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Salazar E, Menger MFS, Faraji S. Ultrafast Photoinduced Dynamics in 1,3-Cyclohexadiene: A Comparison of Trajectory Surface Hopping Schemes†. J Chem Theory Comput 2024; 20:5796-5806. [PMID: 38949625 PMCID: PMC11270829 DOI: 10.1021/acs.jctc.4c00012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
Photoinduced nonadiabatic processes play a crucial role in a wide range of disciplines, from fundamental steps in biology to modern applications in advanced materials science. A theoretical understanding of these processes is highly desirable, and trajectory surface hopping (TSH) has proven to be a well-suited framework for a wide range of systems. In this work, we present a comprehensive comparison between two TSH algorithms, the conventional Tully's fewest switches surface hopping (FSSH) scheme and the Landau-Zener surface hopping (LZSH), to study the photoinduced ring-opening of 1,3-cyclohexadiene (CHD) to 1,3,5-hexatriene at the spin-flip time-dependent density functional theory (SF-TDDFT) level of theory. Additionally, we compare our results with a literature study at the extended multistate complete active space second-order perturbation theory method (XMS-CASPT2) level of theory. Our results show that the average population and lifetimes estimated with LZSH using SF-TDDFT are closer to the literature (using multireference methods) than those estimated with FSSH using SF-TDDFT. The latter speaks in favor of applying LZSH in combination with the SF-TDDFT method to study larger and more complex systems such as molecular photoswitches where the CHD molecule acts as a backbone. In addition, we present an implementation of Tully's FSSH algorithm as an extension to the PySurf software package.
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Affiliation(s)
- Edison
X. Salazar
- Instituut-Lorentz, Universiteit Leiden, 2300 RA Leiden, The Netherlands
- Theoretical
Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maximilian F. S.
J. Menger
- Theoretical
Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Theoretische
Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, 69120 Heidelberg, Germany
| | - Shirin Faraji
- Theoretical
Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Institute
of Theoretical and Computational Chemistry, Faculty of Mathematics
and Natural Sciences, Heinrich Heine University
Düsseldorf, 40225 Düsseldorf, Germany
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2
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Shu Y, Truhlar DG. Generalized Semiclassical Ehrenfest Method: A Route to Wave Function-Free Photochemistry and Nonadiabatic Dynamics with Only Potential Energies and Gradients. J Chem Theory Comput 2024; 20:4396-4426. [PMID: 38819014 DOI: 10.1021/acs.jctc.4c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We reconsider recent methods by which direct dynamics calculations of electronically nonadiabatic processes can be carried out while requiring only adiabatic potential energies and their gradients. We show that these methods can be understood in terms of a new generalization of the well-known semiclassical Ehrenfest method. This is convenient because it eliminates the need to evaluate electronic wave functions and their matrix elements along the mixed quantum-classical trajectories. The new approximations and procedures enabling this advance are the curvature-driven approximation to the time-derivative coupling, the generalized semiclassical Ehrenfest method, and a new gradient correction scheme called the time-derivative matrix (TDM) scheme. When spin-orbit coupling is present, one can carry out dynamics calculations in the fully adiabatic basis using potential energies and gradients calculated without spin-orbit coupling plus the spin-orbit coupling matrix elements. Even when spin-orbit coupling is neglected, the method is useful because it allows calculations by electronic structure methods for which nonadiabatic coupling vectors are unavailable. In order to place the new considerations in context, the article starts out with a review of background material on trajectory surface hopping, the semiclassical Ehrenfest scheme, and methods for incorporating decoherence. We consider both internal conversion and intersystem crossing. We also review several examples from our group of successful applications of the curvature-driven approximation.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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3
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Qiang J, Zhou L, Peng Y, Yu C, Lu P, Pan S, Lu C, Chen G, Lu R, Zhang W, Wu J. Femtosecond Collisional Dissipation of Vibrating D_{2}^{+} in Helium Nanodroplets. PHYSICAL REVIEW LETTERS 2024; 132:103201. [PMID: 38518314 DOI: 10.1103/physrevlett.132.103201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 02/05/2024] [Indexed: 03/24/2024]
Abstract
We explored the collision-induced vibrational decoherence of singly ionized D_{2} molecules inside a helium nanodroplet. By using the pump-probe reaction microscopy with few-cycle laser pulses, we captured in real time the collision-induced ultrafast dissipation of vibrational nuclear wave packet dynamics of D_{2}^{+} ion embedded in the droplet. Because of the strong coupling of excited molecular cations with the surrounding solvent, the vibrational coherence of D_{2}^{+} in the droplet interior only lasts for a few vibrational periods and completely collapses within 140 fs. The observed ultrafast coherence loss is distinct from that of isolated D_{2}^{+} in the gas phase, where the vibrational coherence persists for a long time with periodic quantum revivals. Our findings underscore the crucial role of ultrafast collisional dissipation in shaping the molecular decoherence and solvation dynamics during solution chemical reactions, particularly when the solute molecules are predominantly in ionic states.
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Affiliation(s)
- Junjie Qiang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- School of Physics and Microelectronics Key Laboratory of Materials Physics of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Lianrong Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Yigeng Peng
- Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Chao Yu
- Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Peifen Lu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Shengzhe Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Chenxu Lu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Gang Chen
- School of Physics and Microelectronics Key Laboratory of Materials Physics of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Ruifeng Lu
- Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Wenbin Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Jian Wu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401121, China
- CAS Center for Excellence in Ultra-Intense Laser Science, Shanghai 201800, China
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4
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Li Manni G, Fdez. Galván I, Alavi A, Aleotti F, Aquilante F, Autschbach J, Avagliano D, Baiardi A, Bao JJ, Battaglia S, Birnoschi L, Blanco-González A, Bokarev SI, Broer R, Cacciari R, Calio PB, Carlson RK, Carvalho Couto R, Cerdán L, Chibotaru LF, Chilton NF, Church JR, Conti I, Coriani S, Cuéllar-Zuquin J, Daoud RE, Dattani N, Decleva P, de Graaf C, Delcey M, De Vico L, Dobrautz W, Dong SS, Feng R, Ferré N, Filatov(Gulak) M, Gagliardi L, Garavelli M, González L, Guan Y, Guo M, Hennefarth MR, Hermes MR, Hoyer CE, Huix-Rotllant M, Jaiswal VK, Kaiser A, Kaliakin DS, Khamesian M, King DS, Kochetov V, Krośnicki M, Kumaar AA, Larsson ED, Lehtola S, Lepetit MB, Lischka H, López Ríos P, Lundberg M, Ma D, Mai S, Marquetand P, Merritt ICD, Montorsi F, Mörchen M, Nenov A, Nguyen VHA, Nishimoto Y, Oakley MS, Olivucci M, Oppel M, Padula D, Pandharkar R, Phung QM, Plasser F, Raggi G, Rebolini E, Reiher M, Rivalta I, Roca-Sanjuán D, Romig T, Safari AA, Sánchez-Mansilla A, Sand AM, Schapiro I, Scott TR, Segarra-Martí J, Segatta F, Sergentu DC, Sharma P, Shepard R, Shu Y, Staab JK, Straatsma TP, Sørensen LK, Tenorio BNC, Truhlar DG, Ungur L, Vacher M, Veryazov V, Voß TA, Weser O, Wu D, Yang X, Yarkony D, Zhou C, Zobel JP, Lindh R. The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry. J Chem Theory Comput 2023; 19:6933-6991. [PMID: 37216210 PMCID: PMC10601490 DOI: 10.1021/acs.jctc.3c00182] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Indexed: 05/24/2023]
Abstract
The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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Affiliation(s)
- Giovanni Li Manni
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Ignacio Fdez. Galván
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Ali Alavi
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Yusuf Hamied
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Flavia Aleotti
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Francesco Aquilante
- Theory and
Simulation of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jochen Autschbach
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - Davide Avagliano
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Alberto Baiardi
- ETH Zurich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jie J. Bao
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Stefano Battaglia
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Letitia Birnoschi
- The Department
of Chemistry, The University of Manchester, M13 9PL, Manchester, U.K.
| | - Alejandro Blanco-González
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
| | - Sergey I. Bokarev
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
- Chemistry
Department, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Ria Broer
- Theoretical
Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Roberto Cacciari
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Paul B. Calio
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Rebecca K. Carlson
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Rafael Carvalho Couto
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Luis Cerdán
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
- Instituto
de Óptica (IO−CSIC), Consejo
Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - Liviu F. Chibotaru
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Nicholas F. Chilton
- The Department
of Chemistry, The University of Manchester, M13 9PL, Manchester, U.K.
| | | | - Irene Conti
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Sonia Coriani
- Department
of Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, 2800 Kongens Lyngby, Denmark
| | - Juliana Cuéllar-Zuquin
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
| | - Razan E. Daoud
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Nike Dattani
- HPQC Labs, Waterloo, N2T 2K9 Ontario Canada
- HPQC College, Waterloo, N2T 2K9 Ontario Canada
| | - Piero Decleva
- Istituto
Officina dei Materiali IOM-CNR and Dipartimento di Scienze Chimiche
e Farmaceutiche, Università degli
Studi di Trieste, I-34121 Trieste, Italy
| | - Coen de Graaf
- Department
of Physical and Inorganic Chemistry, Universitat
Rovira i Virgili, Tarragona 43007, Spain
- ICREA, Pg. Lluís
Companys 23, 08010 Barcelona, Spain
| | - Mickaël
G. Delcey
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Luca De Vico
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Werner Dobrautz
- Chalmers
University of Technology, Department of Chemistry
and Chemical Engineering, 41296 Gothenburg, Sweden
| | - Sijia S. Dong
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry and Chemical Biology, Department of Physics, and Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Rulin Feng
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Nicolas Ferré
- Institut
de Chimie Radicalaire (UMR-7273), Aix-Marseille
Univ, CNRS, ICR 13013 Marseille, France
| | | | - Laura Gagliardi
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Marco Garavelli
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Yafu Guan
- State Key
Laboratory of Molecular Reaction Dynamics and Center for Theoretical
Computational Chemistry, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Meiyuan Guo
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Matthew R. Hennefarth
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew R. Hermes
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chad E. Hoyer
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miquel Huix-Rotllant
- Institut
de Chimie Radicalaire (UMR-7273), Aix-Marseille
Univ, CNRS, ICR 13013 Marseille, France
| | - Vishal Kumar Jaiswal
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Andy Kaiser
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Danil S. Kaliakin
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
| | - Marjan Khamesian
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Daniel S. King
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vladislav Kochetov
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Marek Krośnicki
- Institute
of Theoretical Physics and Astrophysics, Faculty of Mathematics, Physics
and Informatics, University of Gdańsk, ul Wita Stwosza 57, 80-952, Gdańsk, Poland
| | | | - Ernst D. Larsson
- Division
of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | - Susi Lehtola
- Molecular
Sciences Software Institute, Blacksburg, Virginia 24061, United States
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 University of Helsinki, Finland
| | - Marie-Bernadette Lepetit
- Condensed
Matter Theory Group, Institut Néel, CNRS UPR 2940, 38042 Grenoble, France
- Theory
Group, Institut Laue Langevin, 38042 Grenoble, France
| | - Hans Lischka
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409-1061, United States
| | - Pablo López Ríos
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Marcus Lundberg
- Department
of Chemistry − Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
| | - Dongxia Ma
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | | | - Francesco Montorsi
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Maximilian Mörchen
- ETH Zurich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Artur Nenov
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Vu Ha Anh Nguyen
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Yoshio Nishimoto
- Graduate
School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Meagan S. Oakley
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Markus Oppel
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Daniele Padula
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Riddhish Pandharkar
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Quan Manh Phung
- Department
of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Felix Plasser
- Department
of Chemistry, Loughborough University, Loughborough, LE11 3TU, U.K.
| | - Gerardo Raggi
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
- Quantum
Materials and Software LTD, 128 City Road, London, EC1V 2NX, United Kingdom
| | - Elisa Rebolini
- Scientific
Computing Group, Institut Laue Langevin, 38042 Grenoble, France
| | - Markus Reiher
- ETH Zurich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Ivan Rivalta
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
| | - Thies Romig
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Arta Anushirwan Safari
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Aitor Sánchez-Mansilla
- Department
of Physical and Inorganic Chemistry, Universitat
Rovira i Virgili, Tarragona 43007, Spain
| | - Andrew M. Sand
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Igor Schapiro
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Thais R. Scott
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Javier Segarra-Martí
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
| | - Francesco Segatta
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Dumitru-Claudiu Sergentu
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
- Laboratory
RA-03, RECENT AIR, A. I. Cuza University of Iaşi, RA-03 Laboratory (RECENT AIR), Iaşi 700506, Romania
| | - Prachi Sharma
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Ron Shepard
- Chemical
Sciences and Engineering Division, Argonne
National Laboratory, Lemont, Illinois 60439, USA
| | - Yinan Shu
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Jakob K. Staab
- The Department
of Chemistry, The University of Manchester, M13 9PL, Manchester, U.K.
| | - Tjerk P. Straatsma
- National
Center for Computational Sciences, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831-6373, United States
- Department
of Chemistry and Biochemistry, University
of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | | | - Bruno Nunes Cabral Tenorio
- Department
of Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, 2800 Kongens Lyngby, Denmark
| | - Donald G. Truhlar
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Liviu Ungur
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Morgane Vacher
- Nantes
Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France
| | - Valera Veryazov
- Division
of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | - Torben Arne Voß
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Oskar Weser
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Dihua Wu
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Xuchun Yang
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
| | - David Yarkony
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chen Zhou
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - J. Patrick Zobel
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Roland Lindh
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
- Uppsala
Center for Computational Chemistry (UC3), Uppsala University, PO Box 576, SE-751 23 Uppsala. Sweden
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5
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Shao C, Shi Z, Xu J, Wang L. Learning Decoherence Time Formulas for Surface Hopping from Quantum Dynamics. J Phys Chem Lett 2023; 14:7680-7689. [PMID: 37606199 DOI: 10.1021/acs.jpclett.3c02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Surface hopping simulations have achieved great success in many different fields, but their reliability has long been limited by the overcoherence problem. We here present a general machine learning assisted approach to identify optimal decoherence time formulas for surface hopping using exact quantum dynamics as references. In order to avoid computationally expensive force calculations, we use the nuclear kinetic energy and the adiabatic energy difference to iteratively generate the descriptor space. Through multilayer screening of the candidate descriptors and discrete optimization of the relevant parameters, we obtain new energy-based decoherence time formulas. As benchmarked in thousands of diverse multilevel systems and six standard scattering models, surface hopping with our new decoherence time formulas nearly reproduces the exact quantum dynamics while maintaining high efficiency. Thereby, our approach provides a promising avenue for systematically improving the accuracy of surface hopping simulations in complex systems from quantum dynamics data.
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Affiliation(s)
- Cancan Shao
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Zhecun Shi
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Jiabo Xu
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Linjun Wang
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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6
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Shu Y, Zhang L, Wu D, Chen X, Sun S, Truhlar DG. New Gradient Correction Scheme for Electronically Nonadiabatic Dynamics Involving Multiple Spin States. J Chem Theory Comput 2023; 19:2419-2429. [PMID: 37079755 DOI: 10.1021/acs.jctc.2c01173] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
It has been recommended that the best representation to use for trajectory surface hopping (TSH) calculations is the fully adiabatic basis in which the Hamiltonian is diagonal. Simulations of intersystem crossing processes with conventional TSH methods require an explicit computation of nonadiabatic coupling vectors (NACs) in the molecular-Coulomb-Hamiltonian (MCH) basis, also called the spin-orbit-free basis, in order to compute the gradient in the fully adiabatic basis (also called the diagonal representation). This explicit requirement destroys some of the advantages of the overlap-based algorithms and curvature-driven algorithms that can be used for the most efficient TSH calculations. Therefore, although these algorithms allow one to perform NAC-free simulations for internal conversion processes, one still requires NACs for intersystem crossing. Here, we show that how the NAC requirement is circumvented by a new computation scheme called the time-derivative-matrix scheme.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Linyao Zhang
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Dihua Wu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Xiye Chen
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Shaozeng Sun
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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7
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Merritt ICD, Jacquemin D, Vacher M. Nonadiabatic Coupling in Trajectory Surface Hopping: How Approximations Impact Excited-State Reaction Dynamics. J Chem Theory Comput 2023; 19:1827-1842. [PMID: 36897995 DOI: 10.1021/acs.jctc.2c00968] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Photochemical reactions are widely modeled using the popular trajectory surface hopping (TSH) method, an affordable mixed quantum-classical approximation to the full quantum dynamics of the system. TSH is able to account for nonadiabatic effects using an ensemble of trajectories, which are propagated on a single potential energy surface at a time and which can hop from one electronic state to another. The occurrences and locations of these hops are typically determined using the nonadiabatic coupling between electronic states, which can be assessed in a number of ways. In this work, we benchmark the impact of some approximations to the coupling term on the TSH dynamics for several typical isomerization and ring-opening reactions. We have identified that two of the schemes tested, the popular local diabatization scheme and a scheme based on biorthonormal wave function overlap implemented in the OpenMOLCAS code as part of this work, reproduce at a much reduced cost the dynamics obtained using the explicitly calculated nonadiabatic coupling vectors. The other two schemes tested can give different results, and in some cases, even entirely incorrect dynamics. Of these two, the scheme based on configuration interaction vectors gives unpredictable failures, while the other scheme based on the Baeck-An approximation systematically overestimates hopping to the ground state as compared to the reference approaches.
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Affiliation(s)
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Morgane Vacher
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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8
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Zhao X, Shu Y, Zhang L, Xu X, Truhlar DG. Direct Nonadiabatic Dynamics of Ammonia with Curvature-Driven Coherent Switching with Decay of Mixing and with Fewest Switches with Time Uncertainty: An Illustration of Population Leaking in Trajectory Surface Hopping Due to Frustrated Hops. J Chem Theory Comput 2023; 19:1672-1685. [PMID: 36877830 DOI: 10.1021/acs.jctc.2c01260] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Mixed quantum-classical nonadiabatic dynamics is a widely used approach to simulate molecular dynamics involving multiple electronic states. There are two main categories of mixed quantum-classical nonadiabatic dynamics algorithms, namely, trajectory surface hopping (TSH) in which the trajectory propagates on a single potential energy surface, interrupted by hops, and self-consistent-potential (SCP) methods, such as semiclassical Ehrenfest, in which propagation occurs on a mean-field surface without hops. In this work, we will illustrate an example of severe population leaking in TSH. We emphasize that such leaking is a combined effect of frustrated hops and long-time simulations that drive the final excited-state population toward zero as a function of time. We further show that such leaking can be alleviated-but not eliminated-by the fewest switches with time uncertainty TSH algorithm (here implemented in the SHARC program); the time uncertainty algorithm slows down the leaking process by a factor of 4.1. The population leaking is not present in coherent switching with decay of mixing (CSDM), which is an SCP method with non-Markovian decoherence included. Another result in this paper is that we find very similar results with the original CSDM algorithm, with time-derivative CSDM (tCSDM), and with curvature-driven CSDM (κCSDM). Not only do we find good agreement for electronically nonadiabatic transition probabilities but also we find good agreement of the norms of the effective nonadiabatic couplings (NACs) that are derived from the curvature-driven time-derivative couplings as implemented in κCSDM with the time-dependent norms of the nonadiabatic coupling vectors computed by state-averaged complete-active-space self-consistent field theory.
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Affiliation(s)
- Xiaorui Zhao
- Center for Combustion Energy, Tsinghua University, Beijing 100084, P. R. China.,School of Aerospace Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Yinan Shu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Linyao Zhang
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Xuefei Xu
- Center for Combustion Energy, Tsinghua University, Beijing 100084, P. R. China
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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9
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Kalita P, Medhi B, Singh HK, Bhattacharyya HP, Gupt N, Sarma M. Perturbing π-clouds with Substituents to Study the Effects on Reaction Dynamics of gauche-1,3-Butadiene to Bicyclobutane Electrocyclization. Chemphyschem 2023; 24:e202200727. [PMID: 36281900 DOI: 10.1002/cphc.202200727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/23/2022] [Indexed: 02/03/2023]
Abstract
The conical intersection (CI) governs the ultra-fast relaxation of excited states in a radiationless manner and are observed mainly in photochemical processes. In the current work, we investigated the effects of substituents on the reaction dynamics for the conversion of gauche-1,3-butadiene to bicyclobutane via photochemical electrocyclization. We incorporated both electron withdrawing (-F) and donating (-CH3 ) groups in the conjugated system. In our study, we optimized the minimum energy conical intersection (MECI) geometries using the multi-configurational state-averaged CASSCF approach, whereas, to study the ground state reaction pathways for the substituted derivatives, dispersion corrected, B3LYP-D3 functional was used. The non-adiabatic surface hopping molecular dynamics simulations were performed to observe the behaviour of electronic states involved throughout the photoconversion process. The results obtained from the multi-reference second-order perturbation correction of energy at the XMS-CASPT2 level of theory, topography analysis, and non-adiabatic dynamics suggest that the -CH3 substituted derivatives can undergo faster thermal conversion to the product in the ground state with a smaller activation energy barrier compared to -F substituted derivative. Our study also reveals that the GBUT to BIBUT conversion follows both conrotatory and disrotatory pathways, whereas, on substitution with -F or -CH3 , the conversion proceeds via the conrotatory pathway.
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Affiliation(s)
- Papu Kalita
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, Indian
| | - Biman Medhi
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, Indian
| | - Haobam Kisan Singh
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, Indian
| | | | - Nikhil Gupt
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, Indian.,Current Address: Indian Institute of Technology Kanpur, Uttar Pradesh, 208016, Indian
| | - Manabendra Sarma
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, Indian
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10
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Shu Y, Truhlar DG. Decoherence and Its Role in Electronically Nonadiabatic Dynamics. J Chem Theory Comput 2023; 19:380-395. [PMID: 36622843 PMCID: PMC9878713 DOI: 10.1021/acs.jctc.2c00988] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Indexed: 01/10/2023]
Abstract
Decoherence is the tendency of a time-evolved reduced density matrix for a subsystem to assume a form corresponding to a statistical ensemble of states rather than a coherent combination of pure-state wave functions. When a molecular process involves changes in the electronic state and the coordinates of the nuclei, as in ultraviolet or visible light photochemistry or electronically inelastic collisions, the reduced density matrix of the electronic subsystem suffers decoherence, due to its interaction with the nuclear subsystem. We present the background necessary to conceptualize this decoherence; in particular, we discuss the density matrix description of pure states and mixed states, and we discuss pointer states and decoherence time. We then discuss how decoherence is treated in the coherent switching with decay of mixing algorithm and the trajectory surface hopping method for semiclassical calculations of electronically nonadiabatic processes.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry,
Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry,
Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota55455-0431, United States
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11
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Jain A, Sindhu A. Pedagogical Overview of the Fewest Switches Surface Hopping Method. ACS OMEGA 2022; 7:45810-45824. [PMID: 36570264 PMCID: PMC9773185 DOI: 10.1021/acsomega.2c04843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The fewest switches surface hopping method continues to grow in popularity to capture electronic nonadiabaticity and quantum nuclear effects due to its simplicity and accuracy. Knowing the basics of the method is essential for the correct implementation and interpretation of results. This review covers the fundamentals of the fewest switches surface hopping method with a detailed discussion of the nuances such as decoherence schemes and frustrated hops and the correct approach to calculating populations. The consequences of incorrect implementation are further discussed toward calculating kinetic and thermodynamic properties. Some tips for practitioners and a step-by-step algorithm for developers are provided. Finally, some of the finer technicalities of the fewest switches surface hopping method that are buried deep in the literature are pointed out to help graduate students better appreciate this method.
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12
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Zhang L, Shu Y, Bhaumik S, Chen X, Sun S, Huang Y, Truhlar DG. Nonadiabatic Dynamics of 1,3-Cyclohexadiene by Curvature-Driven Coherent Switching with Decay of Mixing. J Chem Theory Comput 2022; 18:7073-7081. [PMID: 36350795 DOI: 10.1021/acs.jctc.2c00801] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The photoinduced ring-opening reaction of 1,3-cyclohexadiene to produce 1,3,5-hexatriene is a classic electrocyclic reaction and is also a prototype for many reactions of biological and synthetic importance. Here, we simulate the ultrafast nonadiabatic dynamics of the reaction in the manifold of the three lowest valence electronic states by using extended multistate complete-active-space second-order perturbation theory (XMS-CASPT2) combined with the curvature-driven coherent switching with decay of mixing (κCSDM) dynamical method. We obtain an excited-state lifetime of 79 fs, and a product quantum yield of 40% from the 500 trajectories initiated in the S1 excited state. The obtained lifetime and quantum yield values are very close to previously reported experimental and computed values, showing the capability of performing a reasonable nonadiabatic ring-opening dynamics with the κCSDM method that does not require nonadiabatic coupling vectors, time derivatives, or diabatization. In addition, we study the ring-opening reaction by initiating the trajectories in the dark state S2. We also optimize the S0/S1 and S1/S2 minimum-energy conical intersections (MECIs) by XMS-CASPT2; for S1/S2, we optimized both an inner and an outer local-minimum-energy conical intersections (LMECIs). We provide the potential energy profile along the ring-opening coordinate by joining selected critical points via linear synchronous transit paths. We find the inner S1/S2 LMECI to be more crucial than the outer one.
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Affiliation(s)
- Linyao Zhang
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China.,School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Yinan Shu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Suman Bhaumik
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Xiye Chen
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China.,School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Shaozeng Sun
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Yudong Huang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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13
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Lin K, Peng J, Xu C, Gu FL, Lan Z. Automatic Evolution of Machine-Learning-Based Quantum Dynamics with Uncertainty Analysis. J Chem Theory Comput 2022; 18:5837-5855. [DOI: 10.1021/acs.jctc.2c00702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kunni Lin
- School of Chemistry, South China Normal University, Guangzhou510006, P. R. China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
| | - Jiawei Peng
- School of Chemistry, South China Normal University, Guangzhou510006, P. R. China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou510006, P. R. China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou510006, P. R. China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou510006, P. R. China
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou510006, P. R. China
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14
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Zhao C, Zheng Q, Zhao J. Excited electron and spin dynamics in topological insulator: A perspective from ab initio non-adiabatic molecular dynamics. FUNDAMENTAL RESEARCH 2022; 2:506-510. [PMID: 39077367 PMCID: PMC11284953 DOI: 10.1016/j.fmre.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/15/2022] [Accepted: 03/08/2022] [Indexed: 11/23/2022] Open
Abstract
We perform an ab initio non-adiabatic molecular dynamics simulation to investigate the non-equilibrium spin and electron dynamics in a prototypical topological insulator (TI) Bi2Se3. Different from the ground state, we reveal that backscattering can happen in an oscillating manner between time-reversal pair topological surface states (TSSs) in the non-equilibrium dynamics. Analysis shows the phonon excitation induces orbital composition change by electron-phonon interaction, which further stimulates spin canting through spin-orbit coupling. The spin canting of time-reversal pair TSSs leads to the non-zero non-adiabatic coupling between them and then issues in backscattering. Both the spin canting and backscattering result in ultrafast spin relaxation with a timescale around 100 fs. This study provides critical insights into the non-equilibrium electron and spin dynamics in TI at the ab initio level and paves a way for the design of ultrafast spintronic materials.
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Affiliation(s)
- Chuanyu Zhao
- Department of Physics, ICQD/Hefei National Research Center for Physical Sciences at the Microscale, and CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qijing Zheng
- Department of Physics, ICQD/Hefei National Research Center for Physical Sciences at the Microscale, and CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jin Zhao
- Department of Physics, ICQD/Hefei National Research Center for Physical Sciences at the Microscale, and CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Synergetic Innovation Center of Quantum Information & Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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15
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Xie H, Xu X, Wang L, Zhuang W. Surface hopping dynamics in periodic solid-state materials with a linear vibronic coupling model. J Chem Phys 2022; 156:154116. [PMID: 35459287 DOI: 10.1063/5.0085759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report a surface hopping approach in which the implemented linear vibronic coupling Hamiltonian is constructed and the electronic wavefunction is propagated in the reciprocal space. The parameters of the linear vibronic coupling model, including onsite energies, phonon frequencies, and electron-phonon couplings, are calculated with density-functional theory and density-functional perturbation theory and interpolated in fine sampling points of the Brillouin zone with maximally localized Wannier functions. Using this approach, we studied the relaxation dynamics of the photo-excited hot carrier in a one-dimensional periodic carbon chain. The results show that the completeness of the number of Hilbert space k points and the number of phonon q points plays an important role in the hot carrier relaxation processes. By calculating the relaxation times of hot carriers under different reciprocal space sampling and extrapolating with the stretched-compressed exponential function, the relaxation times of hot electrons and holes in the quasi-continuous energy band are obtained. By considering the feedback effect in the hopping processes and analyzing the time-dependent phonon energy in different normal modes, we found that the long-wave longitudinal optical phonons play a major role in the relaxation dynamics of hot electrons and holes. We, therefore, provided herein an efficient and accurate approach for modeling the photophysical processes in periodic solid-state material systems.
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Affiliation(s)
- Hua Xie
- Key Laboratory of Strongly-Coupled Quantum Matter Physics, Chinese Academy of Sciences, School of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiaoliang Xu
- Key Laboratory of Strongly-Coupled Quantum Matter Physics, Chinese Academy of Sciences, School of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Linjun Wang
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
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16
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Qiu J, Lu Y, Wang L. Multilayer Subsystem Surface Hopping Method for Large-Scale Nonadiabatic Dynamics Simulation with Hundreds of Thousands of States. J Chem Theory Comput 2022; 18:2803-2815. [PMID: 35380833 DOI: 10.1021/acs.jctc.2c00130] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a multilayer subsystem surface hopping (MSSH) method to deal with nonadiabatic dynamics in large-scale systems. A small subsystem instead of the full system is adopted for surface hopping and is updated on-the-fly to achieve a reliable description of important adiabatic states and the wave function evolution. Additional subsystems for molecular dynamics and statistical description are introduced to further improve the simulation reliability. The global flux hopping probabilities with optimal state assignments are utilized to treat the complex surface crossings. As demonstrated in a series of one- and two-dimensional Holstein models with up to hundreds of thousands of states, MSSH shows weak parameter dependence in all investigated systems. Especially, the computational costs are reduced by 2-6 orders of magnitude compared to traditional surface hopping simulations in full systems, and size-independent results are achieved with a large time-step size of 2-5 fs. The new method is compatible with different decoherence correction strategies and achieves a much better balance between efficiency and reliability, thus promising for applications in general charge and exciton dynamics simulations.
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Affiliation(s)
- Jing Qiu
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yao Lu
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Linjun Wang
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
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17
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Xie BB, Jia PK, Wang KX, Chen WK, Liu XY, Cui G. Generalized Ab Initio Nonadiabatic Dynamics Simulation Methods from Molecular to Extended Systems. J Phys Chem A 2022; 126:1789-1804. [PMID: 35266391 DOI: 10.1021/acs.jpca.1c10195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonadiabatic dynamics simulation has become a powerful tool to describe nonadiabatic effects involved in photophysical processes and photochemical reactions. In the past decade, our group has developed generalized trajectory-based ab initio surface-hopping (GTSH) dynamics simulation methods, which can be used to describe a series of nonadiabatic processes, such as internal conversion, intersystem crossing, excitation energy transfer and charge transfer of molecular systems, and photoinduced nonadiabatic carrier dynamics of extended systems with and without spin-orbit couplings. In this contribution, we will first give a brief introduction to our recently developed methods and related numerical implementations at different computational levels. Later, we will present some of our latest applications in realistic systems, which cover organic molecules, biological proteins, organometallic compounds, periodic organic and inorganic materials, etc. Final discussion is given to challenges and outlooks of ab initio nonadiabatic dynamics simulations.
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Affiliation(s)
- Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Pei-Ke Jia
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Ke-Xin Wang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, Sichuan, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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18
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Li B, Xu J, Li G, Shi Z, Wang L. A Mixed Deterministic-Stochastic Algorithm of the Branching Corrected Mean Field Method for Nonadiabatic Dynamics. J Chem Phys 2022; 156:114116. [DOI: 10.1063/5.0084013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new algorithm of the branching corrected mean field (BCMF) method for nonadiabatic dynamics [J. Xu and L. Wang, J. Phys. Chem. Lett. 11, 8283 (2020)], which combines the key advantages of the two existed algorithms, i.e., the deterministic BCMF algorithm based on weights of trajectory branches (BCMF-w) and the stochastic BCMF algorithm with random collapse of the electronic wavefunction (BCMF-s). The resulting mixed deterministic-stochastic BCMF algorithm (BCMF-ws) is benchmarked in a series of standard scattering problems with potential wells on the excited-state surfaces, which are common in realistic systems. In all investigated cases, BCMF-ws holds the same high accuracy while the computational time is reduced about two orders of magnitude compared to the original BCMF-w and BCMF-s algorithms, thus promising for nonadiabatic dynamics simulations of general systems.
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Affiliation(s)
| | | | | | | | - Linjun Wang
- Department of Chemistry, Zhejiang University, China
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19
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Vindel-Zandbergen P, Matsika S, Maitra NT. Exact-Factorization-Based Surface Hopping for Multistate Dynamics. J Phys Chem Lett 2022; 13:1785-1790. [PMID: 35170972 DOI: 10.1021/acs.jpclett.1c04132] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A surface-hopping algorithm recently derived from the exact factorization approach, SHXF [Ha et al. J. Phys. Chem. Lett. 2018, 9, 1097], introduces an additional term in the electronic equation of surface hopping that couples electronic states through the quantum momentum. This term not only provides a first-principles description of decoherence, but here we show it is crucial to accurately capture nonadiabatic dynamics when more than two states are occupied at any given time. Using a vibronic coupling model of the uracil cation, we show that the lack of this term in traditional surface-hopping methods, including those with decoherence corrections, leads to failure to predict the dynamics through a three-state intersection, while SHXF performs similarly to the multiconfiguration time-dependent Hartree quantum dynamics benchmark.
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Affiliation(s)
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
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20
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Shu Y, Zhang L, Chen X, Sun S, Huang Y, Truhlar DG. Nonadiabatic Dynamics Algorithms with Only Potential Energies and Gradients: Curvature-Driven Coherent Switching with Decay of Mixing and Curvature-Driven Trajectory Surface Hopping. J Chem Theory Comput 2022; 18:1320-1328. [PMID: 35104136 DOI: 10.1021/acs.jctc.1c01080] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Direct dynamics by mixed quantum-classical nonadiabatic methods is an important tool for understanding processes involving multiple electronic states. Very often, the computational bottleneck of such direct simulation comes from electronic structure theory. For example, at every time step of a trajectory, nonadiabatic dynamics requires potential energy surfaces, their gradients, and the matrix elements coupling the surfaces. The need for the couplings can be alleviated by employing the time derivatives of the wave functions, which can be evaluated from overlaps of electronic wave functions at successive time steps. However, evaluation of overlap integrals is still expensive for large systems. In addition, for electronic structure methods for which the wave functions or the coupling matrix elements are not available, nonadiabatic dynamics algorithms become inapplicable. In this work, building on recent work by Baeck and An, we propose new nonadiabatic dynamics algorithms that only require adiabatic potential energies and their gradients. The new methods are named curvature-driven coherent switching with decay of mixing (κCSDM) and curvature-driven trajectory surface hopping (κTSH). We show how powerful these new methods are in terms of computation time and accuracy as compared to previous mixed quantum-classical nonadiabatic dynamics algorithms. The lowering of the computational cost will allow longer nonadiabatic trajectories and greater ensemble averaging to be affordable, and the ability to calculate the dynamics without electronic structure coupling matrix elements extends the dynamics capability to new classes of electronic structure methods.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Linyao Zhang
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China.,School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Xiye Chen
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China.,School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Shaozeng Sun
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Yudong Huang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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21
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Lin K, Peng J, Gu FL, Lan Z. Simulation of Open Quantum Dynamics with Bootstrap-Based Long Short-Term Memory Recurrent Neural Network. J Phys Chem Lett 2021; 12:10225-10234. [PMID: 34647736 DOI: 10.1021/acs.jpclett.1c02672] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The recurrent neural network with the long short-term memory cell (LSTM-NN) is employed to simulate the long-time dynamics of open quantum systems. The bootstrap method is applied in the LSTM-NN construction and prediction, which provides a Monte Carlo estimation of a forecasting confidence interval. Within this approach, a large number of LSTM-NNs are constructed by resampling time-series sequences that were obtained from the early stage quantum evolution given by numerically exact multilayer multiconfigurational time-dependent Hartree method. The built LSTM-NN ensemble is used for the reliable propagation of the long-time quantum dynamics, and the simulated result is highly consistent with the exact evolution. The forecasting uncertainty that partially reflects the reliability of the LSTM-NN prediction is also given. This demonstrates the bootstrap-based LSTM-NN approach is a practical and powerful tool to propagate the long-time quantum dynamics of open systems with high accuracy and low computational cost.
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Affiliation(s)
- Kunni Lin
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Jiawei Peng
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
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22
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Wong JC, Kanai Y. First Principles Dynamics Study of Excited Hole Relaxation in DNA. Chemphyschem 2021; 23:e202100521. [PMID: 34494706 DOI: 10.1002/cphc.202100521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/30/2021] [Indexed: 11/08/2022]
Abstract
A recent theoretical work showed that ion irradiation generates excited holes deep within the valence band of DNA. In this work, we investigate the excited hole relaxation toward HOMO using a first-principles computational method following such ionization events. The excited hole relaxation is found to depend significantly on the energetic position of the excited hole generated. The relaxation process is found to be an order of magnitude slower for holes that are generated deeper than 20 eV than those generated within 10 eV, where the probability for the initial ionization events is the highest. However, the excited holes that are generated in different spatial moieties such as DNA nucleotide bases and phosphate backbones do not show noticeable differences in terms of the relaxation time. Our work also shows that decoherence due to nuclei dynamics slows down the relaxation by a factor of two or more. At the same time, the relaxation time is found to be less than a couple of picoseconds, much shorter than typical timescales associated with chemical bond dissociation.
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Affiliation(s)
- Jian Cheng Wong
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yosuke Kanai
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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23
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Vindel-Zandbergen P, Ibele LM, Ha JK, Min SK, Curchod BFE, Maitra NT. Study of the Decoherence Correction Derived from the Exact Factorization Approach for Nonadiabatic Dynamics. J Chem Theory Comput 2021; 17:3852-3862. [PMID: 34138553 PMCID: PMC8280698 DOI: 10.1021/acs.jctc.1c00346] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
![]()
We present a detailed
study of the decoherence correction to surface
hopping that was recently derived from the exact factorization approach.
Ab initio multiple spawning calculations that use the same initial
conditions and the same electronic structure method are used as a
reference for three molecules: ethylene, the methaniminium cation,
and fulvene, for which nonadiabatic dynamics follows a photoexcitation.
A comparison with the Granucci–Persico energy-based decoherence
correction and the augmented fewest-switches surface-hopping scheme
shows that the three decoherence-corrected methods operate on individual
trajectories in a qualitatively different way, but the results averaged
over trajectories are similar for these systems.
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Affiliation(s)
| | - Lea M Ibele
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Jong-Kwon Ha
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Seung Kyu Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Basile F E Curchod
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
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24
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Zhang L, Shu Y, Sun S, Truhlar DG. Direct coherent switching with decay of mixing for intersystem crossing dynamics of thioformaldehyde: The effect of decoherence. J Chem Phys 2021; 154:094310. [PMID: 33685154 DOI: 10.1063/5.0037878] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We evaluate the effect of electronic decoherence on intersystem crossing in the photodynamics of thioformaldehyde. First, we show that the state-averaged complete-active-space self-consistent field electronic structure calculations with a properly chosen active space of 12 active electrons in 10 active orbitals can predict the potential energy surfaces and the singlet-triplet spin-orbit couplings quite well for CH2S, and we use this method for direct dynamics by coherent switching with decay of mixing (CSDM). We obtain similar dynamical results with CSDM or by adding energy-based decoherence to trajectory surface hopping, with the population of triplet states tending to a small steady-state value over 500 fs. Without decoherence, the state populations calculated by the conventional trajectory surface hopping method or the semiclassical Ehrenfest method gradually increase. This difference shows that decoherence changes the nature of the results not just quantitatively but qualitatively.
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Affiliation(s)
- Linyao Zhang
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Yinan Shu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | - Shaozeng Sun
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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25
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Tang D, Shen L, Fang WH. Evaluation of mixed quantum-classical molecular dynamics on cis-azobenzene photoisomerization. Phys Chem Chem Phys 2021; 23:13951-13964. [PMID: 34142685 DOI: 10.1039/d1cp01374b] [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
The quantitative prediction of nonadiabatic transitions between different electronic states is important to understand ultrafast processes in photochemistry. A variety of mixed quantum-classical molecular dynamics methods such as surface hopping and Ehrenfest mean-field have been developed. However, how to choose an appropriate one from a wide diversity of dynamics algorithms to study a realistic photochemical process is still unclear. In this work, we implemented 30 combinations of different mixed quantum-classical dynamics methods, including 24 surface hopping models with 8 decoherence corrections and 3 momentum rescaling strategies as well as 6 mean-field models. Then we performed numerical investigations by simulating the photoisomerization of cis-azobenzene combined with on-the-fly electronic structure calculations. Predictions of the S1 lifetime and the quantum yield of the photoproduct using different models are distinct. Surface hopping is more robust than mean-field in our test system. Moreover, the choice of momentum rescaling methods in surface hopping brings more significant changes than decoherence corrections, while a large discrepancy between simulation results with different mean-field algorithms has been observed.
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Affiliation(s)
- Diandong Tang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Lin Shen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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26
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Uratani H, Morioka T, Yoshikawa T, Nakai H. Fast Nonadiabatic Molecular Dynamics via Spin-Flip Time-Dependent Density-Functional Tight-Binding Approach: Application to Nonradiative Relaxation of Tetraphenylethylene with Locked Aromatic Rings. J Chem Theory Comput 2020; 16:7299-7313. [PMID: 33197192 DOI: 10.1021/acs.jctc.0c00936] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nonadiabatic dynamics around conical intersections between ground and excited states are crucial to understand excited-state phenomena in complex chemical systems. With this background in mind, we present an approach combining fewest-switches trajectory surface hopping and spin-flip (SF) time-dependent (TD) density-functional tight binding (DFTB), which is a simplified version of SF-TD density functional theory (DFT) with semiempirical parametrizations, for computationally efficient nonadiabatic molecular dynamics simulations. The estimated computational time of the SF-TD-DFTB approach is several orders of magnitude lower than that of SF-TD-DFT. In addition, the proposed method reproduces the time scales and quantum yields in photoisomerization reactions of azobenzene at a level comparable with conventional ab initio approaches, demonstrating reasonable accuracy. Finally, we report a practical application of the developed technique to explore the nonradiative relaxation processes of tetraphenylethylene and its derivative with torsionally locked aromatic rings and discuss the effect of locking the rings on the excited-state lifetime.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Toshiki Morioka
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8245, Japan
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27
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Xiao BY, Xu JB, Wang LJ. New energy-based decoherence correction approaches for trajectory surface hopping. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2006098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Bing-yang Xiao
- Center for Chemistry of Novel & High-Performance Materials, and Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Jia-bo Xu
- Center for Chemistry of Novel & High-Performance Materials, and Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Lin-jun Wang
- Center for Chemistry of Novel & High-Performance Materials, and Department of Chemistry, Zhejiang University, Hangzhou 310027, China
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28
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Conti I, Cerullo G, Nenov A, Garavelli M. Ultrafast Spectroscopy of Photoactive Molecular Systems from First Principles: Where We Stand Today and Where We Are Going. J Am Chem Soc 2020; 142:16117-16139. [PMID: 32841559 PMCID: PMC7901644 DOI: 10.1021/jacs.0c04952] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Computational spectroscopy is becoming a mandatory tool for the interpretation of the
complex, and often congested, spectral maps delivered by modern non-linear multi-pulse
techniques. The fields of Electronic Structure Methods,
Non-Adiabatic Molecular Dynamics, and Theoretical
Spectroscopy represent the three pillars of the virtual ultrafast
optical spectrometer, able to deliver transient spectra in
silico from first principles. A successful simulation strategy requires a
synergistic approach that balances between the three fields, each one having its very
own challenges and bottlenecks. The aim of this Perspective is to demonstrate that,
despite these challenges, an impressive agreement between theory and experiment is
achievable now regarding the modeling of ultrafast photoinduced processes in complex
molecular architectures. Beyond that, some key recent developments in the three fields
are presented that we believe will have major impacts on spectroscopic simulations in
the very near future. Potential directions of development, pending challenges, and
rising opportunities are illustrated.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, IFN-CNR, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
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29
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Shu Y, Zhang L, Sun S, Truhlar DG. Time-Derivative Couplings for Self-Consistent Electronically Nonadiabatic Dynamics. J Chem Theory Comput 2020; 16:4098-4106. [PMID: 32456433 DOI: 10.1021/acs.jctc.0c00409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electronically nonadiabatic dynamics methods based on a self-consistent potential, such as semiclassical Ehrenfest and coherent switching with decay of mixing, have a number of advantages but are computationally slower than approximations based on an unaveraged potential because they require evaluation of all components of the nonadiabatic coupling vector. Here we introduce a new approximation to the self-consistent potential that does not have this computational drawback. The new approximation uses time-derivative couplings evaluated by overlap integrals of electronic wave functions to approximate the nonadiabatic coupling terms in the equations of motion. We present a numerical test of the method for ethylene that shows there is little loss of accuracy in the ensemble-averaged results. This new approximation to the self-consistent potential makes direct dynamics calculations with self-consistent potentials more efficient for complex systems and makes them practically affordable for some cases where the cost was previously too high.
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Affiliation(s)
- Yinan Shu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Linyao Zhang
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States.,School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Shaozeng Sun
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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30
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Shu Y, Zhang L, Mai S, Sun S, González L, Truhlar DG. Implementation of Coherent Switching with Decay of Mixing into the SHARC Program. J Chem Theory Comput 2020; 16:3464-3475. [DOI: 10.1021/acs.jctc.0c00112] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yinan Shu
- Department of Chemistry and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Linyao Zhang
- Department of Chemistry and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, People’s Republic of China
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090, Vienna, Austria
| | - Shaozeng Sun
- School of Energy Science and Engineering, Harbin Institute of Technology, Harbin 150001, People’s Republic of China
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090, Vienna, Austria
| | - Donald G. Truhlar
- Department of Chemistry and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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31
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Xie W, Holub D, Kubař T, Elstner M. Performance of Mixed Quantum-Classical Approaches on Modeling the Crossover from Hopping to Bandlike Charge Transport in Organic Semiconductors. J Chem Theory Comput 2020; 16:2071-2084. [PMID: 32176844 DOI: 10.1021/acs.jctc.9b01271] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In the present study, several mixed quantum-classical (MQC) methods are applied to on-the-fly nonadiabatic molecular dynamics simulations of hole transport in molecular organic semiconductors (OSCs). The tested MQC methods contain the mean-field Ehrenfest (MFE), trajectory surface hopping (TSH) approaches based on Tully's fewest switches surface hopping (FSSH) and the global flux surface hopping (GFSH), the latter in the diabatic/adiabatic representation, and a Landau-Zener type trajectory surface hopping (LZSH). We also tested several correction schemes which were proposed to identify trivial crossings and to remove unphysical long-range charge transfers due to decoherence corrections. In addition, several cost-effective approaches for the nuclear velocity adjustment after an energy-allowed/energy-forbidden hop are investigated with respect to detailed balance and internal consistency conditions. To model a broad spectrum of OSCs with different charge transport characteristics, we derived from the anthracene structural model the construction of two additional models by uniformly scaling down the electronic couplings by the factors of 0.1 and 0.5. Anthracene shows a bandlike charge transport mechanism, characterized by slightly delocalized charge carriers 'diffusing' through the crystal. For smaller couplings, the mechanism changes to a hopping type, characteristically differing in the charge delocalization and temperature dependence. The MFE and corrected adiabatic TSH approaches are able to quantitatively reproduce the expected behavior, while the diabatic LZSH method fails for large couplings, as do approaches which are based on the hopping of localized charge between neighboring sites. Moreover, we find that while the hole mobility of the anthracene crystal simulated using the celebrated Marcus theory is in good agreement with the experimental value, its agreement has to be regarded as an accident due to the overestimation of the prefactor in the Marcus rate equation.
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Affiliation(s)
- Weiwei Xie
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Daniel Holub
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany.,Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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32
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R S L, Kurup GB, Vennapusa SR. Identification of a receiver triplet state in the ultrafast intersystem crossing of carbonylpyrenes. Phys Chem Chem Phys 2020; 22:6145-6153. [PMID: 32124884 DOI: 10.1039/c9cp06857k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The near-unity triplet quantum yield of photoexcited carbonyl functionalized pyrenes is theoretically investigated. The estimated energetics of singlet-triplet manifolds and relevant spin-orbit coupling parameters strongly suggest triplet state formation via the S1→ T4/T5 pathway. Quantum wavepacket dynamics of triplet manifolds within the linear vibronic coupling approach reveal that the receiver triplet state would undergo rapid internal conversion decay to the lower triplet state(s), facilitating efficient triplet generation by minimizing the reverse intersystem crossing possibilities. On the basis of these results, a unified mechanism is proposed to describe the ultrafast intersystem crossing process in these molecules.
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Affiliation(s)
- Lekshmi R S
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM), Maruthamala P.O., Vithura, Thiruvananthapuram 695551, Kerala, India.
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33
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Ibele LM, Nicolson A, Curchod BFE. Excited-state dynamics of molecules with classically driven trajectories and Gaussians. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1665199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Lea M. Ibele
- Department of Chemistry, Durham University, Durham, UK
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34
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Shen L, Tang D, Xie B, Fang WH. Quantum Trajectory Mean-Field Method for Nonadiabatic Dynamics in Photochemistry. J Phys Chem A 2019; 123:7337-7350. [PMID: 31373814 DOI: 10.1021/acs.jpca.9b03480] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mixed quantum-classical dynamical approaches have been widely used to study nonadiabatic phenomena in photochemistry and photobiology, in which the time evolutions of the electronic and nuclear subsystems are treated based on quantum and classical mechanics, respectively. The key issue is how to deal with coherence and decoherence during the propagation of the two subsystems, which has been the subject of numerous investigations for a few decades. A brief description on Ehrenfest mean-field and surface-hopping (SH) methods is first provided, and then different algorithms for treatment of quantum decoherence are reviewed in the present paper. More attentions were paid to quantum trajectory mean-field (QTMF) method under the picture of quantum measurements, which is able to overcome the overcoherence problem. Furthermore, the combined QTMF and SH algorithm is proposed in the present work, which takes advantages of the QTMF and SH methods. The potential to extend the applicability of the QTMF method was briefly discussed, such as the generalization to other type of nonadiabatic transitions, the combination with multiscale computational models, and possible improvements on its accuracy and efficiency by using machine-learning techniques.
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Affiliation(s)
- Lin Shen
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , P. R. China
| | - Diandong Tang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , P. R. China
| | - Binbin Xie
- Hangzhou Institute of Advanced Studies , Zhejiang Normal University , 1108 Gengwen Road , Hangzhou 311231 , Zhejiang P. R. China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , P. R. China
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35
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Wang L, Qiu J, Bai X, Xu J. Surface hopping methods for nonadiabatic dynamics in extended systems. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1435] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Linjun Wang
- Center for Chemistry of Novel & High‐Performance Materials, Department of Chemistry Zhejiang University Hangzhou China
| | - Jing Qiu
- Center for Chemistry of Novel & High‐Performance Materials, Department of Chemistry Zhejiang University Hangzhou China
| | - Xin Bai
- Center for Chemistry of Novel & High‐Performance Materials, Department of Chemistry Zhejiang University Hangzhou China
| | - Jiabo Xu
- Center for Chemistry of Novel & High‐Performance Materials, Department of Chemistry Zhejiang University Hangzhou China
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36
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Plasser F, Mai S, Fumanal M, Gindensperger E, Daniel C, González L. Strong Influence of Decoherence Corrections and Momentum Rescaling in Surface Hopping Dynamics of Transition Metal Complexes. J Chem Theory Comput 2019; 15:5031-5045. [DOI: 10.1021/acs.jctc.9b00525] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Felix Plasser
- Institute for Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Loughborough, LE11 3TU, U.K
| | - Sebastian Mai
- Institute for Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 17, 1090 Vienna, Austria
| | - Maria Fumanal
- Laboratoire de Chimie Quantique, Institut de Chimie Strasbourg, UMR7177 CNRS/Université de Strasbourg 4 Rue Blaise Pascal BP296/R8, F-67008 Strasbourg, France
| | - Etienne Gindensperger
- Laboratoire de Chimie Quantique, Institut de Chimie Strasbourg, UMR7177 CNRS/Université de Strasbourg 4 Rue Blaise Pascal BP296/R8, F-67008 Strasbourg, France
| | - Chantal Daniel
- Laboratoire de Chimie Quantique, Institut de Chimie Strasbourg, UMR7177 CNRS/Université de Strasbourg 4 Rue Blaise Pascal BP296/R8, F-67008 Strasbourg, France
| | - Leticia González
- Institute for Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 17, 1090 Vienna, Austria
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37
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Xu J, Wang L. Branching corrected surface hopping: Resetting wavefunction coefficients based on judgement of wave packet reflection. J Chem Phys 2019; 150:164101. [DOI: 10.1063/1.5090927] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Jiabo Xu
- Department of Chemistry, Center for Chemistry of Novel and High-Performance Materials, Zhejiang University, Hangzhou 310027, China
| | - Linjun Wang
- Department of Chemistry, Center for Chemistry of Novel and High-Performance Materials, Zhejiang University, Hangzhou 310027, China
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38
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Xie W, Sapunar M, Došlić N, Sala M, Domcke W. Assessing the performance of trajectory surface hopping methods: Ultrafast internal conversion in pyrazine. J Chem Phys 2019; 150:154119. [DOI: 10.1063/1.5084961] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Weiwei Xie
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Marin Sapunar
- Department of Physical Chemistry, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia
| | - Matthieu Sala
- Laboratoire Interdisciplinaire Carnot de Bourgogne UMR 6303 CNRS, Université de Bourgogne, BP 47870, F-21078 Dijon, France and Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
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39
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Dokukina I, Nenov A, Garavelli M, Marian CM, Weingart O. QM/MM Photodynamics of Retinal in the Channelrhodopsin Chimera C1C2 with OM3/MRCI. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Irina Dokukina
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”Universitá degli Studi di Bologna Viale del Risorgimento, 4 40136 Bologna Italia
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”Universitá degli Studi di Bologna Viale del Risorgimento, 4 40136 Bologna Italia
| | - Christel M. Marian
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
| | - Oliver Weingart
- Institut für Theoretische Chemie und ComputerchemieHeinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf Germany
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40
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Li X, Hu D, Xie Y, Lan Z. Analysis of trajectory similarity and configuration similarity in on-the-fly surface-hopping simulation on multi-channel nonadiabatic photoisomerization dynamics. J Chem Phys 2018; 149:244104. [DOI: 10.1063/1.5048049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Xusong Li
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Sino-Danish Center for Education and Research/Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deping Hu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Xie
- The Environmental Research Institute, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Sino-Danish Center for Education and Research/Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- The Environmental Research Institute, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
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41
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Xie Y, Zheng J, Lan Z. Performance evaluation of the symmetrical quasi-classical dynamics method based on Meyer-Miller mapping Hamiltonian in the treatment of site-exciton models. J Chem Phys 2018; 149:174105. [DOI: 10.1063/1.5047002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu Xie
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
- The Environmental Research Institute; MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Jie Zheng
- Industrial Research Institute of Nonwovens and Technical Textiles, College of Textiles and Clothing, Qingdao University, Qingdao 266071, China
| | - Zhenggang Lan
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, Shandong, China
- The Environmental Research Institute; MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
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42
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COBRAMM 2.0 — A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations. J Mol Model 2018; 24:271. [DOI: 10.1007/s00894-018-3769-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/27/2018] [Indexed: 01/04/2023]
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43
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Alonso JL, Bruscolini P, Castro A, Clemente-Gallardo J, Cuchí JC, Jover-Galtier JA. Ehrenfest Statistical Dynamics in Chemistry: Study of Decoherence Effects. J Chem Theory Comput 2018; 14:3975-3985. [DOI: 10.1021/acs.jctc.8b00511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. L. Alonso
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, ES 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor s/n, Edificio
I+D, ES 50018 Zaragoza, Spain
- Unidad asociada IQFR-BIFI, Universidad de Zaragoza, Edificio I+D-Campus Rı́o Ebro, Mariano Esquillor s/n, ES 50018 Zaragoza, Spain
| | - P. Bruscolini
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, ES 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor s/n, Edificio
I+D, ES 50018 Zaragoza, Spain
| | - A. Castro
- BIFI-Fundación ARAID, Universidad de Zaragoza, Edificio I+D-Campus Río Ebro, Mariano Esquillor s/n, ES 50018 Zaragoza, Spain
| | - J. Clemente-Gallardo
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, ES 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor s/n, Edificio
I+D, ES 50018 Zaragoza, Spain
| | - J. C. Cuchí
- Departament d’Enginyeria Agroforestal, ETSEA-Universitat de Lleida, Avenida Alcalde Rovira Roure 191, ES 25198 Lleida, Spain
| | - J. A. Jover-Galtier
- Departamento de Física Teórica, Universidad de Zaragoza, Pedro Cerbuna 12, ES 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor s/n, Edificio
I+D, ES 50018 Zaragoza, Spain
- Centro Universitario de la Defensa de Zaragoza, Academia General Militar, Carretera de Huesca s/n, ES 50090 Zaragoza, Spain
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44
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Crespo-Otero R, Barbatti M. Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics. Chem Rev 2018; 118:7026-7068. [DOI: 10.1021/acs.chemrev.7b00577] [Citation(s) in RCA: 301] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rachel Crespo-Otero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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45
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Gao LH, Xie BB, Fang WH. Theories and Applications of Mixed Quantum-Classical Non-adiabatic Dynamics. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1712234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Liang-hui Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Bin-bin Xie
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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46
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Xie W, Domcke W. Accuracy of trajectory surface-hopping methods: Test for a two-dimensional model of the photodissociation of phenol. J Chem Phys 2017; 147:184114. [DOI: 10.1063/1.5006788] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Weiwei Xie
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747 Garching, Germany
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47
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Li X, Xie Y, Hu D, Lan Z. Analysis of the Geometrical Evolution in On-the-Fly Surface-Hopping Nonadiabatic Dynamics with Machine Learning Dimensionality Reduction Approaches: Classical Multidimensional Scaling and Isometric Feature Mapping. J Chem Theory Comput 2017; 13:4611-4623. [DOI: 10.1021/acs.jctc.7b00394] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Xusong Li
- CAS
Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Sino-Danish
Center for Education and Research/Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kgs. Lyngby, Denmark
| | - Yu Xie
- CAS
Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Deping Hu
- CAS
Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenggang Lan
- CAS
Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy
and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Sino-Danish
Center for Education and Research/Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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48
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Han Y, Meng Q, Rasulev B, May PS, Berry MT, Kilin DS. Photoinduced Charge Transfer versus Fragmentation Pathways in Lanthanum Cyclopentadienyl Complexes. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00050] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yulun Han
- Department
of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
- Department
of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Qingguo Meng
- Shenyang
Institute of Automation, Guangzhou, Chinese Academy of Sciences, Guangzhou 511458, China
| | - Bakhtiyor Rasulev
- Center
for Computationally Assisted Science and Technology, North Dakota State University, Fargo, North Dakota 58102, United States
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58102, United States
| | - P. Stanley May
- Department
of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
| | - Mary T. Berry
- Department
of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
| | - Dmitri S. Kilin
- Department
of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
- Department
of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
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49
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Time-resolved photoelectron signals from bifurcating electron wavepackets propagated across conical intersection in path-branching dynamics. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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50
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Wolter M, Elstner M, Kleinekathöfer U, Kubař T. Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details. J Phys Chem B 2017; 121:529-549. [PMID: 28045546 DOI: 10.1021/acs.jpcb.6b11384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The transfer of electrons over long distances in complex molecular systems is a phenomenon of significance in both biochemistry and technology. In recent years, we have been developing efficient models to study ET in complex systems, including DNA as a prominent example. Ab initio and model approaches have been combined in an "on-the-fly" calculation of ET parameters, which can be used to propagate nuclear and electronic degrees of freedom simultaneously. These previous efforts have aimed at deriving an efficient nonadiabatic quantum mechanical-molecular mechanical (QM/MM) simulation scheme for ET, making nanosecond simulations of ET in realistic systems possible. This, however, is still insufficient for the treatment of large donor-bridge-acceptor systems, like the ET in DNA, overcoming long adenine bridges. Therefore, we have constructed a theoretical model in a bottom-up manner. All quantum-chemical as well as force-field calculations are substituted by theoretical models of the involved phenomena on a molecular level, including polarization and relaxation of the molecular environment, which are often omitted in other recently developed theoretical models of ET. A nonadiabatic simulation scheme is employed, and no assumptions regarding the ET mechanism are needed. Thus, the predictive power of the simulations is preserved, while pushing the limits of the accessible time scales beyond microseconds. This model-based simulation scheme is applied to ET in various DNA species. Good agreement with the "full" atomistic nonadiabatic QM/MM scheme is observed for the archetypal DNA ET systems, the polyA sequence, as well as the sequences GTnGGG, containing adenines as bridge sites. Furthermore, ET in larger, more complex DNA sequences is simulated, and the results are discussed.
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Affiliation(s)
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen , 28759 Bremen, Germany
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