1
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Acheson K, Kirrander A. Robust Inversion of Time-Resolved Data via Forward-Optimization in a Trajectory Basis. J Chem Theory Comput 2023; 19:2721-2734. [PMID: 37129988 DOI: 10.1021/acs.jctc.2c01113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
An inversion method for time-resolved data from ultrafast experiments is introduced, based on forward-optimization in a trajectory basis. The method is applied to experimental data from X-ray scattering of the photochemical ring-opening reaction of 1,3-cyclohexadiene and electron diffraction of the photodissociation of CS2. In each case, inversion yields a model that reproduces the experimental data, identifies the main dynamic motifs, and agrees with independent experimental observations. Notably, the method explicitly accounts for continuity constraints and is robust even for noisy data.
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Affiliation(s)
- Kyle Acheson
- EaStCHEM, School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Adam Kirrander
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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2
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Moreno Carrascosa A, Coe JP, Simmermacher M, Paterson MJ, Kirrander A. Towards high-resolution X-ray scattering as a probe of electron correlation. Phys Chem Chem Phys 2022; 24:24542-24552. [DOI: 10.1039/d2cp02933b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We demonstrate that X-ray scattering can be used as a probe of electron–electron correlation.
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Affiliation(s)
- Andrés Moreno Carrascosa
- EaStCHEM, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Jeremy P. Coe
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Mats Simmermacher
- EaStCHEM, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Martin J. Paterson
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Adam Kirrander
- EaStCHEM, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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3
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Moreno Carrascosa A, Yang M, Yong H, Ma L, Kirrander A, Weber PM, Lopata K. Mapping static core-holes and ring-currents with X-ray scattering. Faraday Discuss 2021; 228:60-81. [PMID: 33605956 DOI: 10.1039/d0fd00124d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Measuring the attosecond movement of electrons in molecules is challenging due to the high temporal and spatial resolutions required. X-ray scattering-based methods are promising, but many questions remain concerning the sensitivity of the scattering signals to changes in density, as well as the means of reconstructing the dynamics from these signals. In this paper, we present simulations of stationary core-holes and electron dynamics following inner-shell ionization of the oxazole molecule. Using a combination of time-dependent density functional theory simulations along with X-ray scattering theory, we demonstrate that the sudden core-hole ionization produces a significant change in the X-ray scattering response and how the electron currents across the molecule should manifest as measurable modulations to the time dependent X-ray scattering signal. This suggests that X-ray scattering is a viable probe for measuring electronic processes at time scales faster than nuclear motion.
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Affiliation(s)
| | - Mengqi Yang
- Department of Chemistry, 232 Choppin Hall, Baton Rouge, Louisiana 70803, USA
| | - Haiwang Yong
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Lingyu Ma
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Adam Kirrander
- EaStCHEM, School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ Edinburgh, UK
| | - Peter M Weber
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kenneth Lopata
- Department of Chemistry, 232 Choppin Hall, Baton Rouge, Louisiana 70803, USA and Center for Computation and Technology, Louisiana State University, Baton Roug, Louisiana 70803, USA.
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4
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Kim JG, Choi EH, Lee Y, Ihee H. Femtosecond X-ray Liquidography Visualizes Wavepacket Trajectories in Multidimensional Nuclear Coordinates for a Bimolecular Reaction. Acc Chem Res 2021; 54:1685-1698. [PMID: 33733724 DOI: 10.1021/acs.accounts.0c00812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ConspectusVibrational wavepacket motions on potential energy surfaces are one of the critical factors that determine the reaction dynamics of photoinduced reactions. The motions of vibrational wavepackets are often discussed in the interpretation of observables measured with various time-resolved vibrational or electronic spectroscopies but mostly in terms of the frequencies of wavepacket motions, which are approximated by normal modes, rather than the actual positions of the wavepacket. Although the time-dependent positions (that is, the trajectory) of wavepackets are hypothesized or drawn in imagined or calculated potential energy surfaces, it is not trivial to experimentally determine the trajectory of wavepackets, especially in multidimensional nuclear coordinates for a polyatomic molecule. Recently, we performed a femtosecond X-ray liquidography (solution scattering) experiment on a gold trimer complex (GTC), [Au(CN)2-]3, in water at X-ray free-electron lasers (XFELs) and elucidated the time-dependent positions of vibrational wavepackets from the Franck-Condon region to equilibrium structures on both excited and ground states in the course of the formation of covalent bonds between gold atoms.Bond making is an essential process in chemical reactions, but it is challenging to keep track of detailed atomic movements associated with bond making because of its bimolecular nature that requires slow diffusion of two reaction parties to meet each other. Bond formation in the solution phase has been elusive because the diffusion of the reactants limits the reaction rate of a bimolecular process, making it difficult to initiate and track the bond-making processes with an ultrafast time resolution. In principle, if the bimolecular encounter can be controlled to overcome the limitation caused by diffusion, the bond-making processes can be tracked in a time-resolved manner, providing valuable insight into the bimolecular reaction mechanism. In this regard, GTC offers a good model system for studying the dynamics of bond formation in solution. Au(I) atoms in GTC exhibit a noncovalent aurophilic interaction, making GTC an aggregate complex without any covalent bond. Upon photoexcitation of GTC, an electron is excited from an antibonding orbital to a bonding orbital, leading to the formation of covalent bonds among Au atoms. Since Au atoms in the ground state of GTC are located in close proximity within the same solvent cage, the formation of Au-Au covalent bonds occurs without its reaction rate being limited by diffusion through the solvent.Femtosecond time-resolved X-ray liquidography (fs-TRXL) data revealed that the ground state has an asymmetric bent structure. From the wavepacket trajectory determined in three-dimensional nuclear coordinates (two internuclear distances and one bond angle), we found that two covalent bonds are formed between three Au atoms of GTC asynchronously. Specifically, one covalent bond is formed first for the shorter Au-Au pair (of the asymmetric and bent ground-state structure) in 35 fs, and subsequently, the other covalent bond is formed for the longer Au-Au pair within 360 fs. The resultant trimer complex has a symmetric and linear geometry, implying the occurrence of bent-to-linear transformation concomitant with the formation of two equivalent covalent bonds, and exhibits vibrations that can be unambiguously assigned to specific normal modes based on the wavepacket trajectory, even without the vibrational frequencies provided by quantum calculation.
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Affiliation(s)
- Jong Goo Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
- KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Eun Hyuk Choi
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
- KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
- KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
- KI for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
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5
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Kim JG, Nozawa S, Kim H, Choi EH, Sato T, Kim TW, Kim KH, Ki H, Kim J, Choi M, Lee Y, Heo J, Oang KY, Ichiyanagi K, Fukaya R, Lee JH, Park J, Eom I, Chun SH, Kim S, Kim M, Katayama T, Togashi T, Owada S, Yabashi M, Lee SJ, Lee S, Ahn CW, Ahn DS, Moon J, Choi S, Kim J, Joo T, Kim J, Adachi SI, Ihee H. Mapping the emergence of molecular vibrations mediating bond formation. Nature 2020; 582:520-524. [PMID: 32581378 DOI: 10.1038/s41586-020-2417-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/16/2020] [Indexed: 11/09/2022]
Abstract
Fundamental studies of chemical reactions often consider the molecular dynamics along a reaction coordinate using a calculated or suggested potential energy surface1-5. But fully mapping such dynamics experimentally, by following all nuclear motions in a time-resolved manner-that is, the motions of wavepackets-is challenging and has not yet been realized even for the simple stereotypical bimolecular reaction6-8: A-B + C → A + B-C. Here we track the trajectories of these vibrational wavepackets during photoinduced bond formation of the gold trimer complex [Au(CN)2-]3 in an aqueous monomer solution, using femtosecond X-ray liquidography9-12 with X-ray free-electron lasers13,14. In the complex, which forms when three monomers A, B and C cluster together through non-covalent interactions15,16, the distance between A and B is shorter than that between B and C. Tracking the wavepacket in three-dimensional nuclear coordinates reveals that within the first 60 femtoseconds after photoexcitation, a covalent bond forms between A and B to give A-B + C. The second covalent bond, between B and C, subsequently forms within 360 femtoseconds to give a linear and covalently bonded trimer complex A-B-C. The trimer exhibits harmonic vibrations that we map and unambiguously assign to specific normal modes using only the experimental data. In principle, more intense X-rays could visualize the motion not only of highly scattering atoms such as gold but also of lighter atoms such as carbon and nitrogen, which will open the door to the direct tracking of the atomic motions involved in many chemical reactions.
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Affiliation(s)
- Jong Goo Kim
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Shunsuke Nozawa
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies, Tsukuba, Japan
| | - Hanui Kim
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Eun Hyuk Choi
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Tokushi Sato
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany.,European XFEL, Schenefeld, Germany
| | - Tae Wu Kim
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Kyung Hwan Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Hosung Ki
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Jungmin Kim
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Minseo Choi
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Jun Heo
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Key Young Oang
- Radiation Center for Ultrafast Science, Quantum Optics Division, Korea Atomic Energy Research Institute (KAERI), Daejeon, Republic of Korea
| | - Kouhei Ichiyanagi
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Ryo Fukaya
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Jae Hyuk Lee
- Pohang Accelerator Laboratory, Pohang, Republic of Korea
| | - Jaeku Park
- Pohang Accelerator Laboratory, Pohang, Republic of Korea
| | - Intae Eom
- Pohang Accelerator Laboratory, Pohang, Republic of Korea
| | - Sae Hwan Chun
- Pohang Accelerator Laboratory, Pohang, Republic of Korea
| | - Sunam Kim
- Pohang Accelerator Laboratory, Pohang, Republic of Korea
| | - Minseok Kim
- Pohang Accelerator Laboratory, Pohang, Republic of Korea
| | - Tetsuo Katayama
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Japan.,RIKEN SPring-8 Center, Sayo, Japan
| | - Tadashi Togashi
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Japan.,RIKEN SPring-8 Center, Sayo, Japan
| | - Sigeki Owada
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Japan.,RIKEN SPring-8 Center, Sayo, Japan
| | - Makina Yabashi
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Japan.,RIKEN SPring-8 Center, Sayo, Japan
| | - Sang Jin Lee
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Seonggon Lee
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Chi Woo Ahn
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Doo-Sik Ahn
- Department of Chemistry, KAIST, Daejeon, Republic of Korea.,KI for the BioCentury, KAIST, Daejeon, Republic of Korea.,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Jiwon Moon
- Department of Chemistry, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Seungjoo Choi
- Department of Chemistry, Inha University, Incheon, Republic of Korea
| | - Joonghan Kim
- Department of Chemistry, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Taiha Joo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jeongho Kim
- Department of Chemistry, Inha University, Incheon, Republic of Korea
| | - Shin-Ichi Adachi
- Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies, Tsukuba, Japan
| | - Hyotcherl Ihee
- Department of Chemistry, KAIST, Daejeon, Republic of Korea. .,KI for the BioCentury, KAIST, Daejeon, Republic of Korea. .,Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon, Republic of Korea.
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6
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Zotev N, Moreno Carrascosa A, Simmermacher M, Kirrander A. Excited Electronic States in Total Isotropic Scattering from Molecules. J Chem Theory Comput 2020; 16:2594-2605. [DOI: 10.1021/acs.jctc.9b00670] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nikola Zotev
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Andrés Moreno Carrascosa
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Mats Simmermacher
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Adam Kirrander
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
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7
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Pápai M, Rozgonyi T, Penfold TJ, Nielsen MM, Møller KB. Simulation of ultrafast excited-state dynamics and elastic x-ray scattering by quantum wavepacket dynamics. J Chem Phys 2019; 151:104307. [DOI: 10.1063/1.5115204] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Mátyás Pápai
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Tamás Rozgonyi
- Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest, Hungary
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 286, H-1519 Budapest, Hungary
| | - Thomas J. Penfold
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Martin M. Nielsen
- Department of Physics, Technical University of Denmark, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
| | - Klaus B. Møller
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
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8
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Moreno Carrascosa A, Yong H, Crittenden DL, Weber PM, Kirrander A. Ab Initio Calculation of Total X-ray Scattering from Molecules. J Chem Theory Comput 2019; 15:2836-2846. [PMID: 30875212 DOI: 10.1021/acs.jctc.9b00056] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a method to calculate total X-ray scattering cross sections directly from ab initio electronic wave functions in atoms and molecules. The approach can be used in conjunction with multiconfigurational wave functions and exploits analytical integrals of Gaussian-type functions over the scattering operator, which leads to accurate and efficient calculations. The results are validated by comparison to experimental results and previous theory for the molecules H2 and CO2. Importantly, we find that the inelastic component of the total scattering varies strongly with molecular geometry. The method is appropriate for use in conjunction with quantum molecular dynamics simulations for the analysis of new ultrafast X-ray scattering experiments and to interpret accurate gas-phase scattering experiments.
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Affiliation(s)
- Andrés Moreno Carrascosa
- EaStCHEM, School of Chemistry , University of Edinburgh , David Brewster Road , EH9 3FJ Edinburgh , United Kingdom
| | - Haiwang Yong
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Deborah L Crittenden
- Department of Chemistry , University of Canterbury , Private Bag 4800 , Christchurch 8041 , New Zealand
| | - Peter M Weber
- Department of Chemistry , Brown University , Providence , Rhode Island 02912 , United States
| | - Adam Kirrander
- EaStCHEM, School of Chemistry , University of Edinburgh , David Brewster Road , EH9 3FJ Edinburgh , United Kingdom
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9
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Parrish RM, Martínez TJ. Ab Initio Computation of Rotationally-Averaged Pump-Probe X-ray and Electron Diffraction Signals. J Chem Theory Comput 2019; 15:1523-1537. [PMID: 30702882 DOI: 10.1021/acs.jctc.8b01051] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We develop a new algorithm for the computation of the rotationally averaged elastic molecular diffraction signal for the cases of perpendicular or parallel pump-probe geometries. The algorithm first collocates the charge density from an arbitrary ab initio wave function onto a Becke quadrature grid [A. Becke, J. Chem. Phys. 1988 , 88 , 2457 ], providing a high-fidelity multiresolution representation of the charge density. A double sum is then performed over the Becke grid points, and the interaction between points computed using the scattering kernels of Williamson and Zewail [J. C. Williamson and A. H. Zewail, J. Phys. Chem. 1994 , 98 , 2766 ]. These kernels analytically average over the molecular orientations with the cos2 γ selection factor appropriate for one-photon dipole absorption in a perpendicular pump-probe geometry. We show that the method is converged with small grids containing <500 points/atom. We implement the algorithm on a GPU for increased efficiency and emonstrate the algorithm for molecules with up to a few dozen atoms. We explore the accuracy of the independent atom model (IAM) by comparison with our new and more accurate method. We also investigate the possibility of detecting signatures of electronic transitions in polyatomic pump-probe diffraction experiments.
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Affiliation(s)
- Robert M Parrish
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States.,SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Todd J Martínez
- Department of Chemistry and The PULSE Institute , Stanford University , Stanford , California 94305 , United States.,SLAC National Accelerator Laboratory , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
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10
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Fletcher K, Krämer M, Bunz UH, Dreuw A. The π-conjugation length determines the fluorescence quenching mechanism of aromatic aldehydes in water. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Moreno Carrascosa A, Kirrander A. Ab initio calculation of inelastic scattering. Phys Chem Chem Phys 2017; 19:19545-19553. [DOI: 10.1039/c7cp02054f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We calculate nonresonant inelastic electron and X-ray scattering cross sections for bound-to-bound transitions in atoms and molecules from ab initio electronic wavefunctions.
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Affiliation(s)
| | - Adam Kirrander
- EaStCHEM
- School of Chemistry
- University of Edinburgh
- EH9 3FJ Edinburgh
- UK
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12
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Moreno Carrascosa A, Northey T, Kirrander A. Imaging rotations and vibrations in polyatomic molecules with X-ray scattering. Phys Chem Chem Phys 2017; 19:7853-7863. [DOI: 10.1039/c6cp06793j] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An approach for calculating elastic X-ray scattering from polyatomic molecules in specific electronic, vibrational, and rotational states is presented, and is used to consider the characterization of specific states in polyatomic molecules using elastic X-ray scattering.
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Affiliation(s)
| | - Thomas Northey
- EaStCHEM
- School of Chemistry
- University of Edinburgh
- EH9 3FJ Edinburgh
- UK
| | - Adam Kirrander
- EaStCHEM
- School of Chemistry
- University of Edinburgh
- EH9 3FJ Edinburgh
- UK
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13
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Northey T, Moreno Carrascosa A, Schäfer S, Kirrander A. Elastic X-ray scattering from state-selected molecules. J Chem Phys 2016; 145:154304. [PMID: 27782487 DOI: 10.1063/1.4962256] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The characterization of electronic, vibrational, and rotational states using elastic (coherent) X-ray scattering is considered. The scattering is calculated directly from complete active space self-consistent field level ab initio wavefunctions for H2 molecules in the ground-state X1Σg+ and first-excited EF1Σg+ electronic states. The calculated scattering is compared to recent experimental measurements [Y.-W. Liu et al., Phys. Rev. A 89, 014502 (2014)], and the influence of vibrational and rotational states on the observed signal is examined. The scaling of the scattering calculations with basis set is quantified, and it is found that energy convergence of the ab initio calculations is a good indicator of the quality of the scattering calculations.
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Affiliation(s)
- Thomas Northey
- EaStCHEM, School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ Edinburgh, United Kingdom
| | - Andrés Moreno Carrascosa
- EaStCHEM, School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ Edinburgh, United Kingdom
| | - Steffen Schäfer
- Aix-Marseille Université and Institut Matériaux Microélectronique Nanosciences de Provence (IM2NP), Marseille, France
| | - Adam Kirrander
- EaStCHEM, School of Chemistry, University of Edinburgh, David Brewster Road, EH9 3FJ Edinburgh, United Kingdom
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14
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Northey T, Zotev N, Kirrander A. Ab Initio Calculation of Molecular Diffraction. J Chem Theory Comput 2014; 10:4911-20. [PMID: 26584376 DOI: 10.1021/ct500096r] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We discuss the application of ab initio X-ray diffraction (AIXRD) to the interpretation of time-resolved and static X-ray diffraction. In our approach, elastic X-ray scattering is calculated directly from the ab initio multiconfigurational wave function via a Fourier transform of the electron density, using the first Born approximation for elastic scattering. Significant gains in efficiency can be obtained by performing the required Fourier transforms analytically, making it possible to combine the calculation of ab initio X-ray diffraction with expensive quantum dynamics simulations. We show that time-resolved X-ray diffraction can detect not only changes in molecular geometry but also changes in the electronic state of a molecule. Calculations for cis-, trans-, and cyclo-butadiene, as well as benzene and 1,3-cyclohexadiene are included.
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Affiliation(s)
- Thomas Northey
- School of Chemistry, University of Edinburgh , West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - Nikola Zotev
- School of Chemistry, University of Edinburgh , West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - Adam Kirrander
- School of Chemistry, University of Edinburgh , West Mains Road, Edinburgh EH9 3JJ, United Kingdom
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Ebadi H. Tracking of azobenzene isomerization by X-ray emission spectroscopy. J Phys Chem A 2014; 118:7832-7. [PMID: 25134009 DOI: 10.1021/jp506543d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Cis-trans isomerizations are among the fundamental processes in photochemistry. In azobenzene or its derivatives this dynamics is, due to its reversibility, one of the reactions widely used in photostimulation of molecular motors or in molecular electronics. Though intensively investigated in the optical regime, no detailed study exists in the X-ray regime so far. Because the X-ray emission spectroscopy echoes the electronic structure sensitive to the geometry, this theoretical report based on the density functional theory and its time-dependent version presents different nitrogen K-edge X-ray emission spectra for cis and trans isomers with close interrelation to their electron configuration. Considering the spectrum along the isomerization path, these structural signatures can be utilized to probe the isomerization dynamics in the excited molecule. The scheme can further be generalized to the element specific photoreactions.
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Affiliation(s)
- H Ebadi
- Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
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Thekku Veedu S, Raiser D, Kia R, Scholz M, Techert S. Ultrafast Dynamical Study of Pyrene-N,N-dimethylaniline (PyDMA) as an Organic Molecular Diode in Solid State. J Phys Chem B 2014; 118:3291-7. [DOI: 10.1021/jp4121222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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17
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Ioffe IN, Granovsky AA. Photoisomerization of Stilbene: The Detailed XMCQDPT2 Treatment. J Chem Theory Comput 2013; 9:4973-90. [PMID: 26583415 DOI: 10.1021/ct400647w] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the detailed XMCQDPT2/cc-pVTZ study of trans-cis photoisomerization in one of the core systems of both experimental and computational photochemistry-the stilbene molecule. For the first time, the potential energy surface (PES) of the S1 state has been directly optimized and scanned using a multistate multiconfiguration second-order perturbation theory. We characterize the trans-stilbene, pyramidalized (phantom), and DHP-cis-stilbene geometric domains of the S1 state and describe their stationary points including the transition states between them, as well as S1/S0 intersections. Also reported are the minima and the activation barriers in the ground state. Our calculations correctly predict the kinetic isotope effect due to H/D exchange at ethylenic hydrogens, the dynamic behavior of excited cis-stilbene, and trans-cis branching ratio after relaxation to S0 through a rather unsymmetric conical intersection. In general, the XMCQDPT2 results confirm the qualitative adequacy of the TDDFT (especially SF-TDDFT) picture of the excited stilbene but also reveal quantitative discrepancies that deserve further exploration.
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Affiliation(s)
- I N Ioffe
- Department of Chemistry, Lomonosov Moscow State University , Moscow, 119991, Russia
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18
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Dixit G, Santra R. Role of electron-electron interference in ultrafast time-resolved imaging of electronic wavepackets. J Chem Phys 2013; 138:134311. [DOI: 10.1063/1.4798321] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Minezawa N, Gordon MS. Photoisomerization of stilbene: a spin-flip density functional theory approach. J Phys Chem A 2011; 115:7901-11. [PMID: 21639100 DOI: 10.1021/jp203803a] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photoisomerization process of 1,2-diphenylethylene (stilbene) is investigated using the spin-flip density functional theory (SFDFT), which has recently been shown to be a promising approach for locating conical intersection (CI) points (Minezawa, N.; Gordon, M. S. J. Phys. Chem. A2009, 113, 12749). The SFDFT method gives valuable insight into twisted stilbene to which the linear response time-dependent DFT approach cannot be applied. In contrast to the previous SFDFT study of ethylene, a distinct twisted minimum is found for stilbene. The optimized structure has a sizable pyramidalization angle and strong ionic character, indicating that a purely twisted geometry is not a true minimum. In addition, the SFDFT approach can successfully locate two CI points: the twisted-pyramidalized CI that is similar to the ethylene counterpart and another CI that possibly lies on the cyclization pathway of cis-stilbene. The mechanisms of the cis--trans isomerization reaction are discussed on the basis of the two-dimensional potential energy surface along the twisting and pyramidalization angles.
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Affiliation(s)
- Noriyuki Minezawa
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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21
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Debnarova A, Techert S, Schmatz S. Ab initio studies of ultrafast x-ray scattering of the photodissociation of iodine. J Chem Phys 2011; 133:124309. [PMID: 20886934 DOI: 10.1063/1.3475567] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We computationally examine various aspects of the reaction dynamics of the photodissociation and recombination of molecular iodine. We use our recently proposed formalism to calculate time-dependent x-ray scattering signal changes from first principles. Different aspects of the dynamics of this prototypical reaction are studied, such as coherent and noncoherent processes, features of structural relaxation that are periodic in time versus nonperiodic dissociative processes, as well as small electron density changes caused by electronic excitation, all with respect to x-ray scattering. We can demonstrate that wide-angle x-ray scattering offers a possibility to study the changes in electron densities in nonperiodic systems, which render it a suitable technique for the investigation of chemical reactions from a structural dynamics point of view.
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Affiliation(s)
- Andrea Debnarova
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Am Faβberg 11, Germany
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Debnarova A, Techert S, Schmatz S. Computational studies of the x-ray scattering properties of laser aligned stilbene. J Chem Phys 2011; 134:054302. [PMID: 21303115 DOI: 10.1063/1.3523569] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The enhancement of the x-ray scattering signal from partially aligned molecular samples is investigated. The alignment properties of the studied molecular system are modeled based on the method of laser alignment. With the advances in the area of laser alignment of molecules, the application of this sample manipulation technique promises a great potential for x-ray scattering measurements. Preferential alignment of molecules in an otherwise amorphous sample leads to constructive interference and thus increases the scattering intensity. This enhances the structural information encoded in the scattering images and enables improved resolution in studies of reaction dynamics, as in this work is shown for the example of the photo-isomerization of stilbene. We demonstrate that the scattering signal is strongly influenced by the alignment axis. Even the most basic one-dimensional alignment offers significant improvement compared to the structural information provided by a randomly oriented sample. Although the signal is sensitive to the uncertainty in the alignment angle, it offers encouraging results even at realistic alignment uncertainties.
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Affiliation(s)
- Andrea Debnarova
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Møller KB, Henriksen NE. Time-Resolved X-Ray Diffraction: The Dynamics of the Chemical Bond. MOLECULAR ELECTRONIC STRUCTURES OF TRANSITION METAL COMPLEXES I 2011. [DOI: 10.1007/430_2011_58] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Ihee H, Wulff M, Kim J, Adachi SI. Ultrafast X-ray scattering: structural dynamics from diatomic to protein molecules. INT REV PHYS CHEM 2010. [DOI: 10.1080/0144235x.2010.498938] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Jiang CW, Xie RH, Li FL, Allen RE. Photocyclization of trans-stilbene induced by an ultrafast laser pulse. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.01.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Kim TK, Lee JH, Wulff M, Kong Q, Ihee H. Spatiotemporal Kinetics in Solution Studied by Time-Resolved X-Ray Liquidography (Solution Scattering). Chemphyschem 2009; 10:1958-80. [DOI: 10.1002/cphc.200900154] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Jiang C, Xie R, Li F, Allen RE. Trans-to-cis isomerization of stilbene following an ultrafast laser pulse. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.04.079] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Cole JM. Photocrystallography. Acta Crystallogr A 2007; 64:259-71. [DOI: 10.1107/s0108767307065324] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 12/03/2007] [Indexed: 11/10/2022] Open
Abstract
This review describes the development and application of a new crystallographic technique that is starting to enable the three-dimensional structural determination of molecules in their photo-activated states. So called `photocrystallography' has wide applicability, particularly in the currently exciting area of photonics, and a discussion of this applied potential is put into context in this article. Studies are classified into four groups: photo-structural changes that are (i) irreversible; (ii) long-lived but reversible under certain conditions; (iii) transient with photo-active lifetimes of the order of microseconds; (iv) very short lived, existing at the nanosecond or even picosecond level. As photo-structural changes relative to the `ground state' can be subtle, this article necessarily concentrates on small-molecule single-crystal X-ray diffraction given that high atomic resolution is possible. That said, where it is pertinent, references are also made to related major advances in photo-induced macromolecular crystallography. The review concludes with an outlook on this new research area, including the future possibility of studying even more ephemeral, femtosecond-lived, photo-active species.
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Henriksen NE, Møller KB. On the Theory of Time-Resolved X-ray Diffraction. J Phys Chem B 2007; 112:558-67. [DOI: 10.1021/jp075497e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Niels E. Henriksen
- CMM, Department of Chemistry, Building 207, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Klaus B. Møller
- CMM, Department of Chemistry, Building 207, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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