomerization efficiency, and can explain the higher quantum yield of the 7,8-dihydro and 9-cyclopropyl-isorhodopsin analogs.
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12
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Hedegård ED, Reiher M. Polarizable Embedding Density Matrix Renormalization Group. J Chem Theory Comput 2016; 12:4242-53. [PMID: 27537835 DOI: 10.1021/acs.jctc.6b00476] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The polarizable embedding (PE) approach is a flexible embedding model where a preselected region out of a larger system is described quantum mechanically, while the interaction with the surrounding environment is modeled through an effective operator. This effective operator represents the environment by atom-centered multipoles and polarizabilities derived from quantum mechanical calculations on (fragments of) the environment. Thereby, the polarization of the environment is explicitly accounted for. Here, we present the coupling of the PE approach with the density matrix renormalization group (DMRG). This PE-DMRG method is particularly suitable for embedded subsystems that feature a dense manifold of frontier orbitals which requires large active spaces. Recovering such static electron-correlation effects in multiconfigurational electronic structure problems, while accounting for both electrostatics and polarization of a surrounding environment, allows us to describe strongly correlated electronic structures in complex molecular environments. We investigate various embedding potentials for the well-studied first excited state of water with active spaces that correspond to a full configuration-interaction treatment. Moreover, we study the environment effect on the first excited state of a retinylidene Schiff base within a channelrhodopsin protein. For this system, we also investigate the effect of dynamical correlation included through short-range density functional theory.
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Affiliation(s)
- Erik D Hedegård
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich , Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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13
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Ockenfels A, Schapiro I, Gärtner W. Rhodopsins carrying modified chromophores--the 'making of', structural modelling and their light-induced reactivity. Photochem Photobiol Sci 2016; 15:297-308. [PMID: 26860474 DOI: 10.1039/c5pp00322a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A series of vitamin-A aldehydes (retinals) with modified alkyl group substituents (9-demethyl-, 9-ethyl-, 9-isopropyl-, 10-methyl, 10-methyl-13-demethyl-, and 13-demethyl retinal) was synthesized and their 11-cis isomers were used as chromophores to reconstitute the visual pigment rhodopsin. Structural changes were selectively introduced around the photoisomerizing C11=C12 bond. The effect of these structural changes on rhodopsin formation and bleaching was determined. Global fit of assembly kinetics yielded lifetimes and spectral features of the assembly intermediates. Rhodopsin formation proceeds stepwise with prolonged lifetimes especially for 9-demethyl retinal (longest lifetime τ3 = 7500 s, cf., 3500 s for retinal), and for 10-methyl retinal (τ3 = 7850 s). These slowed-down processes are interpreted as either a loss of fixation (9dm) or an increased steric hindrance (10me) during the conformational adjustment within the protein. Combined quantum mechanics and molecular mechanics (QM/MM) simulations provided structural insight into the retinal analogues-assembled, full-length rhodopsins. Extinction coefficients, quantum yields and kinetics of the bleaching process (μs-to-ms time range) were determined. Global fit analysis yielded lifetimes and spectral features of bleaching intermediates, revealing remarkably altered kinetics: whereas the slowest process of wild-type rhodopsin and of bleached and 11-cis retinal assembled rhodopsin takes place with lifetimes of 7 and 3.8 s, respectively, this process for 10-methyl-13-demethyl retinal was nearly 10 h (34670 s), coming to completion only after ca. 50 h. The structural changes in retinal derivatives clearly identify the precise interactions between chromophore and protein during the light-induced changes that yield the outstanding efficiency of rhodopsin.
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Affiliation(s)
- Andreas Ockenfels
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany.
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14
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Laurent AD, Adamo C, Jacquemin D. Dye chemistry with time-dependent density functional theory. Phys Chem Chem Phys 2015; 16:14334-56. [PMID: 24548975 DOI: 10.1039/c3cp55336a] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.
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Affiliation(s)
- Adèle D Laurent
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS no. 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes, Cedex 3, France.
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15
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Schnedermann C, Liebel M, Kukura P. Mode-Specificity of Vibrationally Coherent Internal Conversion in Rhodopsin during the Primary Visual Event. J Am Chem Soc 2015; 137:2886-91. [DOI: 10.1021/ja508941k] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christoph Schnedermann
- Physical
and Theoretical
Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, U.K
| | - Matz Liebel
- Physical
and Theoretical
Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, U.K
| | - Philipp Kukura
- Physical
and Theoretical
Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, U.K
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16
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Walczak E, Andruniów T. Impacts of retinal polyene (de)methylation on the photoisomerization mechanism and photon energy storage of rhodopsin. Phys Chem Chem Phys 2015; 17:17169-81. [DOI: 10.1039/c5cp01939g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Similar to native rhodopsin, a two-mode space-saving isomerization mechanism drives the photoreaction in (de)methylated rhodopsin analogues.
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Affiliation(s)
- Elżbieta Walczak
- Department of Chemistry
- Wroclaw University of Technology
- 50-370 Wroclaw
- Poland
| | - Tadeusz Andruniów
- Department of Chemistry
- Wroclaw University of Technology
- 50-370 Wroclaw
- Poland
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17
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Polli D, Rivalta I, Nenov A, Weingart O, Garavelli M, Cerullo G. Tracking the primary photoconversion events in rhodopsins by ultrafast optical spectroscopy. Photochem Photobiol Sci 2015; 14:213-28. [DOI: 10.1039/c4pp00370e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the most recent experimental and computational efforts aimed at exposing the very early phases of the ultrafast isomerization in visual Rhodopsins and we discuss future advanced experiments and calculations.
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Affiliation(s)
- D. Polli
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- 20133 Milano
- Italy
| | - I. Rivalta
- Université de Lyon
- CNRS
- Institut de Chimie de Lyon
- École Normale Supérieure de Lyon
- F-69364 Lyon Cedex 07
| | - A. Nenov
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - O. Weingart
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- Universitätsstr. 1
- 40225 Düsseldorf
- Germany
| | - M. Garavelli
- Université de Lyon
- CNRS
- Institut de Chimie de Lyon
- École Normale Supérieure de Lyon
- F-69364 Lyon Cedex 07
| | - G. Cerullo
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- 20133 Milano
- Italy
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18
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Femtosecond laser spectroscopy of the rhodopsin photochromic reaction: a concept for ultrafast optical molecular switch creation (ultrafast reversible photoreaction of rhodopsin). Molecules 2014; 19:18351-66. [PMID: 25393597 PMCID: PMC6271421 DOI: 10.3390/molecules191118351] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/04/2014] [Accepted: 11/06/2014] [Indexed: 12/02/2022] Open
Abstract
Ultrafast reverse photoreaction of visual pigment rhodopsin in the femtosecond time range at room temperature is demonstrated. Femtosecond two-pump probe experiments with a time resolution of 25 fs have been performed. The first pump pulse at 500 nm initiated cis-trans photoisomerization of rhodopsin chromophore, 11-cis retinal, which resulted in the formation of the primary ground-state photoproduct within a mere 200 fs. The second pump pulse at 620 nm with a varying delay of 200 to 3750 fs relative to the first pump pulse, initiated the reverse phototransition of the primary photoproduct to rhodopsin. The results of this photoconversion have been observed on the differential spectra obtained after the action of two pump pulses at a time delay of 100 ps. It was found that optical density decreased at 560 nm in the spectral region of bathorhodopsin absorption and increased at 480 nm, where rhodopsin absorbs. Rhodopsin photoswitching efficiency shows oscillations as a function of the time delay between two pump pulses. The quantum yield of reverse photoreaction initiated by the second pump pulse falls within the range 15% ± 1%. The molecular mechanism of the ultrafast reversible photoreaction of visual pigment rhodopsin may be used as a concept for the development of an ultrafast optical molecular switch.
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19
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Blancafort L. Photochemistry and photophysics at extended seams of conical intersection. Chemphyschem 2014; 15:3166-81. [PMID: 25157686 DOI: 10.1002/cphc.201402359] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Indexed: 11/07/2022]
Abstract
The role of extended seams of conical intersection in excited-state mechanisms is reviewed. Seams are crossings of the potential energy surface in many dimensions where the decay from the excited to the ground state can occur, and the extended seam is composed of different segments lying along a reaction coordinate. Every segment is associated with a different primary photoproduct, which gives rise to competing pathways. This idea is first illustrated for fulvene and ethylene, and then it is used to explain more complex cases such as the dependence of the isomerisation of retinal chromophore isomers on the protein environment, the dependence of the efficiency of the azobenzene photochemical switch on the wavelength of irradiation and the direction of the isomerisation, and the coexistence of different mechanisms in the photo-induced Wolff rearrangement of diazonaphthoquinone. The role of extended seams in the photophysics of the DNA nucleobases and the relationship between two-state seams and three-state crossings is also discussed. As an outlook, the design of optical control strategies based on the passage of the excited molecule through the seam is considered, and it is shown how the excited-state lifetime of fulvene can be modulated by shaping the energy of the seam.
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Affiliation(s)
- Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona (Spain).
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20
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Polli D, Weingart O, Brida D, Poli E, Maiuri M, Spillane KM, Bottoni A, Kukura P, Mathies RA, Cerullo G, Garavelli M. Wavepacket Splitting and Two-Pathway Deactivation in the Photoexcited Visual Pigment Isorhodopsin. Angew Chem Int Ed Engl 2014; 53:2504-7. [DOI: 10.1002/anie.201309867] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Indexed: 11/10/2022]
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21
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Polli D, Weingart O, Brida D, Poli E, Maiuri M, Spillane KM, Bottoni A, Kukura P, Mathies RA, Cerullo G, Garavelli M. Aufspaltung des Wellenpakets und Doppelpfad-Desaktivierung im photoangeregten Sehpigment Isorhodopsin. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309867] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 759] [Impact Index Per Article: 75.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
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23
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Gozem S, Melaccio F, Luk HL, Rinaldi S, Olivucci M. Learning from photobiology how to design molecular devices using a computer. Chem Soc Rev 2014; 43:4019-36. [DOI: 10.1039/c4cs00037d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Learning how to model photo-responsive proteins may open the way to the design of lightpowered biomimetic molecular devices.
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Affiliation(s)
- S. Gozem
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
| | - F. Melaccio
- Dipartimento di Chimica
- Università di Siena
- Siena, Italy
| | - H. L. Luk
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
| | - S. Rinaldi
- Dipartimento di Chimica
- Università di Siena
- Siena, Italy
| | - M. Olivucci
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
- Dipartimento di Chimica
- Università di Siena
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24
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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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25
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Cheminal A, Léonard J, Kim S, Jung KH, Kandori H, Haacke S. Steady state emission of the fluorescent intermediate of Anabaena Sensory Rhodopsin as a function of light adaptation conditions. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Ultrafast photochemistry of anabaena sensory rhodopsin: experiment and theory. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:589-97. [PMID: 24099700 DOI: 10.1016/j.bbabio.2013.09.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/28/2013] [Accepted: 09/29/2013] [Indexed: 11/20/2022]
Abstract
Light induced isomerization of the retinal chromophore activates biological function in all retinal protein (RP) driving processes such as ion-pumping, vertebrate vision and phototaxis in organisms as primitive as archea, or as complex as mammals. This process and its consecutive reactions have been the focus of experimental and theoretical research for decades. The aim of this review is to demonstrate how the experimental and theoretical research efforts can now be combined to reach a more comprehensive understanding of the excited state process on the molecular level. Using the Anabaena Sensory Rhodopsin as an example we will show how contemporary time-resolved spectroscopy and recently implemented excited state QM/MM methods consistently describe photochemistry in retinal proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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27
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Böckmann M, Braun S, Doltsinis NL, Marx D. Mimicking photoisomerisation of azo-materials by a force field switch derived from nonadiabatic ab initio simulations: Application to photoswitchable helical foldamers in solution. J Chem Phys 2013; 139:084108. [DOI: 10.1063/1.4818489] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Huntress MM, Gozem S, Malley KR, Jailaubekov AE, Vasileiou C, Vengris M, Geiger JH, Borhan B, Schapiro I, Larsen DS, Olivucci M. Toward an Understanding of the Retinal Chromophore in Rhodopsin Mimics. J Phys Chem B 2013; 117:10053-70. [DOI: 10.1021/jp305935t] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark M. Huntress
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
| | - Samer Gozem
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
| | - Konstantin R. Malley
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
| | - Askat E. Jailaubekov
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824,
United States
| | - Mikas Vengris
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
- Faculty of
Physics, Vilnius University, Sauletekio
10 LT10223 Vilnius,
Lithuania
| | - James H. Geiger
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824,
United States
| | - Babak Borhan
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824,
United States
| | - Igor Schapiro
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California Davis, One Shields Avenure,
Davis, California 95616, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio
43402, United States
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29
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Cascella M, Bärfuss S, Stocker A. Cis-retinoids and the chemistry of vision. Arch Biochem Biophys 2013; 539:187-95. [PMID: 23791723 DOI: 10.1016/j.abb.2013.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/04/2013] [Accepted: 06/10/2013] [Indexed: 11/17/2022]
Abstract
We discuss here principal biochemical transformations of retinoid molecules in the visual cycle. We focus our analysis on the accumulating evidence of alternate pathways and functional redundancies in the cycle. The efficiency of the visual cycle depends, on one hand, on fast regeneration of the photo-bleached chromophores. On the other hand, it is crucial that the cyclic process should be highly selective to avoid accumulation of byproducts. The state-of-the-art knowledge indicates that single enzymatically active components of the cycle are not strictly selective and may require chaperones to enhance their rates. It appears that protein-protein interactions significantly improve the biological stability of the visual cycle. In particular, synthesis of thermodynamically less stable 11-cis-retinoid conformers is favored by physical interactions of the isomerases present in the retina with cellular retinaldehyde binding protein.
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Affiliation(s)
- Michele Cascella
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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30
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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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31
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Böckmann M, Doltsinis NL, Marx D. Enhanced photoswitching of bridged azobenzene studied by nonadiabatic ab initio simulation. J Chem Phys 2012; 137:22A505. [DOI: 10.1063/1.4733673] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Gozem S, Schapiro I, Ferre N, Olivucci M. The Molecular Mechanism of Thermal Noise in Rod Photoreceptors. Science 2012; 337:1225-8. [DOI: 10.1126/science.1220461] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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33
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Laricheva EN, Gozem S, Rinaldi S, Melaccio F, Valentini A, Olivucci M. Origin of Fluorescence in 11-cis Locked Bovine Rhodopsin. J Chem Theory Comput 2012; 8:2559-63. [DOI: 10.1021/ct3002514] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elena N. Laricheva
- Department
of Chemistry, Center
for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Samer Gozem
- Department
of Chemistry, Center
for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
| | - Silvia Rinaldi
- Dipartimento di Chimica, Università
di Siena, via De Gasperi 2, I-53100 Siena, Italy
| | - Federico Melaccio
- Dipartimento di Chimica, Università
di Siena, via De Gasperi 2, I-53100 Siena, Italy
| | - Alessio Valentini
- Dipartimento di Chimica, Università
di Siena, via De Gasperi 2, I-53100 Siena, Italy
| | - Massimo Olivucci
- Department
of Chemistry, Center
for Photochemical Sciences, Bowling Green State University, Bowling
Green, Ohio 43403, United States
- Dipartimento di Chimica, Università
di Siena, via De Gasperi 2, I-53100 Siena, Italy
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34
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Chung WC, Nanbu S, Ishida T. QM/MM Trajectory Surface Hopping Approach to Photoisomerization of Rhodopsin and Isorhodopsin: The Origin of Faster and More Efficient Isomerization for Rhodopsin. J Phys Chem B 2012; 116:8009-23. [DOI: 10.1021/jp212378u] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wilfredo Credo Chung
- Fukui Institute
for Fundamental Chemistry, Kyoto University, 34-4, Takano-nishihirakicho, Sakyo-ku, Kyoto 606-8103, Japan
| | - Shinkoh Nanbu
- Department of Materials
and Life Sciences, Faculty of Science and Engineering, Sophia University, Kioicho, Chiyoda-ku, Tokyo 102-8554,
Japan
| | - Toshimasa Ishida
- Fukui Institute
for Fundamental Chemistry, Kyoto University, 34-4, Takano-nishihirakicho, Sakyo-ku, Kyoto 606-8103, Japan
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35
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Chung WC, Nanbu S, Ishida T. A Nonadiabatic Ab Initio Dynamics Study on Rhodopsin and Its Analog Isorhodopsin: Chemical Dynamics Reasons behind Selection of Rhodopsin by Life. CHEM LETT 2011. [DOI: 10.1246/cl.2011.1395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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36
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Schapiro I, Ryazantsev MN, Frutos LM, Ferré N, Lindh R, Olivucci M. The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects. J Am Chem Soc 2011; 133:3354-64. [DOI: 10.1021/ja1056196] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Igor Schapiro
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Luis Manuel Frutos
- Departamento de Química Física, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Nicolas Ferré
- Laboratoire Chimie Provence UMR 6264, Université de Provence, Campus Saint Jérôme Case 521, 13397 Marseille Cedex 20, France
| | - Roland Lindh
- Department of Quantum Chemistry, Ångströmlab, Lägerhyddsv. 1, Box 518, 751 20 Uppsala University, Sweden
| | - Massimo Olivucci
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Chimica, Università degli Studi di Siena, via Aldo Moro 2, I-53100 Siena, Italy
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37
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Schapiro I, Melaccio F, Laricheva EN, Olivucci M. Using the computer to understand the chemistry of conical intersections. Photochem Photobiol Sci 2011; 10:867-86. [DOI: 10.1039/c0pp00290a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Chung WC, Nanbu S, Ishida T. Nonadiabatic ab Initio Dynamics of a Model Protonated Schiff Base of 9-cis Retinal. J Phys Chem A 2010; 114:8190-201. [DOI: 10.1021/jp103253b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wilfredo Credo Chung
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4, Takano-nishihirakicho, Kyoto 606-8103, Japan
| | - Shinkoh Nanbu
- Department of Materials and Life Sciences, Faculty of Science and Engineering, Sophia University, Chiyodaku Kioicho, Tokyo 102-8554, Japan
| | - Toshimasa Ishida
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4, Takano-nishihirakicho, Kyoto 606-8103, Japan
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39
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Khrenova MG, Nemukhin AV, Grigorenko BL, Krylov AI, Domratcheva TM. Quantum Chemistry Calculations Provide Support to the Mechanism of the Light-Induced Structural Changes in the Flavin-Binding Photoreceptor Proteins. J Chem Theory Comput 2010; 6:2293-302. [DOI: 10.1021/ct100179p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- M. G. Khrenova
- Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation, N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - A. V. Nemukhin
- Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation, N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - B. L. Grigorenko
- Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation, N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - A. I. Krylov
- Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation, N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - T. M. Domratcheva
- Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation, N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
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40
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Khrenova MG, Bochenkova AV, Nemukhin AV. Modeling reaction routes from rhodopsin to bathorhodopsin. Proteins 2010; 78:614-22. [PMID: 19787771 DOI: 10.1002/prot.22590] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The quantum mechanical-molecular mechanical (QM/MM) theory was applied to calculate accurate structural parameters, vibrational and optical spectra of bathorhodopsin (BATHO), one of the primary photoproducts of the functional cycle of the visual pigment rhodopsin (RHO), and to characterize reaction routes from RHO to BATHO. The recently resolved crystal structure of BATHO (PDBID: 2G87) served as an initial source of coordinates of heavy atoms. Protein structures in the ground electronic state and vibrational frequencies were determined by using the density functional theory in the PBE0/cc-pVDZ approximation for the QM part and the AMBER force field parameters in the MM part. Calculated and assigned vibrational spectra of both model protein systems, BATHO and RHO, cover three main regions referring to the hydrogen-out-of-plan (HOOP) motion, the C==C ethylenic stretches, and the C--C single-bond stretches. The S(0)-S(1) electronic excitation energies of the QM part, including the chromophore group in the field of the protein matrix, were estimated by using the advanced quantum chemistry methods. The computed structural parameters as well as the spectral bands match perfectly the experimental findings. A structure of the transition state on the S(0) potential energy surface for the ground electronic state rearrangement from RHO to BATHO was located proving a possible route of the thermal protein activation to the primary photoproduct.
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Affiliation(s)
- M G Khrenova
- Department of Chemistry, MV Lomonosov Moscow State University, Moscow 119991, Russian Federation
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Aquilante F, De Vico L, Ferré N, Ghigo G, Malmqvist PA, Neogrády P, Pedersen TB, Pitonák M, Reiher M, Roos BO, Serrano-Andrés L, Urban M, Veryazov V, Lindh R. MOLCAS 7: the next generation. J Comput Chem 2010; 31:224-47. [PMID: 19499541 DOI: 10.1002/jcc.21318] [Citation(s) in RCA: 1301] [Impact Index Per Article: 92.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies.
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Affiliation(s)
- Francesco Aquilante
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland
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Coto PB, Roca-Sanjuán D, Serrano-Andrés L, Martín-Pendás A, Martí S, Andrés J. Toward Understanding the Photochemistry of Photoactive Yellow Protein: A CASPT2/CASSCF and Quantum Theory of Atoms in Molecules Combined Study of a Model Chromophore in Vacuo. J Chem Theory Comput 2009; 5:3032-8. [DOI: 10.1021/ct900401z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. B. Coto
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - D. Roca-Sanjuán
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - L. Serrano-Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - A. Martín-Pendás
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - S. Martí
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
| | - J. Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia, Spain, Departamento de Química-Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006, Oviedo, Spain, Departamento de Química-Física y Analítica, Universidad Jaume I, 224, 12071, Castellón, Spain
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Filippi C, Zaccheddu M, Buda F. Absorption Spectrum of the Green Fluorescent Protein Chromophore: A Difficult Case for ab Initio Methods? J Chem Theory Comput 2009; 5:2074-87. [DOI: 10.1021/ct900227j] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claudia Filippi
- Instituut-Lorentz, Universiteit Leiden, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands, Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Maurizio Zaccheddu
- Instituut-Lorentz, Universiteit Leiden, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands, Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Francesco Buda
- Instituut-Lorentz, Universiteit Leiden, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands, Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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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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Ishida T, Nanbu S, Nakamura H. Nonadiabatic ab Initio Dynamics of Two Models of Schiff Base Retinal. J Phys Chem A 2009; 113:4356-66. [DOI: 10.1021/jp8110315] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Toshimasa Ishida
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4, Takano-nishihirakicho, Kyoto 606-8103, Japan
| | - Shinkoh Nanbu
- Research Institute for Information Technology, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Hiroki Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, 444-8585, Japan
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González-Navarrete P, Coto PB, Polo V, Andrés J. A theoretical study on the thermal ring opening rearrangement of 1H-bicyclo[3.1.0]hexa-3,5-dien-2-one: a case of two state reactivity. Phys Chem Chem Phys 2009; 11:7189-96. [DOI: 10.1039/b906404d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abstract
The accurate ab initio quantum chemical (QM) method multiconfigurational second-order perturbation (CASSPT2)/complete active space self-consistent field (CASSCF) has been used in conjunction with molecular mechanics (MM) procedures to compute molecular properties and photoinduced reactivity of DNA/RNA nucleobases (NABs) in isolation and within a realistic environment, in which the double helix strand, the aqueous media, and the external counterions are included. It is illustrated that the use of an MM model is helpful both to account for short- and long-range effects of the system surrounding the QM molecular core and to provide the proper structural constraints that allow more accurate QM geometry determinations.
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Schapiro I, Weingart O, Buss V. Bicycle-Pedal Isomerization in a Rhodopsin Chromophore Model. J Am Chem Soc 2008; 131:16-7. [DOI: 10.1021/ja805586z] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Igor Schapiro
- Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Oliver Weingart
- Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Volker Buss
- Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
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Coto PB, Martí S, Oliva M, Olivucci M, Merchán M, Andrés J. Origin of the Absorption Maxima of the Photoactive Yellow Protein Resolved via Ab Initio Multiconfigurational Methods. J Phys Chem B 2008; 112:7153-6. [DOI: 10.1021/jp711396b] [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)
- Pedro B. Coto
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Sergio Martí
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Mónica Oliva
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Massimo Olivucci
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Manuela Merchán
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
| | - Juan Andrés
- Instituto de Ciencia Molecular (ICMOL), Universidad de Valencia, Apdo. 22085, ES-46071, Valencia (Spain), Departament de Química Física i Analítica, Universitat Jaume I, 224, 12071, Castellón (Spain), Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403 (U.S.A.), and Dipartimento di Chimica, Università di Siena, Via Aldo Moro I-53100, Siena, (Italy)
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