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Ayuso D, Palacios A, Decleva P, Martín F. Ultrafast charge dynamics in glycine induced by attosecond pulses. Phys Chem Chem Phys 2018. [PMID: 28631783 DOI: 10.1039/c7cp01856h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The combination of attosecond pump-probe techniques with mass spectrometry methods has recently led to the first experimental demonstration of ultrafast charge dynamics in a biomolecule, the amino acid phenylalanine [Calegari et al., Science, 2014, 346, 336]. Using an extension of the static-exchange density functional theory (DFT) method, the observed dynamics was explained as resulting from the coherent superposition of ionic states produced by the broadband attosecond pulse. Here, we have used the static-exchange DFT method to investigate charge migration induced by attosecond pulses in the glycine molecule. We show that the observed dynamics follows patterns similar to those previously found in phenylalanine, namely that charge fluctuations occur all over the molecule and that they can be explained in terms of a few typical frequencies of the system. We have checked the validity of our approach by explicitly comparing with the photoelectron spectra obtained in synchrotron radiation experiments and with the charge dynamics that follows the removal of an electron from a given molecular orbital, for which fully correlated ab initio results are available in the literature. From this comparison, we conclude that our method provides an accurate description of both the coherent superposition of cationic states generated by the attosecond pulse and its subsequent time evolution. Hence, we expect that the static-exchange DFT method should perform equally well for other medium-size and large molecules, for which the use of fully correlated ab initio methods is not possible.
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Affiliation(s)
- David Ayuso
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Ayuso D, Kimura M, Kooser K, Patanen M, Plésiat E, Argenti L, Mondal S, Travnikova O, Sakai K, Palacios A, Kukk E, Decleva P, Ueda K, Martín F, Miron C. Vibrationally Resolved B 1s Photoionization Cross Section of BF3. J Phys Chem A 2015; 119:5971-8. [DOI: 10.1021/jp511416h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Ayuso
- Departamento de
Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - M. Kimura
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - K. Kooser
- Department
of Physics and Astronomy, University of Turku, 20014 Turku, Finland
| | - M. Patanen
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin,
BP 48, 91192 Gif-sur-Yvette
Cedex, France
| | - E. Plésiat
- Departamento de
Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - L. Argenti
- Departamento de
Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - S. Mondal
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - O. Travnikova
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin,
BP 48, 91192 Gif-sur-Yvette
Cedex, France
| | - K. Sakai
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - A. Palacios
- Departamento de
Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - E. Kukk
- Department
of Physics and Astronomy, University of Turku, 20014 Turku, Finland
| | - P. Decleva
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste and CNR–Istituto Officina dei Materiali, 34127 Trieste, Italy
| | - K. Ueda
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - F. Martín
- Departamento de
Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Cantoblanco, 28049 Madrid, Spain
- Condensed Matter Physics
Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - C. Miron
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin,
BP 48, 91192 Gif-sur-Yvette
Cedex, France
- Extreme Light Infrastructure
- Nuclear Physics (ELI-NP), “Horia Hulubei” National Institute for Physics and Nuclear Engineering, 30 Reactorului Street, RO-077125 Măgurele, Jud.
Ilfov, Romania
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Okada K, Suemitsu A, Terashima T, Iwasaki Y, Tamenori Y, Suzuki IH, Nagaoka S, Tabayashi K. Photofragmentation of the K-shell excited perfluorocyclobutane: anisotropies in the fragments and breakdown pathways. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:635-639. [PMID: 21671438 DOI: 10.1002/jms.1932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Total ion yield spectrum of perfluorocyclobutane (c-C(4)F(8)) has been measured in the C and F K-shell excitation regions. The peak assignments are presented based on angle-resolved photofragment ion mass spectrometry. The peaks at 291.34 and 688.5 eV are found to come from the transitions from the C 1s and the F 1s to the lowest unoccupied b(2)σ(CF)* orbital, respectively. A photoelectron-photoion-photoion coincidence spectrum is acquired at 700.1 eV for clarifying the breakdown pathways of c-C(4)F(8)(2+). Two series of the pathways are identified; fission of F atom(s) followed by charge separation and elimination of CF(2) or CF(3) followed by charge separation.
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Affiliation(s)
- K Okada
- Department of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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Lucchese RR, Montuoro R, Kotsis K, Tashiro M, Ehara M, Bozek JD, Das A, Landry A, Rathbone J, Poliakoff E. The effect of vibrational motion on the dynamics of shape resonant photoionization of BF3leading to the state of. Mol Phys 2010. [DOI: 10.1080/00268971003641866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Ueda K, Muramatsu Y, Shimizu Y, Chiba H, Sato Y, Kitajima M, Tanaka H, Nakamatsu H. Quasi-isotropic fragmentation of PF5 following P 2p photoabsorption. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)00578-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Shimizu Y, Ueda K, Chiba H, Okunishi M, Ohmori K, West JB, Sato Y, Hayaishi T. Symmetries and dissociation dynamics of F 1s core excited states of BF3. J Chem Phys 1997. [DOI: 10.1063/1.474585] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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