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Schlathölter T, Poully JC. Radiation-Induced Molecular Processes in DNA: A Perspective on Gas-Phase Interaction Studies. Chemistry 2024; 30:e202400633. [PMID: 38888393 DOI: 10.1002/chem.202400633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Indexed: 06/20/2024]
Abstract
Studying the direct effects of DNA irradiation is essential for understanding the impact of radiation on biological systems. Gas-phase interactions are especially well suited to uncover the molecular mechanisms underlying these direct effects. Only relatively recently, isolated DNA oligonucleotides were irradiated by ionizing particles such as VUV or X-ray photons or ion beams, and ionic products were analyzed by mass spectrometry. This article provides a comprehensive review of primarily experimental investigations in this field over the past decade, emphasizing the description of processes such as ionization, fragmentation, charge and hydrogen transfer triggered by photoabsorption or ion collision, and the recent progress made thanks to specific atomic photoabsorption. Then, we outline ongoing experimental developments notably involving ion-mobility spectrometry, crossed beams or time-resolved measurements. The discussion extends to potential research directions for the future.
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Affiliation(s)
- Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, AG Groningen, The Netherlands
- University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718, BG Groningen, The Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA, CNRS, ENSICAEN, Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
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Svensson PHW, Schwob L, Grånäs O, Unger I, Björneholm O, Timneanu N, Lindblad R, Vieli AL, Zamudio-Bayer V, Timm M, Hirsch K, Caleman C, Berholts M. Heavy element incorporation in nitroimidazole radiosensitizers: molecular-level insights into fragmentation dynamics. Phys Chem Chem Phys 2024; 26:770-779. [PMID: 37888897 DOI: 10.1039/d3cp03800a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The present study investigates the photofragmentation behavior of iodine-enhanced nitroimidazole-based radiosensitizer model compounds in their protonated form using near-edge X-ray absorption mass spectrometry and quantum mechanical calculations. These molecules possess dual functionality: improved photoabsorption capabilities and the ability to generate species that are relevant to cancer sensitization upon photofragmentation. Four samples were investigated by scanning the generated fragments in the energy regions around C 1s, N 1s, O 1s, and I 3d-edges with a particular focus on NO2+ production. The experimental summed ion yield spectra are explained using the theoretical near-edge X-ray absorption fine structure spectrum based on density functional theory. Born-Oppenheimer-based molecular dynamics simulations were performed to investigate the fragmentation processes.
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Affiliation(s)
- Pamela H W Svensson
- Department of Physics and Astronomy, University of Uppsala, SE-75120 Uppsala, Sweden.
| | - Lucas Schwob
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oscar Grånäs
- Department of Physics and Astronomy, University of Uppsala, SE-75120 Uppsala, Sweden.
| | - Isaak Unger
- Department of Physics and Astronomy, University of Uppsala, SE-75120 Uppsala, Sweden.
| | - Olle Björneholm
- Department of Physics and Astronomy, University of Uppsala, SE-75120 Uppsala, Sweden.
| | - Nicusor Timneanu
- Department of Physics and Astronomy, University of Uppsala, SE-75120 Uppsala, Sweden.
| | - Rebecka Lindblad
- Department of Physics and Astronomy, University of Uppsala, SE-75120 Uppsala, Sweden.
| | - Anna-Lydia Vieli
- Department of Physics and Astronomy, University of Uppsala, SE-75120 Uppsala, Sweden.
| | - Vicente Zamudio-Bayer
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz Zentrum Berlin für Materialien und Energie, 12489 Berlin-Adlershof, Germany
| | - Martin Timm
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz Zentrum Berlin für Materialien und Energie, 12489 Berlin-Adlershof, Germany
| | - Konstantin Hirsch
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz Zentrum Berlin für Materialien und Energie, 12489 Berlin-Adlershof, Germany
| | - Carl Caleman
- Department of Physics and Astronomy, University of Uppsala, SE-75120 Uppsala, Sweden.
- Center for Free-Electron Laser Science, DESY, DE-22607 Hamburg, Germany
| | - Marta Berholts
- Institute of Physics, University of Tartu, W. Ostwald 1, EST-50411, Tartu, Estonia.
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Leroux J, Kotobi A, Hirsch K, Lau T, Ortiz-Mahecha C, Maksimov D, Meißner R, Oostenrijk B, Rossi M, Schubert K, Timm M, Trinter F, Unger I, Zamudio-Bayer V, Schwob L, Bari S. Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy. Phys Chem Chem Phys 2023; 25:25603-25618. [PMID: 37721108 DOI: 10.1039/d3cp02524a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Near-edge X-ray absorption mass spectrometry (NEXAMS) around the nitrogen and oxygen K-edges was employed on gas-phase peptides to probe the electronic transitions related to their protonation sites, namely at basic side chains, the N-terminus and the amide oxygen. The experimental results are supported by replica exchange molecular dynamics and density-functional theory and restricted open-shell configuration with single calculations to attribute the transitions responsible for the experimentally observed resonances. We studied five tailor-made glycine-based pentapeptides, where we identified the signature of the protonation site of N-terminal proline, histidine, lysine and arginine, at 406 eV, corresponding to N 1s → σ*(NHx+) (x = 2 or 3) transitions, depending on the peptides. We compared the spectra of pentaglycine and triglycine to evaluate the sensitivity of NEXAMS to protomers. Separate resonances have been identified to distinguish two protomers in triglycine, the protonation site at the N-terminus at 406 eV and the protonation site at the amide oxygen characterized by a transition at 403.1 eV.
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Affiliation(s)
- Juliette Leroux
- CIMAP, CEA/CNRS/ENSICAEN/Université de Caen Normandie, 14050 Caen, France
- Deutsches Elektronen-Synchrotron DESY, Germany.
| | - Amir Kotobi
- Deutsches Elektronen-Synchrotron DESY, Germany.
- Helmholtz-Zentrum Hereon, Institute of Surface Science, 21502 Geesthacht, Germany
| | - Konstantin Hirsch
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Tobias Lau
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Carlos Ortiz-Mahecha
- Hamburg University of Technology, Institute of Polymers and Composites, 21073 Hamburg, Germany
| | - Dmitrii Maksimov
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | - Robert Meißner
- Helmholtz-Zentrum Hereon, Institute of Surface Science, 21502 Geesthacht, Germany
- Hamburg University of Technology, Institute of Polymers and Composites, 21073 Hamburg, Germany
| | | | - Mariana Rossi
- Max Planck Institute for the Structure and Dynamics of Matter, 22761 Hamburg, Germany
| | | | - Martin Timm
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | - Florian Trinter
- Institut für Kernphysik, Goethe-Universität Frankfurt am Main, 60438 Frankfurt am Main, Germany
- Molecular Physics, Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Isaak Unger
- Department of Physics and Astronomy, Uppsala University, 75120 Uppsala, Sweden
| | - Vicente Zamudio-Bayer
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, 12489 Berlin, Germany
| | | | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Germany.
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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Carravetta V, Couto RC, Ågren H. X-ray absorption of molecular cations-a new challenge for electronic structure theory. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:363002. [PMID: 35767974 DOI: 10.1088/1361-648x/ac7d2a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
In this paper we put forward some historical notes on the development of computational chemistry toward applications of x-ray spectroscopies. We highlight some of the important contributions by Enrico Clementi as method and program developer and as a supporter of this branch of computational research. We bring up a modern example based on the very recent experimental development of x-ray absorption of cationic molecules. As we show this spectroscopy poses new challenges for electronic structure theory and the electron correlation problem.
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Affiliation(s)
- V Carravetta
- Institute of Physical Chemical Processes-CNR, via Moruzzi 1, 56124 Pisa, Italy
| | - R C Couto
- Department of Theoretical Chemistry and Biology, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - H Ågren
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
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