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Nakao T, Takasu R, Tsuchida H, Saito M, Majima T. Delayed fragmentation of isolated nucleobases induced by MeV ions. J Chem Phys 2024; 161:054302. [PMID: 39087542 DOI: 10.1063/5.0215222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024] Open
Abstract
We evaluated the dissociation of isolated gas-phase nucleobase molecules induced by mega electron volt (MeV)-energy ions to gain fundamental insights into the reactions of nucleobases upon fast ion irradiation. We studied five nucleobase molecules-adenine, guanine, cytosine, thymine, and uracil-as gas-phase targets. We compared the fragmentation patterns obtained from carbon ion impacts with those obtained from proton impacts to clarify the effect of heavy ion irradiation. We also compared the results with electron impact and photoionization results. In addition, we identified several delayed fragmentation pathways by analyzing the correlation between fragment pairs generated from singly and doubly charged intermediate ions. To determine the lifetimes of delayed fragmentation from singly charged intermediate ions, we evaluated the detection efficiencies of the microchannel plate detector for the neutral fragment HCN as a function of kinetic energy using a new methodology. As the first demonstration of this method, we estimated the lifetimes of C5H5N5+ generated by 1.2-MeV C+ and 0.5-MeV H+ collisions to be 0.87 ± 0.43 and 0.67 ± 0.09 µs, respectively. These lifetimes were approximately one order of magnitude longer than those of the doubly charged intermediate ion C5H5N52+.
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Affiliation(s)
- T Nakao
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
| | - R Takasu
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
| | - H Tsuchida
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
- Quantum Science and Engineering Center, Kyoto University, Uji 611-0011, Japan
| | - M Saito
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
- Quantum Science and Engineering Center, Kyoto University, Uji 611-0011, Japan
| | - T Majima
- Department of Nuclear Engineering, Kyoto University, Kyoto 615-8540, Japan
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Hervé du Penhoat MA, Souchaud A, Rajpal A, Vuilleumier R, Gaigeot MP, Tavernelli I, Fujii K, Yokoya A, Díaz-Tendero S, Politis MF. Ultrafast fragmentation of highly-excited doubly-ionized deoxyribose: role of the liquid water environment. Phys Chem Chem Phys 2024; 26:15693-15704. [PMID: 38766756 DOI: 10.1039/d4cp00489b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Ab initio molecular dynamics simulations are used to investigate the fragmentation dynamics following the double ionization of 2-deoxy-D-ribose (DR), a major component in the DNA chain. Different ionization scenarios are considered to provide a complete picture. First focusing on isolated DR2+, fragmentation patterns are determined for the ground electronic state, adding randomly distributed excitation energy to the nuclei. These patterns differ for the two isomers studied. To compare thermal and electronic excitation effects, Ehrenfest dynamics are also performed, allowing to remove the two electrons from selected molecular orbitals. Two intermediate-energy orbitals, localized on the carbon chain, were selected. The dissociation pattern corresponds to the most frequent pattern obtained when adding thermal excitation. On the contrary, targeting the four deepest orbitals, localized on the oxygen atoms, leads to selective ultrafast C-O and/or O-H bond dissociation. To probe the role of environment, a system consisting of a DR molecule embedded in liquid water is then studied. The two electrons are removed from either the DR or the water molecules directly linked to the sugar through hydrogen bonds. Although the dynamics onset is similar to that of isolated DR when removing the same deep orbitals localized on the sugar oxygen atoms, the subsequent fragmentation patterns differ. Sugar damage also occurs following the Coulomb explosion of neighboring H2O2+ molecules due to interaction with the emitted O or H atoms.
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Affiliation(s)
| | | | - Aashini Rajpal
- IMPMC, Sorbonne Université, UMR CNRS 7590, MNHN, Paris, France.
| | - Rodolphe Vuilleumier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | | | - Kentaro Fujii
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Akinari Yokoya
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Sergio Díaz-Tendero
- Departamento de Química, Universidad Autónoma de Madrid, Madrid, Spain
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Marie-Françoise Politis
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
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Ascenzi D, Erdmann E, Bolognesi P, Avaldi L, Castrovilli MC, Thissen R, Romanzin C, Alcaraz C, Rabadan I, Mendez L, Díaz-Tendero S, Cartoni A. H 2O˙ + and OH + reactivity versus furan: experimental low energy absolute cross sections for modeling radiation damage. Phys Chem Chem Phys 2023; 25:24643-24656. [PMID: 37665608 DOI: 10.1039/d3cp02772d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Radiotherapy is one of the most widespread and efficient strategies to fight malignant tumors. Despite its broad application, the mechanisms of radiation-DNA interaction are still under investigation. Theoretical models to predict the effects of a particular delivered dose are still in their infancy due to the difficulty of simulating a real cell environment, as well as the inclusion of a large variety of secondary processes. This work reports the first experimental study of the ion-molecule reactions of the H2O˙+ and OH+ ions, produced by photoionization with synchrotron radiation, with a furan (c-C4H4O) molecule, a template for deoxyribose sugar in DNA. The present experiments, performed as a function of the collision energy of the ions and the tunable photoionization energy, provide key parameters for the theoretical modelling of the effect of radiation dose, like the absolute cross sections for producing protonated furan (furanH+) and a radical cation (furan˙+), the most abundant products, which can amount up to 200 Å2 at very low collision energies (<1.0 eV). The experimental results show that furanH+ is more fragile, indicating how the protonation of the sugar component of the DNA may favor its dissociation with possible major radiosensitizing effects. Moreover, the ring opening of furanH+ isomers and the potential energy surface of the most important fragmentation channels have been explored by molecular dynamics simulations and quantum chemistry calculations. The results show that, in the most stable isomer of furanH+, the ring opening occurs via a low energy pathway with carbon-oxygen bond cleavage, followed by the loss of neutral carbon monoxide and the formation of the allyl cation CH2CHCH2+, which instead is not observed in the fragmentation of furan˙+. At higher energies the ring opening through the carbon-carbon bond is accompanied by the loss of formaldehyde, producing HCCCH2+, the most intense fragment ion detected in the experiments. This work highlights the importance of the secondary processes, like the ion-molecule reactions at low energies in the radiation damage due to their very large cross sections, and it aims to provide benchmark data for the development of suitable models to approach this low collision energy range.
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Affiliation(s)
- Daniela Ascenzi
- Department of Physics, University of Trento, Via Sommarive 14, 38123 Trento, Italy
| | - Ewa Erdmann
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Paola Bolognesi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015, Monterotondo, Italy
| | - Lorenzo Avaldi
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015, Monterotondo, Italy
| | - Mattea Carmen Castrovilli
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015, Monterotondo, Italy
| | - Roland Thissen
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Claire Romanzin
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Christian Alcaraz
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Saint Aubin, Gif-sur-Yvette, France
| | - Ismanuel Rabadan
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Luis Mendez
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Antonella Cartoni
- Department of Chemistry, Sapienza University of Rome, P. le Aldo Moro 5, Rome, 00185, Italy.
- Institute of Structure of Matter-CNR (ISM-CNR), Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015, Monterotondo, Italy
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Carlini L, Montorsi F, Wu Y, Bolognesi P, Borrego-Varillas R, Casavola AR, Castrovilli MC, Chiarinelli J, Mocci D, Vismarra F, Lucchini M, Nisoli M, Mukamel S, Garavelli M, Richter R, Nenov A, Avaldi L. Electron and ion spectroscopy of azobenzene in the valence and core shells. J Chem Phys 2023; 158:054201. [PMID: 36754795 DOI: 10.1063/5.0133824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Azobenzene is a prototype and a building block of a class of molecules of extreme technological interest as molecular photo-switches. We present a joint experimental and theoretical study of its response to irradiation with light across the UV to x-ray spectrum. The study of valence and inner shell photo-ionization and excitation processes combined with measurement of valence photoelectron-photoion coincidence and mass spectra across the core thresholds provides a detailed insight into the site- and state-selected photo-induced processes. Photo-ionization and excitation measurements are interpreted via the multi-configurational restricted active space self-consistent field method corrected by second order perturbation theory. Using static modeling, we demonstrate that the carbon and nitrogen K edges of azobenzene are suitable candidates for exploring its photoinduced dynamics thanks to the transient signals appearing in background-free regions of the NEXAFS and XPS.
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Affiliation(s)
- L Carlini
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - F Montorsi
- Dipartimento di Chimica Industriale, Università Degli Studi di Bologna, Bologna, Italy
| | - Y Wu
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - P Bolognesi
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - R Borrego-Varillas
- CNR-Istituto di Fotonica e Nanotecnologie, CNR-IFN, Piazza Leonardo da Vinci 32, Milano, Italy
| | - A R Casavola
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - M C Castrovilli
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - J Chiarinelli
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
| | - D Mocci
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - F Vismarra
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - M Lucchini
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - M Nisoli
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milano, Italy
| | - S Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
| | - M Garavelli
- Dipartimento di Chimica Industriale, Università Degli Studi di Bologna, Bologna, Italy
| | - R Richter
- Elettra Sincrotrone Trieste, Area Science Park, Basovizza, Italy
| | - A Nenov
- Dipartimento di Chimica Industriale, Università Degli Studi di Bologna, Bologna, Italy
| | - L Avaldi
- CNR-Istituto di Struttura Della Materia, CNR-ISM, Area Della Ricerca di Roma 1, Monterotondo, Italy
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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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