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Bull JN, West CW, Anstöter CS, da Silva G, Bieske EJ, Verlet JRR. Ultrafast photoisomerisation of an isolated retinoid. Phys Chem Chem Phys 2019; 21:10567-10579. [PMID: 31073587 DOI: 10.1039/c9cp01624d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The photoinduced excited state dynamics of gas-phase trans-retinoate (deprotonated trans-retinoic acid, trans-RA-) are studied using tandem ion mobility spectrometry coupled with laser spectroscopy, and frequency-, angle- and time-resolved photoelectron imaging. Photoexcitation of the bright S3(ππ*) ← S0 transition leads to internal conversion to the S1(ππ*) state on a ≈80 fs timescale followed by recovery of S0 and concomitant isomerisation to give the 13-cis (major) and 9-cis (minor) photoisomers on a ≈180 fs timescale. The sub-200 fs stereoselective photoisomerisation parallels that for the retinal protonated Schiff base chromophore in bacteriorhodopsin. Measurements on trans-RA- in methanol using the solution photoisomerisation action spectroscopy technique show that 13-cis-RA- is also the principal photoisomer, although the 13-cis and 9-cis photoisomers are formed with an inverted branching ratio with photon energy in methanol when compared with the gas phase, presumably due to solvent-induced modification of potential energy surfaces and inhibition of electron detachment processes. Comparison of the gas-phase time-resolved data with transient absorption spectroscopy measurements on retinoic acid in methanol suggest that photoisomerisation is roughly six times slower in solution. This work provides clear evidence that solvation significantly affects the photoisomerisation dynamics of retinoid molecules.
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Affiliation(s)
- James N Bull
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Christopher W West
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Cate S Anstöter
- Department of Chemistry, Durham University, Durham DH1 3LE, UK
| | - Gabriel da Silva
- Department of Chemical Engineering, University of Melbourne, Parkville, VIC 3010, Australia
| | - Evan J Bieske
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jan R R Verlet
- Department of Chemistry, Durham University, Durham DH1 3LE, UK
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2
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Marín MDC, De Vico L, Dong SS, Gagliardi L, Truhlar DG, Olivucci M. Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins. J Chem Theory Comput 2019; 15:1915-1923. [PMID: 30721054 PMCID: PMC7096677 DOI: 10.1021/acs.jctc.8b01069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-binding rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodopsin Modeling (ARM), and it involves the use of the complete active space self-consistent field (CASSCF) method followed by a multiconfiguration second-order perturbation theory (in particular, CASPT2) calculation of external correlation energies. Although it was shown that ARM is capable of successfully reproducing and predicting spectroscopic property trends in chromophore-embedding protein sets, practical applications of such technology are limited by the high computational costs of the multiconfiguration perturbation theory calculations. In the present work we benchmark the more affordable multiconfiguration pair-density functional theory (MC-PDFT) method whose accuracy has been recently validated for retinal chromophores in the gas phase, indicating that MC-PDFT could potentially be used to analyze large (e.g., few hundreds) sets of rhodopsin proteins. Here, we test this theory for a set of rhodopsin QM/MM models whose experimental absorption maxima (λ a max) have been measured. The results indicate that MC-PDFT may be employed to calculate λ a max values for this important class of photoresponsive proteins.
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Affiliation(s)
- María Del Carmen Marín
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , 43403 Ohio , United States
| | - Luca De Vico
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
| | - Sijia S Dong
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Massimo Olivucci
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , 43403 Ohio , United States
- USIAS Institut d'Études Avanceés , Université de Strasbourg , 67083 Strasbourg , France
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3
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Wolański Ł, Grabarek D, Andruniów T. Is the choice of a standard zeroth-order hamiltonian in CASPT2 ansatz optimal in calculations of excitation energies in protonated and unprotonated schiff bases of retinal? J Comput Chem 2018; 39:1470-1480. [PMID: 29635695 DOI: 10.1002/jcc.25217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 11/07/2022]
Abstract
To account for systematic error of CASPT2 method empirical modification of the zeroth-order Hamiltonian with Ionization Potential-Electron Affinity (IPEA) shift was introduced. The optimized IPEA value (0.25 a.u.), called standard IPEA (S-IPEA), was recommended but due to its unsatisfactory performance in multiple metallic and organic compounds it has been questioned lately as a general parameter working properly for all molecules under CASPT2 study. As we are interested in Schiff bases of retinal, an important question emerging from this conflict of choice, to use or not to use S-IPEA, is whether the introduction of the modified zeroth-order Hamiltonian into CASPT2 ansatz does really improve their energetics. To achieve this goal, we assessed an impact of the IPEA shift value, in a range of 0-0.35 a.u., on vertical excitation energies to low-lying singlet states of two protonated (RPSBs) and two unprotonated (RSBs) Schiff bases of retinal for which experimental data in gas phase are available. In addition, an effect of geometry, basis set, and active space on computed VEEs is also reported. We find, that for these systems, the choice of S-IPEA significantly overestimates both S0 →S1 and S0 →S2 energies and the best theoretical estimate, in reference to the experimental data, is provided with either unmodified zeroth-order Hamiltonian or small value of the IPEA shift in a range of 0.05-0.15 a.u., depending on active space and basis set size, equilibrium geometry, and character of the excited state. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Łukasz Wolański
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
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4
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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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5
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Dong SS, Gagliardi L, Truhlar DG. Excitation spectra of retinal by multiconfiguration pair-density functional theory. Phys Chem Chem Phys 2018; 20:7265-7276. [PMID: 29484326 DOI: 10.1039/c7cp07275a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Retinal is the chromophore in proteins responsible for vision. The absorption maximum of retinal is sensitive to mutations of the protein. However, it is not easy to predict the absorption spectrum of retinal accurately, and questions remain even after intensive investigation. Retinal poses a challenge for Kohn-Sham density functional theory (KS-DFT) because of the charge transfer character in its excitations, and it poses a challenge for wave function theory because the large size of the molecule makes multiconfigurational perturbation theory methods expensive. In this study, we demonstrate that multiconfiguration pair-density functional theory (MC-PDFT) provides an efficient way to predict the vertical excitation energies of 11-Z retinal, and it reproduces the experimentally determined absorption band widths and peak positions better than complete active space second-order perturbation theory (CASPT2). The consistency between complete active space self-consistent field (CASSCF) and KS-DFT dipole moments is demonstrated to be a useful criterion in selecting the active space. We also found that the nature of the terminal groups and the conformations of retinal play a significant role in the absorption spectrum. By considering a thermal distribution of conformations, we predict an absorption spectrum of retinal that is consistent with the experimental gas-phase spectrum. The location of the absorption peak and the spectral broadening based on MC-PDFT calculations agree better with experiments than those of CASPT2.
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Affiliation(s)
- Sijia S Dong
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
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6
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Isomerization of the RPSB chromophore in the gas phase along the torsional pathways using QTAIM. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.07.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Coughlan NJA, Wallace CM, Adamson BD, Bieske EJ. Photoisomerization of β-Ionone Protonated Schiff Base in the Gas Phase. J Phys Chem A 2016; 120:6557-62. [PMID: 27483192 DOI: 10.1021/acs.jpca.6b05645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The photoisomerization of β-ionone protonated Schiff base (BIPSB) is investigated in the gas phase by irradiating mobility-selected ions in a tandem ion mobility spectrometer with tunable radiation. Four distinguishable isomers are produced by electrospray ionization whose structures are deduced from their collision cross sections and photoisomerization behavior along with density functional theory calculations. They include two geometric isomers of BIPSB with trans or cis configurations about the polyene chain's terminal C═N double bond, a bicyclic structure formed through electrocyclization of the polyene chain, and a Z-retro-γ-ionone isomer. Although trans-BIPSB and 9-cis-BIPSB have similar photoisomerization action spectra, with a maximum response at 375 nm, they photoconvert to different isomers. The trans-BIPSB isomer transforms to the bicyclic form upon exposure to light over the 320-400 nm range, whereas the cis-BIPSB isomer is prevented by steric hindrance from forming the bicyclic BIPSB isomer following irradiation and is proposed instead to form the 7,9-di-cis isomer. Neither the bicyclic isomer nor the Z-retro-γ-ionone isomer respond strongly to near-UV light.
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Affiliation(s)
| | - Claire M Wallace
- School of Chemistry, The University of Melbourne , Victoria 3010, Australia
| | - Brian D Adamson
- School of Chemistry, The University of Melbourne , Victoria 3010, Australia
| | - Evan J Bieske
- School of Chemistry, The University of Melbourne , Victoria 3010, Australia
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8
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Coughlan NJA, Catani KJ, Adamson BD, Wille U, Bieske EJ. Photoisomerization action spectrum of retinal protonated Schiff base in the gas phase. J Chem Phys 2015; 140:164307. [PMID: 24784270 DOI: 10.1063/1.4871883] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The photophysical behaviour of the isolated retinal protonated n-butylamine Schiff base (RPSB) is investigated in the gas phase using a combination of ion mobility spectrometry and laser spectroscopy. The RPSB cations are introduced by electrospray ionisation into an ion mobility mass spectrometer where they are exposed to tunable laser radiation in the region of the S1 ← S0 transition (420-680 nm range). Four peaks are observed in the arrival time distribution of the RPSB ions. On the basis of predicted collision cross sections with nitrogen gas, the dominant peak is assigned to the all-trans isomer, whereas the subsidiary peaks are assigned to various single, double and triple cis geometric isomers. RPSB ions that absorb laser radiation undergo photoisomerization, leading to a detectable change in their drift speed. By monitoring the photoisomer signal as a function of laser wavelength an action spectrum, extending from 480 to 660 nm with a clear peak at 615 ± 5 nm, is obtained. The photoisomerization action spectrum is related to the absorption spectrum of isolated retinal RPSB molecules and should help benchmark future electronic structure calculations.
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Affiliation(s)
- N J A Coughlan
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - K J Catani
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - B D Adamson
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - U Wille
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - E J Bieske
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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9
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Coughlan NJA, Adamson BD, Gamon L, Catani K, Bieske EJ. Retinal shows its true colours: photoisomerization action spectra of mobility-selected isomers of the retinal protonated Schiff base. Phys Chem Chem Phys 2015; 17:22623-31. [DOI: 10.1039/c5cp03611a] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isomers of the retinal protonated Schiff base are separated and probed using laser radiation in a tandem ion mobility spectrometer yielding isomer-specific electronic spectra.
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Affiliation(s)
| | - B. D. Adamson
- School of Chemistry
- The University of Melbourne
- Melbourne
- Australia
| | - L. Gamon
- School of Chemistry
- The University of Melbourne
- Melbourne
- Australia
| | - K. Catani
- School of Chemistry
- The University of Melbourne
- Melbourne
- Australia
| | - E. J. Bieske
- School of Chemistry
- The University of Melbourne
- Melbourne
- Australia
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10
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Faber C, Boulanger P, Attaccalite C, Duchemin I, Blase X. Excited states properties of organic molecules: from density functional theory to the GW and Bethe-Salpeter Green's function formalisms. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:20130271. [PMID: 24516185 DOI: 10.1098/rsta.2013.0271] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Many-body Green's function perturbation theories, such as the GW and Bethe-Salpeter formalisms, are starting to be routinely applied to study charged and neutral electronic excitations in molecular organic systems relevant to applications in photovoltaics, photochemistry or biology. In parallel, density functional theory and its time-dependent extensions significantly progressed along the line of range-separated hybrid functionals within the generalized Kohn-Sham formalism designed to provide correct excitation energies. We give an overview and compare these approaches with examples drawn from the study of gas phase organic systems such as fullerenes, porphyrins, bacteriochlorophylls or nucleobases molecules. The perspectives and challenges that many-body perturbation theory is facing, such as the role of self-consistency, the calculation of forces and potential energy surfaces in the excited states, or the development of embedding techniques specific to the GW and Bethe-Salpeter equation formalisms, are outlined.
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Affiliation(s)
- C Faber
- Institut Néel, CNRS and University Joseph Fourier, , BP 166, 38042 Grenoble Cedex 09, France
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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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Malrieu JP, Caballol R, Calzado CJ, de Graaf C, Guihéry N. Magnetic interactions in molecules and highly correlated materials: physical content, analytical derivation, and rigorous extraction of magnetic Hamiltonians. Chem Rev 2013; 114:429-92. [PMID: 24102410 DOI: 10.1021/cr300500z] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jean Paul Malrieu
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse 3 , 118 route de Narbonne, 31062 Toulouse, France
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13
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Huix-Rotllant M, Filatov M, Gozem S, Schapiro I, Olivucci M, Ferré N. Assessment of Density Functional Theory for Describing the Correlation Effects on the Ground and Excited State Potential Energy Surfaces of a Retinal Chromophore Model. J Chem Theory Comput 2013; 9:3917-32. [PMID: 26592387 DOI: 10.1021/ct4003465] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In the quest for a cost-effective level of theory able to describe a large portion of the ground and excited potential energy surfaces of large chromophores, promising approaches are rooted in various approximations to the exact density functional theory (DFT). In the present work, we investigate how generalized Kohn-Sham DFT (GKS-DFT), time-dependent DFT (TDDFT), and spin-restricted ensemble-DFT (REKS) methods perform along three important paths characterizing a model retinal chromophore (the penta-2,4-dieniminium cation) in a region of near-degeneracy (close to a conical intersection) with respect to reference high-level multiconfigurational wave function methods. If GKS-DFT correctly describes the closed-shell charge transfer state, only TDDFT and REKS approaches give access to the open-shell diradical, one which sometimes corresponds to the electronic ground state. It is demonstrated that the main drawback of the usual DFT-based methods lies in the absence of interactions between the charge transfer and the diradicaloid configurations. Hence, we test a new computational scheme based on the State-averaged REKS (SA-REKS) approach, which explicitly includes these interactions into account. The State-Interaction SA-REKS (SI-SA-REKS) method significantly improves on the REKS and the SA-REKS results for the target system. The similarities and differences between DFT and wave function-based approaches are analyzed according to (1) the active space dimensions of the wave function-based methods and (2) the relative electronegativities of the allyl and protonated Schiff base moieties.
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Affiliation(s)
- Miquel Huix-Rotllant
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire , 13397 Marseille Cedex 20, France
| | - Michael Filatov
- Institut für Physicalische und Theoretische Chemie, Universität Bonn , Beringstr. 4, 53115 Bonn, Germany
| | - Samer Gozem
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States
| | - Igor Schapiro
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States.,Max Planck Institute for Chemical Energy Conversion , Stiftstr. 34 - 36, Mülheim an der Ruhr, Germany
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States.,Dipartimento di Chimica, Università di Siena , Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire , 13397 Marseille Cedex 20, France
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14
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Valsson O, Campomanes P, Tavernelli I, Rothlisberger U, Filippi C. Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls. J Chem Theory Comput 2013; 9:2441-54. [PMID: 26583734 DOI: 10.1021/ct3010408] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of the protein matrix in modulating the absorption of retinal chromophore in rhodopsin, but, while generally agreeing in predicting the correct location of the absorption maximum, they often reached contradicting conclusions on how the environment tunes the spectrum. To address this controversial issue, we combine here a thorough structural and dynamical characterization of rhodopsin with a careful validation of its excited-state properties via the use of a wide range of state-of-the-art quantum chemical approaches including various flavors of time-dependent density functional theory (TDDFT), different multireference perturbative schemes (CASPT2 and NEVPT2), and quantum Monte Carlo (QMC) methods. Through extensive quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, we obtain a comprehensive structural description of the chromophore-protein system and sample a wide range of thermally accessible configurations. We show that, in order to obtain reliable excitation properties, it is crucial to employ a sufficient number of representative configurations of the system. In fact, the common use of a single, ad hoc structure can easily lead to an incorrect model and an agreement with experimental absorption spectra due to cancelation of errors. Finally, we show that, to properly account for polarization effects on the chromophore and to quench the large blue-shift induced by the counterion on the excitation energies, it is necessary to adopt an enhanced description of the protein environment as given by a large quantum region including as many as 250 atoms.
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Affiliation(s)
- Omar Valsson
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Pablo Campomanes
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
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15
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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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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, 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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