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Yamazaki K, Niitsu N, Kanno M, Ueda K, Kono H. Capturing the photo-induced dynamics of nano-molecules by X-ray free electron laser induced Coulomb explosion. J Chem Phys 2019; 151:124305. [PMID: 31575189 DOI: 10.1063/1.5115072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We performed reaction dynamics simulations to demonstrate that the vibrational dynamics of C60 induced by infrared (IR) pulses can be traced by triggering Coulomb explosion with intense femtosecond X-ray free electron laser (XFEL) probe pulses. The time series of the angular anisotropy β(t) of fast C+ and C2+ fragments of C60 60+ produced by such an XFEL pulse reflects the instantaneous structure of C60 vibrationally excited by IR pulses. The phases and amplitudes of excited vibrational modes and the coupling between excited modes can be successfully extracted from the expansion of β(t) in terms of vibrational modes. This proof-of-principle simulation clearly demonstrates that various information of the structures and reaction dynamics of large clusters or biomolecules can be retrieved by decomposing the experimentally determined β(t) into vibrational modes.
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Affiliation(s)
- Kaoru Yamazaki
- Institute for Materials Research, Tohoku University, Sendai 980-8577, Japan
| | - Naoyuki Niitsu
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-9578, Japan
| | - Manabu Kanno
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-9578, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Hirohiko Kono
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-9578, Japan
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Inhester L, Oostenrijk B, Patanen M, Kokkonen E, Southworth SH, Bostedt C, Travnikova O, Marchenko T, Son SK, Santra R, Simon M, Young L, Sorensen SL. Chemical Understanding of the Limited Site-Specificity in Molecular Inner-Shell Photofragmentation. J Phys Chem Lett 2018; 9:1156-1163. [PMID: 29444399 DOI: 10.1021/acs.jpclett.7b03235] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In many cases fragmentation of molecules upon inner-shell ionization is very unspecific with respect to the initially localized ionization site. Often this finding is interpreted in terms of an equilibration of internal energy into vibrational degrees of freedom after Auger decay. We investigate the X-ray photofragmentation of ethyl trifluoroacetate upon core electron ionization at environmentally distinct carbon sites using photoelectron-photoion-photoion coincidence measurements and ab initio electronic structure calculations. For all four carbon ionization sites, the Auger decay weakens the same bonds and transfers the two charges to opposite ends of the molecule, which leads to a rapid dissociation into three fragments, followed by further fragmentation steps. The lack of site specificity is attributed to the character of the dicationic electronic states after Auger decay instead of a fast equilibration of internal energy.
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Affiliation(s)
- Ludger Inhester
- Center for Free-Electron Laser Science, DESY , Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Bart Oostenrijk
- Department of Physics, Lund University , Box 118, 221 00 Lund, Sweden
| | - Minna Patanen
- Faculty of Science, Nano and Molecular Systems Research Unit, University of Oulu , Box 3000, FIN-90014 Oulu, Finland
| | - Esko Kokkonen
- Faculty of Science, Nano and Molecular Systems Research Unit, University of Oulu , Box 3000, FIN-90014 Oulu, Finland
| | - Stephen H Southworth
- Chemical Sciences and Engineering Division, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Christoph Bostedt
- Chemical Sciences and Engineering Division, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Physics, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Oksana Travnikova
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique - Matière et Rayonnement, LCPMR , F-75005 Paris, France
| | - Tatiana Marchenko
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique - Matière et Rayonnement, LCPMR , F-75005 Paris, France
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, DESY , Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY , Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg , Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Marc Simon
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique - Matière et Rayonnement, LCPMR , F-75005 Paris, France
| | - Linda Young
- Chemical Sciences and Engineering Division, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Physics and James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Stacey L Sorensen
- Department of Physics, Lund University , Box 118, 221 00 Lund, Sweden
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Takanashi T, Nakamura K, Kukk E, Motomura K, Fukuzawa H, Nagaya K, Wada SI, Kumagai Y, Iablonskyi D, Ito Y, Sakakibara Y, You D, Nishiyama T, Asa K, Sato Y, Umemoto T, Kariyazono K, Ochiai K, Kanno M, Yamazaki K, Kooser K, Nicolas C, Miron C, Asavei T, Neagu L, Schöffler M, Kastirke G, Liu XJ, Rudenko A, Owada S, Katayama T, Togashi T, Tono K, Yabashi M, Kono H, Ueda K. Ultrafast Coulomb explosion of a diiodomethane molecule induced by an X-ray free-electron laser pulse. Phys Chem Chem Phys 2017; 19:19707-19721. [DOI: 10.1039/c7cp01669g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Coulomb explosion mechanism of a CH2I2 molecule is rather different to that of CH3I. The kinetic energy of iodine ions is ∼3 times larger due to Coulomb repulsion of the two iodine ions, while that of carbon ions is almost the same for both, as indicated by the red arrows that represent kinetic energies of the atomic ions.
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Ha DT, Yamazaki K, Wang Y, Alcamí M, Maeda S, Kono H, Martín F, Kukk E. Fragmentation network of doubly charged methionine: Interpretation using graph theory. J Chem Phys 2016; 145:094302. [DOI: 10.1063/1.4962061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. T. Ha
- Department of Physics and Astronomy, University of Turku, 20014 Turku, Finland
| | - K. Yamazaki
- Department of Chemistry, Graduate School of Science, Tohoku University, 980-8578 Sendai, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Y. Wang
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain
| | - M. Alcamí
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain
| | - S. Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - H. Kono
- Department of Chemistry, Graduate School of Science, Tohoku University, 980-8578 Sendai, Japan
| | - F. Martín
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain
- Condensed Matter Physics Center, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - E. Kukk
- Department of Physics and Astronomy, University of Turku, 20014 Turku, Finland
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Itälä E, Levola H, Ha DT, Kooser K, Rachlew E, Kukk E. Photofragmentation of Serine Following C 1s Core Ionization—Comparison with Cysteine. J Phys Chem A 2016; 120:5419-26. [DOI: 10.1021/acs.jpca.6b02554] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eero Itälä
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Helena Levola
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Dang Trinh Ha
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
- Departamento
de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Kuno Kooser
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
- Institute
of Physics, University of Tartu, 50411, Tartu, Estonia
| | - Elisabeth Rachlew
- Physics
Department, Royal Institute of Technology KTH, S-10691 Stockholm, Sweden
| | - Edwin Kukk
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
- Turku University Centre for Materials and Surfaces (MatSurf), FIN-20014 Turku, Finland
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Nagaya K, Motomura K, Kukk E, Takahashi Y, Yamazaki K, Ohmura S, Fukuzawa H, Wada S, Mondal S, Tachibana T, Ito Y, Koga R, Sakai T, Matsunami K, Nakamura K, Kanno M, Rudenko A, Nicolas C, Liu XJ, Miron C, Zhang Y, Jiang Y, Chen J, Anand M, Kim DE, Tono K, Yabashi M, Yao M, Kono H, Ueda K. Femtosecond charge and molecular dynamics of I-containing organic molecules induced by intense X-ray free-electron laser pulses. Faraday Discuss 2016; 194:537-562. [DOI: 10.1039/c6fd00085a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We studied the electronic and nuclear dynamics of I-containing organic molecules induced by intense hard X-ray pulses at the XFEL facility SACLA in Japan. The interaction with the intense XFEL pulse causes absorption of multiple X-ray photons by the iodine atom, which results in the creation of many electronic vacancies (positive charges) via the sequential electronic relaxation in the iodine, followed by intramolecular charge redistribution. In a previous study we investigated the subsequent fragmentation by Coulomb explosion of the simplest I-substituted hydrocarbon, iodomethane (CH3I). We carried out three-dimensional momentum correlation measurements of the atomic ions created via Coulomb explosion of the molecule and found that a classical Coulomb explosion model including charge evolution (CCE-CE model), which accounts for the concerted dynamics of nuclear motion and charge creation/charge redistribution, reproduces well the observed momentum correlation maps of fragment ions emitted after XFEL irradiation. Then we extended the study to 5-iodouracil (C4H3IN2O2, 5-IU), which is a more complex molecule of biological relevance, and confirmed that, in both CH3I and 5-IU, the charge build-up takes about 10 fs, while the charge is redistributed among atoms within only a few fs. We also adopted a self-consistent charge density-functional based tight-binding (SCC-DFTB) method to treat the fragmentations of highly charged 5-IU ions created by XFEL pulses. Our SCC-DFTB modeling reproduces well the experimental and CCE-CE results. We have also investigated the influence of the nuclear dynamics on the charge redistribution (charge transfer) using nonadiabatic quantum-mechanical molecular dynamics (NAQMD) simulation. The time scale of the charge transfer from the iodine atomic site to the uracil ring induced by nuclear motion turned out to be only ∼5 fs, indicating that, besides the molecular Auger decay in which molecular orbitals delocalized over the iodine site and the uracil ring are involved, the nuclear dynamics also play a role for ultrafast charge redistribution. The present study illustrates that the CCE-CE model as well as the SCC-DFTB method can be used for reconstructing the positions of atoms in motion, in combination with the momentum correlation measurement of the atomic ions created via XFEL-induced Coulomb explosion of molecules.
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Yamazaki K, Nakamura T, Niitsu N, Kanno M, Ueda K, Kono H. Erratum: “Communication: Two-step explosion processes of highly charged fullerene cations C60q+ (q = 20–60)” [J. Chem. Phys. 141, 121105 (2014)]. J Chem Phys 2014. [DOI: 10.1063/1.4904913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Kaoru Yamazaki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Takashi Nakamura
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Naoyuki Niitsu
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
- Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Manabu Kanno
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Hirohiko Kono
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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