1
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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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2
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Toldo JM, Mattos RS, Pinheiro M, Mukherjee S, Barbatti M. Recommendations for Velocity Adjustment in Surface Hopping. J Chem Theory Comput 2024; 20:614-624. [PMID: 38207213 DOI: 10.1021/acs.jctc.3c01159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
This study investigates velocity adjustment directions after hopping in surface hopping dynamics. Using fulvene and a protonated Schiff base (PSB4) as case studies, we investigate the population decay and reaction yields of different sets of dynamics with the velocity adjusted in either the nonadiabatic coupling, gradient difference, or momentum directions. For the latter, in addition to the conventional algorithm, we investigated the performance of a reduced kinetic energy reservoir approach recently proposed. Our evaluation also considered velocity adjustment in the directions of approximate nonadiabatic coupling vectors. While results for fulvene are susceptible to the adjustment approach, PSB4 is not. We correlated this dependence to the topography near the conical intersections. When nonadiabatic coupling vectors are unavailable, the gradient difference direction is the best adjustment option. If the gradient difference is also unavailable, a semiempirical vector direction or the momentum direction with a reduced kinetic energy reservoir becomes an excellent option to prevent an artificial excess of back hoppings. The precise velocity adjustment direction is less crucial for describing the nonadiabatic dynamics than the kinetic energy reservoir's size.
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Affiliation(s)
- Josene M Toldo
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | - Rafael S Mattos
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | - Max Pinheiro
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | | | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
- Institut Universitaire de France, Paris 75231, France
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3
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Barneschi L, Kaliakin D, Huix-Rotllant M, Ferré N, Filatov Gulak M, Olivucci M. Assessment of the Electron Correlation Treatment on the Quantum-Classical Dynamics of Retinal Protonated Schiff Base Models: XMS-CASPT2, RMS-CASPT2, and REKS Methods. J Chem Theory Comput 2023; 19:8189-8200. [PMID: 37937990 DOI: 10.1021/acs.jctc.3c00879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
We compare the performance of three different multiconfigurational wave function-based electronic structure methods and two implementations of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method. The study is characterized by three features: (i) it uses a small set of quantum-classical trajectories rather than potential energy surface mapping, (ii) it focuses, exclusively, on the photoisomerization of retinal protonated Schiff base models, and (iii) it probes the effect of both methyl substitution and the increase in length of the conjugate π-system. For each tested method, the corresponding analytical gradients are used to drive the quantum-classical (Tully's FSSH method) trajectory propagation, including the recent multistate XMS-CASPT2 and RMS-CASPT2 gradients. It is shown that while CASSCF, XMS-CASPT2, and RMS-CASPT2 yield consistent photoisomerization dynamics descriptions, REKS produces, in some of these systems, qualitatively different behavior that is attributed to a flatter and topographically different excited state potential energy surface. The origin of this behavior can be traced back to the effect of the employed density functional approximation. The above studies are further expanded by benchmarking, at the CASSCF and REKS levels, the electronic structure methods using a QM/MM model of the visual pigment rhodopsin.
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Affiliation(s)
- Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
| | - Danil Kaliakin
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Miquel Huix-Rotllant
- Aix-Marseille Université, CNRS, Institut Chimie Radicalaire, 13013 Marseille, France
| | - Nicolas Ferré
- Aix-Marseille Université, CNRS, Institut Chimie Radicalaire, 13013 Marseille, France
| | - Michael Filatov Gulak
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
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4
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Sirimatayanant S, Andruniów T. Benchmarking two-photon absorption strengths of rhodopsin chromophore models with CC3 and CCSD methodologies: An assessment of popular density functional approximations. J Chem Phys 2023; 158:094106. [PMID: 36889953 DOI: 10.1063/5.0135594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
This work presents the investigations of the impact of an increasing electron correlation in the hierarchy of coupled-cluster methods, i.e., CC2, CCSD, and CC3, on two-photon absorption (2PA) strengths for the lowest excited state of the minimal rhodopsin's chromophore model-cis-penta-2,4-dieniminium cation (PSB3). For a larger chromophore's model [4-cis-hepta-2,4,6-trieniminium cation (PSB4)], CC2 and CCSD calculations of 2PA strengths were performed. Additionally, 2PA strengths predicted by some popular density functional theory (DFT) functionals differing in HF exchange contribution were assessed against the reference CC3/CCSD data. For PSB3, the accuracy of 2PA strengths increases in the following order: CC2 < CCSD < CC3, with the CC2 deviation from both higher-level methods exceeding 10% at 6-31+G* basis sets and 2% at aug-cc-pVDZ basis set. However, for PSB4, this trend is reversed and CC2-based 2PA strength is larger than the corresponding CCSD value. Among the DFT functionals investigated, CAM-B3LYP and BHandHLYP provide 2PA strengths in best compliance with reference data, however, with the error approaching an order of magnitude.
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Affiliation(s)
- Saruti Sirimatayanant
- Institute of Advanced Materials, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Tadeusz Andruniów
- Institute of Advanced Materials, Department of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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5
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Hricovíni M, Asher JR, Hricovíni M. A study of the photochemical behaviour and relaxation mechanisms of anti– syn isomerisation around quinazolinone –N–N bonds. RSC Adv 2022; 12:27442-27452. [DOI: 10.1039/d2ra04529j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/17/2022] [Indexed: 11/21/2022] Open
Abstract
High-resolution NMR experiments revealed that differently substituted quinazolinone-based Schiff bases undergo anti to syn isomerisation on exposure to ultraviolet light in DMSO solution.
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Affiliation(s)
- Michal Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovak Republic
| | - James R. Asher
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 36 Bratislava, Slovak Republic
- Faculty of Natural Sciences, Department of Inorganic Chemistry, Comenius University, Mlynská Dolina, CH2, 84215, Bratislava, Slovak Republic
| | - Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovak Republic
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Marefat Khah A, Grimmelsmann L, Knorr J, Nuernberger P, Hättig C. How a linear triazene photoisomerizes in a volume-conserving fashion. Phys Chem Chem Phys 2018; 20:28075-28087. [PMID: 30383059 DOI: 10.1039/c8cp05208e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding deactivation mechanisms of functional groups is a key step to design novel photo-active devices and molecular imaging agents. Here, we elucidate the photochemistry of linear triazenes, an extended analogue of the photo-switchable azo group, exemplarily for the widely used DNA-minor-groove binder berenil. Combining ultrafast spectroscopy and ab initio calculations unveils that the E-azo,s-trans structure of berenil predominates in the gas phase and in aqueous solution, and ADC(2) intrinsic reaction coordinate calculations disclose that the excited-state relaxation to the S1 minima/conical intersections follows a two-step mechanism: N[double bond, length as m-dash]N bond stretching followed by a bicycle-pedal rotation in the triazene bridge. Furthermore, studying the ground-state pathways shows that a fraction of the molecules relaxes back to the E-azo,s-trans isomer while the other part photoisomerizes to the Z-azo,s-trans via a hula-twist motion, as evidenced by experimental quantum yields of Φ ≈ 0.5 found for berenil in water, ethylene glycol, or bound to β-trypsin. Moreover, our studies show that while the excited-state relaxation is insensitive to the environment, the ground-state dynamics depend on biomolecular binding partners.
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7
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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8
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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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9
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Schapiro I. The Origin of Bond Selectivity and Excited-State Reactivity in Retinal Analogues. J Phys Chem A 2016; 120:3353-65. [DOI: 10.1021/acs.jpca.6b00701] [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)
- Igor Schapiro
- Fritz Haber
Center for Molecular
Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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10
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Eng J, Daniel C. Structural Properties and UV–Visible Absorption Spectroscopy of Retinal-pyridyl-CN Re(I) Carbonyl Bipyridine Complex: A Theoretical Study. J Phys Chem A 2015; 119:10645-53. [DOI: 10.1021/acs.jpca.5b08047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julien Eng
- Laboratoire de Chimie Quantique,
Institut de Chimie Strasbourg, UMR-7177 CNRS/Université de Strasbourg 1 Rue Blaise Pascal BP 296/R8, F-67008 STRASBOURG, France
| | - Chantal Daniel
- Laboratoire de Chimie Quantique,
Institut de Chimie Strasbourg, UMR-7177 CNRS/Université de Strasbourg 1 Rue Blaise Pascal BP 296/R8, F-67008 STRASBOURG, France
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11
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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12
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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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13
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Punwong C, Owens J, Martínez TJ. Direct QM/MM Excited-State Dynamics of Retinal Protonated Schiff Base in Isolation and Methanol Solution. J Phys Chem B 2014; 119:704-14. [DOI: 10.1021/jp5038798] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chutintorn Punwong
- Department
of Physics, Faculty of Science, and Trace
Analysis and Biosensor Research Center, Prince of Songkla University, Songkhla 90112, Thailand
| | - Jane Owens
- Department
of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, United States
| | - Todd J. Martínez
- Department
of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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14
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An overview of nonadiabatic dynamics simulations methods, with focus on the direct approach versus the fitting of potential energy surfaces. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1526-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Rivalta I, Nenov A, Garavelli M. Modelling retinal chromophores photoisomerization: from minimal models in vacuo to ultimate bidimensional spectroscopy in rhodopsins. Phys Chem Chem Phys 2014; 16:16865-79. [DOI: 10.1039/c3cp55211j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modelling of retinal photoisomerization in different environments is reviewed and ultimate ultrafast electronic spectroscopy is proposed for obtaining new insights.
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Affiliation(s)
- Ivan Rivalta
- Université de Lyon
- CNRS
- 69364 Lyon, Cedex 07, France
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
| | - Artur Nenov
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna, Italy
| | - Marco Garavelli
- Université de Lyon
- CNRS
- 69364 Lyon, Cedex 07, France
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
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16
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Álvarez R, Vaz B, Gronemeyer H, de Lera ÁR. Functions, therapeutic applications, and synthesis of retinoids and carotenoids. Chem Rev 2013; 114:1-125. [PMID: 24266866 DOI: 10.1021/cr400126u] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rosana Álvarez
- Departamento de Química Orgánica, Centro de Investigación Biomédica (CINBIO), and Instituto de Investigación Biomédica de Vigo (IBIV), Universidade de Vigo , 36310 Vigo, Spain
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17
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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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18
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Ultrafast photochemistry of anabaena sensory rhodopsin: experiment and theory. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:589-97. [PMID: 24099700 DOI: 10.1016/j.bbabio.2013.09.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/28/2013] [Accepted: 09/29/2013] [Indexed: 11/20/2022]
Abstract
Light induced isomerization of the retinal chromophore activates biological function in all retinal protein (RP) driving processes such as ion-pumping, vertebrate vision and phototaxis in organisms as primitive as archea, or as complex as mammals. This process and its consecutive reactions have been the focus of experimental and theoretical research for decades. The aim of this review is to demonstrate how the experimental and theoretical research efforts can now be combined to reach a more comprehensive understanding of the excited state process on the molecular level. Using the Anabaena Sensory Rhodopsin as an example we will show how contemporary time-resolved spectroscopy and recently implemented excited state QM/MM methods consistently describe photochemistry in retinal proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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19
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Ruckenbauer M, Barbatti M, Müller T, Lischka H. Nonadiabatic photodynamics of a retinal model in polar and nonpolar environment. J Phys Chem A 2013; 117:2790-9. [PMID: 23470211 PMCID: PMC3619535 DOI: 10.1021/jp400401f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The nonadiabatic photodynamics of
the all-trans-2,4-pentadiene-iminium cation (protonated
Schiff base 3, PSB3) and
the all-trans-3-methyl-2,4-pentadiene-iminium cation
(MePSB3) were investigated in the gas phase and in polar (aqueous)
and nonpolar (n-hexane) solutions by means of surface
hopping using a multireference configuration-interaction (MRCI) quantum
mechanical/molecular mechanics (QM/MM) level. Spectra, lifetimes for
radiationless deactivation to the ground state, and structural and
electronic parameters are compared. A strong influence of the polar
solvent on the location of the crossing seam, in particular in the
bond length alternation (BLA) coordinate, is found. Additionally,
inclusion of the polar solvent changes the orientation of the intersection
cone from sloped in the gas phase to peaked, thus enhancing considerably
its efficiency for deactivation of the molecular system to the ground
state. These factors cause, especially for MePSB3, a substantial decrease
in the lifetime of the excited state despite the steric inhibition
by the solvent.
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Affiliation(s)
- Matthias Ruckenbauer
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria
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20
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Vuković L, Burmeister CF, Král P, Groenhof G. Control Mechanisms of Photoisomerization in Protonated Schiff Bases. J Phys Chem Lett 2013; 4:1005-1011. [PMID: 26291368 DOI: 10.1021/jz400133u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We performed ab initio excited-state molecular dynamics simulations of a gas-phase photoexcited protonated Schiff base (C1-N2═C3-C4═C5-C6) to search for control mechanisms of its photoisomerization. The excited molecule twists by ∼90° around either the N2C3 bond or the C4C5 bond and relaxes to the ground electronic state through a conical intersection with either a trans or cis outcome. We show that a large initial distortion of several dihedral angles and a specific normal vibrational mode combining pyramidalization and double-bond twisting can lead to a preferential rotation of atoms around the C4C5 bond. We also show that selective pretwisting of several dihedral angles in the initial ground state thermal ensemble (by analogy to a protein pocket) can significantly increase the fraction of photoreactive (cis → trans) trajectories. We demonstrate that new ensembles with higher degrees of control over the photoisomerization reaction can be obtained by a computational directed evolution approach on the ensembles of molecules with the pretwisted geometries.
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Affiliation(s)
- Lela Vuković
- †Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Carl F Burmeister
- †Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | | | - Gerrit Groenhof
- †Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
- ∥Department of Chemistry and Nanoscience Center, University of Jyväskylä, P.O. Box 35 FI-40014 Jyväskylä, Finland
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21
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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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22
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Kaila VRI, Send R, Sundholm D. The effect of protein environment on photoexcitation properties of retinal. J Phys Chem B 2012; 116:2249-58. [PMID: 22166007 DOI: 10.1021/jp205918m] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Retinal is the photon absorbing chromophore of rhodopsin and other visual pigments, enabling the vertebrate vision process. The effects of the protein environment on the primary photoexcitation process of retinal were studied by time-dependent density functional theory (TDDFT) and the algebraic diagrammatic construction through second order (ADC(2)) combined with our recently introduced reduction of virtual space (RVS) approximation method. The calculations were performed on large full quantum chemical cluster models of the bluecone (BC) and rhodopsin (Rh) pigments with 165-171 atoms. Absorption wavelengths of 441 and 491 nm were obtained at the B3LYP level of theory for the respective models, which agree well with the experimental values of 414 and 498 nm. Electrostatic rather than structural strain effects were shown to dominate the spectral tuning properties of the surrounding protein. The Schiff base retinal and a neighboring Glu-113 residue were found to have comparable proton affinities in the ground state of the BC model, whereas in the excited state, the proton affinity of the Schiff base is 5.9 kcal/mol (0.26 eV) higher. For the ground and excited states of the Rh model, the proton affinity of the Schiff base is 3.2 kcal/mol (0.14 eV) and 7.9 kcal/mol (0.34 eV) higher than for Glu-113, respectively. The protein environment was found to enhance the bond length alternation (BLA) of the retinyl chain and blueshift the first absorption maxima of the protonated Schiff base in the BC and Rh models relative to the chromophore in the gas phase. The protein environment was also found to decrease the intensity of the second excited state, thus improving the quantum yield of the photoexcitation process. Relaxation of the BC model on the excited state potential energy surface led to a vanishing BLA around the isomerization center of the conjugated retinyl chain, rendering the retinal accessible for cis-trans isomerization. The energy of the relaxed excited state was found to be 30 kcal/mol (1.3 eV) above the minimum ground state energy, and might be related to the transition state of the thermal activation process.
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Affiliation(s)
- Ville R I Kaila
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Plasser F, Barbatti M, Aquino AJA, Lischka H. Electronically excited states and photodynamics: a continuing challenge. Theor Chem Acc 2012. [DOI: 10.1007/s00214-011-1073-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Klaffki N, Weingart O, Garavelli M, Spohr E. Sampling excited state dynamics: influence of HOOP mode excitations in a retinal model. Phys Chem Chem Phys 2012; 14:14299-305. [DOI: 10.1039/c2cp41994g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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25
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Lin L, Fan W, Chen S, Ma J, Hu W, Lin Y, Zhang H, Huang R. Photochromism of (E)-4-phenyl-1-(pyridine-2-ylmethylene)semicarbazide. NEW J CHEM 2012. [DOI: 10.1039/c2nj40468k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Li X, Chung LW, Morokuma K. Photodynamics of All-trans Retinal Protonated Schiff Base in Bacteriorhodopsin and Methanol Solution. J Chem Theory Comput 2011; 7:2694-8. [DOI: 10.1021/ct200549z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Lung Wa Chung
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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27
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Nenov A, de Vivie-Riedle R. Geometrical and substituent effects in conical intersections: Linking chemical structure and photoreactivity in polyenes. J Chem Phys 2011; 135:034304. [DOI: 10.1063/1.3608924] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Nonadiabatic dynamics with trajectory surface hopping method. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.64] [Citation(s) in RCA: 279] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Schapiro I, Ryazantsev MN, Frutos LM, Ferré N, Lindh R, Olivucci M. The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects. J Am Chem Soc 2011; 133:3354-64. [DOI: 10.1021/ja1056196] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Igor Schapiro
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Luis Manuel Frutos
- Departamento de Química Física, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Nicolas Ferré
- Laboratoire Chimie Provence UMR 6264, Université de Provence, Campus Saint Jérôme Case 521, 13397 Marseille Cedex 20, France
| | - Roland Lindh
- Department of Quantum Chemistry, Ångströmlab, Lägerhyddsv. 1, Box 518, 751 20 Uppsala University, Sweden
| | - Massimo Olivucci
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Chimica, Università degli Studi di Siena, via Aldo Moro 2, I-53100 Siena, Italy
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30
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Nenov A, Cordes T, Herzog TT, Zinth W, de Vivie-Riedle R. Molecular Driving Forces for Z/E Isomerization Mediated by Heteroatoms: The Example Hemithioindigo. J Phys Chem A 2010; 114:13016-30. [DOI: 10.1021/jp107899g] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Artur Nenov
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Thorben Cordes
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Teja T. Herzog
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Wolfgang Zinth
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
| | - Regina de Vivie-Riedle
- Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 11, D-81377 München, Germany, and BioMolecular Optics and Munich Center for Integrated Protein Science CIPSM, Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, D-80538 München, Germany
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31
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Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping. Proc Natl Acad Sci U S A 2010; 107:20172-7. [PMID: 21048087 DOI: 10.1073/pnas.1007000107] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantum mechanics/molecular mechanics calculations based on ab initio multiconfigurational second order perturbation theory are employed to construct a computer model of Bacteriorhodopsin that reproduces the observed static and transient electronic spectra, the dipole moment changes, and the energy stored in the photocycle intermediate K. The computed reaction coordinate indicates that the isomerization of the retinal chromophore occurs via a complex motion accounting for three distinct regimes: (i) production of the excited state intermediate I, (ii) evolution of I toward a conical intersection between the excited state and the ground state, and (iii) formation of K. We show that, during stage ii, a space-saving mechanism dominated by an asynchronous double bicycle-pedal deformation of the C10═C11─C12═C13─C14═N moiety of the chromophore dominates the isomerization. On this same stage a N─H/water hydrogen bond is weakened and initiates a breaking process that is completed during stage iii.
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Rostov IV, Amos RD, Kobayashi R, Scalmani G, Frisch MJ. Studies of the ground and excited-state surfaces of the retinal chromophore using CAM-B3LYP. J Phys Chem B 2010; 114:5547-55. [PMID: 20369810 DOI: 10.1021/jp911329g] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer (PSBT) is examined. Optimized structures on both the ground state and the excited state are calculated, and the dependence on torsional angles in the carbon chain is investigated. Time-dependent density functional theory is used to produce excitation energies and the excited-state surface. To avoid problems with the description of excited states that can arise with standard DFT methods, the CAM-B3LYP functional was used. Comparing CAM-B3LYP with B3LYP results indicates that the former is significantly more accurate, as a consequence of which detailed cross sections of the retinal excited-state surface are obtained.
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Affiliation(s)
- Ivan V Rostov
- Australian National University Supercomputer Facility, Mills Road, Canberra, ACT 0200, Australia
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Ruckenbauer M, Barbatti M, Müller T, Lischka H. Nonadiabatic Excited-State Dynamics with Hybrid ab Initio Quantum-Mechanical/Molecular-Mechanical Methods: Solvation of the Pentadieniminium Cation in Apolar Media. J Phys Chem A 2010; 114:6757-65. [DOI: 10.1021/jp103101t] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matthias Ruckenbauer
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria, Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Mario Barbatti
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria, Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Thomas Müller
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria, Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria, Institute of Advanced Simulation, Jülich Supercomputer Centre, Research Centre Jülich, D-52425 Jülich, Germany, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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34
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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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