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Gerlach M, Schaffner D, Preitschopf T, Karaev E, Bozek J, Holzmeier F, Fischer I. X-ray induced fragmentation of fulminic acid, HCNO. J Chem Phys 2023; 159:114306. [PMID: 37721327 DOI: 10.1063/5.0167395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/24/2023] [Indexed: 09/19/2023] Open
Abstract
The fragmentation of fulminic acid, HCNO, after excitation and ionization of core electrons was investigated using Auger-electron-photoion coincidence spectroscopy. A considerable degree of site-selectivity is observed. Ionization of the carbon and oxygen 1s electron leads to around 70% CH+ + NO+, while ionization at the central N-atom produces only 37% CH+ + NO+, but preferentially forms O+ + HCN+ and O+ + CN+. The mass-selected Auger-electron spectra show that these fragments are associated with higher binding energy final states. Furthermore, ionization of the C 1s electron leads to a higher propensity for C-H bond fission compared to O 1s ionization. Following resonant Auger-Meitner decay after 1s → 3π excitation, 12 different ionic products are formed. At the C 1s edge, the parent ion HCNO+ is significantly more stable compared to the other two edges, which we also attribute to the higher contribution of final states with low binding energies in the C 1s resonant Auger electron spectra.
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Affiliation(s)
- Marius Gerlach
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Dorothee Schaffner
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Tobias Preitschopf
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Emil Karaev
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - John Bozek
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | | | - Ingo Fischer
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
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2
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Tiefenthaler L, Scheier P, Erdmann E, Aguirre NF, Díaz-Tendero S, Luxford TFM, Kočišek J. Non-ergodic fragmentation upon collision-induced activation of cysteine-water cluster cations. Phys Chem Chem Phys 2023; 25:5361-5371. [PMID: 36647750 PMCID: PMC9930733 DOI: 10.1039/d2cp04172c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cysteine-water cluster cations Cys(H2O)3,6+ and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collision-induced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies from DFT calculations showing that clusters do not only fragment exclusively by sequential emission of single water molecules but also by the release of small water clusters. Release of clustered water is observed also in the ADMP (atom centered density matrix propagation) molecular dynamics model of small Cys(H2O)3+ and Cys(H2O)3H+ clusters. For large clusters Cys(H2O)6+ and Cys(H2O)6H+ the less computationally demanding statistical Microcanonical Metropolis Monte-Carlo method (M3C) is used to model the experimental fragmentation patterns. We are able to detail the energy redistribution in clusters upon collision activation. In the present case, about two thirds of the collision energy redistribute via an ergodic process, while the remaining one third is transferred into a non-ergodic channel leading to ejection of a single water molecule from the cluster. In contrast to molecular fragmentation, which can be well described by statistical models, modelling of collision-induced activation of weakly bound clusters requires inclusion of non-ergodic processes.
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Affiliation(s)
- Lukas Tiefenthaler
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Austria.
| | - Paul Scheier
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Austria.
| | - Ewa Erdmann
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.,Departamento de Química, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | | | - Sergio Díaz-Tendero
- Departamento de Química, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in ChemicalSciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Thomas F. M. Luxford
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of SciencesDolejškova 318223 PragueCzechia
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czechia.
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3
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Bolognesi P, Avaldi L. Photoelectron-photoion(s) coincidence studies of molecules of biological interest. Phys Chem Chem Phys 2022; 24:22356-22370. [PMID: 36124990 DOI: 10.1039/d2cp03079a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoelectron-photoion(s) coincidence, PEPICO, experiments with synchrotron radiation have become one of the most powerful tools to investigate dissociative photoionization thanks to their selectivity. In this paper their application to the study of molecular species of biological interest in the gas phase is reviewed. Some applications of PEPICO to the study of potential radiosensitizers, amino acids and small peptides and opportunities offered by the advent of novel methods for the production of beams of these molecules are discussed.
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Affiliation(s)
- P Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 00015 Monterotondo Scalo, Italy.
| | - L Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 00015 Monterotondo Scalo, Italy.
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Gopakumar G, Svensson PHW, Grånäs O, Brena B, Schwob L, Unger I, Saak CM, Timm M, Bülow C, Kubin M, Zamudio-Bayer V, Lau JT, von Issendorff B, Abid AR, Lindblad A, Danielsson E, Koerfer E, Caleman C, Björneholm O, Lindblad R. X-ray Induced Fragmentation of Protonated Cystine. J Phys Chem A 2022; 126:1496-1503. [PMID: 35213156 PMCID: PMC8919253 DOI: 10.1021/acs.jpca.1c10158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate site-specific X-ray induced fragmentation across the sulfur L-edge of protonated cystine, the dimer of the amino acid cysteine. Ion yield NEXAFS were performed in the gas phase using electrospray ionization (ESI) in combination with an ion trap. The interpretation of the sulfur L-edge NEXAFS spectrum is supported by Restricted Open-Shell Configuration Interaction (ROCIS) calculations. The fragmentation pathway of triply charged cystine ions was modeled by Molecular Dynamics (MD) simulations. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons. The disulfide bridge breaks for resonant excitation at lower photon energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments initially formed subsequently break into smaller fragments.
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Affiliation(s)
- Geethanjali Gopakumar
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Pamela H W Svensson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Oscar Grånäs
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Barbara Brena
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Lucas Schwob
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Isaak Unger
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Clara-Magdalena Saak
- Department of Physical Chemistry, University of Vienna, Währingerstraßze 42, 1090 Vienna, Austria
| | - Martin Timm
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.,Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, DE-10623 Berlin, Germany
| | - Christine Bülow
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.,Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany
| | - Markus Kubin
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany
| | - Vicente Zamudio-Bayer
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany
| | - J Tobias Lau
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.,Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany
| | - Bernd von Issendorff
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany
| | - Abdul R Abid
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.,Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, P.O. Box 3000, 90570 Oulu, Finland
| | - Andreas Lindblad
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Emma Danielsson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Ebba Koerfer
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Olle Björneholm
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Rebecka Lindblad
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.,Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.,Department of Physics, Lund University, Box 118, SE-22100 Lund, Sweden.,Department of Chemistry - Ångström Laboratory, Uppsala University, Box 538, SE-75121 Uppsala, Sweden
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5
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H-atom rearrangement in NH3 under ion impact. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2021. [DOI: 10.1007/s43538-021-00019-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Futamata N, Yamamura R, Trinh Ha D, Takahashi O. Fragmentation pathways of methylbenzoate cations following core excitation: Theoretical approach using graph theory. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Abundance of molecular triple ionization by double Auger decay. Sci Rep 2018; 8:16405. [PMID: 30401877 PMCID: PMC6219609 DOI: 10.1038/s41598-018-34807-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/26/2018] [Indexed: 11/29/2022] Open
Abstract
Systematic measurements of electron emission following formation of single 1s or 2p core holes in molecules with C, O, F, Si, S and Cl atoms show that overall triple ionization can make up as much as 20% of the decay. The proportion of triple ionization is observed to follow a linear trend correlated to the number of available valence electrons on the atom bearing the initial core hole and on closest neighbouring atoms, where the interatomic distance is assumed to play a large role. The amounts of triple ionization (double Auger decay) after 1s or 2p core hole formation follow the same linear trend, which indicates that the hole identity is not a crucial determining factor in the number of electrons emitted. The observed linear trend for the percentage of double Auger decay follows a predictive line equation of the form DA = 0.415 · Nve + 5.46.
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8
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Roos AH, Eland JHD, Andersson J, Zagorodskikh S, Singh R, Squibb RJ, Feifel R. Relative extent of double and single Auger decay in molecules containing C, N and O atoms. Phys Chem Chem Phys 2018; 18:25705-25710. [PMID: 27711372 DOI: 10.1039/c6cp02414a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We show that the proportion of double Auger decay following creation of single 1s core holes in molecules containing C, N and O atoms is greater than usually assumed, amounting to about 10% of single Auger decay in many cases. It varies from molecule to molecule, where the size of the molecule has a positive correlation to the amount of double Auger decay. In neon, examined as a related benchmark, the proportion of double Auger decay is similar to that in methane, and is in the order of 5%.
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Affiliation(s)
- A Hult Roos
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Gothenburg, Sweden.
| | - J H D Eland
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Gothenburg, Sweden. and Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, UK
| | - J Andersson
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Gothenburg, Sweden.
| | - S Zagorodskikh
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Gothenburg, Sweden. and Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala, Sweden
| | - R Singh
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Gothenburg, Sweden.
| | - R J Squibb
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Gothenburg, Sweden.
| | - R Feifel
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Gothenburg, Sweden.
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9
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Takahashi O, Kooser K, Ha DT, Myllynen H, Laksman J, Rachlew E, Kukk E. Site-selective bond scission of methylbenzoate following core excitation. Phys Chem Chem Phys 2018; 20:9591-9599. [DOI: 10.1039/c7cp08428e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Relative ion yield of methylbenzoate depending on photon energy show site-specificity.
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Affiliation(s)
- Osamu Takahashi
- Institute for Sustainable Science and Development
- Hiroshima University
- Higashi-Hiroshima 739-8526
- Japan
| | - Kuno Kooser
- Department of Physics and Astronomy
- University of Turku
- FIN-20014 Turku
- Finland
- Institute of Physics
| | - Dang Trinh Ha
- Institute for Sustainable Science and Development
- Hiroshima University
- Higashi-Hiroshima 739-8526
- Japan
- Department of Physics and Astronomy
| | - Hanna Myllynen
- Department of Physics and Astronomy
- University of Turku
- FIN-20014 Turku
- Finland
| | | | - Elisabeth Rachlew
- Royal Institute of Technology KTH
- Physics Department
- S-10691 Stockholm
- Sweden
| | - Edwin Kukk
- Department of Physics and Astronomy
- University of Turku
- FIN-20014 Turku
- Finland
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10
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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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