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Plante I, West DW, Weeks J, Risca VI. Simulation of Radiation-Induced DNA Damage and Protection by Histones Using the Code RITRACKS. BIOTECH 2024; 13:17. [PMID: 38921049 PMCID: PMC11201919 DOI: 10.3390/biotech13020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/10/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024] Open
Abstract
(1) Background: DNA damage is of great importance in the understanding of the effects of ionizing radiation. Various types of DNA damage can result from exposure to ionizing radiation, with clustered types considered the most important for radiobiological effects. (2) Methods: The code RITRACKS (Relativistic Ion Tracks), a program that simulates stochastic radiation track structures, was used to simulate DNA damage by photons and ions spanning a broad range of linear energy transfer (LET) values. To perform these simulations, the transport code was modified to include cross sections for the interactions of ions or electrons with DNA and amino acids for ionizations, dissociative electron attachment, and elastic collisions. The radiochemistry simulations were performed using a step-by-step algorithm that follows the evolution of all particles in time, including reactions between radicals and DNA structures and amino acids. Furthermore, detailed DNA damage events, such as base pair positions, DNA fragment lengths, and fragment yields, were recorded. (3) Results: We report simulation results using photons and the ions 1H+, 4He2+, 12C6+, 16O8+, and 56Fe26+ at various energies, covering LET values from 0.3 to 164 keV/µm, and performed a comparison with other codes and experimental results. The results show evidence of DNA protection from damage at its points of contacts with histone proteins. (4) Conclusions: RITRACKS can provide a framework for studying DNA damage from a variety of ionizing radiation sources with detailed representations of DNA at the atomic scale, DNA-associated proteins, and resulting DNA damage events and statistics, enabling a broader range of future comparisons with experiments such as those based on DNA sequencing.
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Affiliation(s)
| | - Devany W. West
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY 10065, USA; (D.W.W.); (V.I.R.)
| | - Jason Weeks
- NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY 10065, USA; (D.W.W.); (V.I.R.)
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2
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Shafranyosh MI, Zapotokova M, Sukhoviya MI, Petrulyak VI, Shafranyosh II. Electronic Ionization of Cytosine Molecules. SURFACE ENGINEERING AND APPLIED ELECTROCHEMISTRY 2022. [DOI: 10.3103/s1068375522010100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Bandurin YA, Zavilopulo AN, Molnar S, Shpenik OO. Excitation of L-valine molecules by electrons and photons. THE EUROPEAN PHYSICAL JOURNAL. D, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 2022; 76:9. [PMID: 35069006 PMCID: PMC8761534 DOI: 10.1140/epjd/s10053-021-00331-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Excitation of L-valine molecules was studied by optical spectroscopy. Optical emission spectra of the L-valine molecule and optical excitation functions of molecular bands and the Hβ spectral line were measured in the gas phase using electron impact. In the spectra of optical emission in the wavelength range of 250-500 nm, intense emission bands were found at energies of incident electrons of 30, 50 and 70 eV. Analysis of structural features of the valine molecule suggested a fragmentation scheme with the formation of excited particles in collisions with electrons. A notable feature of the presented optical excitation functions is a different growth dynamics with an increase in the energy of exciting electrons and the presence of a number of features and kinks, which are especially pronounced for λ = 305 nm and λ = 311 nm. The excitation thresholds were determined from the initial sections of the excitation functions of the most intense spectral lines by the least-squares method. The photoluminescence spectra of L-valine were measured for the first time on a Shimadzu RF-6000 spectrofluorophotometer in the spectral range of 400-800 nm for excitation wavelengths of 250, 275, 333, 351, and 380 nm.
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Affiliation(s)
- Yu. A. Bandurin
- Institute of Electron Physics, National Academy of Sciences of Ukraine, Uzhhorod, 88017 Ukraine
| | - A. N. Zavilopulo
- Institute of Electron Physics, National Academy of Sciences of Ukraine, Uzhhorod, 88017 Ukraine
| | - Sh. Molnar
- Ukrainian-Hungarian Educational-Scientific Institute of Uzhhorod National University, Uzhhorod, 88000 Ukraine
| | - O. O. Shpenik
- Ukrainian-Hungarian Educational-Scientific Institute of Uzhhorod National University, Uzhhorod, 88000 Ukraine
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4
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Liu C, Zheng Y, Sanche L. Damage Induced to DNA and Its Constituents by 0-3 eV UV Photoelectrons †. Photochem Photobiol 2021; 98:546-563. [PMID: 34767635 DOI: 10.1111/php.13559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/07/2021] [Indexed: 11/28/2022]
Abstract
The complex physical and chemical interactions between DNA and 0-3 eV electrons released by UV photoionization can lead to the formation of various lesions such as base modifications and cleavage, crosslinks and single strand breaks. Furthermore, in the presence of platinum chemotherapeutic agents, these electrons can cause clustered lesions, including double strand breaks. We explain the mechanisms responsible for these damages via the production 0-3 eV electrons by UVC radiation, and by UV photons of any wavelengths, when they are produced by photoemission from nanoparticles lying within about 10 nm from DNA. We review experimental evidence showing that a single 0-3 eV electron can produce these damages. The foreseen benefits UV-irradiation of nanoparticles targeted to the cell nucleus are mentioned in the context of cancer therapy, as well as the potential hazards to human health when they are present in cells.
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Affiliation(s)
- Chaochao Liu
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, China
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, China
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada
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5
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Muftakhov M, Shchukin P, Khatymov R. Thymidine and stavudine molecules in reactions with low-energy electrons. Radiat Phys Chem Oxf Engl 1993 2021. [DOI: 10.1016/j.radphyschem.2021.109464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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6
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Stokes PW, Foster SP, Casey MJE, Cocks DG, González-Magaña O, de Urquijo J, García G, Brunger MJ, White RD. An improved set of electron-THFA cross sections refined through a neural network-based analysis of swarm data. J Chem Phys 2021; 154:084306. [PMID: 33639749 DOI: 10.1063/5.0043759] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We review experimental and theoretical cross sections for electron transport in α-tetrahydrofurfuryl alcohol (THFA) and, in doing so, propose a plausible complete set. To assess the accuracy and self-consistency of our proposed set, we use the pulsed-Townsend technique to measure drift velocities, longitudinal diffusion coefficients, and effective Townsend first ionization coefficients for electron swarms in admixtures of THFA in argon, across a range of density-reduced electric fields from 1 to 450 Td. These measurements are then compared to simulated values derived from our proposed set using a multi-term solution of Boltzmann's equation. We observe discrepancies between the simulation and experiment, which we attempt to address by employing a neural network model that is trained to solve the inverse swarm problem of unfolding the cross sections underpinning our experimental swarm measurements. What results from our neural network-based analysis is a refined set of electron-THFA cross sections, which we confirm is of higher consistency with our swarm measurements than that which we initially proposed. We also use our database to calculate electron transport coefficients in pure THFA across a range of reduced electric fields from 0.001 to 10 000 Td.
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Affiliation(s)
- P W Stokes
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - S P Foster
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - M J E Casey
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - D G Cocks
- Research School of Physics, Australian National University, Canberra, ACT 0200, Australia
| | - O González-Magaña
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, 62251 Cuernavaca, Morelos, Mexico
| | - J de Urquijo
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, 62251 Cuernavaca, Morelos, Mexico
| | - G García
- Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid, Spain
| | - M J Brunger
- College of Science and Engineering, Flinders University, Bedford Park, Adelaide SA 5042, Australia
| | - R D White
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
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7
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Kochur AG, Chaynikov AP, Yavna VA. Monte Carlo study of the relative role of energy absorption mechanisms in solid disordered neon under irradiation with photons in the energy range of 4 to 800 Ry. Appl Radiat Isot 2020; 160:109144. [PMID: 32351211 DOI: 10.1016/j.apradiso.2020.109144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 11/18/2022]
Abstract
Mechanisms of energy absorption in solid disordered neon under 4 to 800 Ry photon irradiation are studied by Monte Carlo simulation with accounting for the cascade decays of vacancies produced by primary and secondary ionization processes. The dominating channel for the transfer of energy to the sample giving about 55% of total absorbed energy is through ionization and excitation of atoms of the medium by secondary electrons produced by primary photoionization and secondary inelastic processes, and by vacancy decay cascades. The portion of energy absorbed in the acts of primary photoionization is significant only at incident photon energies fewer than 10 Ry, it is about 5% at incident photon energy near the Ne1s ionization threshold, and decreases rapidly at higher photon energies. The energy absorbed in secondary photoionization processes makes 3-5% of total absorbed energy on the whole incident photon energy interval. About 40% of total absorbed energy is transferred by low-energy electrons and photons that cannot ionize or excite atomic electrons. In the problems of radiation cancer therapy, at high energies of incident photons, the low-energy electrons produced in great quantities may contribute to DNA strand breaks via dissociative electron attachment.
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Affiliation(s)
- A G Kochur
- Rostov State Transport University, 2 Narodnogo Opolcheniya, Rostov-on-Don, 344038, Russia.
| | - A P Chaynikov
- Rostov State Transport University, 2 Narodnogo Opolcheniya, Rostov-on-Don, 344038, Russia
| | - V A Yavna
- Rostov State Transport University, 2 Narodnogo Opolcheniya, Rostov-on-Don, 344038, Russia
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8
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Lemelin V, Bass AD, Sanche L. Low energy (6-18 eV) electron scattering from condensed thymidine (dT) III: absolute electronic excitation cross sections. Phys Chem Chem Phys 2020; 22:8364-8372. [PMID: 32266899 DOI: 10.1039/d0cp00198h] [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
Absolute cross sections (CSs) for electronic excitation by low-energy electron (LEE) scattering, from condensed thymidine (dT) in the 6-18 eV incident energy range, were measured by high-resolution electron energy loss spectroscopy (HREELS). Various electron energy loss (EEL) spectra were acquired using 1 ML of dT condensed on a multilayer film of Ar held at about 20 K under ultra-high vacuum (∼1 × 10-11 Torr). dT is one of the most complex DNA constituents to be studied by HREELS and these spectra provide the first LEE energy-loss data for electronic excitation of a nucleoside. CSs for transitions to the states 13A', 13A'', 23A', 21A', 33A', 23A'', 43A', 33A'', 53A' and 51A' of dT were extracted from the EEL spectra. These states correlate to those previously measured for the thymine moiety. Two broad resonances are observed in the energy dependence of the CSs at around 8 and 10 eV; these energies are close to those found in earlier gas- and solid-phase studies on the interaction of LEEs with dT, thymine and related molecules. A quantitative comparison between the electronic CSs of dT and those of thymine and tetrahydrofuran indicates that no variation is induced in the electronic CSs of thymine upon chemically binding to a deoxyribose group.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
| | - A D Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
| | - L Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des radiations, Université de Sherbrooke, Québec J1H 5N4, Canada.
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9
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Maioli LS, Kossoski F, Bettega MHF. Low-energy electron scattering by cyanamide: anion spectra and dissociation pathways. Phys Chem Chem Phys 2020; 22:7894-7902. [PMID: 32227067 DOI: 10.1039/d0cp00806k] [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
The low-energy anion spectra of cyanamide and its rare tautomer carbodiimide were surveyed with elastic electron scattering calculations. Our assignments differ qualitatively and quantitatively from a previous theoretical report. We support that both tautomers present two π* and two shape resonances, while cyanamide should also display a dipole bound state and a shape resonance. Available dissociative electron attachment measurements have shown several structures for dehydrogenation below 4 eV, but no sharp peaks related to vibrational Feshbach resonances. The absence of these resonances is explained by the lack of a potential barrier for tunneling of the hydrogen atom, despite the coupling between dipole bound and states. We found that the π* resonances initiate the dynamics that lead to hydrogen loss at 1.5, 2.5 and 3 eV. The later two structures arise from the anion states of cyanamide, while carbodiimide should account for the lower-lying one. The rarity of the second tautomer would be offset by its larger dissociative electron attachment cross section, enough to leave a distinct signature in the measured ion yield spectra. Low-energy electrons should thus decompose carbodiimide much more efficiently than cyanamide.
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Affiliation(s)
- Leticia S Maioli
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba, Paraná, Brazil
| | | | - Márcio H F Bettega
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba, Paraná, Brazil
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10
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Bhunia S, Kumar A, Ojha AK. Tuning of structural and magnetic properties by intriguing radical-radical interaction by double electron oxidation in U-A-U′ triplex formation. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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de Urquijo J, Casey MJE, Serkovic-Loli LN, Cocks DG, Boyle GJ, Jones DB, Brunger MJ, White RD. Assessment of the self-consistency of electron-THF cross sections using electron swarm techniques: Mixtures of THF–Ar and THF–N2. J Chem Phys 2019. [DOI: 10.1063/1.5108619] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J. de Urquijo
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, 62251, Cuernavaca, Morelos, Mexico
| | - M. J. E. Casey
- College of Science and Engineering, James Cook University, Townsville QLD 4811, Australia
| | - L. N. Serkovic-Loli
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, 62251, Cuernavaca, Morelos, Mexico
| | - D. G. Cocks
- College of Science and Engineering, James Cook University, Townsville QLD 4811, Australia
| | - G. J. Boyle
- College of Science and Engineering, James Cook University, Townsville QLD 4811, Australia
| | - D. B. Jones
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
| | - M. J. Brunger
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide SA 5001, Australia
| | - R. D. White
- College of Science and Engineering, James Cook University, Townsville QLD 4811, Australia
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12
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Cercola R, Matthews E, Dessent CEH. Near-threshold electron transfer in anion-nucleobase clusters: does the identity of the anion matter? Mol Phys 2019. [DOI: 10.1080/00268976.2019.1596327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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13
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Lemelin V, Bass AD, Sanche L. Note: Absolute electronic excitation cross sections for 8.5-17.5 eV electron scattering from condensed dimethyl phosphate (DMP). J Chem Phys 2018; 149:246101. [DOI: 10.1063/1.5059387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- V. Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Québec J1H 5N4, Canada
| | - A. D. Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Québec J1H 5N4, Canada
| | - L. Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Québec J1H 5N4, Canada
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14
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Cunha T, Mendes M, Ferreira da Silva F, Eden S, García G, Bacchus-Montabonel MC, Limão-Vieira P. Electron transfer driven decomposition of adenine and selected analogs as probed by experimental and theoretical methods. J Chem Phys 2018; 148:134301. [PMID: 29626890 DOI: 10.1063/1.5021888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on a combined experimental and theoretical study of electron-transfer-induced decomposition of adenine (Ad) and a selection of analog molecules in collisions with potassium (K) atoms. Time-of-flight negative ion mass spectra have been obtained in a wide collision energy range (6-68 eV in the centre-of-mass frame), providing a comprehensive investigation of the fragmentation patterns of purine (Pu), adenine (Ad), 9-methyl adenine (9-mAd), 6-dimethyl adenine (6-dimAd), and 2-D adenine (2-DAd). Following our recent communication about selective hydrogen loss from the transient negative ions (TNIs) produced in these collisions [T. Cunha et al., J. Chem. Phys. 148, 021101 (2018)], this work focuses on the production of smaller fragment anions. In the low-energy part of the present range, several dissociation channels that are accessible in free electron attachment experiments are absent from the present mass spectra, notably NH2 loss from adenine and 9-methyl adenine. This can be understood in terms of a relatively long transit time of the K+ cation in the vicinity of the TNI tending to enhance the likelihood of intramolecular electron transfer. In this case, the excess energy can be redistributed through the available degrees of freedom inhibiting fragmentation pathways. Ab initio theoretical calculations were performed for 9-methyl adenine (9-mAd) and adenine (Ad) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.
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Affiliation(s)
- T Cunha
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - M Mendes
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - F Ferreira da Silva
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - S Eden
- School of Physical Sciences, The Open University, Walton Hall, MK7 6AA Milton Keynes, United Kingdom
| | - G García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain
| | - M-C Bacchus-Montabonel
- Institut Lumiére Matiére, Université Lyon, Université Claude Bernard Lyon 1, CNRS, 69622 Villeurbanne, France
| | - P Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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15
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Lemelin V, Bass AD, Wagner JR, Sanche L. Absolute vibrational excitation cross sections for 1-18 eV electron scattering from condensed dimethyl phosphate (DMP). J Chem Phys 2017; 147:234305. [DOI: 10.1063/1.5008486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- V. Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - A. D. Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - J. R. Wagner
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - L. Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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16
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Casey MJE, de Urquijo J, Serkovic Loli LN, Cocks DG, Boyle GJ, Jones DB, Brunger MJ, White RD. Self-consistency of electron-THF cross sections using electron swarm techniques. J Chem Phys 2017; 147:195103. [DOI: 10.1063/1.5004717] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. J. E. Casey
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - J. de Urquijo
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de Mexico, 62251 Cuernavaca, Morelos, Mexico
| | - L. N. Serkovic Loli
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de Mexico, 62251 Cuernavaca, Morelos, Mexico
| | - D. G. Cocks
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - G. J. Boyle
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - D. B. Jones
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - M. J. Brunger
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - R. D. White
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
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17
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Liu W, Tan Z, Zhang L, Champion C. Calculation on spectrum of direct DNA damage induced by low-energy electrons including dissociative electron attachment. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2017; 56:99-110. [PMID: 28185000 DOI: 10.1007/s00411-016-0681-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 12/30/2016] [Indexed: 06/06/2023]
Abstract
In this work, direct DNA damage induced by low-energy electrons (sub-keV) is simulated using a Monte Carlo method. The characteristics of the present simulation are to consider the new mechanism of DNA damage due to dissociative electron attachment (DEA) and to allow determining damage to specific bases (i.e., adenine, thymine, guanine, or cytosine). The electron track structure in liquid water is generated, based on the dielectric response model for describing electron inelastic scattering and on a free-parameter theoretical model and the NIST database for calculating electron elastic scattering. Ionization cross sections of DNA bases are used to generate base radicals, and available DEA cross sections of DNA components are applied for determining DNA-strand breaks and base damage induced by sub-ionization electrons. The electron elastic scattering from DNA components is simulated using cross sections from different theoretical calculations. The resulting yields of various strand breaks and base damage in cellular environment are given. Especially, the contributions of sub-ionization electrons to various strand breaks and base damage are quantitatively presented, and the correlation between complex clustered DNA damage and the corresponding damaged bases is explored. This work shows that the contribution of sub-ionization electrons to strand breaks is substantial, up to about 40-70%, and this contribution is mainly focused on single-strand break. In addition, the base damage induced by sub-ionization electrons contributes to about 20-40% of the total base damage, and there is an evident correlation between single-strand break and damaged base pair A-T.
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Affiliation(s)
- Wei Liu
- School of Electrical Engineering, Shandong University, Jinan, 250061, Shandong, People's Republic of China
| | - Zhenyu Tan
- School of Electrical Engineering, Shandong University, Jinan, 250061, Shandong, People's Republic of China.
| | - Liming Zhang
- School of Electrical Engineering, Shandong University, Jinan, 250061, Shandong, People's Republic of China
- Electric Power Research Institute of Tianjin Electric Power Corporation, Tianjin, 300384, People's Republic of China
| | - Christophe Champion
- Centre d'Etudes Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, BP 120, 33175, Gradignan, France
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18
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Lemelin V, Bass AD, Cloutier P, Sanche L. Absolute cross sections for electronic excitation of condensed tetrahydrofuran (THF) by 11-16 eV electrons. J Chem Phys 2017; 145:174703. [PMID: 27825202 DOI: 10.1063/1.4966650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Absolute cross section (CS) data on the interaction of low energy electrons with DNA and its molecular constituents are required as input parameters in Monte-Carlo type simulations, for several radiobiological applications. Previously [V. Lemelin et al., J. Chem. Phys. 144, 074701 (2016)], we measured absolute vibrational CSs for low-energy electron scattering from condensed tetrahydrofuran, a convenient surrogate for the deoxyribose. Here we report absolute electronic CSs for energy losses of between 6 and 11.5 eV, by electrons with energies between 11 and 16 eV. The variation of these CSs with incident electron energy shows no evidence of transient anion states, consistent with theoretical and other experimental results, indicating that initial electron capture leading to DNA strand breaks occurs primarily on DNA bases or the phosphate group.
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Affiliation(s)
- V Lemelin
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - A D Bass
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - P Cloutier
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - L Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences des Radiations, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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19
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Fromm M, Boulanouar O. Low energy electrons and ultra-soft X-rays irradiation of plasmid DNA. Technical innovations. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Francés-Monerris A, Segarra-Martí J, Merchán M, Roca-Sanjuán D. Complete-active-space second-order perturbation theory (CASPT2//CASSCF) study of the dissociative electron attachment in canonical DNA nucleobases caused by low-energy electrons (0-3 eV). J Chem Phys 2016; 143:215101. [PMID: 26646889 DOI: 10.1063/1.4936574] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Low-energy (0-3 eV) ballistic electrons originated during the irradiation of biological material can interact with DNA/RNA nucleobases yielding transient-anion species which undergo decompositions. Since the discovery that these reactions can eventually lead to strand breaking of the DNA chains, great efforts have been dedicated to their study. The main fragmentation at the 0-3 eV energy range is the ejection of a hydrogen atom from the specific nitrogen positions. In the present study, the methodological approach introduced in a previous work on uracil [I. González-Ramírez et al., J. Chem. Theory Comput. 8, 2769-2776 (2012)] is employed to study the DNA canonical nucleobases fragmentations of N-H bonds induced by low-energy electrons. The approach is based on minimum energy path and linear interpolation of internal coordinates computations along the N-H dissociation channels carried out at the complete-active-space self-consistent field//complete-active-space second-order perturbation theory level. On the basis of the calculated theoretical quantities, new assignations for the adenine and cytosine anion yield curves are provided. In addition, the π1 (-) and π2 (-) states of the pyrimidine nucleobases are expected to produce the temporary anions at electron energies close to 1 and 2 eV, respectively. Finally, the present theoretical results do not allow to discard neither the dipole-bound nor the valence-bound mechanisms in the range of energies explored, suggesting that both possibilities may coexist in the experiments carried out with the isolated nucleobases.
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Affiliation(s)
| | - Javier Segarra-Martí
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071 València, Spain
| | - Manuela Merchán
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071 València, Spain
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071 València, Spain
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21
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Kopyra J, Abdoul-Carime H. Temperature dependence of the cross section for the fragmentation of thymine via dissociative electron attachment. J Chem Phys 2015; 142:174303. [PMID: 25956096 DOI: 10.1063/1.4919638] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Providing experimental values for absolute Dissociative Electron Attachment (DEA) cross sections for nucleobases at realistic biological conditions is a considerable challenge. In this work, we provide the temperature dependence of the cross section, σ, of the dehydrogenated thymine anion (T - H)(-) produced via DEA. Within the 393-443 K temperature range, it is observed that σ varies by one order of magnitude. By extrapolating to a temperature of 313 K, the relative DEA cross section for the production of the dehydrogenated thymine anion at an incident energy of 1 eV decreases by 2 orders of magnitude and the absolute value reaches approximately 6 × 10(-19) cm(2). These quantitative measurements provide a benchmark for theoretical prediction and also a contribution to a more accurate description of the effects of ionizing radiation on molecular medium.
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Affiliation(s)
- Janina Kopyra
- Faculty of Science, Siedlce University, 3 Maja 54, 08-110 Siedlce, Poland
| | - Hassan Abdoul-Carime
- Université de Lyon; Université Claude Bernard Lyon1; Institut de Physique Nucléaire de Lyon, CNRS/IN2P3 UMR 5822, 43 Bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
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22
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Minaev BF, Shafranyosh MI, Svida YY, Sukhoviya MI, Shafranyosh II, Baryshnikov GV, Minaeva VA. Fragmentation of the adenine and guanine molecules induced by electron collisions. J Chem Phys 2015; 140:175101. [PMID: 24811665 DOI: 10.1063/1.4871881] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Secondary electron emission is the most important stage in the mechanism of radiation damage to DNA biopolymers induced by primary ionizing radiation. These secondary electrons ejected by the primary electron impacts can produce further ionizations, initiating an avalanche effect, leading to genome damage through the energy transfer from the primary objects to sensitive biomolecular targets, such as nitrogenous bases, saccharides, and other DNA and peptide components. In this work, the formation of positive and negative ions of purine bases of nucleic acids (adenine and guanine molecules) under the impact of slow electrons (from 0.1 till 200 eV) is studied by the crossed electron and molecular beams technique. The method used makes it possible to measure the molecular beam intensity and determine the total cross-sections for the formation of positive and negative ions of the studied molecules, their energy dependences, and absolute values. It is found that the maximum cross section for formation of the adenine and guanine positive ions is reached at about 90 eV energy of the electron beam and their absolute values are equal to 2.8 × 10(-15) and 3.2 × 10(-15) cm(2), respectively. The total cross section for formation of the negative ions is 6.1 × 10(-18) and 7.6 × 10(-18) cm(2) at the energy of 1.1 eV for adenine and guanine, respectively. The absolute cross-section values for the molecular ions are measured and the cross-sections of dissociative ionization are determined. Quantum chemical calculations are performed for the studied molecules, ions and fragments for interpretation of the crossed beams experiments.
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Affiliation(s)
- B F Minaev
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
| | | | - Yu Yu Svida
- Uzhgorod National University, 88000 Uzhgorod, Ukraine
| | - M I Sukhoviya
- Uzhgorod National University, 88000 Uzhgorod, Ukraine
| | | | - G V Baryshnikov
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
| | - V A Minaeva
- Bohdan Khmelnitsky National University, 18031 Cherkasy, Ukraine
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23
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Do TPT, Duque HV, Lopes MCA, Konovalov DA, White RD, Brunger MJ, Jones DB. Differential cross sections for electron-impact vibrational-excitation of tetrahydrofuran at intermediate impact energies. J Chem Phys 2015; 142:124306. [PMID: 25833578 DOI: 10.1063/1.4915888] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We report differential cross sections (DCSs) for electron-impact vibrational-excitation of tetrahydrofuran, at intermediate incident electron energies (15-50 eV) and over the 10°-90° scattered electron angular range. These measurements extend the available DCS data for vibrational excitation for this species, which have previously been obtained at lower incident electron energies (≤20 eV). Where possible, our data are compared to the earlier measurements in the overlapping energy ranges. Here, quite good agreement was generally observed where the measurements overlapped.
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Affiliation(s)
- T P T Do
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - H V Duque
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - M C A Lopes
- Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais, Brazil
| | - D A Konovalov
- College of Science, Technology and Engineering, James Cook University, Townsville, Australia
| | - R D White
- College of Science, Technology and Engineering, James Cook University, Townsville, Australia
| | - M J Brunger
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - D B Jones
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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24
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Kossoski F, Kopyra J, Varella MTDN. Anion states and fragmentation of 2-chloroadenine upon low-energy electron collisions. Phys Chem Chem Phys 2015; 17:28958-65. [DOI: 10.1039/c5cp04967a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a joint theoretical and experimental investigation into the electron-induced fragmentation of 2-chloroadenine, for electrons up to 12 eV. Our results suggest that 2-chloroadenine can be considered as potential radiosensitiser.
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Affiliation(s)
- F. Kossoski
- Instituto de Física
- Universidade de São Paulo
- São Paulo
- Brazil
| | - J. Kopyra
- Siedlce University
- Faculty of Science
- 08-110 Siedlce
- Poland
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25
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Almeida D, Ferreira da Silva F, Eden S, García G, Limão-Vieira P. New Fragmentation Pathways in K–THF Collisions As Studied by Electron-Transfer Experiments: Negative Ion Formation. J Phys Chem A 2014; 118:690-6. [DOI: 10.1021/jp407997w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Almeida
- Laboratório
de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Fı́sica, Faculdade de Ciências
e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - F. Ferreira da Silva
- Laboratório
de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Fı́sica, Faculdade de Ciências
e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - S. Eden
- Department
of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - G. García
- Instituto de Fı́sica Fundamental, Consejo Superior de Investigaciones Cientı́ficas, Serrano 113-bis, 28006 Madrid, Spain
- Centre
for Medical Radiation Physics, University of Wollongong, NSW 2522, Australia
| | - P. Limão-Vieira
- Laboratório
de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Fı́sica, Faculdade de Ciências
e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department
of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
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26
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da Silva FF, Matias C, Almeida D, García G, Ingólfsson O, Flosadóttir HD, Ómarsson B, Ptasinska S, Puschnigg B, Scheier P, Limão-Vieira P, Denifl S. NCO(-), a key fragment upon dissociative electron attachment and electron transfer to pyrimidine bases: site selectivity for a slow decay process. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1787-97. [PMID: 24043519 DOI: 10.1007/s13361-013-0715-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 05/25/2023]
Abstract
We report gas phase studies on NCO(-) fragment formation from the nucleobases thymine and uracil and their N-site methylated derivatives upon dissociative electron attachment (DEA) and through electron transfer in potassium collisions. For comparison, the NCO(-) production in metastable decay of the nucleobases after deprotonation in matrix assisted laser desorption/ionization (MALDI) is also reported. We show that the delayed fragmentation of the dehydrogenated closed-shell anion into NCO(-) upon DEA proceeds few microseconds after the electron attachment process, indicating a rather slow unimolecular decomposition. Utilizing partially methylated thymine, we demonstrate that the remarkable site selectivity of the initial hydrogen loss as a function of the electron energy is preserved in the prompt as well as the metastable NCO(-) formation in DEA. Site selectivity in the NCO(-) yield is also pronounced after deprotonation in MALDI, though distinctly different from that observed in DEA. This is discussed in terms of the different electronic states subjected to metastable decay in these experiments. In potassium collisions with 1- and 3-methylthymine and 1- and 3-methyluracil, the dominant fragment is the NCO(-) ion and the branching ratios as a function of the collision energy show evidence of extraordinary site-selectivity in the reactions yielding its formation.
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Affiliation(s)
- Filipe Ferreira da Silva
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
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27
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de Oliveira EM, da Costa RF, Sanchez SD, Natalense APP, Bettega MHF, Lima MAP, Varella MTDN. Low-energy electron scattering by cellulose and hemicellulose components. Phys Chem Chem Phys 2013; 15:1682-9. [PMID: 23247550 DOI: 10.1039/c2cp43375c] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report elastic integral, differential and momentum transfer cross sections for low-energy electron scattering by the cellulose components β-D-glucose and cellobiose (β(1 → 4) linked glucose dimer), and the hemicellulose component β-D-xylose. For comparison with the β forms, we also obtain results for the amylose subunits α-D-glucose and maltose (α(1 → 4) linked glucose dimer). The integral cross sections show double peaked broad structures between 8 eV and 20 eV similar to previously reported results for tetrahydrofuran and 2-deoxyribose, suggesting a general feature of molecules containing furanose and pyranose rings. These broad structures would reflect OH, CO and/or CC σ* resonances, where inspection of low-lying virtual orbitals suggests significant contribution from anion states. Though we do not examine dissociation pathways, these anion states could play a role in dissociative electron attachment mechanisms, in case they were coupled to the long-lived π* anions found in lignin subunits [de Oliveira et al., Phys. Rev. A, 2012, 86, 020701(R)]. Altogether, the resonance spectra of lignin, cellulose and hemicellulose components establish a physical-chemical basis for electron-induced biomass pretreatment that could be applied to biofuel production.
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Affiliation(s)
- Eliane M de Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE/CNPEM), CP 6170, 13083-970, Campinas, SP, Brazil
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28
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Mašín Z, Gorfinkiel JD. Shape and core excited resonances in electron collisions with diazines. J Chem Phys 2012. [DOI: 10.1063/1.4767345] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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Homem MGP, López-Castillo A, Barbatti M, Rosa LFS, Iza P, Cavasso-Filho RL, Farenzena LS, Lee MT, Iga I. Experimental and theoretical investigations on photoabsorption and photoionization of trimethylphosphate in the vacuum-ultraviolet energy range. J Chem Phys 2012; 137:184305. [PMID: 23163369 DOI: 10.1063/1.4765336] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In this work, we report a joint experimental-theoretical investigation on interaction of vacuum-ultraviolet radiation with trimethylphosphate (TMP) molecule (C(3)H(9)O(4)P) in gas phase. This species together with tetrahydrofuran (THF) are model compounds of deoxyribose nucleic acids (DNA)/ribose nucleic acids (RNA) backbone. Absolute photoabsorption cross sections (σ(a)) and ionization yields (η) are measured using the double-ion-chamber technique in the 11.0-21.45 eV energy range. Photoionization (σ(i)) and neutral-decay (σ(n)) cross sections in absolute scale are also derived. Moreover, theoretical photoabsorption cross sections are calculated using the time-dependent density functional theory from the excitation threshold up to 16 eV. Good agreement between the present calculated and experimental photoabsorption cross sections in the 11.0-14.5 eV range is encouraging. Also, the present measured data of σ(a) and σ(i) for TMP are about 1.3 and 1.5 times of those of THF, respectively. Thus, the experimental evidences that the majority of strand breaks being located at sugar rings in the irradiated DNA/RNA backbone moiety may be induced by a possible migration of the hole, initially created at phosphate group, to the linked sugar groups. Finally, absolute partial photoionization cross sections are derived from the experimental time-of-flight mass spectra.
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Affiliation(s)
- M G P Homem
- Departamento de Física, UFSC, 88040-970 Florianópolis, SC, Brazil
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30
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Michaud M, Bazin M, Sanche L. Absolute cross sections for vibrational excitations of cytosine by low energy electron impact. J Chem Phys 2012; 137:115103. [PMID: 22998289 PMCID: PMC3812122 DOI: 10.1063/1.4752655] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The absolute cross sections (CSs) for vibrational excitations of cytosine by electron impact between 0.5 and 18 eV were measured by electron-energy loss (EEL) spectroscopy of the molecule deposited at monolayer coverage on an inert Ar substrate. The vibrational energies compare to those that have been reported from IR spectroscopy of cytosine isolated in Ar matrix, IR and Raman spectra of polycrystalline cytosine, and ab initio calculation. The CSs for the various H bending modes at 142 and 160 meV are both rising from their energy threshold up to 1.7 and 2.1 × 10(-17) cm(2) at about 4 eV, respectively, and then decrease moderately while maintaining some intensity at 18 eV. The latter trend is displayed as well for the CS assigned to the NH(2) scissor along with bending of all H at 179 meV. This overall behavior in electron-molecule collision is attributed to direct processes such as the dipole, quadrupole, and polarization contributions, etc. of the interaction of the incident electron with a molecule. The CSs for the ring deformation at 61 meV, the ring deformation with N-H symmetric wag at 77 meV, and the ring deformations with symmetric bending of all H at 119 meV exhibit common enhancement maxima at 1.5, 3.5, and 5.5 eV followed by a broad hump at about 12 eV, which are superimposed on the contribution due to the direct processes. At 3.5 eV, the CS values for the 61-, 77-, and 119-meV modes reach 4.0, 3.0, and 4.5 × 10(-17) cm(2), respectively. The CS for the C-C and C-O stretches at 202 meV, which dominates in the intermediate EEL region, rises sharply until 1.5 eV, reaches its maximum of 5.7 × 10(-17) cm(2) at 3.5 eV and then decreases toward 18 eV. The present vibrational enhancements, correspond to the features found around 1.5 and 4.5 eV in electron transmission spectroscopy (ETS) and those lying within 1.5-2.1 eV, 5.2-6.8 eV, and 9.5-10.9 eV range in dissociative electron attachment (DEA) experiments with cytosine in gas phase. While the ETS features are ascribed to shape resonances associated with the electron occupation of the second and third antibonding π-orbitals of the molecule in its ground state, the correspondence with DEA features suggests the existence of common precursor anion states decaying with certain probabilities into the vibrationally excited ground state.
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Affiliation(s)
- M Michaud
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada.
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31
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Dora A, Bryjko L, van Mourik T, Tennyson J. Low-energy electron scattering with the purine bases of DNA/RNA using the R-matrix method. J Chem Phys 2012; 136:024324. [DOI: 10.1063/1.3675448] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Michaud M, Bazin M, Sanche L. Measurement of inelastic cross sections for low-energy electron scattering from DNA bases. Int J Radiat Biol 2012; 88:15-21. [PMID: 21615242 PMCID: PMC3828174 DOI: 10.3109/09553002.2011.577505] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To determine experimentally the absolute cross sections (CS) to deposit various amount of energies into DNA bases by low-energy electron (LEE) impact. MATERIALS AND METHODS Electron energy loss (EEL) spectra of DNA bases were recorded for different LEE impact energies on the molecules deposited at very low coverage on an inert argon (Ar) substrate. Following their normalisation to the effective incident electron current and molecular surface number density, the EEL spectra were then fitted with multiple Gaussian functions in order to delimit the various excitation energy regions. The CS to excite a molecule into its various excitation modes were finally obtained from computing the area under the corresponding Gaussians. RESULTS The EEL spectra and absolute CS for the electronic excitations of pyrimidine and the DNA bases thymine, adenine, and cytosine by electron impacts below 18 eV were reported for the molecules deposited at about monolayer coverage on a solid Ar substrate. CONCLUSIONS The CS for electronic excitations of DNA bases by LEE impact were found to lie within the 10(216) to 10(218) cm(2) range. The large value of the total ionisation CS indicated that ionisation of DNA bases by LEE is an important dissipative process via which ionising radiation degrades and is absorbed in DNA.
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Affiliation(s)
- Marc Michaud
- Department of Nuclear Medicine and Radiobiology, Sherbrooke, Quebec, Canada.
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33
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Mašín Z, Gorfinkiel JD. Elastic and inelastic low-energy electron collisions with pyrazine. J Chem Phys 2011; 135:144308. [DOI: 10.1063/1.3650236] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Zubkov AS, Artyukhov VI, Chernozatonskii LA, Nedelina OS. A model of single-electron transport. Calculation of the thermodynamic parameters for electron capture by the bound proton of oxyacids. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2011. [DOI: 10.1134/s1990793111090259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Cheng HY, Chen CW. Energy and Lifetime of Temporary Anion States of Uracil by Stabilization Method. J Phys Chem A 2011; 115:10113-21. [DOI: 10.1021/jp205986z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hsiu-Yao Cheng
- Department of Chemistry, Tunghai University, Taichung 40704, Taiwan, R.O.C
| | - Chi-Wei Chen
- Department of Chemistry, Tunghai University, Taichung 40704, Taiwan, R.O.C
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36
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Park Y, Li Z, Cloutier P, Sanche L, Wagner JR. DNA damage induced by low-energy electrons: conversion of thymine to 5,6-dihydrothymine in the oligonucleotide trimer TpTpT. Radiat Res 2010; 175:240-6. [PMID: 21268718 DOI: 10.1667/rr2381.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Low-energy electrons (LEE) induce single- and double-strand breaks in DNA. To investigate the mechanism of LEE-induced DNA damage, nucleotides and short oligonucleotide were irradiated with monoenergetic electrons in the solid state and the modifications were observed by chemical analyses. With 10 eV electrons and TpTpT as the target, approximately one-third of the total damage of TpTpT involves cleavage of the phosphodiester-sugar bond (C-O) and the N-glycosidic bond (C-N). Here we focus on the remaining two-thirds of the damage. The major products were observed to elute between TpT and TpTpT on the HPLC chromatogram. Of these products, three modifications were identified as XpTpT, TpXpT and TpTpX, where X = 5,6-dihydrothymine, on the basis of comparison with standard compounds using HPLC and mass spectrometry. These results suggest that 5,6-dihydrothymine is a major product of the reaction of LEE with DNA.
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Affiliation(s)
- Yeunsoo Park
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Heath Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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37
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Bazin M, Michaud M, Sanche L. Absolute cross sections for electronic excitations of cytosine by low energy electron impact. J Chem Phys 2010; 133:155104. [PMID: 20969430 PMCID: PMC3817082 DOI: 10.1063/1.3505301] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The absolute cross sections (CSs) for electronic excitations of cytosine by electron impact between 5 and 18 eV were measured by electron-energy-loss (EEL) spectroscopy of the molecule deposited at low coverage on an inert Ar substrate. The lowest EEL features found at 3.55 and 4.02 eV are ascribed to transitions from the ground state to the two lowest triplet 1 (3)A(')(π→π(∗)) and 2 (3)A(')(π→π(∗)) valence states of the molecule. Their energy dependent CSs exhibit essentially a common maximum at about 6 eV with a value of 1.84×10(-17) cm(2) for the former and 4.94×10(-17) cm(2) for the latter. In contrast, the CS for the next EEL feature at 4.65 eV, which is ascribed to the optically allowed transition to the 2 (1)A(')(π→π(∗)) valence state, shows only a steep rise to about 1.04×10(-16) cm(2) followed by a monotonous decrease with the incident electron energy. The higher EEL features at 5.39, 6.18, 6.83, and 7.55 eV are assigned to the excitations of the 3 (3,1)A(')(π→π(∗)), 4 (1)A(')(π→π(∗)), 5 (1)A(')(π→π(∗)), and 6 (1)A(')(π→π(∗)) valence states, respectively. The CSs for the 3 (3,1)A(') and 4 (1)A(') states exhibit a common enhancement at about 10 eV superimposed on a more or less a steep rise, reaching, respectively, a maximum of 1.27 and 1.79×10(-16) cm(2), followed by a monotonous decrease. This latter enhancement and the maximum seen at about 6 eV in the lowest triplet states correspond to the core-excited electron resonances that have been found by dissociative electron attachment experiments with cytosine in the gas phase. The weak EEL feature found at 5.01 eV with a maximum CS of 3.8×10(-18) cm(2) near its excitation threshold is attributed to transitions from the ground state to the 1 (3,1)A(")(n→π(∗)) states. The monotonous rise of the EEL signal above 8 eV is attributed to the ionization of the molecule. It is partitioned into four excitation energy regions at about 8.55, 9.21, 9.83, and 11.53 eV, which correspond closely to the ionization energies of the four highest occupied molecular orbitals of cytosine. The sum of the ionization CS for these four excitation regions reaches a maximum of 8.1×10(-16) cm(2) at the incident energy of 13 eV.
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Affiliation(s)
- M. Bazin
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke Québec, Canada J1H 5N4
| | - M. Michaud
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke Québec, Canada J1H 5N4
| | - L. Sanche
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et Sciences de la Santé, Université de Sherbrooke, Sherbrooke Québec, Canada J1H 5N4
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Champion C, Lekadir H, Galassi ME, Fojón O, Rivarola RD, Hanssen J. Theoretical predictions for ionization cross sections of DNA nucleobases impacted by light ions. Phys Med Biol 2010; 55:6053-67. [DOI: 10.1088/0031-9155/55/20/002] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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de Oliveira EM, Lima MAP, Bettega MHF, Sanchez SD, da Costa RF, Varella MTDN. Low-energy electron collisions with pyrrole. J Chem Phys 2010; 132:204301. [DOI: 10.1063/1.3428620] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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40
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Zhang L, Tan Z. A new calculation on spectrum of direct DNA damage induced by low-energy electrons. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2010; 49:15-26. [PMID: 20039050 DOI: 10.1007/s00411-009-0262-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Accepted: 12/11/2009] [Indexed: 05/28/2023]
Abstract
In this work, direct DNA damage induced by low-energy electrons (<5 keV) is simulated using Monte Carlo methods, and the resulting yield of various strand breaks and base damages in cellular environment is presented. The simulation is based on a new inelastic cross section for the production of electron track structure in liquid water, and on ionization cross sections of DNA bases to generate base radical. Especially, a systematic approach of simulating detailed base damage is suggested. This approach includes improvement of a volume model of DNA, generation of the DNA base sequence, conversion of ionization events in liquid water at hit site to the ionization interaction of electrons with DNA bases and development of an algorithm to convert a base radical to a damage. The results obtained in terms of strand breaks are compared with those of experiments and other theoretical calculations, and good agreement was obtained. The yield of detailed base damages and clustered DNA damages caused by the combination of various strand breaks and base damages is presented, and the corresponding distribution characteristics are analyzed. The influence of the relative content of base pairs A-T and G-C in a DNA segment on the yield of both strand breaks and base damages is also explored. The present work provides fundamental information on DNA damage and represents the first effort toward the goal of obtaining the spectrum of clustered DNA damage including detailed base damages, for the mechanistic interpretation and prediction of radiation effects.
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Affiliation(s)
- Liming Zhang
- School of Electrical Engineering, Shandong University, Southern Campus, 250061, Jinan, Shandong, People's Republic of China
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41
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Dora A, Tennyson J, Bryjko L, van Mourik T. R-matrix calculation of low-energy electron collisions with uracil. J Chem Phys 2009; 130:164307. [PMID: 19405579 DOI: 10.1063/1.3119667] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
R-matrix calculations on electron-uracil collisions are presented within the static exchange, static exchange plus polarization, and close-coupling approximations. Particularly as input for the close-coupling calculations, a series of target calculations is performed which considers low-lying singlet and triplet excited states of the uracil target. The scattering calculations find three low-lying shape resonances of (2)A(") symmetry and three higher-energy Feshbach resonances of (2)A(') symmetry. In both symmetries the precise resonance parameters are found to be sensitive to the treatment of polarization effects employed. Cross sections are presented for both elastic scattering and electronic excitation. Comparisons are made with energy-dependent, differential cross section measurements at 90 degrees angle and good agreement is found for scattering energies above 0.5 eV.
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Affiliation(s)
- Amar Dora
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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42
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Dampc M, Mielewska B, Siggel-King MR, King GC, Zubek M. Threshold photoelectron spectra of tetrahydrofuran over the energy range 9–29eV. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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44
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Burrow PD, Gallup GA, Modelli A. Are there pi* shape resonances in electron scattering from phosphate groups? J Phys Chem A 2008; 112:4106-13. [PMID: 18366196 DOI: 10.1021/jp7109143] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The temporary anion states of trimethyl phosphate and several compounds bearing the P=O group were explored using electron transmission spectroscopy and ab initio calculations to determine if these states have the characteristics of the pi* resonances usually associated with multiple bonds. No evidence was found for this in (CH3O)3PO and, by extension, we do not expect them to appear in the phosphate group of DNA. Cl3PO, however, does display such characteristics to some extent, and we show that they arise from the spatial properties of the sigma* (P-Cl) orbitals rather than from multiple PO bonding. A novel computational means to explore effects due to the relative size of a molecular orbital and that of the angular momentum barrier responsible for confining the additional electron is presented.
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Affiliation(s)
- Paul D Burrow
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0111, USA.
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45
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Kim S, Lind MC, Schaefer HF. Structures and Energetics of the Deprotonated Adenine−Uracil Base Pair, Including Proton-Transferred Systems. J Phys Chem B 2008; 112:3545-51. [DOI: 10.1021/jp711518n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sunghwan Kim
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
| | - Maria C. Lind
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
| | - Henry F. Schaefer
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
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46
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Solomun T, Skalický T. The interaction of a protein–DNA surface complex with low-energy electrons. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2007.12.078] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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47
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Ibănescu BC, May O, Allan M. Cleavage of the ether bond by electron impact: differences between linear ethers and tetrahydrofuran. Phys Chem Chem Phys 2008; 10:1507-11. [PMID: 18327306 DOI: 10.1039/b718130b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dissociative electron attachment (DEA) to diethyl ether yielded primarily the C(2)H(5)O(-) ion, with a strong Feshbach resonance band at 9.1 eV and a weaker shape resonance band at 3.89 eV. Very similar spectra were obtained for dibutyl ether, with C(4)H(9)O(-) bands at 8.0 and 3.6 eV. Some of these primary ions subsequently lost H(2) and yielded weaker signals of the C(2)H(3)O(-) and C(4)H(7)O(-) ions. In contrast, DEA to the cyclic ether tetrahydrofuran (THF) yielded mainly a fragment of mass 41, presumably deprotonated ketene, at 7.65 eV. The low-energy band was missing in THF. H(-) with two bands at 6.88 and 8.61 eV, and an ion of mass 43 (presumably deprotonated acetaldehyde) with two bands at 6.7 and 8.50 eV were also observed. We propose that in the primary DEA step the C-O bond is cleaved in both the open-chain and the cyclic ethers. In the open-chain ethers the excess energy is partitioned between the (internal and kinetic) energies of two fragments, resulting in an RO(-) ion cool enough to be observed. The CH(2)(CH(2))(3)O(-) ion resulting from cleavage of the C-O bond in THF contains the entire excess energy (more than 6 eV at an electron energy of 7.65 eV) and is too short-lived with respect to further dissociation and thermal autodetachment to be detected in a mass spectrometer. These findings imply that there could be a substantial difference between the fragmentation in the gas phase described here and fragmentation in the condensed phase where the initially formed fragments can be rapidly cooled by the environment.
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Affiliation(s)
- Bogdan C Ibănescu
- Department of Chemistry, University of Fribourg, Chemin du Musée, 9, CH-1700 Fribourg, Switzerland
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48
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Radiation Effects On DNA: Theoretical Investigations Of Electron, Hole And Excitation Pathways To DNA Damage. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8184-2_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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Vasil’ev YV, Figard BJ, Barofsky DF, Deinzer ML. Resonant electron capture by some amino acids esters. J Am Chem Soc 2007; 268:106-121. [PMID: 19838328 PMCID: PMC2762707 DOI: 10.1016/j.ijms.2007.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Resonant electron capture by Gly, Ala and Phe esters have shown that the most efficient negative ion (NI) fragmentations are associated with the C-termini. A new mechanism for the negative ion-forming processes at energies lower than those associated with the pi*(OO) shape resonance involves coupling between dipole-bound and valence negative ion states of the same symmetry for amino acid conformers with high permanent dipoles. The interaction avoids crossing of the NI states and instead leads to formation of two adiabatic potential energy surfaces. Underivatized amino acids most effectively fragment from the bottom adiabatic surface via generation of [M-H](-) carboxylate anions by hydrogen-atom tunneling through the barrier; fragmentation of the their esters with formation of analogues [M-X](-) NIs occurs through the upper adiabatic state without penetration of the barrier in which the energy of the valence sigma*OX resonance exceeds the bond dissociation energy of the neutral molecule. Low and high temperature resonant electron capture experiments point to the importance of conformational preferences of the amino acids for optimum dissociation of the parent NIs in the gas phase.
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Affiliation(s)
- Yury V. Vasil’ev
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331
- Department of Physics, Bashkir State Agricultural University, Ufa, Russia
| | - Benjamin J. Figard
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | | | - Max L. Deinzer
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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