1
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Hu Z, Deng ZY, Feng HJ. Effects of BPQ binding on the nonadiabatic dynamics of excited electrons in poly(dG)-poly(dC) DNA under proton irradiation. Phys Chem Chem Phys 2024. [PMID: 39192749 DOI: 10.1039/d4cp01917b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
The interaction between DNA and small molecules is important for understanding the mechanisms of DNA-based multifunctional devices and has been extensively studied. However, there are few reports on such interactions in irradiation environments. Here, we investigate the nonadiabatic dynamic behaviors of excited electrons in double-stranded DNA bound to BPQ molecule upon proton irradiation, focusing on the energy deposition and electronic excitation dynamics as protons traverse the DNA along different channels. Our results reveal that the presence of BPQ significantly influences charge migration and DNA damage, with notable differences between CGvdW and CGcovalent adducts. The energy deposition process is highly dependent on charge density, and guanine exhibits higher excitation propensity than cytosine due to its structural characteristics. The BPQ molecule enhances DNA charge migration and promotes damage through secondary electron migration. These findings provide insights into the nonadiabatic dynamics of DNA under ionizing radiation and have implications for designing targeted electrophilic organics to improve radiotherapy efficacy.
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Affiliation(s)
- Zhihua Hu
- School of Physics, Northwest University, Xi'an 710127, China.
| | - Zun-Yi Deng
- School of Physics, Northwest University, Xi'an 710127, China.
| | - Hong-Jian Feng
- School of Physics, Northwest University, Xi'an 710127, China.
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2
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Solov’yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov’yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 PMCID: PMC11240271 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
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Affiliation(s)
| | | | - Nigel J. Mason
- School
of Physics and Astronomy, University of
Kent, Canterbury CT2 7NH, United
Kingdom
| | - Richard A. Amos
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université
Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université,
CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre
for Light Matter Interactions, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty
of Engineering, University of Applied Sciences
Aschaffenburg, Würzburger
Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European
Innovation Center, Bořivojova
2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université
Claude Bernard Lyon 1, CNRS, Institut Lumière
Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Kate Ricketts
- Department
of Targeted Intervention, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- University
College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E. H. Wheatley
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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3
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Mortensen JJ, Larsen AH, Kuisma M, Ivanov AV, Taghizadeh A, Peterson A, Haldar A, Dohn AO, Schäfer C, Jónsson EÖ, Hermes ED, Nilsson FA, Kastlunger G, Levi G, Jónsson H, Häkkinen H, Fojt J, Kangsabanik J, Sødequist J, Lehtomäki J, Heske J, Enkovaara J, Winther KT, Dulak M, Melander MM, Ovesen M, Louhivuori M, Walter M, Gjerding M, Lopez-Acevedo O, Erhart P, Warmbier R, Würdemann R, Kaappa S, Latini S, Boland TM, Bligaard T, Skovhus T, Susi T, Maxson T, Rossi T, Chen X, Schmerwitz YLA, Schiøtz J, Olsen T, Jacobsen KW, Thygesen KS. GPAW: An open Python package for electronic structure calculations. J Chem Phys 2024; 160:092503. [PMID: 38450733 DOI: 10.1063/5.0182685] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 03/08/2024] Open
Abstract
We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.
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Affiliation(s)
- Jens Jørgen Mortensen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ask Hjorth Larsen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mikael Kuisma
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Aleksei V Ivanov
- Riverlane Ltd., St Andrews House, 59 St Andrews Street, Cambridge CB2 3BZ, United Kingdom
| | - Alireza Taghizadeh
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Andrew Peterson
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Anubhab Haldar
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Asmus Ougaard Dohn
- Department of Physics, Technical University of Denmark, 2800 Lyngby, Denmark and Science Institute and Faculty of Physical Sciences, VR-III, University of Iceland, Reykjavík 107, Iceland
| | - Christian Schäfer
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Eric D Hermes
- Quantum-Si, 29 Business Park Drive, Branford, Connecticut 06405, USA
| | | | - Georg Kastlunger
- CatTheory, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Gianluca Levi
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Hannu Häkkinen
- Departments of Physics and Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Jakub Fojt
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Jiban Kangsabanik
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Joachim Sødequist
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jouko Lehtomäki
- Department of Applied Physics, Aalto University, P.O. Box 11100, 00076 Aalto, Finland
| | - Julian Heske
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jussi Enkovaara
- CSC-IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Kirsten Trøstrup Winther
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Marcin Dulak
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Marko M Melander
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Martin Ovesen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Martti Louhivuori
- CSC-IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Michael Walter
- FIT Freiburg Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Morten Gjerding
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Olga Lopez-Acevedo
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia
| | - Paul Erhart
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Robert Warmbier
- School of Physics and Mandelstam Institute for Theoretical Physics, University of the Witwatersrand, 1 Jan Smuts Avenue, 2001 Johannesburg, South Africa
| | - Rolf Würdemann
- Freiburger Materialforschungszentrum, Universität Freiburg, Stefan-Meier-Straße 21, D-79104 Freiburg, Germany
| | - Sami Kaappa
- Computational Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Simone Latini
- Nanomade, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Tara Maria Boland
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Thomas Bligaard
- Department of Energy Conversion and Storage, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Thorbjørn Skovhus
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Toma Susi
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Tristan Maxson
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, USA
| | - Tuomas Rossi
- CSC-IT Center for Science Ltd., P.O. Box 405, FI-02101 Espoo, Finland
| | - Xi Chen
- School of Physical Science and Technology, Lanzhou University, Lanzhou, Gansu 730000, China
| | | | - Jakob Schiøtz
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Thomas Olsen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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4
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Zhao X, Merritt ICD, Lei R, Shu Y, Jacquemin D, Zhang L, Xu X, Vacher M, Truhlar DG. Nonadiabatic Coupling in Trajectory Surface Hopping: Accurate Time Derivative Couplings by the Curvature-Driven Approximation. J Chem Theory Comput 2023; 19:6577-6588. [PMID: 37772732 DOI: 10.1021/acs.jctc.3c00813] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Trajectory surface hopping (TSH) is a widely used mixed quantum-classical dynamics method that is used to simulate molecular dynamics with multiple electronic states. In TSH, time-derivative coupling is employed to propagate the electronic coefficients and in that way to determine when the electronic state on which the nuclear trajectory is propagated switches. In this work, we discuss nonadiabatic TSH dynamics algorithms employing the curvature-driven approximation and overlap-based time derivative couplings, and we report test calculations on six photochemical reactions where we compare the results to one another and to calculations employing analytic nonadiabatic coupling vectors. We correct previous published results thanks to a bug found in the software. We also provide additional, more detailed studies of the time-derivative couplings. Our results show good agreement between curvature-driven algorithms and overlap-based algorithms.
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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
| | | | - Ruiqing Lei
- Center for Combustion Energy, Tsinghua University, Beijing 100084, P. R. China
| | - Yinan Shu
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
- Institut Universitaire de France (IUF), Paris 75005, France
| | - 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
- Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, P. R. China
| | - Morgane Vacher
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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5
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Melander MM. Frozen or dynamic? — An atomistic simulation perspective on the timescales of electrochemical reactions. Electrochim Acta 2023. [DOI: 10.1016/j.electacta.2023.142095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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6
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Wu X, Wen S, Song H, Frauenheim T, Tretiak S, Yam C, Zhang Y. Nonadiabatic Molecular Dynamics Simulations Based on Time-Dependent Density Functional Tight-Binding Method. J Chem Phys 2022; 157:084114. [DOI: 10.1063/5.0100339] [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
Nonadiabatic excited-state molecular dynamics underpin many photophysical and photochemical phenomena, such as exciton dynamics, charge separation and transport. In this work, we present an efficient nonadiabatic molecular dynamic (NAMD) simulation method based on time-dependent density functional tight-binding (TDDFTB) theory. Specifically, the adiabatic electronic structure, an essential NAMD input, is described at the TDDFTB level. The nonadiabatic effects originating from the coupled motions of electrons and nuclei are treated by the trajectory surface hopping algorithm. To improve the computational efficiency, nonadiabatic couplings between excited states within the TDDFTB method are derived and implemented using an analytical approach. Further, the time-dependent nonadiabatic coupling scalars are calculated based on the overlap between molecular orbitals rather than the Slater determinants to speed up the simulations. In addition, the electronic decoherence scheme and a state reassigned unavoided crossings algorithm, which has been implemented in the NEXMD software, are used to improve the accuracy of the simulated dynamics and handle trivial unavoided crossings. Finally, the photoinduced nonadiabatic dynamics of a benzene molecule are simulated to demonstrate our implementation. The results for excited state NAMD simulations of benzene molecule based on TDDFTB method compare well that obtained with numerically expensive time-dependent density functional theory. The proposed methodology provides an attractive theoretical simulation tool for predicting the photophysical and photochemical properties of complex materials.
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Affiliation(s)
- Xiaoyan Wu
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen JL Computational Science and Applied Research Institute, China
| | | | - Huajing Song
- Los Alamos National Laboratory, United States of America
| | | | - Sergei Tretiak
- Theoretical Division, T-1, Los Alamos National Laboratory, United States of America
| | - ChiYung Yam
- Beijing Computational Science Research Center, Beijing Computational Science Research Center, China
| | - Yu Zhang
- Theoretical Division, Los Alamos National Laboratory, United States of America
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7
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Yamijala SSRKC, Shinde R, Hanasaki K, Ali ZA, Wong BM. Photo-induced degradation of PFASs: Excited-state mechanisms from real-time time-dependent density functional theory. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127026. [PMID: 34481387 DOI: 10.1016/j.jhazmat.2021.127026] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
Per- and polyfluoroalkyl substances (PFASs) are hazardous, carcinogenic, and bioaccumulative contaminants found in drinking water sources. To mitigate and remove these persistent pollutants, recent experimental efforts have focused on photo-induced processes to accelerate their degradation; however, the mechanistic details of these promising degradation processes remain unclear. To shed crucial insight on these electronic-excited state processes, we present the first study of photo-induced degradation of explicitly-solvated PFASs using excited-state, real-time time-dependent density functional theory (RT-TDDFT) calculations. Furthermore, our large-scale RT-TDDFT calculations show that these photo-induced excitations can be highly selective by enabling a charge-transfer process that only dissociates the CF bond while keeping the surrounding water molecules intact. Collectively, the RT-TDDFT techniques used in this work (1) enable a new capability for probing photo-induced mechanisms that cannot be gleaned from conventional ground-state DFT calculations and (2) provide a rationale for understanding ongoing experiments that are actively exploring photo-induced degradation of PFASs and other environmental contaminants.
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Affiliation(s)
- Sharma S R K C Yamijala
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California Riverside, Riverside, CA 92521, USA; Department of Chemistry and Center for Atomistic Modelling and Materials Design, Indian Institute of Technology Madras, Chennai 600036, India
| | - Ravindra Shinde
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California Riverside, Riverside, CA 92521, USA
| | - Kota Hanasaki
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California Riverside, Riverside, CA 92521, USA
| | - Zulfikhar A Ali
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California Riverside, Riverside, CA 92521, USA
| | - Bryan M Wong
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California Riverside, Riverside, CA 92521, USA.
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8
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Shepard C, Zhou R, Yost DC, Yao Y, Kanai Y. Simulating electronic excitation and dynamics with real-time propagation approach to TDDFT within plane-wave pseudopotential formulation. J Chem Phys 2021; 155:100901. [PMID: 34525811 DOI: 10.1063/5.0057587] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We give a perspective on simulating electronic excitation and dynamics using the real-time propagation approach to time-dependent density functional theory (RT-TDDFT) in the plane-wave pseudopotential formulation. RT-TDDFT is implemented in various numerical formalisms in recent years, and its practical application often dictates the most appropriate implementation of the theory. We discuss recent developments and challenges, emphasizing numerical aspects of studying real systems. Several applications of RT-TDDFT simulation are discussed to highlight how the approach is used to study interesting electronic excitation and dynamics phenomena in recent years.
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Affiliation(s)
- Christopher Shepard
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - Ruiyi Zhou
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - Dillon C Yost
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Yi Yao
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
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9
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Schnappinger T, de Vivie-Riedle R. Coupled nuclear and electron dynamics in the vicinity of a conical intersection. J Chem Phys 2021; 154:134306. [PMID: 33832271 DOI: 10.1063/5.0041365] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ultrafast optical techniques allow us to study ultrafast molecular dynamics involving both nuclear and electronic motion. To support interpretation, theoretical approaches are needed that can describe both the nuclear and electron dynamics. Hence, we revisit and expand our ansatz for the coupled description of the nuclear and electron dynamics in molecular systems (NEMol). In this purely quantum mechanical ansatz, the quantum-dynamical description of the nuclear motion is combined with the calculation of the electron dynamics in the eigenfunction basis. The NEMol ansatz is applied to simulate the coupled dynamics of the molecule NO2 in the vicinity of a conical intersection (CoIn) with a special focus on the coherent electron dynamics induced by the non-adiabatic coupling. Furthermore, we aim to control the dynamics of the system when passing the CoIn. The control scheme relies on the carrier envelope phase of a few-cycle IR pulse. The laser pulse influences both the movement of the nuclei and the electrons during the population transfer through the CoIn.
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10
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Aierken Y, Agrawal A, Sun M, Melander M, Crumlin EJ, Helms BA, Prendergast D. Revealing Charge-Transfer Dynamics at Electrified Sulfur Cathodes Using Constrained Density Functional Theory. J Phys Chem Lett 2021; 12:739-744. [PMID: 33405937 DOI: 10.1021/acs.jpclett.0c03334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To understand and control the behavior of electrochemical systems, including batteries and electrocatalysts, we seek molecular-level details of the charge transfer mechanisms at electrified interfaces. Recognizing some key limitations of standard equilibrium electronic structure methods to model materials and their interfaces, we propose applying charge constraints to effectively separate electronic and nuclear degrees of freedom, which are especially beneficial to the study of conversion electrodes, where electronic charge carriers are converted to much slower polarons within a material that is nonmetallic. We demonstrate the need for such an approach within the context of sulfur cathodes and the arrival of Li ions during discharge of a Li-S cell. The requirement that electronic degrees of freedom are arrested is justified by comparison with real-time evolution of the electronic structure. Long-lived metastable configurations provide plenty of time for nuclear dynamics and relaxation in response to the electrification of the interface, a process that would be completely missed without applying charge constraints. This approach will be vital to the study of dynamics at electrified interfaces which may be created deliberately, adding charge to the electrode, or spontaneously, due to finite temperature dynamics in the electrolyte.
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Affiliation(s)
- Yierpan Aierken
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Ankit Agrawal
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Meiling Sun
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Marko Melander
- Nanoscience Center, Department of Chemistry, University of Jyväskylä, P.O. Box 35 (YN), Jyväskylä FI-40014, Finland
| | - Ethan J Crumlin
- Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Brett A Helms
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - David Prendergast
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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11
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Buntov EA, Zatsepin AF. Carbon Bond Breaking under Ar +-Ion Irradiation in Dependence on sp Hybridization: Car–Parrinello, Ehrenfest, and Classical Dynamics Study. J Phys Chem A 2020; 124:9128-9132. [DOI: 10.1021/acs.jpca.0c05739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evgeny A. Buntov
- Institute of Physics and Technology, Ural Federal University, Ekaterinburg 620002, Russia
| | - Anatoly F. Zatsepin
- Institute of Physics and Technology, Ural Federal University, Ekaterinburg 620002, Russia
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12
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You P, Chen D, Lian C, Zhang C, Meng S. First‐principles dynamics of photoexcited molecules and materials towards a quantum description. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1492] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Peiwei You
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Daqiang Chen
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Chao Lian
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
| | - Cui Zhang
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
- Songshan Lake Materials Laboratory Dongguan China
| | - Sheng Meng
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics Chinese Academy of Sciences Beijing China
- School of Physical Sciences University of Chinese Academy of Sciences Beijing China
- Songshan Lake Materials Laboratory Dongguan China
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13
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He X, Liu J. A new perspective for nonadiabatic dynamics with phase space mapping models. J Chem Phys 2019; 151:024105. [DOI: 10.1063/1.5108736] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xin He
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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14
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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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15
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Foglia NO, Morzan UN, Estrin DA, Scherlis DA, Gonzalez Lebrero MC. Role of Core Electrons in Quantum Dynamics Using TDDFT. J Chem Theory Comput 2016; 13:77-85. [DOI: 10.1021/acs.jctc.6b00771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicolás O. Foglia
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Uriel N. Morzan
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Dario A. Estrin
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Damian A. Scherlis
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Mariano C. Gonzalez Lebrero
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
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16
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Andermatt S, Cha J, Schiffmann F, VandeVondele J. Combining Linear-Scaling DFT with Subsystem DFT in Born–Oppenheimer and Ehrenfest Molecular Dynamics Simulations: From Molecules to a Virus in Solution. J Chem Theory Comput 2016; 12:3214-27. [DOI: 10.1021/acs.jctc.6b00398] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Jinwoong Cha
- Department
of Materials, ETH Zürich, Zürich, Switzerland
| | - Florian Schiffmann
- Department
of Materials, ETH Zürich, Zürich, Switzerland
- Centre
of Policy Studies, Victoria University, Melbourne, Australia
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17
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Baczewski AD, Shulenburger L, Desjarlais MP, Hansen SB, Magyar RJ. X-ray Thomson Scattering in Warm Dense Matter without the Chihara Decomposition. PHYSICAL REVIEW LETTERS 2016; 116:115004. [PMID: 27035307 DOI: 10.1103/physrevlett.116.115004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 06/05/2023]
Abstract
X-ray Thomson scattering is an important experimental technique used to measure the temperature, ionization state, structure, and density of warm dense matter (WDM). The fundamental property probed in these experiments is the electronic dynamic structure factor. In most models, this is decomposed into three terms [J. Chihara, J. Phys. F 17, 295 (1987)] representing the response of tightly bound, loosely bound, and free electrons. Accompanying this decomposition is the classification of electrons as either bound or free, which is useful for gapped and cold systems but becomes increasingly questionable as temperatures and pressures increase into the WDM regime. In this work we provide unambiguous first principles calculations of the dynamic structure factor of warm dense beryllium, independent of the Chihara form, by treating bound and free states under a single formalism. The computational approach is real-time finite-temperature time-dependent density functional theory (TDDFT) being applied here for the first time to WDM. We compare results from TDDFT to Chihara-based calculations for experimentally relevant conditions in shock-compressed beryllium.
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Affiliation(s)
- A D Baczewski
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - L Shulenburger
- Pulsed Power Sciences Center, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - M P Desjarlais
- Pulsed Power Sciences Center, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - S B Hansen
- Pulsed Power Sciences Center, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - R J Magyar
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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18
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Kolesov G, Grånäs O, Hoyt R, Vinichenko D, Kaxiras E. Real-Time TD-DFT with Classical Ion Dynamics: Methodology and Applications. J Chem Theory Comput 2015; 12:466-76. [DOI: 10.1021/acs.jctc.5b00969] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Grigory Kolesov
- John
A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Oscar Grånäs
- John
A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department
of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box
516, SE-75120 Uppsala, Sweden
| | - Robert Hoyt
- Department
of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Dmitry Vinichenko
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Efthimios Kaxiras
- John
A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department
of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
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19
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Krishtal A, Ceresoli D, Pavanello M. Subsystem real-time time dependent density functional theory. J Chem Phys 2015; 142:154116. [DOI: 10.1063/1.4918276] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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21
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Sakko A, Rossi TP, Nieminen RM. Dynamical coupling of plasmons and molecular excitations by hybrid quantum/classical calculations: time-domain approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:315013. [PMID: 25028486 DOI: 10.1088/0953-8984/26/28/315013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The presence of plasmonic material influences the optical properties of nearby molecules in untrivial ways due to the dynamical plasmon-molecule coupling. We combine quantum and classical calculation schemes to study this phenomenon in a hybrid system that consists of a Na(2) molecule located in the gap between two Au/Ag nanoparticles. The molecule is treated quantum-mechanically with time-dependent density-functional theory, and the nanoparticles with quasistatic classical electrodynamics. The nanoparticle dimer has a plasmon resonance in the visible part of the electromagnetic spectrum, and the Na(2) molecule has an electron-hole excitation in the same energy range. Due to the dynamical interaction of the two subsystems the plasmon and the molecular excitations couple, creating a hybridized molecular-plasmon excited state. This state has unique properties that yield e.g. enhanced photoabsorption compared to the freestanding Na(2) molecule. The computational approach used enables decoupling of the mutual plasmon-molecule interaction, and our analysis verifies that it is not legitimate to neglect the back coupling effect when describing the dynamical interaction between plasmonic material and nearby molecules. Time-resolved analysis shows nearly instantaneous formation of the coupled state, and provides an intuitive picture of the underlying physics.
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22
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Schleife A, Draeger EW, Kanai Y, Correa AA. Plane-wave pseudopotential implementation of explicit integrators for time-dependent Kohn-Sham equations in large-scale simulations. J Chem Phys 2012; 137:22A546. [DOI: 10.1063/1.4758792] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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