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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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Howell RW. Advancements in the use of Auger electrons in science and medicine during the period 2015-2019. Int J Radiat Biol 2020; 99:2-27. [PMID: 33021416 PMCID: PMC8062591 DOI: 10.1080/09553002.2020.1831706] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/01/2020] [Accepted: 09/28/2020] [Indexed: 02/06/2023]
Abstract
Auger electrons can be highly radiotoxic when they are used to irradiate specific molecular sites. This has spurred basic science investigations of their radiobiological effects and clinical investigations of their potential for therapy. Focused symposia on the biophysical aspects of Auger processes have been held quadrennially. This 9th International Symposium on Physical, Molecular, Cellular, and Medical Aspects of Auger Processes at Oxford University brought together scientists from many different fields to review past findings, discuss the latest studies, and plot the future work to be done. This review article examines the research in this field that was published during the years 2015-2019 which corresponds to the period since the last meeting in Japan. In addition, this article points to future work yet to be done. There have been a plethora of advancements in our understanding of Auger processes. These advancements range from basic atomic and molecular physics to new ways to implement Auger electron emitters in radiopharmaceutical therapy. The highly localized doses of radiation that are deposited within a 10 nm of the decay site make them precision tools for discovery across the physical, chemical, biological, and medical sciences.
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Affiliation(s)
- Roger W Howell
- Division of Radiation Research, Department of Radiology, New Jersey Medical School, Rutgers University, Newark, NJ, USA
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Ab Initio Molecular Dynamics Simulations to Interpret the Molecular Fragmentation Induced in Deoxyribose by Synchrotron Soft X-Rays. QUANTUM BEAM SCIENCE 2019. [DOI: 10.3390/qubs3040024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
It has been suggested that core ionization in DNA atoms could induce complex, irreparable damage. Synchrotron soft X-rays have been used to probe the damage induced by such events in thin films of DNA components. In a complementary approach, we investigate the fragmentation dynamics following a carbon or oxygen K-shell ionization in 2-deoxy-D-ribose (DR), a major component in the DNA chain. Core ionization of the sugars hydration layer is also studied. To that aim, we use state-of-the-art ab initio Density Functional Theory-based Molecular Dynamics (MD) simulations. The ultrafast dissociation dynamics of the core ionized molecule, prior Auger decay, is modeled for about 10 fs. We show that the core-ionization of oxygen atoms within DR or its hydration layer may induce proton transfers towards nearby molecules, before Auger decay. In a second step, we model an Auger effect occurring either at the beginning or at the end of the core–hole dynamics. Two electrons are removed from the deepest valence molecular orbitals localized on the initially core-ionized oxygen atom (O*), and this electronic state is propagated by means of Ehrenfest MD. We show an ultrafast dissociation of the DR2+ molecule C-O* bonds, which, in most cases, seems independent of the time at which Auger decay occurs.
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Hervé du Penhoat MA, Moraga NRG, Gaigeot MP, Vuilleumier R, Tavernelli I, Politis MF. Proton Collision on Deoxyribose Originating from Doubly Ionized Water Molecule Dissociation. J Phys Chem A 2018; 122:5311-5320. [PMID: 29846073 DOI: 10.1021/acs.jpca.8b04787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we studied the fragmentation dynamics of 2-deoxy-d-ribose (DR) in solution that arises from the double ionization of a water molecule in its primary hydration shell. This process was modeled in the framework of ab initio molecular dynamics. The charge unbalanced in the solvent molecules produces a Coulomb explosion with the consequent release of protons with kinetic energy in the few electronvolts range, which collide with the surrounding molecules in solution inducing further chemical reactions. In particular, we observe proton collisions with the solute molecule DR, which leads to a complete ring opening. In DNA, damage to the DR moiety may lead to DNA strand breaking. This mechanism can be understood as one of the possible steps in the radiation-induced fragmentation of DNA chains.
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Affiliation(s)
| | | | - Marie-Pierre Gaigeot
- LAMBE UMR8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement , Université d'Evry val d'Essonne, Université Paris-Saclay, CEA, CNRS , Blvd F. Mitterrand , 91025 Evry , France
| | - Rodolphe Vuilleumier
- PASTEUR, Département de chimie, École normale supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Ivano Tavernelli
- IBM Research-Zurich , Säumerstrasse 4 , 8803 Rüschlikon , Switzerland
| | - Marie-Fraņcoise Politis
- LAMBE UMR8587, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement , Université d'Evry val d'Essonne, Université Paris-Saclay, CEA, CNRS , Blvd F. Mitterrand , 91025 Evry , France
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Fujii K, Izumi Y, Narita A, Ghose KK, López-Tarifa P, Touati A, Spezia R, Vuilleumier R, Gaigeot MP, Politis MF, Du Penhoat MAH, Yokoya A. Roles of Hydration for Inducing Decomposition of 2-Deoxy-d-ribose by Ionization of Oxygen K-Shell Electrons. Radiat Res 2018; 189:264-272. [DOI: 10.1667/rr14225.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kentaro Fujii
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Japan
| | - Yudai Izumi
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Ayumi Narita
- Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Krishna Kamol Ghose
- LAMBE UMR CNRS 8587, Université d'Evry val d'Essonne, Evry, & Université Paris-Sacley, France France
| | - Pablo López-Tarifa
- École Polytechnique Fédérale de Lausanne, EPFL SB-ISIC-LCBC-BCH, 1015, Lausanne, Switzerland
| | - Alain Touati
- IMPMC, Sorbonne Universités - UPMC Univ Paris 06, UMR CNRS 7590, MNHN, IRD UMR 206, Paris, France
| | - Riccardo Spezia
- LAMBE UMR CNRS 8587, Université d'Evry val d'Essonne, Evry, & Université Paris-Sacley, France France
| | - Rodolphe Vuilleumier
- PASTEUR, Département de chimie, École normale supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Paris 75005, France
| | - Marie-Pierre Gaigeot
- LAMBE UMR CNRS 8587, Université d'Evry val d'Essonne, Evry, & Université Paris-Sacley, France France
| | - Marie-Françoise Politis
- LAMBE UMR CNRS 8587, Université d'Evry val d'Essonne, Evry, & Université Paris-Sacley, France France
| | | | - Akinari Yokoya
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Japan
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Inhester L, Oostenrijk B, Patanen M, Kokkonen E, Southworth SH, Bostedt C, Travnikova O, Marchenko T, Son SK, Santra R, Simon M, Young L, Sorensen SL. Chemical Understanding of the Limited Site-Specificity in Molecular Inner-Shell Photofragmentation. J Phys Chem Lett 2018; 9:1156-1163. [PMID: 29444399 DOI: 10.1021/acs.jpclett.7b03235] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In many cases fragmentation of molecules upon inner-shell ionization is very unspecific with respect to the initially localized ionization site. Often this finding is interpreted in terms of an equilibration of internal energy into vibrational degrees of freedom after Auger decay. We investigate the X-ray photofragmentation of ethyl trifluoroacetate upon core electron ionization at environmentally distinct carbon sites using photoelectron-photoion-photoion coincidence measurements and ab initio electronic structure calculations. For all four carbon ionization sites, the Auger decay weakens the same bonds and transfers the two charges to opposite ends of the molecule, which leads to a rapid dissociation into three fragments, followed by further fragmentation steps. The lack of site specificity is attributed to the character of the dicationic electronic states after Auger decay instead of a fast equilibration of internal energy.
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Affiliation(s)
- Ludger Inhester
- Center for Free-Electron Laser Science, DESY , Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Bart Oostenrijk
- Department of Physics, Lund University , Box 118, 221 00 Lund, Sweden
| | - Minna Patanen
- Faculty of Science, Nano and Molecular Systems Research Unit, University of Oulu , Box 3000, FIN-90014 Oulu, Finland
| | - Esko Kokkonen
- Faculty of Science, Nano and Molecular Systems Research Unit, University of Oulu , Box 3000, FIN-90014 Oulu, Finland
| | - Stephen H Southworth
- Chemical Sciences and Engineering Division, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Christoph Bostedt
- Chemical Sciences and Engineering Division, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Physics, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Oksana Travnikova
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique - Matière et Rayonnement, LCPMR , F-75005 Paris, France
| | - Tatiana Marchenko
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique - Matière et Rayonnement, LCPMR , F-75005 Paris, France
| | - Sang-Kil Son
- Center for Free-Electron Laser Science, DESY , Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY , Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging , Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, University of Hamburg , Jungiusstrasse 9, 20355 Hamburg, Germany
| | - Marc Simon
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique - Matière et Rayonnement, LCPMR , F-75005 Paris, France
| | - Linda Young
- Chemical Sciences and Engineering Division, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, Illinois 60439, United States
- Department of Physics and James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Stacey L Sorensen
- Department of Physics, Lund University , Box 118, 221 00 Lund, Sweden
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Aguirre NF, Díaz-Tendero S, Hervieux PA, Alcamí M, Martín F. M 3C: A Computational Approach To Describe Statistical Fragmentation of Excited Molecules and Clusters. J Chem Theory Comput 2017; 13:992-1009. [PMID: 28005371 DOI: 10.1021/acs.jctc.6b00984] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Microcanonical Metropolis Monte Carlo method, based on a random sampling of the density of states, is revisited for the study of molecular fragmentation in the gas phase (isolated molecules, atomic and molecular clusters, complex biomolecules, etc.). A random walk or uniform random sampling in the configurational space (atomic positions) and a uniform random sampling of the relative orientation, vibrational energy, and chemical composition of the fragments is used to estimate the density of states of the system, which is continuously updated as the random sampling populates individual states. The validity and usefulness of the method is demonstrated by applying it to evaluate the caloric curve of a weakly bound rare gas cluster (Ar13), to interpret the fragmentation of highly excited small neutral and singly positively charged carbon clusters (Cn, n = 5,7,9 and Cn+, n = 4,5) and to simulate the mass spectrum of the acetylene molecule (C2H2).
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Affiliation(s)
- Néstor F Aguirre
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , 28049 Madrid, Spain
| | - Paul-Antoine Hervieux
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg , 67000 Strasbourg, France
| | - Manuel Alcamí
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencias (IMDEA-Nanociencia) , 28049 Madrid, Spain
| | - Fernando Martín
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , 28049 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencias (IMDEA-Nanociencia) , 28049 Madrid, Spain
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