1
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Taylor JT, Tozer DJ, Curchod BFE. On the description of conical intersections between excited electronic states with LR-TDDFT and ADC(2). J Chem Phys 2023; 159:214115. [PMID: 38059547 DOI: 10.1063/5.0176140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023] Open
Abstract
Conical intersections constitute the conceptual bedrock of our working understanding of ultrafast, nonadiabatic processes within photochemistry (and photophysics). Accurate calculation of potential energy surfaces within the vicinity of conical intersections, however, still poses a serious challenge to many popular electronic structure methods. Multiple works have reported on the deficiency of methods like linear-response time-dependent density functional theory within the adiabatic approximation (AA LR-TDDFT) or algebraic diagrammatic construction to second-order [ADC(2)]-approaches often used in excited-state molecular dynamics simulations-to describe conical intersections between the ground and excited electronic states. In the present study, we focus our attention on conical intersections between excited electronic states and probe the ability of AA LR-TDDFT and ADC(2) to describe their topology and topography, using protonated formaldimine and pyrazine as two exemplar molecules. We also take the opportunity to revisit the performance of these methods in describing conical intersections involving the ground electronic state in protonated formaldimine-highlighting in particular how the intersection ring exhibited by AA LR-TDDFT can be perceived either as a (near-to-linear) seam of intersection or two interpenetrating cones, depending on the magnitude of molecular distortions within the branching space.
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Affiliation(s)
- Jack T Taylor
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - David J Tozer
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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2
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Park JW. Analytical Gradient Theory for Resolvent-Fitted Second-Order Extended Multiconfiguration Perturbation Theory (XMCQDPT2). J Chem Theory Comput 2021; 17:6122-6133. [PMID: 34582217 DOI: 10.1021/acs.jctc.1c00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We present the formulation and implementation of an analytical gradient algorithm for extended multiconfiguration quasidegenerate perturbation theory (XMCQDPT2) with the resolvent-fitting approximation by Granovsky. This algorithm is powerful when optimizing molecular configurations with a moderate-sized active space and many electronic states. First, we present the powerfulness and accuracy of resolvent-fitting approximations compared to canonical XMCQDPT2 theory. Then, we demonstrate the utility of the current algorithm in frequency analyses, optimizing the minimum energy conical intersection geometries of the retinal chromophore model RPSB6 and evaluating nuclear gradients when there are many electronic states. Furthermore, we parallelize the algorithm using the OpenMP/MPI hybrid approach. Additionally, we report the computational cost and parallel efficiency of the program.
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Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University (CBNU), Cheongju 28644, Korea
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3
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Kretz B, Egger DA. Accurate Molecular Geometries in Complex Excited-State Potential Energy Surfaces from Time-Dependent Density Functional Theory. J Chem Theory Comput 2021; 17:357-366. [PMID: 33284603 DOI: 10.1021/acs.jctc.0c00858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The interplay of electronic excitations and structural changes in molecules impacts nonradiative decay and charge transfer in the excited state, thus influencing excited-state lifetimes and photocatalytic reaction rates in optoelectronic and energy devices. To capture such effects requires computational methods providing an accurate description of excited-state potential energy surfaces and geometries. We suggest time-dependent density functional theory using optimally tuned range-separated hybrid (OT-RSH) functionals as an accurate approach to obtain excited-state molecular geometries. We show that OT-RSH provides accurate molecular geometries in excited-state potential energy surfaces that are complex and involve an interplay of local and charge-transfer excitations, for which conventional semilocal and hybrid functionals fail. At the same time, the nonempirical OT-RSH approach maintains the high accuracy of parametrized functionals (e.g., B3LYP) for predicting excited-state geometries of small organic molecules showing valence excited states.
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Affiliation(s)
- Bernhard Kretz
- Department of Physics, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| | - David A Egger
- Department of Physics, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
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4
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Brahim S, Brahim H, Humbel S, Rahmouni A. Computational studies of Ni(II) photosensitizers complexes containing 1,1′-bis(diphenylphosphino)ferrocene and dithio ligands. CAN J CHEM 2020. [DOI: 10.1139/cjc-2019-0168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Detailed theoretical studies of Ni(II) complexes in a distorted square planar form and containing dithio and (P, P) chelating ligands were performed. These Ni(II) complexes are investigated for their use in dye-sensitized solar cells (DSSC). Structures and UV–vis spectra are calculated at density functional theory (DFT) and time-dependent density functional theory (TD-DFT) theories using B3LYP and CAM-B3LYP functionals and 6-31G(d,p) and 6-31G+(d) basis sets. Geometry optimizations result in excellent agreement with the experimental results. Moreover, the analysis of the frontier molecular orbitals (FMOs) allowed a detailed assignment and a clear analysis of the electronic transitions. The TD-DFT calculations reproduce the main spectroscopic properties observed and substituent effects. The results reveal that all absorption spectra are characterized by mixed character mainly dominated by metal to ligand and ligand to ligand charge transfers (MLCT and LLCT). We unveil how the substituent variations affect the DSSCs features of the complexes.
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Affiliation(s)
- Sefia Brahim
- Modeling and Calculation Methods Laboratory, University of Saida, Saida 20002, Algeria
| | - Houari Brahim
- Department of Chemistry, University of Saida, Saida 20000, Algeria
| | - Stéphane Humbel
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Ali Rahmouni
- Modeling and Calculation Methods Laboratory, University of Saida, Saida 20002, Algeria
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5
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Park JW. Single-State Single-Reference and Multistate Multireference Zeroth-Order Hamiltonians in MS-CASPT2 and Conical Intersections. J Chem Theory Comput 2019; 15:3960-3973. [DOI: 10.1021/acs.jctc.9b00067] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jae Woo Park
- Department of Chemistry, Chungbuk National University (CBNU), Cheongju 28644, Korea
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6
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Lee IS, Filatov M, Min SK. Formulation and Implementation of the Spin-Restricted Ensemble-Referenced Kohn–Sham Method in the Context of the Density Functional Tight Binding Approach. J Chem Theory Comput 2019; 15:3021-3032. [DOI: 10.1021/acs.jctc.9b00132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- In Seong Lee
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Seung Kyu Min
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
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7
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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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8
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Marsili E, Farag MH, Yang X, De Vico L, Olivucci M. Two-State, Three-Mode Parametrization of the Force Field of a Retinal Chromophore Model. J Phys Chem A 2019; 123:1710-1719. [PMID: 30753077 DOI: 10.1021/acs.jpca.8b10010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, the potential energy surfaces of the penta-2,4-dieniminium cation have been investigated using several electronic structure methods. The resulting pool of geometrical, electronic, and energy data provides a suitable basis for the construction of a topographically correct analytical model of the molecule force field and, therefore, for a better understanding of this class of molecules, which includes the chromophore of visual pigments. In the present contribution, we report the construction of such a model for regions of the force field that drive the photochemical and thermal isomerization of the central double bound of the cation. While previous models included only two modes, it is here shown that the proposed three-mode model and corresponding set of parameters are able to reproduce the complex topographical and electronic structure features seen in electronically correlated data obtained at the XMCQDPT2//CASSCF/6-31G* level of theory.
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Affiliation(s)
- Emanuele Marsili
- Dipartimento di Biotecnologie, Chimica e Farmacia , Università di Siena , via A. Moro 2 , I-53100 Siena , Italy
| | - Marwa H Farag
- Department of Chemistry , University of Southern California , Los Angeles , California 90089-0482 , United States
| | - Xuchun Yang
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States and
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia , Università di Siena , via A. Moro 2 , I-53100 Siena , Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia , Università di Siena , via A. Moro 2 , I-53100 Siena , Italy.,Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States and.,Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 , Université de Strasbourg-CNRS , F-67034 Strasbourg , France
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9
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Ai Y, Xing J, Zhang A, Zhao C, Liu Y, Xie B, Chen W, Cui G, Lu Z, Wang X. Computational Study on the Excited-State Decay of 5-Methylcytosine and 5-Hydroxymethylcytosine: The Common Form of DNA Methylation and Its Oxidation Product. J Phys Chem B 2018; 122:10424-10434. [DOI: 10.1021/acs.jpcb.8b07830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | | | | | - Binbin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | | | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | | | - Xiangke Wang
- NAAM Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences, Soochow University, Suzhou 215123, P. R. China
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10
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Grabarek D, Andruniów T. Initial excited-state relaxation of locked retinal protonated schiff base chromophore. An insight from coupled cluster and multireference perturbation theory calculations. J Comput Chem 2018; 39:1720-1727. [PMID: 29727036 DOI: 10.1002/jcc.25346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/06/2018] [Accepted: 04/12/2018] [Indexed: 11/07/2022]
Abstract
The initial S1 excited-state relaxation of retinal protonated Schiff base (RPSB) analog with central C11C12 double bond locked by eight-membered ring (locked-11.8) was investigated by means of multireference perturbation theory methods (XMCQDPT2, XMS-CASPT2, MS-CASPT2) as well as single-reference coupled-cluster CC2 method. The analysis of XMCQDPT2-based geometries reveals rather weak coupling between in-plane and out-of-plane structural evolution and minor energetical relaxation of three locked-11.8 conformers. Therefore, a strong coupling between bonds length inversion and backbone out-of-plane deformation resulting in a very steep S1 energy profile predicted by CASSCF/CASPT2 calculations is in clear contradiction with the reference XMCQDPT2 results. Even though CC2 method predicts good quality ground-state structures, the excited-state structures display more advanced torsional deformation leading to ca. 0.2 eV exaggerated energy relaxation and significantly red shifted (0.4-0.7 eV) emission maxima. According to our findings, the initial photoisomerization process in locked-11.8, and possibly in other RPSB analogs, studied fully (both geometries and energies) by multireference perturbation theory may be somewhat slower than predicted by CASSCF/CASPT2 or CC2 methods. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- 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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11
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Filatov M, Min SK, Kim KS. Direct Nonadiabatic Dynamics by Mixed Quantum-Classical Formalism Connected with Ensemble Density Functional Theory Method: Application to trans-Penta-2,4-dieniminium Cation. J Chem Theory Comput 2018; 14:4499-4512. [DOI: 10.1021/acs.jctc.8b00217] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Michael Filatov
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Seung Kyu Min
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Kwang S. Kim
- Department of Chemistry, School of Natural Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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12
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Theoretical Investigations on Mechanisms and Pathways of C₂H₅O₂ with BrO Reaction in the Atmosphere. Molecules 2018; 23:molecules23061268. [PMID: 29799497 PMCID: PMC6100565 DOI: 10.3390/molecules23061268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 11/17/2022] Open
Abstract
In this work, feasible mechanisms and pathways of the C2H5O2 + BrO reaction in the atmosphere were investigated using quantum chemistry methods, i.e., QCISD(T)/6-311++G(2df,2p)//B3LYP/6-311++G(2df,2p) levels of theory. Our result indicates that the title reaction occurs on both the singlet and triplet potential energy surfaces (PESs). Kinetically, singlet C2H5O3Br and C2H5O2BrO were dominant products under the atmospheric conditions below 300 K. CH3CHO2 + HOBr, CH3CHO + HOBrO, and CH3CHO + HBrO2 are feasible to a certain extent thermodynamically. Because of high energy barriers, all products formed on the triplet PES are negligible. Moreover, time-dependent density functional theory (TDDFT) calculation implies that C2H5O3Br and C2H5O2BrO will photolyze under the sunlight.
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13
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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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14
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Nabavi SH, Khodabandeh MH, Golbabaee M, Moshaii A, Davari MD. Excited states study reveals the twisted geometry induced large stokes shift in DCM fluorescent dye. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Xing J, Ai Y, Liu Y, Du J, Chen W, Lu Z, Wang X. Theoretical Studies on the Photophysics and Photochemistry of 5-Formylcytosine and 5-Carboxylcytosine: The Oxidative Products of Epigenetic Modification of Cytosine in DNA. J Phys Chem B 2018; 122:2704-2714. [DOI: 10.1021/acs.jpcb.7b10218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jinlu Xing
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Yuejie Ai
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
| | - Yang Liu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
| | - Jia Du
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Weiqiang Chen
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Zhanhui Lu
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Xiangke Wang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
- NAAM Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences, Soochow University, Suzhou 215123, P. R. China
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16
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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17
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Szefczyk B, Grabarek D, Walczak E, Andruniów T. Excited-state minima and emission energies of retinal chromophore analogues: Performance of CASSCF and CC2 methods as compared with CASPT2. J Comput Chem 2017; 38:1799-1810. [PMID: 28512740 DOI: 10.1002/jcc.24821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/10/2017] [Accepted: 04/13/2017] [Indexed: 11/08/2022]
Abstract
This study provides gas-phase S1 excited-state geometries along with emission and adiabatic energies for methylated/demethylated and ring-locked analogues of protonated Schiff base retinal models comprising system of five conjugated double bonds (PSB5), using second order multiconfiguration perturbation theory (CASPT2). CASPT2 results serve as reference data to assess the performance of CC2 (second-order approximate coupled cluster singles and doubles) and a commonly used CASSCF/CASPT2 protocol, that is, complete active space self-consistent field (CASSCF) geometry optimization followed by CASPT2 energy calculation. We find that the CASSCF methodology fails to locate planar S1 minimum energy structures for four out of five investigated planar models in contrast to CC2 and CASPT2 methods. However, for those which were found: one planar and two twisted minima, there is an excellent agreement between CASSCF and CASPT2 results in terms of geometrical parameters, one-electron properties, as well as emission and adiabatic energies. CC2 performs well for in-plane S1 minima and their spectroscopic and electronic properties. However, this picture deteriorates for twisted minima. As expected, the CC2 description of the S2 electronic state, with strong multireference and significant double excitation character, is very poor, exhibiting errors in transition energies exceeding 1 eV. They may be substantially diminished by recalculating transition energies with CASPT2 method. Our work shows that CASSCF/CASPT2 and CC2 shortcomings may influence gas-phase retinal analogues' excited state description in a dramatic way. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Borys Szefczyk
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Dawid Grabarek
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Elżbieta Walczak
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, Wroclaw, 50-370, Poland
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18
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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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19
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Ai Y, Xia S, Liao RZ. Theoretical Studies on the Photochemistry of Pentose Aminooxazoline, a Hypothetical Intermediate Product in the Prebiotic Synthetic Scenario of RNA Nucleotides. J Phys Chem B 2016; 120:9329-37. [PMID: 27525736 DOI: 10.1021/acs.jpcb.6b06061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
2-Aminooxazole is generally considered a prebiotic precursor of ribonucleotides on the early earth. Its pentose compound, pentose aminooxazoline, has been suggested to be a key intermediate in the prebiotic synthetic scenario. In this article, detailed mechanism of the photochemistry of pentose aminooxazoline has been studied by performing density functional theory and multireference complete active space self-consistent field calculations. Parallel to the "ring-puckering" process, which leads to ultrafast nonradiative deactivation, several other photodissociation channels are explored in detail. In addition, the influences of the pentose structure and solvation effects with both implicit and explicit water models have been uncovered for both neutral and protonated forms. The current theoretical results provide very important information not only for the photostability of RNA nucleotides but also for an in-depth understanding of the synthesis of other prebiotic nucleotides.
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Affiliation(s)
- Yuejie Ai
- School of Environmental and Chemical Engineering, North China Electric Power University , Beijing 102206, China
| | - Shuhua Xia
- College of Life and Environmental Science, Minzu University of China , Beijing 100081, China
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
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Grabarek D, Walczak E, Andruniów T. Assessing the Accuracy of Various Ab Initio Methods for Geometries and Excitation Energies of Retinal Chromophore Minimal Model by Comparison with CASPT3 Results. J Chem Theory Comput 2016; 12:2346-56. [DOI: 10.1021/acs.jctc.6b00108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dawid Grabarek
- Advanced Materials Engineering
and Modelling Group, Wroclaw University of Technology, Wyb. Wyspianskiego
27, 50-370 Wroclaw, Poland
| | - Elżbieta Walczak
- Advanced Materials Engineering
and Modelling Group, Wroclaw University of Technology, Wyb. Wyspianskiego
27, 50-370 Wroclaw, Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering
and Modelling Group, Wroclaw University of Technology, Wyb. Wyspianskiego
27, 50-370 Wroclaw, Poland
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21
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Tuna D, Lefrancois D, Wolański Ł, Gozem S, Schapiro I, Andruniów T, Dreuw A, Olivucci M. Assessment of Approximate Coupled-Cluster and Algebraic-Diagrammatic-Construction Methods for Ground- and Excited-State Reaction Paths and the Conical-Intersection Seam of a Retinal-Chromophore Model. J Chem Theory Comput 2015; 11:5758-81. [PMID: 26642989 DOI: 10.1021/acs.jctc.5b00022] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
As a minimal model of the chromophore of rhodopsin proteins, the penta-2,4-dieniminium cation (PSB3) poses a challenging test system for the assessment of electronic-structure methods for the exploration of ground- and excited-state potential-energy surfaces, the topography of conical intersections, and the dimensionality (topology) of the branching space. Herein, we report on the performance of the approximate linear-response coupled-cluster method of second order (CC2) and the algebraic-diagrammatic-construction scheme of the polarization propagator of second and third orders (ADC(2) and ADC(3)). For the ADC(2) method, we considered both the strict and extended variants (ADC(2)-s and ADC(2)-x). For both CC2 and ADC methods, we also tested the spin-component-scaled (SCS) and spin-opposite-scaled (SOS) variants. We have explored several ground- and excited-state reaction paths, a circular path centered around the S1/S0 surface crossing, and a 2D scan of the potential-energy surfaces along the branching space. We find that the CC2 and ADC methods yield a different dimensionality of the intersection space. While the ADC methods yield a linear intersection topology, we find a conical intersection topology for the CC2 method. We present computational evidence showing that the linear-response CC2 method yields a surface crossing between the reference state and the first response state featuring characteristics that are expected for a true conical intersection. Finally, we test the performance of these methods for the approximate geometry optimization of the S1/S0 minimum-energy conical intersection and compare the geometries with available data from multireference methods. The present study provides new insight into the performance of linear-response CC2 and polarization-propagator ADC methods for molecular electronic spectroscopy and applications in computational photochemistry.
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Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, University of Heidelberg , 69120 Heidelberg, Germany
| | - Łukasz Wolański
- Department of Chemistry, Wrocław University of Technology , 50370 Wrocław, Poland
| | - Samer Gozem
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Igor Schapiro
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504 , Strasbourg 67034, France
| | - Tadeusz Andruniów
- Department of Chemistry, Wrocław University of Technology , 50370 Wrocław, Poland
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, University of Heidelberg , 69120 Heidelberg, Germany
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States.,Dipartimento di Biotecnologie, Chimica e Farmacia, Universitá de Siena , 53100 Siena, Italy
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22
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Valsson O, Filippi C, Casida ME. Regarding the use and misuse of retinal protonated Schiff base photochemistry as a test case for time-dependent density-functional theory. J Chem Phys 2015; 142:144104. [DOI: 10.1063/1.4916354] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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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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Gozem S, Melaccio F, Lindh R, Krylov AI, Granovsky AA, Angeli C, Olivucci M. Mapping the Excited State Potential Energy Surface of a Retinal Chromophore Model with Multireference and Equation-of-Motion Coupled-Cluster Methods. J Chem Theory Comput 2013; 9:4495-506. [DOI: 10.1021/ct400460h] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Federico Melaccio
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, I-53100 Siena, Italy
| | - Roland Lindh
- Department
of Chemistry, Ångström, the Theoretical Chemistry Programme, POB 518, SE-751 20 Uppsala, Sweden
| | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | | | - Celestino Angeli
- Dipartimento
di Chimica, Università di Ferrara, via Borsari 46, I-44121 Ferrara, Italy
| | - 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
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25
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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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26
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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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27
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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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28
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Gozem S, Krylov AI, Olivucci M. Conical Intersection and Potential Energy Surface Features of a Model Retinal Chromophore: Comparison of EOM-CC and Multireference Methods. J Chem Theory Comput 2012; 9:284-92. [DOI: 10.1021/ct300759z] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samer Gozem
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
| | - Anna I. Krylov
- Department of Chemistry, University
of Southern California, Los Angeles, California 90089-0482, United
States
| | - Massimo Olivucci
- Department of Chemistry, 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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29
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Gozem S, Huntress M, Schapiro I, Lindh R, Granovsky AA, Angeli C, Olivucci M. Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model. J Chem Theory Comput 2012; 8:4069-80. [DOI: 10.1021/ct3003139] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samer Gozem
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
| | - Mark Huntress
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Department of Chemistry, Bowling
Green State University, Bowling Green, Ohio 43403, United States
| | - Roland Lindh
- Department of Chemistry −
Ångström, the Theoretical Chemistry Programme, POB 518,
SE-751 20 Uppsala, Sweden
| | | | - Celestino Angeli
- Dipartimento di
Chimica, Università
di Ferrara, via Borsari 46, I-44121 Ferrara, Italy
| | - Massimo Olivucci
- Department of Chemistry, 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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30
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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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31
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Fazzi D, Grancini G, Maiuri M, Brida D, Cerullo G, Lanzani G. Ultrafast internal conversion in a low band gap polymer for photovoltaics: experimental and theoretical study. Phys Chem Chem Phys 2012; 14:6367-74. [DOI: 10.1039/c2cp23917e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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A computational approach to the electronic and optical properties of Ru(II) and Ir(III) polypyridyl complexes: Applications to DSC, OLED and NLO. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2011.03.008] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Conte AM, Guidoni L, Del Sole R, Pulci O. Many-body study of the photoisomerization of the minimal model of the retinal protonated Schiff base. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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34
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Sun QC, Liu JY, Hao Y, Yang XC. Volume-conserved Twist Excited-state of π-Conjugated Molecules. CHINESE J CHEM PHYS 2010. [DOI: 10.1088/1674-0068/23/06/637-642] [Citation(s) in RCA: 2] [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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35
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Valsson O, Filippi C. Photoisomerization of Model Retinal Chromophores: Insight from Quantum Monte Carlo and Multiconfigurational Perturbation Theory. J Chem Theory Comput 2010. [DOI: 10.1021/ct900692y] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Omar Valsson
- Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Claudia Filippi
- Faculty of Science and Technology and MESA+ Research Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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36
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Schapiro I, Ryazantsev MN, Ding WJ, Huntress MM, Melaccio F, Andruniow T, Olivucci M. Computational Photobiology and Beyond. Aust J Chem 2010. [DOI: 10.1071/ch09563] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.
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Adrover M, Frau J, Caldés C, Vilanova B, Donoso J, Muñoz F. Theoretical and experimental study of the vertical excitation energies in the ionic and tautomeric forms of 4-aminomethylpyridine. J Photochem Photobiol A Chem 2010. [DOI: 10.1016/j.jphotochem.2009.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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38
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Sumita M, Ryazantsev MN, Saito K. Acceleration of the Z to E photoisomerization of penta-2,4-dieniminium by hydrogen out-of-plane motion: theoretical study on a model system of retinal protonated Schiff base. Phys Chem Chem Phys 2009; 11:6406-14. [PMID: 19809672 DOI: 10.1039/b900882a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the result of comparison between two reaction coordinates [on the potential energy surface of the first excited state (S(1))] produced by CASSCF and these energies recalculated by MRMP2 in the Z to E photoisomerization of penta-2,4-dieniminium (PDI) as the minimal model of the retinal protonated Schiff base (RPSB). One coordinate is the S(1) state minimum-energy-path (MEP) in mass-weighted coordinates from the S(1) vertically excited point, where a strong hydrogen-out-of plane (HOOP) motion is not exhibited. The energy profile of the S(1) MEP at the MRMP2//CASSCF level shows a barrier for the rotation around the reactive C-C and hits the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by 65 degrees . The other coordinate is an S(1) coordinate obtained by the relaxed scan strategy. The relaxed coordinate along the central C-C-C-C dihedral angle, which we call the HOOP coordinate, shows strong HOOP motion. According to the MRMP2//CASSCF calculation, there is no barrier on the HOOP coordinate. Furthermore, the S(1) to S(0) transition may be possible without the large skeletal deformation by HOOP motion because the HOOP coordinate encounters the S(1)/S(0) degeneracy space where the central C-C-C-C dihedral angle is distorted by only 40 degrees . Consequently, if PDI is a suitable model molecule for the RPSB as often assumed, the 11-cis to all-trans photoisomerization is predicted to be accelerated by the HOOP motion.
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Affiliation(s)
- Masato Sumita
- Department of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, 305-8571, Japan
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39
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Keal TW, Wanko M, Thiel W. Assessment of semiempirical methods for the photoisomerisation of a protonated Schiff base. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0546-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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40
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Ortiz-Sánchez JM, Gelabert R, Moreno M, Lluch JM. Electronic-structure and quantum dynamical study of the photochromism of the aromatic Schiff base salicylideneaniline. J Chem Phys 2008; 129:214308. [DOI: 10.1063/1.3032215] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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41
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De Angelis F, Fantacci S, Selloni A. Alignment of the dye's molecular levels with the TiO(2) band edges in dye-sensitized solar cells: a DFT-TDDFT study. NANOTECHNOLOGY 2008; 19:424002. [PMID: 21832662 DOI: 10.1088/0957-4484/19/42/424002] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a theoretical study of the lineup of the LUMO of Ru(II)-polypyridyl (N3 and N719) molecular dyes with the conduction band edge of a TiO(2) anatase nanoparticle. We use density functional theory (DFT) and the Car-Parrinello scheme for efficient optimization of the dye-nanoparticle systems, followed by hybrid B3LYP functional calculations of the electronic structure and time-dependent DFT (TDDFT) determination of the lowest vertical excitation energies. The electronic structure and TDDFT calculations are performed in water solution, using a continuum model. Various approximate procedures to compute the excited state oxidation potential of dye sensitizers are discussed. Our calculations show that the level alignment for the interacting nanoparticle-sensitizer system is very similar, within about 0.1 eV, to that for the separated TiO(2) and dye. The excellent agreement of our results with available experimental data indicates that the approach of this work could be used as an efficient predictive tool to help the optimization of dye-sensitized solar cells.
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Affiliation(s)
- Filippo De Angelis
- Istituto CNR di Scienze e Tecnologie Molecolari (ISTM-CNR), c/o Dipartimento di Chimica, Università di Perugia, Via elce di Sotto 8, I-06213 Perugia, Italy
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Abstract
Functions of biologically active molecules are frequently initiated by elementary chemical reactions such as energy and electron transfer, cis-trans isomerizations, and proton transfer. The nature of these reactions generally makes them very fast and efficient, occurring on picosecond and femtosecond timescales. Ultrafast spectroscopy has played an important role in the study of a number of biological processes and has provided unique information about several of nature's responses to light. Here I review the current understanding of light-energy collection and conversion in photosynthesis, the function of carotenoid molecules in photosynthesis, and the primary light-initiated reactions of the photoreceptors rhodopsin, bacteriorhodopsin, photoactive yellow protein, phytochrome, and a new type of blue-light receptor based on flavin chromophores.
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Affiliation(s)
- Villy Sundström
- Department of Chemical Physics, Lund University, S-221 00 Lund, Sweden.
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43
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Röhrig UF, Sebastiani D. NMR Chemical Shifts of the Rhodopsin Chromophore in the Dark State and in Bathorhodopsin: A Hybrid QM/MM Molecular Dynamics Study. J Phys Chem B 2008; 112:1267-74. [DOI: 10.1021/jp075662q] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ute F. Röhrig
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Sebastiani
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Cordova F, Doriol LJ, Ipatov A, Casida ME, Filippi C, Vela A. Troubleshooting time-dependent density-functional theory for photochemical applications: Oxirane. J Chem Phys 2007; 127:164111. [DOI: 10.1063/1.2786997] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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LÜ LL, LIU XW, YUAN K, WANG YC, WANG HQ. Spin-orbit Coupling and Intersystem Crossing in 4H-Pyran-4-thione: CASSCF//TD-B3LYP Study. CHINESE J CHEM 2007. [DOI: 10.1002/cjoc.200790270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hoffmann M, Wanko M, Strodel P, König PH, Frauenheim T, Schulten K, Thiel W, Tajkhorshid E, Elstner M. Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc 2007; 128:10808-18. [PMID: 16910676 DOI: 10.1021/ja062082i] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of color tuning in the rhodopsin family of proteins has been studied by comparing the optical properties of the light-driven proton pump bacteriorhodopsin (bR) and the light detector sensory rhodopsin II (sRII). Despite a high structural similarity, the maximal absorption is blue-shifted from 568 nm in bR to 497 nm in sRII. The molecular mechanism of this shift is still a matter of debate, and its clarification sheds light onto the general mechanisms of color tuning in retinal proteins. The calculations employ a combined quantum mechanical/molecular mechanical (QM/MM) technique, using a DFT-based method for ground state properties and the semiempirical OM2/MRCI method and ab initio SORCI method for excited state calculations. The high efficiency of the methodology has allowed us to study a wide variety of aspects including dynamical effects. The absorption shift as well as various mutation experiments and vibrational properties have been successfully reproduced. Our results indicate that several sources contribute to the spectral shift between bR and sRII. The main factors are the counterion region at the extracellular side of retinal and the amino acid composition of the binding pocket. Our analysis allows a distinction and identification of the different effects in detail and leads to a clear picture of the mechanism of color tuning, which is in good agreement with available experimental data.
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Affiliation(s)
- Michael Hoffmann
- Theoretische Physik, Universität Paderborn, Warburger Str. 100, 33098 Paderborn, Germany
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Coto PB, Sinicropi A, De Vico L, Ferré N, Olivucci M. Characterization of the conical intersection of the visual pigment rhodopsin at the CASPT2//CASSCF/AMBER level of theory. Mol Phys 2007. [DOI: 10.1080/00268970500415865] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- P. B. Coto
- a Dipartimento di Chimica , Università di Siena , Via Aldo Moro I-53100 Siena, Italy
| | - A. Sinicropi
- a Dipartimento di Chimica , Università di Siena , Via Aldo Moro I-53100 Siena, Italy
| | - L. De Vico
- b Department of Theoretical Chemistry , Lund University , Chemical Centre, P.O. Box 124, S-221 00 Lund, Sweden
| | - N. Ferré
- c Laboratoire de Chimie Théorique et de Modélisation Moléculaire , Unité Mixte de Recherche 6517, Université de Provence , Case 521, Faculté de Saint Jérôme, 13397 Marseille Cedex 20, France
| | - M. Olivucci
- a Dipartimento di Chimica , Università di Siena , Via Aldo Moro I-53100 Siena, Italy
- d Centro per lo Studio dei Sistemi Complessi , Via Tommaso Pendola 37, I-53100 , Siena, Italy
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Spezia R, Burghardt I, Hynes JT. Conical intersections in solution: non-equilibrium versus equilibrium solvation. Mol Phys 2007. [DOI: 10.1080/00268970500417895] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Riccardo Spezia
- a Département de Chimie , Ecole Normale Supérieure , 24 rue Lhomond, F-75231 Paris cedex 05, France
| | - Irene Burghardt
- a Département de Chimie , Ecole Normale Supérieure , 24 rue Lhomond, F-75231 Paris cedex 05, France
| | - James T. Hynes
- a Département de Chimie , Ecole Normale Supérieure , 24 rue Lhomond, F-75231 Paris cedex 05, France
- b Department of Chemistry and Biochemistry , University of Colorado , Boulder, CO 80309-0215, USA
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De Angelis F, Fantacci S, Sgamellotti A. An integrated computational tool for the study of the optical properties of nanoscale devices: application to solar cells and molecular wires. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0224-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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