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Bai Y, Buren B, Yang Z, Zhou B, Chen M. Feshbach resonances in D + HD(v = 1, j = 0) reaction at low collision energies. J Comput Chem 2021; 42:2334-2340. [PMID: 34613618 DOI: 10.1002/jcc.26763] [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: 07/16/2021] [Revised: 08/30/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022]
Abstract
Feshbach resonances in D + HD(v = 1, j = 0) reaction are studied by using the time-independent quantum method. The integral cross section (ICS) results present three Feshbach resonance peaks, which are different from H + HD(v = 1, j = 0) reaction dominated by only one peak. These resonances are attributed to coupling with adiabatic effective potentials of D + HD(v = 1, j = 1) reaction, and the most obvious peak is contributed by J = 1 at 83.16 cm-1 collision energy. For J = 0 and 2, the resonances are related with the same L partial wave and present a double-peak structure in total ICS. The characteristics of product angular distribution show that the resonance of J = 1 is long-lived, while the lifetimes are relatively shorter for the resonance of J = 0 and 2.
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Affiliation(s)
- Yuwen Bai
- Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams (Ministry of Education), School of Physics, Dalian University of Technology, Dalian, China
| | - Bayaer Buren
- Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams (Ministry of Education), School of Physics, Dalian University of Technology, Dalian, China
| | - Zijiang Yang
- Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams (Ministry of Education), School of Physics, Dalian University of Technology, Dalian, China
| | - Boyi Zhou
- Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams (Ministry of Education), School of Physics, Dalian University of Technology, Dalian, China
| | - Maodu Chen
- Key Laboratory of Materials Modification by Laser, Electron, and Ion Beams (Ministry of Education), School of Physics, Dalian University of Technology, Dalian, China
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Makoś MZ, Verma N, Larson EC, Freindorf M, Kraka E. Generative adversarial networks for transition state geometry prediction. J Chem Phys 2021; 155:024116. [PMID: 34266275 DOI: 10.1063/5.0055094] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work introduces a novel application of generative adversarial networks (GANs) for the prediction of starting geometries in transition state (TS) searches based on the geometries of reactants and products. The multi-dimensional potential energy space of a chemical reaction often complicates the location of a starting TS geometry, leading to the correct TS combining reactants and products in question. The proposed TS-GAN efficiently maps the space between reactants and products and generates reliable TS guess geometries, and it can be easily combined with any quantum chemical software package performing geometry optimizations. The TS-GAN was trained and applied to generate TS guess structures for typical chemical reactions, such as hydrogen migration, isomerization, and transition metal-catalyzed reactions. The performance of the TS-GAN was directly compared to that of classical approaches, proving its high accuracy and efficiency. The current TS-GAN can be extended to any dataset that contains sufficient chemical reactions for training. The software is freely available for training, experimentation, and prediction at https://github.com/ekraka/TS-GAN.
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Affiliation(s)
- Małgorzata Z Makoś
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Niraj Verma
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Eric C Larson
- Computer Science Department, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
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Vincent UE, McClintock PVE, Khovanov IA, Rajasekar S. Vibrational and stochastic resonances in driven nonlinear systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200226. [PMID: 33455554 DOI: 10.1098/rsta.2020.0226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/08/2020] [Indexed: 05/22/2023]
Abstract
Nonlinear systems are abundant in nature. Their dynamics have been investigated very extensively, motivated partly by their multidisciplinary applicability, ranging from all branches of physical and mathematical sciences through engineering to the life sciences and medicine. When driven by external forces, nonlinear systems can exhibit a plethora of interesting and important properties-one of the most prominent being that of resonance. In the presence of a second, higher frequency, driving force, whether stochastic or deterministic/periodic, a resonance phenomenon arises that can generally be termed stochastic resonance or vibrational resonance. Operating a system in or out of resonance promises applications in several advanced technologies, such as the creation of novel materials at the nano, micro and macroscales including, but not limited to, materials having photonic band gaps, quantum control of atoms and molecules as well as miniature condensed matter systems. Motivated in part by these potential applications, this 2-part Theme Issue provides a concrete up-to-date overview of vibrational and stochastic resonances in driven nonlinear systems. It assembles state-of-the-art, original contributions on such induced resonances-addressing their analysis, occurrence and applications from either the theoretical, numerical or experimental perspectives, or through combinations of these. This article is part of the theme issue 'Vibrational and stochastic resonance in driven nonlinear systems (part 1)'.
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Affiliation(s)
- U E Vincent
- Department of Physical Sciences, Redeemer's University, P.M.B. 230, Ede, Nigeria
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - P V E McClintock
- Department of Physics, Lancaster University, Lancaster LA1 4YB, UK
| | - I A Khovanov
- School of Engineering, University of Warwick, Coventry CV4 7Al, UK
| | - S Rajasekar
- School of Physics, Bharathidasan University, Tiruchirappalli 620 024, Tamilnadu, India
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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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