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Martins JB, de Moura CEV, Goldsztejn G, Travnikova O, Guillemin R, Ismail I, Journel L, Koulentianos D, Barbatti M, Lago AF, Céolin D, Rocco MLM, Püttner R, Piancastelli MN, Simon M, Marchenko T. Electron delocalisation in conjugated sulfur heterocycles probed by resonant Auger spectroscopy. Phys Chem Chem Phys 2022; 24:8477-8487. [PMID: 35404373 DOI: 10.1039/d1cp05910f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We propose a novel approach for an indirect probing of conjugation and hyperconjugation in core-excited molecules using resonant Auger spectroscopy. Our work demonstrates that the changes in the electronic structure of thiophene (C4H4S) and thiazole (C3H3NS), occurring in the process of resonant sulfur K-shell excitation and Auger decay, affect the stabilisation energy resulting from π-conjugation and hyperconjugation. The variations in the stabilisation energy manifest themselves in the resonant S KL2,3L2,3 Auger spectra of thiophene and thiazole. The comparison of the results obtained for the conjugated molecules and for thiolane (C4H8S), the saturated analogue of thiophene, has been performed. The experimental observations are interpreted using high-level quantum-mechanical calculations and the natural bond orbital analysis.
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Affiliation(s)
- Jessica B Martins
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France.
| | - Carlos E V de Moura
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.,Aix-Marseille University, CNRS, ICR, Marseille, France
| | - Gildas Goldsztejn
- Université Paris-Saclay, Institut des Sciences Moléculaires d'Orsay ISMO, UMR CNRS 8214, F-91405 Orsay, France
| | - Oksana Travnikova
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France. .,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette Cedex, France
| | - Renaud Guillemin
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France. .,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette Cedex, France
| | - Iyas Ismail
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France. .,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette Cedex, France
| | - Loïc Journel
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France. .,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette Cedex, France
| | - Dimitrios Koulentianos
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France. .,Department of Physics, University of Gothenburg, Origovägen 6B, SE-412 96 Gothenburg, Sweden
| | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille, France.,Institut Universitaire de France, 75231 Paris, France
| | - Alexsandre F Lago
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), 09210-580, Santo André, São Paulo, Brazil
| | - Denis Céolin
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette Cedex, France
| | - Maria Luiza M Rocco
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Ralph Püttner
- Fachbereich Physik, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Maria Novella Piancastelli
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France. .,Department of Physics and Astronomy, Uppsala University, SE-751 20 Uppsala, Sweden
| | - Marc Simon
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France. .,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette Cedex, France
| | - Tatiana Marchenko
- Sorbonne Université, CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris, France. .,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, F-91192 Gif-sur-Yvette Cedex, France
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2
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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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3
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Varas LR, Fantuzzi F, Coutinho LH, Bernini RB, Nascimento MAC, de Souza GGB. Are disulfide bonds resilient to double ionization? Insights from coincidence spectroscopy and ab initio calculations. RSC Adv 2020; 10:35039-35048. [PMID: 35515687 PMCID: PMC9056841 DOI: 10.1039/d0ra05979j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
Disulfide bonds (–S–S–) are severely damaged as a consequence of sulfur core–shell ionization processes, which is related to their low thermodynamic stability in multiply-charged systems.
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Affiliation(s)
- Lautaro R. Varas
- Escuela de Ingeniería Química
- Universidad de Costa Rica
- Ciudad de la Investigación
- Facultad de Ingeniería
- 11501-2060 San José
| | - Felipe Fantuzzi
- Instituto de Química
- Universidade Federal do Rio de Janeiro
- Cidade Universitária
- 21949-909, Rio de Janeiro
- Brazil
| | | | - Rafael B. Bernini
- Instituto Federal de Ciência e Tecnologia do Rio de Janeiro (IFRJ)
- Duque de Caxias
- Brazil
| | | | - G. G. B. de Souza
- Instituto de Química
- Universidade Federal do Rio de Janeiro
- Cidade Universitária
- 21949-909, Rio de Janeiro
- Brazil
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4
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Tenorio BNC, Oliveira RR, Nascimento MAC, Rocha AB. Coupled Cluster and Time-Dependent Density Functional Theory Description of Inner Shell Photoabsorption Cross Sections of Molecules. J Chem Theory Comput 2018; 14:5324-5338. [DOI: 10.1021/acs.jctc.8b00375] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Bruno Nunes Cabral Tenorio
- UFRJ - Universidade Federal do Rio de Janeiro, Instituto
de Química, Av. Athos da Silveira Ramos, 149, Rio de Janeiro 21941-909, Brasil
| | - Ricardo Rodrigues Oliveira
- UFRJ - Universidade Federal do Rio de Janeiro, Instituto
de Química, Av. Athos da Silveira Ramos, 149, Rio de Janeiro 21941-909, Brasil
| | - Marco Antonio Chaer Nascimento
- UFRJ - Universidade Federal do Rio de Janeiro, Instituto
de Química, Av. Athos da Silveira Ramos, 149, Rio de Janeiro 21941-909, Brasil
| | - Alexandre Braga Rocha
- UFRJ - Universidade Federal do Rio de Janeiro, Instituto
de Química, Av. Athos da Silveira Ramos, 149, Rio de Janeiro 21941-909, Brasil
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5
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Tenório BN, de Moura CE, Oliveira RR, Rocha AB. Transitions energies, optical oscillator strengths and partial potential energy surfaces of inner-shell states of water clusters. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Salles RCM, Coutinho LH, da Veiga AG, Sant’Anna MM, de Souza GGB. Surface damage in cystine, an amino acid dimer, induced by keV ions. J Chem Phys 2018; 148:045107. [DOI: 10.1063/1.5011816] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- R. C. M. Salles
- Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-909 Rio de Janeiro, RJ, Brazil
| | - L. H. Coutinho
- Instituto de Física, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-972 Rio de Janeiro, RJ, Brazil
| | - A. G. da Veiga
- Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-909 Rio de Janeiro, RJ, Brazil
| | - M. M. Sant’Anna
- Instituto de Física, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-972 Rio de Janeiro, RJ, Brazil
| | - G. G. B. de Souza
- Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21941-909 Rio de Janeiro, RJ, Brazil
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