1
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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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2
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Liu L, Fang WH, Martinez TJ. A Nitrogen Out-of-Plane (NOOP) Mechanism for Imine-Based Light-Driven Molecular Motors. J Am Chem Soc 2023; 145:6888-6898. [PMID: 36920260 DOI: 10.1021/jacs.3c00275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Light-driven molecular motors have generated considerable interest due to their potential applications in material and biological systems. Recently, Greb and Lehn reported a new class of molecular motors, chiral N-alkyl imines, which undergo unidirectional rotation induced by light and heat. The mechanism of unidirectional motion in molecular motors containing a C═N group has been assumed to consist of photoinduced torsion about the double bond. In this work, we present a computational study of the photoisomerization dynamics of a chiral N-alkyl imine motor. We find that the location and energetics of minimal energy conical intersections (MECIs) alone are insufficient to understand the mechanism of the motor. Furthermore, a key part of the mechanism consists of out-of-plane distortions of the N atom (followed by isomerization about the double bond). Dynamic effects and out-of-plane distortions are critical to understand the observed (rather low) quantum yield for photoisomerization. Our results provide hints as to how the photoisomerization quantum yield might be increased, improving the efficiency of this class of molecular motors.
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Affiliation(s)
- Lihong Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.,Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Todd J Martinez
- Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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3
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List NH, Jones CM, Martínez TJ. Internal conversion of the anionic GFP chromophore: in and out of the I-twisted S 1/S 0 conical intersection seam. Chem Sci 2022; 13:373-385. [PMID: 35126970 PMCID: PMC8729814 DOI: 10.1039/d1sc05849e] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/11/2021] [Indexed: 11/21/2022] Open
Abstract
The functional diversity of the green fluorescent protein (GFP) family is intimately connected to the interplay between competing photo-induced transformations of the chromophore motif, anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI-). Its ability to undergo Z/E-isomerization is of particular importance for super-resolution microscopy and emerging opportunities in optogenetics. Yet, key dynamical features of the underlying internal conversion process in the native HBDI- chromophore remain largely elusive. We investigate the intrinsic excited-state behavior of isolated HBDI- to resolve competing decay pathways and map out the factors governing efficiency and the stereochemical outcome of photoisomerization. Based on non-adiabatic dynamics simulations, we demonstrate that non-selective progress along the two bridge-torsional (i.e., phenolate, P, or imidazolinone, I) pathways accounts for the three decay constants reported experimentally, leading to competing ultrafast relaxation primarily along the I-twisted pathway and S1 trapping along the P-torsion. The majority of the population (∼70%) is transferred to S0 in the vicinity of two approximately enantiomeric minima on the I-twisted intersection seam (MECI-Is). Despite their sloped, reactant-biased topographies (suggesting low photoproduct yields), we find that decay through these intersections leads to products with a surprisingly high quantum yield of ∼30%. This demonstrates that E-isomer generation results at least in part from direct isomerization on the excited state. A photoisomerization committor analysis reveals a difference in intrinsic photoreactivity of the two MECI-Is and that the observed photoisomerization is the combined result of two effects: early, non-statistical dynamics around the less reactive intersection followed by later, near-statistical behavior around the more reactive MECI-I. Our work offers new insight into internal conversion of HBDI- that both establishes the intrinsic properties of the chromophore and enlightens principles for the design of chromophore derivatives and protein variants with improved photoswitching properties.
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Affiliation(s)
- Nanna H List
- Department of Chemistry and the PULSE Institute, Stanford University Stanford CA 94305 USA .,SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Chey M Jones
- Department of Chemistry and the PULSE Institute, Stanford University Stanford CA 94305 USA .,SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Todd J Martínez
- Department of Chemistry and the PULSE Institute, Stanford University Stanford CA 94305 USA .,SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
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4
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Liu Y, Zhu C. Trajectory surface hopping molecular dynamics simulations for retinal protonated Schiff-base photoisomerization. Phys Chem Chem Phys 2021; 23:23861-23874. [PMID: 34651159 DOI: 10.1039/d1cp03401d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Global switching trajectory surface hopping molecular dynamics simulations are performed using accurate on-the-fly (TD)CAM-B3LYP/6-31G potential energy surfaces to study retinal protonated Schiff-base photoisomerization up to S1 excitation. The simulations detected two-layer conical intersection networks: one is at an energy as high as 8 eV and the other is in the energy range around 3-4 eV. Six conical intersections within the low-layer energy region that correspond to active conical intersections under experimental conditions are found via the use of pairwise isomers, within which nonadiabatic molecular dynamics simulations are performed. Eight isomer products are populated with simulated sampling trajectories from which the simulated quantum yield in the gas phase is estimated to be 0.11 (0.08) moving from the all-trans isomer to the 11-cis (11-cis to all-trans) isomer in comparison with an experimental value of 0.09 (0.2) in the solution phase. Each conical intersection is related to one specific twist angle accompanying a related CC double bond motion during photoisomerization. Nonplanar distortion of the entire dynamic process has a significant role in the formation of the relevant photoisomerization products. The present simulation indicates that all hopping points show well-behaved potential energy surface topology, as calculated via the conventional TDDFT method, at conical intersections between S1 and S0 states. Therefore, the present nonadiabatic dynamics simulations with the TDDFT method are very encouraging for simulating various large systems related to retinal Schiff-base photoisomerization in the real world.
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Affiliation(s)
- Yuxiu Liu
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao-Tung University, Hsinchu 30010, Taiwan.
| | - Chaoyuan Zhu
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao-Tung University, Hsinchu 30010, Taiwan. .,Department of Applied Chemistry and Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
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5
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Matsika S. Electronic Structure Methods for the Description of Nonadiabatic Effects and Conical Intersections. Chem Rev 2021; 121:9407-9449. [PMID: 34156838 DOI: 10.1021/acs.chemrev.1c00074] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonadiabatic effects are ubiquitous in photophysics and photochemistry, and therefore, many theoretical developments have been made to properly describe them. Conical intersections are central in nonadiabatic processes, as they promote efficient and ultrafast nonadiabatic transitions between electronic states. A proper theoretical description requires developments in electronic structure and specifically in methods that describe conical intersections between states and nonadiabatic coupling terms. This review focuses on the electronic structure aspects of nonadiabatic processes. We discuss the requirements of electronic structure methods to describe conical intersections and nonadiabatic couplings, how the most common excited state methods perform in describing these effects, and what the recent developments are in expanding the methodology and implementing nonadiabatic couplings.
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Affiliation(s)
- Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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6
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Pieroni C, Marsili E, Lauvergnat D, Agostini F. Relaxation dynamics through a conical intersection: Quantum and quantum-classical studies. J Chem Phys 2021; 154:034104. [PMID: 33499611 DOI: 10.1063/5.0036726] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We study the relaxation process through a conical intersection of a photo-excited retinal chromophore model. The analysis is based on a two-electronic-state two-dimensional Hamiltonian developed by Hahn and Stock [J. Phys. Chem. B 104 1146 (2000)] to reproduce, with a minimal model, the main features of the 11-cis to all-trans isomerization of the retinal of rhodopsin. In particular, we focus on the performance of various trajectory-based schemes to nonadiabatic dynamics, and we compare quantum-classical results to the numerically exact quantum vibronic wavepacket dynamics. The purpose of this work is to investigate, by analyzing electronic and nuclear observables, how the sampling of initial conditions for the trajectories affects the subsequent dynamics.
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Affiliation(s)
- Carlotta Pieroni
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Emanuele Marsili
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
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7
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Marsili E, Olivucci M, Lauvergnat D, Agostini F. Quantum and Quantum-Classical Studies of the Photoisomerization of a Retinal Chromophore Model. J Chem Theory Comput 2020; 16:6032-6048. [PMID: 32931266 DOI: 10.1021/acs.jctc.0c00679] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report an in-depth analysis of the photo-induced isomerization of the 2-cis-penta-2,4-dieniminium cation: a minimal model of the 11-cis retinal protonated Schiff base chromophore of the dim-light photoreceptor rhodopsin. Based on recently developed three-dimensional potentials parametrized on ab initio multi-state multi-configurational second-order perturbation theory data, we perform quantum-dynamical studies. In addition, simulations based on various quantum-classical methods, among which Tully surface hopping and the coupled-trajectory approach derived from the exact factorization, allow us to validate their performance against vibronic wavepacket propagation and, therefore, a purely quantum treatment. Quantum-dynamics results uncover qualitative differences with respect to the two-dimensional Hahn-Stock potentials, widely used as model potentials for the isomerization of the same chromophore, due to the increased dimensionality and three-mode correlation. Quantum-classical simulations show, instead, that three-dimensional model potentials are capable of capturing a number of features revealed by atomistic simulations and experimental observations. In particular, a recently reported vibrational phase relationship between double-bond torsion and hydrogen-out-of-plane modes critical for rhodopsin isomerization efficiency is correctly reproduced.
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Affiliation(s)
- Emanuele Marsili
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France.,Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
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8
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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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9
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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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10
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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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11
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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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12
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Migani A, Blancafort L. Excitonic Interfacial Proton-Coupled Electron Transfer Mechanism in the Photocatalytic Oxidation of Methanol to Formaldehyde on TiO2(110). J Am Chem Soc 2016; 138:16165-16173. [DOI: 10.1021/jacs.6b11067] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Annapaola Migani
- Catalan
Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Lluís Blancafort
- Institut
de Química Computacional i Catàlisi and Departament
de Química, Facultat de Ciències, Universitat de Girona, C/M. A. Campmany 69, 17003 Girona, Spain
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13
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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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14
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Manathunga M, Yang X, Luk HL, Gozem S, Frutos LM, Valentini A, Ferrè N, Olivucci M. Probing the Photodynamics of Rhodopsins with Reduced Retinal Chromophores. J Chem Theory Comput 2016; 12:839-50. [PMID: 26640959 DOI: 10.1021/acs.jctc.5b00945] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While the light-induced population dynamics of different photoresponsive proteins has been investigated spectroscopically, systematic computational studies have not yet been possible due to the phenomenally high cost of suitable high level quantum chemical methods and the need of propagating hundreds, if not thousands, of nonadiabatic trajectories. Here we explore the possibility of studying the photodynamics of rhodopsins by constructing and investigating quantum mechanics/molecular mechanics (QM/MM) models featuring reduced retinal chromophores. In order to do so we use the sensory rhodopsin found in the cyanobacterium Anabaena PCC7120 (ASR) as a benchmark system. We find that the basic mechanistic features associated with the excited state dynamics of ASR QM/MM models are reproduced using models incorporating a minimal (i.e., three double-bond) chromophore. Furthermore, we show that ensembles of nonadiabatic ASR trajectories computed using the same abridged models replicate, at both the CASPT2 and CASSCF levels of theory, the trends in spectroscopy and lifetimes estimated using unabridged models and observed experimentally at room temperature. We conclude that a further expansion of these studies may lead to low-cost QM/MM rhodopsin models that may be used as effective tools in high-throughput in silico mutant screening.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Hoi Ling Luk
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Samer Gozem
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Luis Manuel Frutos
- Departamento de Química Física, Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid, Spain
| | - Alessio Valentini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena , via A. Moro 2, I-53100 Siena, Siena, Italy.,Departamento de Química Física, Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid, Spain
| | - Nicolas Ferrè
- Aix-Marseille Université, CNRS, Institut de Chimie Radicalaire, 13397 Marseille, Cedex 20, France
| | - 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, Siena, Italy.,University of Strasbourg Institute for Advanced Studies, 5, allée du Général Rouvillois, F-67083 Strasbourg, France
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15
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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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16
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Aquilante F, Autschbach J, Carlson RK, Chibotaru LF, Delcey MG, De Vico L, Fdez Galván I, Ferré N, Frutos LM, Gagliardi L, Garavelli M, Giussani A, Hoyer CE, Li Manni G, Lischka H, Ma D, Malmqvist PÅ, Müller T, Nenov A, Olivucci M, Pedersen TB, Peng D, Plasser F, Pritchard B, Reiher M, Rivalta I, Schapiro I, Segarra-Martí J, Stenrup M, Truhlar DG, Ungur L, Valentini A, Vancoillie S, Veryazov V, Vysotskiy VP, Weingart O, Zapata F, Lindh R. Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table. J Comput Chem 2015; 37:506-41. [PMID: 26561362 DOI: 10.1002/jcc.24221] [Citation(s) in RCA: 1105] [Impact Index Per Article: 122.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 12/17/2022]
Abstract
In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
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Affiliation(s)
- Francesco Aquilante
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden.,Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York, 14260-3000, USA
| | - Rebecca K Carlson
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA
| | - Liviu F Chibotaru
- Division of Quantum and Physical Chemistry, and INPAC, Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven Celestijnenlaan, 200F, 3001, Belgium
| | - Mickaël G Delcey
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden
| | - Luca De Vico
- Department of Chemistry, Copenhagen University, Universitetsparken 5, Copenhagen Ø, 2100, Denmark
| | - Ignacio Fdez Galván
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden.,Uppsala Center for Computational Chemistry - UC3, Uppsala University, Box 518, Uppsala, 751 20, Sweden
| | - Nicolas Ferré
- Université d'Aix-Marseille, CNRS, Institut de Chimie Radicalaire, Campus Étoile/Saint-Jérôme Case 521, Avenue Esc. Normandie Niemen, Marseille Cedex 20, 13397, France
| | - Luis Manuel Frutos
- Unidad Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Laura Gagliardi
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy.,Université de Lyon, CNRS, École Normale Supérieure de Lyon, 46 Allée d'Italie, Lyon Cedex 07, F-69364, France
| | - Angelo Giussani
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy
| | - Chad E Hoyer
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA
| | - Giovanni Li Manni
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA.,Max Planck Institut für Festkörperforschung, Heisenbergstraße 1, Stuttgart, 70569, Germany
| | - Hans Lischka
- Department of Chemistry and Biochemistry, Texas Tech University, Memorial Circle and Boston, Lubbock, Texas, 79409-1061, USA.,Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, Vienna, A-1090, Austria
| | - Dongxia Ma
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA.,Max Planck Institut für Festkörperforschung, Heisenbergstraße 1, Stuttgart, 70569, Germany
| | - Per Åke Malmqvist
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O.B 124 S-221 00, Lund, Sweden
| | - Thomas Müller
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Institute for Advanced Simulation (IAS), Wilhelm-Johnen-Straße, Jülich, 52425, Germany
| | - Artur Nenov
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena, 53100, Italy.,Chemistry Department, Bowling Green State University, 141 Overman Hall, Bowling Green, Ohio, 43403, USA.,Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504, 23 Rue du Loess, Strasbourg, 67034, France
| | - Thomas Bondo Pedersen
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, Oslo, 0315, Norway
| | - Daoling Peng
- College of Chemistry and Environment, South China Normal University, Guangzhou, 510006, China
| | - Felix Plasser
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, Vienna, A-1090, Austria
| | - Ben Pritchard
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York, 14260-3000, USA
| | - Markus Reiher
- ETH Zurich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, Zurich, CH-8093, Switzerland
| | - Ivan Rivalta
- Université de Lyon, CNRS, École Normale Supérieure de Lyon, 46 Allée d'Italie, Lyon Cedex 07, F-69364, France
| | - Igor Schapiro
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504, 23 Rue du Loess, Strasbourg, 67034, France.,Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, IT-40126, Bologna, Italy
| | - Michael Stenrup
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden.,Uppsala Center for Computational Chemistry - UC3, Uppsala University, Box 518, Uppsala, 751 20, Sweden
| | - Donald G Truhlar
- Department of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota, 55455-0431, USA
| | - Liviu Ungur
- Division of Quantum and Physical Chemistry, and INPAC, Institute for Nanoscale Physics and Chemistry, Katholieke Universiteit Leuven Celestijnenlaan, 200F, 3001, Belgium
| | - Alessio Valentini
- Unidad Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain.,Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena, 53100, Italy
| | - Steven Vancoillie
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O.B 124 S-221 00, Lund, Sweden
| | - Valera Veryazov
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O.B 124 S-221 00, Lund, Sweden
| | - Victor P Vysotskiy
- Department of Theoretical Chemistry, Lund University, Chemical Center, P.O.B 124 S-221 00, Lund, Sweden
| | - Oliver Weingart
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
| | - Felipe Zapata
- Unidad Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Roland Lindh
- Department of Chemistry - Ångström, The Theoretical Chemistry Programme, Uppsala University, Box 518, Uppsala, 751 20, Sweden.,Uppsala Center for Computational Chemistry - UC3, Uppsala University, Box 518, Uppsala, 751 20, Sweden
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17
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18
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Schapiro I, Roca-Sanjuán D, Lindh R, Olivucci M. A surface hopping algorithm for nonadiabatic minimum energy path calculations. J Comput Chem 2015; 36:312-20. [DOI: 10.1002/jcc.23805] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 10/21/2014] [Accepted: 11/16/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Igor Schapiro
- Department of Chemistry; Bowling Green State University; Bowling Green Ohio 43403
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular; Universitat de València; P. O. Box 22085 València 46071 Spain
| | - Roland Lindh
- Department of Chemistry-Ångström; Theoretical Chemistry Programme, Uppsala University; P. O. Box 518 Uppsala 75120 Sweden
- Uppsala Center for Computational Chemistry - UC 3; Uppsala University; P. O. Box 518 Uppsala 75120 Sweden
| | - Massimo Olivucci
- Department of Chemistry; Bowling Green State University; Bowling Green Ohio 43403
- Dipartimento di Biotechnologie, Chimica e Farmacia; Università di Siena; Siena 53100 Italy
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19
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Akimov AV, Prezhdo OV. Advanced Capabilities of the PYXAID Program: Integration Schemes, Decoherence Effects, Multiexcitonic States, and Field-Matter Interaction. J Chem Theory Comput 2014; 10:789-804. [DOI: 10.1021/ct400934c] [Citation(s) in RCA: 342] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alexey V. Akimov
- Department
of Chemistry, University of Rochester, Rochester, New York 14627
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York, 11973
| | - Oleg V. Prezhdo
- Department
of Chemistry, University of Rochester, Rochester, New York 14627
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20
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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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21
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Akimov AV, Prezhdo OV. The PYXAID Program for Non-Adiabatic Molecular Dynamics in Condensed Matter Systems. J Chem Theory Comput 2013; 9:4959-72. [DOI: 10.1021/ct400641n] [Citation(s) in RCA: 425] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Alexey V. Akimov
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Oleg V. Prezhdo
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
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22
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Maeda S, Taketsugu T, Morokuma K. Exploring Pathways of Photoaddition Reactions by Artificial Force Induced Reaction Method: A Case Study on the Paternò–Büchi Reaction. Z PHYS CHEM 2013. [DOI: 10.1524/zpch.2013.0401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Nakayama A, Harabuchi Y, Yamazaki S, Taketsugu T. Photophysics of cytosine tautomers: new insights into the nonradiative decay mechanisms from MS-CASPT2 potential energy calculations and excited-state molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:12322-39. [DOI: 10.1039/c3cp51617b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Malhado JP, Hynes JT. Photoisomerization for a model protonated Schiff base in solution: Sloped/peaked conical intersection perspective. J Chem Phys 2012; 137:22A543. [DOI: 10.1063/1.4754505] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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25
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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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26
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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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27
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Boggio-Pasqua M, Burmeister CF, Robb MA, Groenhof G. Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations. Phys Chem Chem Phys 2012; 14:7912-28. [DOI: 10.1039/c2cp23628a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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28
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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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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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Schapiro I, Melaccio F, Laricheva EN, Olivucci M. Using the computer to understand the chemistry of conical intersections. Photochem Photobiol Sci 2011; 10:867-86. [DOI: 10.1039/c0pp00290a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Leyva V, Corral I, Feixas F, Migani A, Blancafort L, González-Vázquez J, González L. A non-adiabatic quantum-classical dynamics study of the intramolecular excited state hydrogen transfer in ortho-nitrobenzaldehyde. Phys Chem Chem Phys 2011; 13:14685-93. [DOI: 10.1039/c1cp20620f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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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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33
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Ončák M, Lischka H, Slavíček P. Photostability and solvation: photodynamics of microsolvated zwitterionic glycine. Phys Chem Chem Phys 2010; 12:4906-14. [DOI: 10.1039/b925246k] [Citation(s) in RCA: 8] [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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34
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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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35
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Computer Simulations of Photobiological Processes: The Effect of the Protein Environment. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
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36
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Asturiol D, Lasorne B, Robb MA, Blancafort L. Photophysics of the pi,pi* and n,pi* states of thymine: MS-CASPT2 minimum-energy paths and CASSCF on-the-fly dynamics. J Phys Chem A 2009; 113:10211-8. [PMID: 19722485 DOI: 10.1021/jp905303g] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photodynamics along the main decay paths of thymine after excitation to the lowest pi,pi* state have been studied with MS-CASPT2 calculations and semiclassical CASSCF dynamics calculations including a surface hopping algorithm. The static calculations show that there are two decay paths from the Franck-Condon structure that lead to a conical intersection with the ground state. The first path goes directly to the intersection, while the second one is indirect and involves a minimum of the pi,pi* state, a small barrier, and a crossing between the pi,pi* and n,pi* states. From the static calculations, both paths have similar slopes. The dynamics calculations along the indirect path show that, after the barrier, part of the trajectories are funneled to the intersection with the ground state, where they are efficiently quenched to the ground state. The remaining trajectories populate the n,pi* state. They are also quenched to the ground state in less than 1 ps, but the static calculations show that the decay rate of the n,pi* state is largely overestimated at the CASSCF level used for the dynamics. Overall, these results suggest that both direct and indirect paths contribute to the subpicosecond decay components found experimentally. The indirect path also provides a way for fast population of the n,pi* state, which will account for the experimental picosecond decay component.
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Affiliation(s)
- David Asturiol
- Institut de Química Computacional, Parc Científic i Tecnològic de la Universitat de Girona, Edifici Jaume Casademont, Pic de Peguera 15 (la Creueta), 17003 Girona, Spain
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37
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Tao H, Levine BG, Martínez TJ. Ab Initio Multiple Spawning Dynamics Using Multi-State Second-Order Perturbation Theory. J Phys Chem A 2009; 113:13656-62. [DOI: 10.1021/jp9063565] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hongli Tao
- Department of Chemistry, Stanford University, Stanford, California, 94305, and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Benjamin G. Levine
- Department of Chemistry, Stanford University, Stanford, California, 94305, and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Todd J. Martínez
- Department of Chemistry, Stanford University, Stanford, California, 94305, and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Lasorne B, Bearpark MJ, Robb MA, Worth GA. Controlling S1/S0 decay and the balance between photochemistry and photostability in benzene: a direct quantum dynamics study. J Phys Chem A 2009; 112:13017-27. [PMID: 18826292 DOI: 10.1021/jp803740a] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this work, we investigate general mechanistic principles that control reaction selectivity following S(1)/S(0) internal conversion in benzene. A systematic relationship is drawn between the varying topology of an extended seam of conical intersection and the balance between two competitive radiationless decay channels: photophysical (benzene reactant regeneration) and photochemical (prefulvene product formation). This is supported by a model quantum dynamics study, using a direct dynamics approach based on variational multiconfiguration Gaussian wavepackets, where initial excitation of specific vibrational modes is designed to generate dynamical pathways that reach selected targets regions of the seam. High-energy regions of the seam are found to be sloped and in favor of the photophysical channel, while lower-energy regions are peaked and give access to the photochemical channel. This changeover could in principle be exploited to define targets for optimal control, by exciting different combinations of specific vibronic levels in S(1), accessing different regions of the seam, and giving different products.
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Affiliation(s)
- Benjamin Lasorne
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
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Szymczak JJ, Barbatti M, Lischka H. Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process? J Phys Chem A 2009; 113:11907-18. [DOI: 10.1021/jp903329j] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jaroslaw J. Szymczak
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090, Vienna, Austria, 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, 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, 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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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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Ishida T, Nanbu S, Nakamura H. Nonadiabatic ab Initio Dynamics of Two Models of Schiff Base Retinal. J Phys Chem A 2009; 113:4356-66. [DOI: 10.1021/jp8110315] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Toshimasa Ishida
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4, Takano-nishihirakicho, Kyoto 606-8103, Japan
| | - Shinkoh Nanbu
- Research Institute for Information Technology, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka, 812-8581, Japan
| | - Hiroki Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, 444-8585, Japan
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42
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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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43
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Pittner J, Lischka H, Barbatti M. Optimization of mixed quantum-classical dynamics: Time-derivative coupling terms and selected couplings. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.10.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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44
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Coe JD, Ong MT, Levine BG, Martínez TJ. On the Extent and Connectivity of Conical Intersection Seams and the Effects of Three-State Intersections. J Phys Chem A 2008; 112:12559-67. [DOI: 10.1021/jp806072k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joshua D. Coe
- Department of Chemistry, Beckman Institute, and Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Mitchell T. Ong
- Department of Chemistry, Beckman Institute, and Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Benjamin G. Levine
- Department of Chemistry, Beckman Institute, and Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Todd J. Martínez
- Department of Chemistry, Beckman Institute, and Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
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Szymczak JJ, Barbatti M, Lischka H. Mechanism of Ultrafast Photodecay in Restricted Motions in Protonated Schiff Bases: The Pentadieniminium Cation. J Chem Theory Comput 2008; 4:1189-99. [DOI: 10.1021/ct800148n] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jaroslaw J. Szymczak
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria
| | - Mario Barbatti
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria
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46
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Antol I, Eckert-Maksić M, Barbatti M, Lischka H. Simulation of the photodeactivation of formamide in the nO-pi* and pi-pi* states: an ab initio on-the-fly surface-hopping dynamics study. J Chem Phys 2008; 127:234303. [PMID: 18154378 DOI: 10.1063/1.2804862] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The short-time photodynamics (1 ps) of formamide in its low-lying singlet excited n(O)-pi(*) and pi-pi(*) states have been investigated by the direct trajectory surface-hopping method based on multiconfigurational ab initio calculations. The simulations showed that in both states, the primary deactivation process is C-N bond dissociation. In the ground state, the energy is transferred to (a) translational motion of the HCO and NH(2) fragments, (b) additional C-H dissociation from the vibrationally hot HCO fragment, or (c) formation of NH(3) and CO. In addition to the C-N dissociation pathway, C-O bond fission is found to be an additional primary deactivation path in the pi-pi(*) dynamics. From fractional occupations of trajectories, lifetimes of formamide were estimated: tau(S(1))=441 fs and tau(S(2))=66 fs.
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Affiliation(s)
- Ivana Antol
- Division of Organic Chemistry and Biochemistry, Rudjer Bosković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia
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Barbatti M, Ruckenbauer M, Szymczak JJ, Aquino AJA, Lischka H. Nonadiabatic excited-state dynamics of polar π-systems and related model compounds of biological relevance. Phys Chem Chem Phys 2008; 10:482-94. [DOI: 10.1039/b709315m] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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49
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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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50
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Barbatti M, Granucci G, Persico M, Ruckenbauer M, Vazdar M, Eckert-Maksić M, Lischka H. The on-the-fly surface-hopping program system Newton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2006.12.008] [Citation(s) in RCA: 380] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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