101
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McKee AD, Schaible MJ, Rosenberg RA, Kundu S, Orlando TM. Low energy secondary electron induced damage of condensed nucleotides. J Chem Phys 2019; 150:204709. [PMID: 31153208 DOI: 10.1063/1.5090491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Radiation damage and stimulated desorption of nucleotides 2'-deoxyadenosine 5'-monophosphate (dAMP), adenosine 5'-monophosphate (rAMP), 2'-deoxycytidine 5'-monophosphate (dCMP), and cytidine 5'-monophosphate (rCMP) deposited on Au have been measured using x-rays as both the probe and source of low energy secondary electrons. The fluence dependent behavior of the O-1s, C-1s, and N-1s photoelectron transitions was analyzed to obtain phosphate, sugar, and nucleobase damage cross sections. Although x-ray induced reactions in nucleotides involve both direct ionization and excitation, the observed bonding changes were likely dominated by the inelastic energy-loss channels associated with secondary electron capture and transient negative ion decay. Growth of the integrated peak area for the O-1s component at 531.3 eV, corresponding to cleavage of the C-O-P phosphodiester bond, yielded effective damage cross sections of about 23 Mb and 32 Mb (1 Mb = 10-18 cm2) for AMP and CMP molecules, respectively. The cross sections for sugar damage, as determined from the decay of the C-1s component at 286.4 eV and the glycosidic carbon at 289.0 eV, were slightly lower (about 20 Mb) and statistically similar for the r- and d- forms of the nucleotides. The C-1s component at 287.6 eV, corresponding to carbons in the nucleobase ring, showed a small initial increase and then decayed slowly, yielding a low damage cross section (∼5 Mb). Although there is no statistical difference between the sugar forms, changing the nucleobase from adenine to cytidine has a slight effect on the damage cross section, possibly due to differing electron capture and transfer probabilities.
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Affiliation(s)
- A D McKee
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - R A Rosenberg
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - S Kundu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - T M Orlando
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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102
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Dong Y, Gao Y, Liu W, Gao T, Zheng Y, Sanche L. Clustered DNA Damage Induced by 2-20 eV Electrons and Transient Anions: General Mechanism and Correlation to Cell Death. J Phys Chem Lett 2019; 10:2985-2990. [PMID: 31099579 DOI: 10.1021/acs.jpclett.9b01063] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The mechanisms of action of low-energy electrons (LEEs) generated in large quantities by ionizing radiation constitute an essential element of our understanding of early events in radiolysis and radiobiology. We present the 2-20 eV electron energy dependence of the yields of base damage (BD), BD-related cross-links (CLs), and non-double-strand break (NDSB) clustered damage induced in DNA. These new yield functions are generated by the impact of LEEs on plasmid DNA films. The damage is analyzed by gel electrophoresis with and without enzyme treatment. Maxima at 5 and 10 eV in BDs and BD-related CLs yield functions, and two others, at 6 and 10 eV, in those of NDSB clustered damage are ascribed to core-excited transient anions that decay into bond-breaking channels. The mechanism causing all types of DNA damages can be attributed to the capture of a single electron by a base followed by multiple different electron transfer pathways.
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Affiliation(s)
- Yanfang Dong
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Yingxia Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Wenhui Liu
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Ting Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Faculty of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology and Clinical Research Center, Faculty of Medicine , Université de Sherbrooke , Sherbrooke , QC , Canada J1H 5N4
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103
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Karashima S, Suzuki T. Charge-Transfer-to-Solvent Reaction in a Hydrophobic Tetrabutylammonium Iodide Molecular Layer in Aqueous Solution. J Phys Chem B 2019; 123:3769-3775. [PMID: 30827113 DOI: 10.1021/acs.jpcb.8b12210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present ultrafast photoelectron spectroscopy of the charge-transfer-to-solvent reaction in a segregated TBAI (tetrabutylammonium iodide) molecular layer in aqueous solution. The reaction times and electron binding energies of transient species vary with TBAI concentration from a very low value of 1 × 10-3 mol L-1, which is in contrast to NaI solution exhibiting no concentration (0.01-1.0 mol L-1) dependence. The result from soft X-ray N(1s) spectroscopy indicates that the photoelectron intensity in TBAI aqueous solution is about 70 times enhanced as compared to that in NH4Cl aqueous solution for an identical salt concentration, and TBA+ drags I- to the surface region. At high TBAI concentrations, electrons released from I- are trapped and held in the TBAI molecular layer owing to electrostatic attraction by TBA+.
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Affiliation(s)
- Shutaro Karashima
- Department of Chemistry, Graduate School of Science , Kyoto University , Kitashirakawa-Oiwakecho , Sakyo-Ku, Kyoto 606-8502 , Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science , Kyoto University , Kitashirakawa-Oiwakecho , Sakyo-Ku, Kyoto 606-8502 , Japan
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104
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Robertson JC, Coote ML, Bissember AC. Synthetic applications of light, electricity, mechanical force and flow. Nat Rev Chem 2019. [DOI: 10.1038/s41570-019-0094-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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105
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Holden ZC, Rana B, Herbert JM. Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron. J Chem Phys 2019; 150:144115. [DOI: 10.1063/1.5089673] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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106
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Kunin A, Neumark DM. Time-resolved radiation chemistry: femtosecond photoelectron spectroscopy of electron attachment and photodissociation dynamics in iodide-nucleobase clusters. Phys Chem Chem Phys 2019; 21:7239-7255. [PMID: 30855623 DOI: 10.1039/c8cp07831a] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Iodide-nucleobase (I-·N) clusters studied by time-resolved photoelectron spectroscopy (TRPES) are an opportune model system for examining radiative damage of DNA induced by low-energy electrons. By initiating charge transfer from iodide to the nucleobase and following the dynamics of the resulting transient negative ions (TNIs) with femtosecond time resolution, TRPES provides a novel window into the chemistry triggered by the attachment of low-energy electrons to nucleobases. In this Perspective, we examine and compare the dynamics of electron attachment, autodetachment, and photodissociation in a variety of I-·N clusters, including iodide-uracil (I-·U), iodide-thymine (I-·T), iodide-uracil-water (I-·U·H2O), and iodide-adenine (I-·A), to develop a more unified representation of our understanding of nucleobase TNIs. The experiments probe whether dipole-bound or valence-bound TNIs are formed initially and the subsequent time evolution of these species. We also provide an outlook for forthcoming applications of TRPES to larger iodide-containing complexes to enable the further investigation of microhydration dynamics in nucleobases, as well as electron attachment and photodissociation in more complex nucleic acid constituents.
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Affiliation(s)
- Alice Kunin
- Department of Chemistry, University of California, Berkeley, California 94720, USA.
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107
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Tippayamontri T, Guérin B, Ouellet R, Sarrhini O, Rousseau J, Lecomte R, Paquette B, Sanche L. Intratumoral 18F-FLT infusion in metabolic targeted radiotherapy. EJNMMI Res 2019; 9:33. [PMID: 30972596 PMCID: PMC6458198 DOI: 10.1186/s13550-019-0496-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/11/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The goal of targeted radiotherapy (TRT) is to administer radionuclides to tumor cells, while limiting radiation exposure to normal tissues. 3'-Deoxy-3'-[18F]-fluorothymidine (18F-FLT) is able to target tumor cells and emits a positron with energy appropriate for local (~ 1 mm range) radiotherapy. In the present work, we investigated the potential of TRT with a local administration of 18F-FLT alone or in combination with 5-fluorouracil (5FU), which acts as a chemotherapeutic agent and radiosensitizer. Treatment efficiency of 18F-FLT combined or not with 5FU was evaluated by intratumoral (i.t.) infusion into subcutaneous HCT116 colorectal tumors implanted in nu/nu mice. The tumor uptake and kinetics of 18F-FLT were determined and compared to 2-deoxy-2-[18F]-fluoro-D-glucose (18F-FDG) by dynamic positron emission tomography (PET) imaging following i.t. injection. The therapeutic responses of 18F-FLT alone and with 5FU were evaluated and compared with 18F-FDG and external beam radiotherapy (EBRT). The level of prostaglandin E2 (PGE2) biosynthesis was measured by liquid chromatography/tandem mass spectrometry (LC/MS/MS) in order to determine the level of inflammation to healthy tissues surrounding the tumor, after i.t. injection of 18F-FLT, and compared to EBRT. RESULTS We found that i.t. administration of 18F-FLT offers (1) the highest tumor-to-muscle uptake ratio not only in the injected tumor, but also in distant tumors, suggesting potential for concurrent metastases treatment and (2) a sixfold gain in radiotherapeutic efficacy in the primary tumor relative to EBRT, which can be further enhanced with concurrent i.t. administration of the radiosensitizer 5FU. While EBRT stimulated PGE2 production in peritumoral tissues, no significant increase of PGE2 was measured in this area following i.t. administration of 18F-FLT. CONCLUSION Considering the biochemical stability of 18F-FLT and the physical properties of localized 18F, this study shows that TRT via intratumoral infusion of 18F-FLT and 5FU could provide a new effective treatment option for solid tumors. Using this approach in a colorectal tumor model, the tumor and its metastases could be efficiently irradiated locally with much lower doses absorbed by healthy tissues than with i.t. administration of 18F-FDG or conventional EBRT.
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Affiliation(s)
- Thititip Tippayamontri
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada. .,Center of Radiotherapy Research, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC, Canada. .,Department of Radiological Technology and Medical Physics, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
| | - Brigitte Guérin
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.,Sherbrooke Molecular Imaging Center, CRCHUS, Sherbrooke, QC, Canada
| | - René Ouellet
- Sherbrooke Molecular Imaging Center, CRCHUS, Sherbrooke, QC, Canada
| | - Otman Sarrhini
- Sherbrooke Molecular Imaging Center, CRCHUS, Sherbrooke, QC, Canada
| | - Jacques Rousseau
- Sherbrooke Molecular Imaging Center, CRCHUS, Sherbrooke, QC, Canada
| | - Roger Lecomte
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.,Sherbrooke Molecular Imaging Center, CRCHUS, Sherbrooke, QC, Canada
| | - Benoit Paquette
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.,Center of Radiotherapy Research, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC, Canada
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada.,Center of Radiotherapy Research, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC, Canada
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108
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Nayek U, Unnikrishnan VK, Abdul Salam AA, Vasa P, Chidangil S, Mathur D. Strong Strand Breaks in DNA Induced by Thermal Energy Particles and Their Electrostatic Inhibition by Na + Nanostructures. J Phys Chem A 2019; 123:3241-3247. [PMID: 30920832 DOI: 10.1021/acs.jpca.9b00650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Low-power laser pulses of 6 ns duration (1064 nm wavelength) have been used to create plasma in an aqueous solution of plasmid DNA (pUC19). Thermal energy electrons and •OH radicals in the plasma induce strand breakages in DNA, including double strand breaks and possible base oxidation/base degradation. The time evolution of these modifications shows that it takes barely 30 s for damage to DNA to occur. Addition of physiologically relevant concentrations of a salt (NaCl) significantly inhibits such damage. We rationalize such inhibition using simple electrostatic considerations. The observation that DNA damage is induced by plasma-induced photolysis of water suggests implications beyond studies of DNA and opens new vistas for using simple nanosecond lasers to probe how ultralow energy radiation may affect living matter under physiological conditions.
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Affiliation(s)
| | | | | | - Parinda Vasa
- Department of Physics , Indian Institute of Technology Bombay , Powai, Mumbai 400 076 , India
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109
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LaForge AC, Michiels R, Bohlen M, Callegari C, Clark A, von Conta A, Coreno M, Di Fraia M, Drabbels M, Huppert M, Finetti P, Ma J, Mudrich M, Oliver V, Plekan O, Prince KC, Shcherbinin M, Stranges S, Svoboda V, Wörner HJ, Stienkemeier F. Real-Time Dynamics of the Formation of Hydrated Electrons upon Irradiation of Water Clusters with Extreme Ultraviolet Light. PHYSICAL REVIEW LETTERS 2019; 122:133001. [PMID: 31012607 DOI: 10.1103/physrevlett.122.133001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Indexed: 06/09/2023]
Abstract
Free electrons in a polar liquid can form a bound state via interaction with the molecular environment. This so-called hydrated electron state in water is of fundamental importance, e.g., in cellular biology or radiation chemistry. Hydrated electrons are highly reactive radicals that can either directly interact with DNA or enzymes, or form highly excited hydrogen (H^{*}) after being captured by protons. Here, we investigate the formation of the hydrated electron in real-time employing extreme ultraviolet femtosecond pulses from a free electron laser, in this way observing the initial steps of the hydration process. Using time-resolved photoelectron spectroscopy we find formation timescales in the low picosecond range and resolve the prominent dynamics of forming excited hydrogen states.
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Affiliation(s)
- A C LaForge
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
| | - R Michiels
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
| | - M Bohlen
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
| | - C Callegari
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - A Clark
- Laboratory of Molecular Nanodynamics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - A von Conta
- Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - M Coreno
- ISM-CNR, Istituto di Struttura della Materia, LD2 Unit, 34149 Trieste, Italy
| | - M Di Fraia
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - M Drabbels
- Laboratory of Molecular Nanodynamics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - M Huppert
- Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - P Finetti
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - J Ma
- Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - M Mudrich
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark
| | - V Oliver
- Laboratory of Molecular Nanodynamics, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - O Plekan
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - K C Prince
- Elettra-Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - M Shcherbinin
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark
| | - S Stranges
- Department of Chemistry and Drug Technologies, University Sapienza, 00185 Rome, Italy, and Tasc IOM-CNR, Basovizza, Trieste, Italy
| | - V Svoboda
- Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - H J Wörner
- Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
| | - F Stienkemeier
- Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
- Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg, 79104 Freiburg, Germany
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110
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Abstract
Electron attachment onto water clusters to form water cluster anions is studied by varying the point of electron attachment along a molecular beam axis and probing the produced cluster anions using photoelectron spectroscopy. The results show that the point of electron attachment has a clear effect on the final distribution of isomers for a cluster containing 78 water molecules, with isomer I formed preferentially near the start of the expansion and isomer II formed preferentially once the molecular beam has progressed for several millimeters. These changes can be accounted for by the cluster growth rate along the beam. Near the start of the expansion, cluster growth is proceeding rapidly with condensing water molecules solvating the electron, while further along the expansion, the growth has terminated and electrons are attached to large and cold preformed clusters, leading to the isomer associated with a loosely bound surface state.
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Affiliation(s)
- Aude Lietard
- Department of Chemistry , Durham University , Durham DH1 3LE , United Kingdom
| | - Jan R R Verlet
- Department of Chemistry , Durham University , Durham DH1 3LE , United Kingdom
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111
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Li Z, Ryszka M, Dawley MM, Carmichael I, Bravaya KB, Ptasińska S. Dipole-Supported Electronic Resonances Mediate Electron-Induced Amide Bond Cleavage. PHYSICAL REVIEW LETTERS 2019; 122:073002. [PMID: 30848645 DOI: 10.1103/physrevlett.122.073002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/11/2018] [Indexed: 05/28/2023]
Abstract
Dissociative electron attachment (DEA) plays a key role in radiation damage of biomolecules under high-energy radiation conditions. The initial step in DEA is often rationalized in terms of resonant electron capture into one of the metastable valence states of a molecule followed by its fragmentation. Our combined theoretical and experimental investigations indicate that the manifold of states responsible for electron capture in the DEA process can be dominated by core-excited (shake-up) dipole-supported resonances. Specifically, we present the results of experimental and computational studies of the gas-phase DEA to three prototypical peptide molecules, formamide, N-methylformamide (NMF), and N,N-dimethyl-formamide (DMF). In contrast to the case of electron capture by positively charged peptides in which amide bond rupture is rare compared to N─C_{α} bond cleavage, fragmentation of the amide bond was observed in each of these three molecules. The ion yield curves for ions resulting from this amide bond cleavage, such as NH_{2}^{-} for formamide, NHCH_{3}^{-} for NMF, and N(CH_{3})_{2}^{-} for DMF, showed a double-peak structure in the region between 5 and 8 eV. The peaks are assigned to Feshbach resonances including core-excited dipole-supported resonances populated upon electron attachment based on high-level electronic structure calculations. Moreover, the lower energy peak is attributed to formation of the core-excited resonance that correlates with the triplet state of the neutral molecule. The latter process highlights the role of optically spin-forbidden transitions promoted by electron impact in the DEA process.
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Affiliation(s)
- Zhou Li
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Michal Ryszka
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - M Michele Dawley
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Sylwia Ptasińska
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
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112
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Meißner R, Makurat S, Kozak W, Limão-Vieira P, Rak J, Denifl S. Electron-Induced Dissociation of the Potential Radiosensitizer 5-Selenocyanato-2'-deoxyuridine. J Phys Chem B 2019; 123:1274-1282. [PMID: 30657689 DOI: 10.1021/acs.jpcb.8b11523] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
5-Selenocyanato-2'-deoxyuridine (SeCNdU) is a recently proposed radiosensitizer based on 2'-deoxyuridine (dU) with the electron-affinic selenocyanato (-SeCN) side group attached at the C5 position of uracil. Since electron interaction processes may be an important source of DNA damage by ionizing radiation, we have studied low-energy dissociative electron attachment to SeCNdU in the gas phase. Negative ion formation has been obtained by means of mass spectrometry, where a rich fragmentation pattern is observed even at ∼0 eV. The reaction pathways exhibiting the highest ion yields are C4N2O2H2Se•- and CN-, both involving a cleavage of the Se-CN bond. The heaviest fragment anion observed is C9N2O5H10Se•-, where besides the charged species, the hydrogen and cyano radicals are also formed. Further decomposition channels also yield the highly reactive hydroxyl radical, which possesses a high DNA damage potential. All observed channels have experimentally determined onsets at 0 eV, which are supported by calculations performed at the M06-2X/aug-cc-pVTZ level. The calculations comprise the thermochemical thresholds at standard and experimental (428.15 K, 3 × 10-11 atm) conditions together with the adiabatic electron affinities. The present study shows that low-energy electrons very effectively decompose SeCNdU upon attachment of thermal electrons, producing a large variety of charged fragments and radicals.
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Affiliation(s)
- Rebecca Meißner
- Institut für Ionenphysik und Angewandte Physik and Center for Biomolecular Sciences Innsbruck , Leopold-Franzens Universität Innsbruck , Technikerstrasse 25 , A-6020 Innsbruck , Austria.,Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics , Universidade NOVA de Lisboa , 2829-516 Caparica , Portugal
| | - Samanta Makurat
- Laboratory of Biological Sensitizers, Physical Chemistry Department, Faculty of Chemistry , University of Gdańsk , 80-308 Gdańsk , Poland
| | - Witold Kozak
- Laboratory of Biological Sensitizers, Physical Chemistry Department, Faculty of Chemistry , University of Gdańsk , 80-308 Gdańsk , Poland
| | - Paulo Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics , Universidade NOVA de Lisboa , 2829-516 Caparica , Portugal
| | - Janusz Rak
- Laboratory of Biological Sensitizers, Physical Chemistry Department, Faculty of Chemistry , University of Gdańsk , 80-308 Gdańsk , Poland
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Biomolecular Sciences Innsbruck , Leopold-Franzens Universität Innsbruck , Technikerstrasse 25 , A-6020 Innsbruck , Austria
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113
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Zhao-Qi W, Hai-Yan W, Zeng ZY, Yan C. Ab initio investigation of possible lower-energy candidate structure for cationic water cluster (H2O) 12+ via particle swarm optimization method. Struct Chem 2019. [DOI: 10.1007/s11224-018-1182-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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114
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Zhang Y, Xie P, Yang S, Han K. Ionization and Electron Attachment for Nucleobases in Water. J Phys Chem B 2019; 123:1237-1247. [DOI: 10.1021/acs.jpcb.8b09435] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yan Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao, Binhai Road 72, Qingdao 266237, China
| | - Peng Xie
- School of Chemistry & Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Songqiu Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
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115
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Ma J, Kumar A, Muroya Y, Yamashita S, Sakurai T, Denisov SA, Sevilla MD, Adhikary A, Seki S, Mostafavi M. Observation of dissociative quasi-free electron attachment to nucleoside via excited anion radical in solution. Nat Commun 2019; 10:102. [PMID: 30626877 PMCID: PMC6327028 DOI: 10.1038/s41467-018-08005-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 12/11/2018] [Indexed: 01/28/2023] Open
Abstract
Damage to DNA via dissociative electron attachment has been well-studied in both the gas and condensed phases; however, understanding this process in bulk solution at a fundamental level is still a challenge. Here, we use a picosecond pulse of a high energy electron beam to generate electrons in liquid diethylene glycol and observe the electron attachment dynamics to ribothymidine at different stages of electron relaxation. Our transient spectroscopic results reveal that the quasi-free electron with energy near the conduction band effectively attaches to ribothymidine leading to a new absorbing species that is characterized in the UV-visible region. This species exhibits a nearly concentration-independent decay with a time constant of ~350 ps. From time-resolved studies under different conditions, combined with data analysis and theoretical calculations, we assign this intermediate to an excited anion radical that undergoes N1-C1′ glycosidic bond dissociation rather than relaxation to its ground state. Radiation-induced low-energy electrons in solution are implicated in DNA damage, but their relaxation dynamics are not well understood. Here the authors observe how quasi-free electrons dissociate glycosidic bonds via an excited nucleoside anion radical, whereas solvated electrons reside on the nucleoside as a relatively stable anion radical.
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Affiliation(s)
- Jun Ma
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, 615-8510, Japan.
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI, 48309, USA
| | - Yusa Muroya
- Department of Beam Materials Science, Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Shinichi Yamashita
- Nuclear Professional School, School of Engineering, The University of Tokyo, 2-22 Shirakata Shirane, Tokai-mura, Naka-gun, Ibaraki, 319-1188, Japan
| | - Tsuneaki Sakurai
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Sergey A Denisov
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, 91405, Orsay, Cedex, France
| | - Michael D Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI, 48309, USA
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI, 48309, USA
| | - Shu Seki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, 615-8510, Japan.
| | - Mehran Mostafavi
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, 91405, Orsay, Cedex, France.
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116
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Abstract
A cavity or excluded-volume structure best explains the experimental properties of the aqueous or “hydrated” electron.
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Affiliation(s)
- John M. Herbert
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus
- USA
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117
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Zhang Y, Wang J, Yang S. Notable effect of water on excess electron attachment to aqueous DNA deoxyribonucleosides. Phys Chem Chem Phys 2019; 21:8925-8932. [DOI: 10.1039/c9cp00536f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
As excess electrons are vertically attached to aqueous deoxyribonucleosides, ∼50% of excess electrons would be delocalized over the water molecules.
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Affiliation(s)
- Yan Zhang
- Institute of Molecular Sciences and Engineering
- Shandong University, Qingdao
- Qingdao 266237
- China
| | - Jiayue Wang
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- Dalian 116023
- China
| | - Songqiu Yang
- State Key Laboratory of Molecular Reaction Dynamics
- Dalian Institute of Chemical Physics
- Chinese Academy of Science
- Dalian 116023
- China
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118
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Richter C, Hollas D, Saak CM, Förstel M, Miteva T, Mucke M, Björneholm O, Sisourat N, Slavíček P, Hergenhahn U. Competition between proton transfer and intermolecular Coulombic decay in water. Nat Commun 2018; 9:4988. [PMID: 30478319 PMCID: PMC6255891 DOI: 10.1038/s41467-018-07501-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/06/2018] [Indexed: 12/01/2022] Open
Abstract
Intermolecular Coulombic decay (ICD) is a ubiquitous relaxation channel of electronically excited states in weakly bound systems, ranging from dimers to liquids. As it is driven by electron correlation, it was assumed that it will dominate over more established energy loss mechanisms, for example fluorescence. Here, we use electron-electron coincidence spectroscopy to determine the efficiency of the ICD process after 2a1 ionization in water clusters. We show that this efficiency is surprisingly low for small water clusters and that it gradually increases to 40-50% for clusters with hundreds of water units. Ab initio molecular dynamics simulations reveal that proton transfer between neighboring water molecules proceeds on the same timescale as ICD and leads to a configuration in which the ICD channel is closed. This conclusion is further supported by experimental results from deuterated water. Combining experiment and theory, we infer an intrinsic ICD lifetime of 12-52 fs for small water clusters.
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Affiliation(s)
- Clemens Richter
- Leibniz Institute of Surface Engineering (IOM), Permoserstr. 15, 04318, Leipzig, Germany
| | - Daniel Hollas
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, 16628, Prague 6, Czech Republic
| | - Clara-Magdalena Saak
- Department of Physics and Astronomy, Uppsala University, Box 516, 751 20, Uppsala, Sweden
| | - Marko Förstel
- Max Planck Institute for Plasma Physics, Boltzmannstr. 2, 85748, Garching, Germany
- Institute for Optics and Atomic Physics, Technical University Berlin, Hardenbergstr. 36, 10623, Berlin, Germany
| | - Tsveta Miteva
- Laboratoire de Chimie Physique Matière et Rayonnement, UMR 7614, Sorbonne Université, CNRS, F-75005, Paris, France
| | - Melanie Mucke
- Department of Physics and Astronomy, Uppsala University, Box 516, 751 20, Uppsala, Sweden
| | - Olle Björneholm
- Department of Physics and Astronomy, Uppsala University, Box 516, 751 20, Uppsala, Sweden
| | - Nicolas Sisourat
- Laboratoire de Chimie Physique Matière et Rayonnement, UMR 7614, Sorbonne Université, CNRS, F-75005, Paris, France
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, 16628, Prague 6, Czech Republic.
| | - Uwe Hergenhahn
- Leibniz Institute of Surface Engineering (IOM), Permoserstr. 15, 04318, Leipzig, Germany.
- Max Planck Institute for Plasma Physics, Wendelsteinstr. 1, 17491, Greifswald, Germany.
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119
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Ameixa J, Arthur-Baidoo E, Meißner R, Makurat S, Kozak W, Butowska K, Ferreira da Silva F, Rak J, Denifl S. Low-energy electron-induced decomposition of 5-trifluoromethanesulfonyl-uracil: A potential radiosensitizer. J Chem Phys 2018; 149:164307. [PMID: 30384761 DOI: 10.1063/1.5050594] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
5-trifluoromethanesulfonyl-uracil (OTfU), a recently proposed radiosensitizer, is decomposed in the gas-phase by attachment of low-energy electrons. OTfU is a derivative of uracil with a triflate (OTf) group at the C5-position, which substantially increases its ability to undergo effective electron-induced dissociation. We report a rich assortment of fragments formed upon dissociative electron attachment (DEA), mostly by simple bond cleavages (e.g., dehydrogenation or formation of OTf-). The most favorable DEA channel corresponds to the formation of the triflate anion alongside with the reactive uracil-5-yl radical through the cleavage of the O-C5 bond, particularly at about 0 eV. Unlike for halouracils, the parent anion was not detected in our experiments. The experimental findings are accounted by a comprehensive theoretical study carried out at the M06-2X/aug-cc-pVTZ level. The latter comprises the thermodynamic thresholds for the formation of the observed anions calculated under the experimental conditions (383.15 K and 3 × 10-11 atm). The energy-resolved ion yield of the dehydrogenated parent anion, (OTfU-H)-, is discussed in terms of vibrational Feshbach resonances arising from the coupling between the dipole bound state and vibrational levels of the transient negative ion. We also report the mass spectrum of the cations obtained through ionization of OTfU by electrons with a kinetic energy of 70 eV. The current study endorses OTfU as a potential radiosensitizer agent with possible applications in radio-chemotherapy.
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Affiliation(s)
- J Ameixa
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences (CMBI), Leopold-Franzens Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
| | - E Arthur-Baidoo
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences (CMBI), Leopold-Franzens Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
| | - R Meißner
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences (CMBI), Leopold-Franzens Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
| | - S Makurat
- Laboratory of Biological Sensitizers, Physical Chemistry Department, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - W Kozak
- Laboratory of Biological Sensitizers, Physical Chemistry Department, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - K Butowska
- Laboratory of Biophysics, Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and Medical University of Gdańsk, 80-307 Gdańsk, Poland
| | - F 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
| | - J Rak
- Laboratory of Biological Sensitizers, Physical Chemistry Department, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - S Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences (CMBI), Leopold-Franzens Universität Innsbruck, Technikerstraße 25/3, 6020 Innsbruck, Austria
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120
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Ab initio investigation of the lower-energy candidate structures for (H2O)10+ water cluster. Struct Chem 2018. [DOI: 10.1007/s11224-018-1109-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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121
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Ma J, Denisov SA, Marignier JL, Pernot P, Adhikary A, Seki S, Mostafavi M. Ultrafast Electron Attachment and Hole Transfer Following Ionizing Radiation of Aqueous Uridine Monophosphate. J Phys Chem Lett 2018; 9:5105-5109. [PMID: 30132673 PMCID: PMC6126959 DOI: 10.1021/acs.jpclett.8b02170] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The primary localization process of radiation-induced charges (holes (cation radical sites) and excess electrons) remains poorly understood, even at the level of monomeric DNA/RNA models, in particular, in an aqueous environment. We report the first spectroscopic study of charge transfer occurring in radiolysis of aqueous uridine 5'-monophosphate (UMP) solutions and its components: uridine, uracil, ribose, and phosphate. Our results show that prehydrated electrons effectively attach to the base site of UMP; the holes in UMP formed by either direct ionization or reaction of UMP with the radiation-mediated water cation radical (H2O•+) facilely localize on the ribose site, despite the fact that a part of them were initially created on either the phosphate or uracil. The nature of phosphate-to-sugar hole transfer is characterized as a barrierless intramolecular electron transfer with a time constant of 2.5 ns, while the base-to-sugar hole transfer occurs much faster, within a 5 ps electron pulse.
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Affiliation(s)
- Jun Ma
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
- Corresponding Author:,
| | - Sergey A. Denisov
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
| | - Jean-Louis Marignier
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
| | - Pascal Pernot
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
| | - Amitava Adhikary
- Department of Chemistry, 146 Library Drive, Oakland University, Rochester, Michigan 48309, USA
| | - Shu Seki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510
| | - Mehran Mostafavi
- Laboratoire de Chimie Physique, UMR 8000 CNRS/Université Paris-Sud, Bât. 349, Orsay 91405 Cedex, France
- Corresponding Author:,
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122
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Gartmann TE, Hartweg S, Ban L, Chasovskikh E, Yoder BL, Signorell R. Electron scattering in large water clusters from photoelectron imaging with high harmonic radiation. Phys Chem Chem Phys 2018; 20:16364-16371. [PMID: 29872831 DOI: 10.1039/c8cp02148a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low-energy electron scattering in water clusters (H2O)n with average cluster sizes of n < 700 is investigated by angle-resolved photoelectron spectroscopy using high harmonic radiation at photon energies of 14.0, 20.3, and 26.5 eV for ionization from the three outermost valence orbitals. The measurements probe the evolution of the photoelectron anisotropy parameter β as a function of cluster size. A remarkably steep decrease of β with increasing cluster size is observed, which for the largest clusters reaches liquid bulk values. Detailed electron scattering calculations reveal that neither gas nor condensed phase scattering can explain the cluster data. Qualitative agreement between experiment and simulations is obtained with scattering calculations that treat cluster scattering as an intermediate case between gas and condensed phase scattering.
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Affiliation(s)
- Thomas E Gartmann
- Department of Chemistry and Applied Biosciences, Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland.
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123
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Hahn MB, Meyer S, Schröter MA, Seitz H, Kunte HJ, Solomun T, Sturm H. Direct electron irradiation of DNA in a fully aqueous environment. Damage determination in combination with Monte Carlo simulations. Phys Chem Chem Phys 2018; 19:1798-1805. [PMID: 28059422 DOI: 10.1039/c6cp07707b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report on a study in which plasmid DNA in water was irradiated with 30 keV electrons generated by a scanning electron microscope and passed through a 100 nm thick Si3N4 membrane. The corresponding Monte Carlo simulations suggest that the kinetic energy spectrum of the electrons throughout the water is dominated by low energy electrons (<100 eV). The DNA radiation damage, single-strand breaks (SSBs) and double-strand breaks (DSBs), was determined by gel electrophoresis. The median lethal dose of D1/2 = 1.7 ± 0.3 Gy was found to be much smaller as compared to partially or fully hydrated DNA irradiated under vacuum conditions. The ratio of the DSBs to SSBs was found to be 1 : 12 as compared to 1 : 88 found for hydrated DNA. Our method enables quantitative measurements of radiation damage to biomolecules (DNA, proteins) in solutions under varying conditions (pH, salinity, co-solutes) for an electron energy range which is difficult to probe by standard methods.
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Affiliation(s)
- Marc Benjamin Hahn
- Free University Berlin, Department of Physics, D-14195 Berlin, Germany. and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Susann Meyer
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany. and University of Potsdam, Institute of Biochemistry and Biology, D-14476 Potsdam, Germany
| | | | - Harald Seitz
- Fraunhofer-Institut für Zelltherapie und Immunologie, Institutsteil Bioanalytik und Bioprozesse, D-14476 Potsdam, Germany
| | - Hans-Jörg Kunte
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Tihomir Solomun
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Heinz Sturm
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany. and Technical University Berlin, D-10587 Berlin, Germany
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124
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Kočišek J, Sedmidubská B, Indrajith S, Fárník M, Fedor J. Electron Attachment to Microhydrated Deoxycytidine Monophosphate. J Phys Chem B 2018; 122:5212-5217. [PMID: 29706064 DOI: 10.1021/acs.jpcb.8b03033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA constituents are effectively decomposed via dissociative electron attachment (DEA). However, the DEA contribution to radiation damage in living tissues is a subject of ongoing discussion. We address an essential question, how aqueous environment influences the DEA to DNA. In particular, we report experimental fragmentation patterns for DEA to microhydrated 2-deoxycytidine 5-monophosphate (dCMP). Isolated dCMP was previously set as a model to describe mechanisms of DNA-strand breaks induced by secondary electrons and decomposes primarily by dissociation of the C-O phosphoester bond. We show that hydrated molecules decompose via dissociation of the C-N glycosidic bond followed by dissociation of the P-O bond. This significant change of the proposed mechanism can be interpreted by a reactive role of water in the postattachment dynamics. Comparison of the fragmentation with previous macroscopic irradiation studies suggests that the actual contribution of DEA to DNA radiation damage in living tissue is rather small.
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Affiliation(s)
- Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences , Dolejškova 3 , 18223 Prague , Czech Republic
| | - Barbora Sedmidubská
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences , Dolejškova 3 , 18223 Prague , Czech Republic.,Deptartment of Nuclear Chemistry, Faculty of Nuclear Sciences and Physical Engineering , Czech Technical University in Prague , Brehová 7 , 115 19 Prague , Czech Republic
| | | | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences , Dolejškova 3 , 18223 Prague , Czech Republic
| | - Juraj Fedor
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences , Dolejškova 3 , 18223 Prague , Czech Republic
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125
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Abstract
The ionizing radiation in aqueous solutions of gold nanoparticles, stabilized by electrostatic non-covalent intermolecular forces and steric interactions, with antimicrobial compounds, are investigated with picosecond pulse radiolysis techniques. Upon pulse radiolysis of an aqueous solution containing very low concentrations of gold nanoparticles with naked surfaces available in water (not obstructed by chemical bonds), a change to Cerenkov spectrum over a large range of wavelengths are observed and pre-solvated electrons are captured by gold nanoparticles exclusively (not by ionic liquid surfactants used to stabilize the nanoparticles). The solvated electrons are also found to decay rapidly compared with the decay kinetics in water. These very fast reactions with electrons in water could provide an enhanced oxidizing zone around gold nanoparticles and this could be the reason for radio sensitizing behavior of gold nanoparticles in radiation therapy.
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126
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Pshenichnyuk SA, Modelli A, Komolov AS. Interconnections between dissociative electron attachment and electron-driven biological processes. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1461347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Stanislav A. Pshenichnyuk
- Institute of Molecule and Crystal Physics – Subdivision of the Ufa Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Alberto Modelli
- Dipartimento di Chimica ‘G. Ciamician’, Università di Bologna, Bologna, Italy
- Centro Interdipartimentale di Ricerca in Scienze Ambientali, Ravenna, Italy
| | - Alexei S. Komolov
- Department of Solid State Electronics, St. Petersburg State University, St. Petersburg, Russia
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127
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Borek D, Bromberg R, Hattne J, Otwinowski Z. Real-space analysis of radiation-induced specific changes with independent component analysis. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:451-467. [PMID: 29488925 PMCID: PMC5829680 DOI: 10.1107/s1600577517018148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/19/2017] [Indexed: 05/06/2023]
Abstract
A method of analysis is presented that allows for the separation of specific radiation-induced changes into distinct components in real space. The method relies on independent component analysis (ICA) and can be effectively applied to electron density maps and other types of maps, provided that they can be represented as sets of numbers on a grid. Here, for glucose isomerase crystals, ICA was used in a proof-of-concept analysis to separate temperature-dependent and temperature-independent components of specific radiation-induced changes for data sets acquired from multiple crystals across multiple temperatures. ICA identified two components, with the temperature-independent component being responsible for the majority of specific radiation-induced changes at temperatures below 130 K. The patterns of specific temperature-independent radiation-induced changes suggest a contribution from the tunnelling of electron holes as a possible explanation. In the second case, where a group of 22 data sets was collected on a single thaumatin crystal, ICA was used in another type of analysis to separate specific radiation-induced effects happening on different exposure-level scales. Here, ICA identified two components of specific radiation-induced changes that likely result from radiation-induced chemical reactions progressing with different rates at different locations in the structure. In addition, ICA unexpectedly identified the radiation-damage state corresponding to reduced disulfide bridges rather than the zero-dose extrapolated state as the highest contrast structure. The application of ICA to the analysis of specific radiation-induced changes in real space and the data pre-processing for ICA that relies on singular value decomposition, which was used previously in data space to validate a two-component physical model of X-ray radiation-induced changes, are discussed in detail. This work lays a foundation for a better understanding of protein-specific radiation chemistries and provides a framework for analysing effects of specific radiation damage in crystallographic and cryo-EM experiments.
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Affiliation(s)
- Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Raquel Bromberg
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Johan Hattne
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
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128
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Hahn MB, Meyer S, Schröter MA, Kunte HJ, Solomun T, Sturm H. DNA protection by ectoine from ionizing radiation: molecular mechanisms. Phys Chem Chem Phys 2018; 19:25717-25722. [PMID: 28913528 DOI: 10.1039/c7cp02860a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ectoine, a compatible solute and osmolyte, is known to be an effective protectant of biomolecules and whole cells against heating, freezing and extreme salinity. Protection of cells (human keratinocytes) by ectoine against ultraviolet radiation has also been reported by various authors, although the underlying mechanism is not yet understood. We present the first electron irradiation of DNA in a fully aqueous environment in the presence of ectoine and at high salt concentrations. The results demonstrate effective protection of DNA by ectoine against the induction of single-strand breaks by ionizing radiation. The effect is explained by an increase in low-energy electron scattering at the enhanced free-vibrational density of states of water due to ectoine, as well as the use of ectoine as an ˙OH-radical scavenger. This was demonstrated by Raman spectroscopy and electron paramagnetic resonance (EPR).
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Affiliation(s)
- Marc Benjamin Hahn
- Free University Berlin, Department of Physics, D-14195 Berlin, Germany. and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Susann Meyer
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany. and University of Potsdam, Institute of Biochemistry and Biology, D-14476 Potsdam, Germany
| | | | - Hans-Jörg Kunte
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Tihomir Solomun
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Heinz Sturm
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany. and Technical University Berlin, D-10587 Berlin, Germany
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129
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Fennimore MA, Matsika S. Core-excited and shape resonances of uracil. Phys Chem Chem Phys 2018; 18:30536-30545. [PMID: 27785493 DOI: 10.1039/c6cp05342d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Attachment of an electron to nucleobases leads to metastable anion states called resonances. There are two types of electronic resonances present in the nucleobases. Shape resonances occur when the electron is attached to one of the previously unoccupied π* orbitals of the base. An electron can also be attached to an electronically excited state leading to core-excited or Feshbach resonances. In this work we present both types of resonances of uracil, a nucleobase present in RNA. Both the positions and widths of the resonances have been calculated using a stabilization method coupled with high level electronic structure methods. Core-excited resonances which are accessed with electrons of energy >4.6 eV are expected to play an important role in the dissociative electron attachment of uracil. Mixing between configurations corresponding to shape and core-excited resonances is also present which complicates the theoretical treatment of this system and necessitates multiconfigurational approaches for a proper description.
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130
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Liu G, Landry C, Ghandi K. Prediction of rate constants of important chemical reactions in water radiation chemistry in sub and supercritical water – non-equilibrium reactions. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The rate constants for reactions involved in the radiolysis of water under relevant thermodynamic conditions in supercritical water-cooled reactors are estimated for inputs in simulations of the radiation chemistry in Generation IV nuclear reactors. We have discussed the mechanism of each chemical reaction with a focus on non-equilibrium reactions. We found most of the reactions are activation controlled above the critical point and that the rate constants are not significantly pressure dependent below 300 °C. This work will aid industry with developing chemical control strategies to suppress the concentration of eroding species.
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Affiliation(s)
- Guangdong Liu
- Department of Physics, Mount Allison University, Sackville, NB E4L 1E2, Canada
| | - Cody Landry
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB E4L 1E2, Canada
| | - Khashayar Ghandi
- Department of Physics, Mount Allison University, Sackville, NB E4L 1E2, Canada
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB E4L 1E2, Canada
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131
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Loupas A, Regeta K, Allan M, Gorfinkiel JD. Shape and Core-Excited Resonances in Thiophene. J Phys Chem A 2018; 122:1146-1155. [DOI: 10.1021/acs.jpca.7b11865] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexandra Loupas
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus
de Caparica, Lisboa, 2829-516 Portugal
- School of Physical Sciences, The Open University,
Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Khrystyna Regeta
- Department of Chemistry, University of Fribourg, Fribourg 1700, Switzerland
| | - Michael Allan
- Department of Chemistry, University of Fribourg, Fribourg 1700, Switzerland
| | - Jimena D. Gorfinkiel
- School of Physical Sciences, The Open University,
Walton Hall, Milton Keynes MK7 6AA, United Kingdom
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132
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Gaiduk AP, Pham TA, Govoni M, Paesani F, Galli G. Electron affinity of liquid water. Nat Commun 2018; 9:247. [PMID: 29339731 PMCID: PMC5770385 DOI: 10.1038/s41467-017-02673-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/15/2017] [Indexed: 11/09/2022] Open
Abstract
Understanding redox and photochemical reactions in aqueous environments requires a precise knowledge of the ionization potential and electron affinity of liquid water. The former has been measured, but not the latter. We predict the electron affinity of liquid water and of its surface from first principles, coupling path-integral molecular dynamics with ab initio potentials, and many-body perturbation theory. Our results for the surface (0.8 eV) agree well with recent pump-probe spectroscopy measurements on amorphous ice. Those for the bulk (0.1-0.3 eV) differ from several estimates adopted in the literature, which we critically revisit. We show that the ionization potential of the bulk and surface are almost identical; instead their electron affinities differ substantially, with the conduction band edge of the surface much deeper in energy than that of the bulk. We also discuss the significant impact of nuclear quantum effects on the fundamental gap and band edges of the liquid.
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Affiliation(s)
- Alex P Gaiduk
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
| | - Tuan Anh Pham
- Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
| | - Marco Govoni
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.,Materials Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, Materials Science and Engineering, San Diego Supercomputer Center, University of California, San Diego, 92093, USA.
| | - Giulia Galli
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA. .,Materials Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
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133
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Ambrosio F, Pasquarello A. Reactivity and energy level of a localized hole in liquid water. Phys Chem Chem Phys 2018; 20:30281-30289. [DOI: 10.1039/c8cp03682a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reaction and redox level of hole capture in liquid water from first principles.
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Affiliation(s)
- Francesco Ambrosio
- Chaire de Simulation à l’Echelle Atomique (CSEA)
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- CH-1015 Lausanne
- Switzerland
| | - Alfredo Pasquarello
- Chaire de Simulation à l’Echelle Atomique (CSEA)
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- CH-1015 Lausanne
- Switzerland
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134
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Cornetta LM, Kossoski F, Varella MTDN. Transient anion spectra of the potential radiosensitizers 5-cyanateuracil and 5-thiocyanateuracil. J Chem Phys 2017; 147:214310. [DOI: 10.1063/1.5007050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- L. M. Cornetta
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
| | - F. Kossoski
- Instituto de Física “Gleb Wataghin,” Universidade Estadual de Campinas, 13083-859 Campinas, São Paulo, Brazil
- Aix Marseille University, CNRS, ICR, Marseille, France
| | - M. T. do N. Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
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135
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Ma J, Wang F, Denisov SA, Adhikary A, Mostafavi M. Reactivity of prehydrated electrons toward nucleobases and nucleotides in aqueous solution. SCIENCE ADVANCES 2017; 3:e1701669. [PMID: 29250599 PMCID: PMC5732001 DOI: 10.1126/sciadv.1701669] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/13/2017] [Indexed: 05/28/2023]
Abstract
DNA damage induced via dissociative attachment by low-energy electrons (0 to 20 eV) is well studied in both gas and condensed phases. However, the reactivity of ultrashort-lived prehydrated electrons ([Formula: see text]) with DNA components in a biologically relevant environment has not been fully explored to date. The electron transfer processes of [Formula: see text] to the DNA nucleobases G, A, C, and T and to nucleosides/nucleotides were investigated by using 7-ps electron pulse radiolysis coupled with pump-probe transient absorption spectroscopy in aqueous solutions. In contrast to previous results, obtained by using femtosecond laser pump-probe spectroscopy, we show that G and A cannot scavenge [Formula: see text] at concentrations of ≤50 mM. Observation of a substantial decrease of the initial yield of hydrated electrons ([Formula: see text]) and formation of nucleobase/nucleotide anion radicals at increasing nucleobase/nucleotide concentrations present direct evidence for the earliest step in reductive DNA damage by ionizing radiation. Our results show that [Formula: see text] is more reactive with pyrimidine than purine nucleobases/nucleotides with a reactivity order of T > C > A > G. In addition, analyses of transient signals show that the signal due to formation of the resulting anion radical directly correlates with the loss of the initial [Formula: see text] signal. Therefore, our results do not agree with the previously proposed dissociation of transient negative ions in nucleobase/nucleotide solutions within the timescale of these experiments. Moreover, in a molecularly crowded medium (for example, in the presence of 6 M phosphate), the scavenging efficiency of [Formula: see text] by G is significantly enhanced. This finding implies that reductive DNA damage by ionizing radiation depends on the microenvironment around [Formula: see text].
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Affiliation(s)
- Jun Ma
- Laboratoire de Chimie Physique, CNRS–Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France
| | - Furong Wang
- Laboratoire de Chimie Physique, CNRS–Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France
| | - Sergey A. Denisov
- Laboratoire de Chimie Physique, CNRS–Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309, USA
| | - Mehran Mostafavi
- Laboratoire de Chimie Physique, CNRS–Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France
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136
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Hobbs RG, Putnam WP, Fallahi A, Yang Y, Kärtner FX, Berggren KK. Mapping Photoemission and Hot-Electron Emission from Plasmonic Nanoantennas. NANO LETTERS 2017; 17:6069-6076. [PMID: 28926275 DOI: 10.1021/acs.nanolett.7b02495] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding plasmon-mediated electron emission and energy transfer on the nanometer length scale is critical to controlling light-matter interactions at nanoscale dimensions. In a high-resolution lithographic material, electron emission and energy transfer lead to chemical transformations. In this work, we employ such chemical transformations in two different high-resolution electron-beam lithography resists, poly(methyl methacrylate) (PMMA) and hydrogen silsesquioxane (HSQ), to map local electron emission and energy transfer with nanometer resolution from plasmonic nanoantennas excited by femtosecond laser pulses. We observe exposure of the electron-beam resists (both PMMA and HSQ) in regions on the surface of nanoantennas where the local field is significantly enhanced. Exposure in these regions is consistent with previously reported optical-field-controlled electron emission from plasmonic hotspots as well as earlier work on low-electron-energy scanning probe lithography. For HSQ, in addition to exposure in hotspots, we observe resist exposure at the centers of rod-shaped nanoantennas in addition to exposure in plasmonic hotspots. Optical field enhancement is minimized at the center of nanorods suggesting that exposure in these regions involves a different mechanism to that in plasmonic hotspots. Our simulations suggest that exposure at the center of nanorods results from the emission of hot electrons produced via plasmon decay in the nanorods. Overall, the results presented in this work provide a means to map both optical-field-controlled electron emission and hot-electron transfer from nanoparticles via chemical transformations produced locally in lithographic materials.
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Affiliation(s)
- Richard G Hobbs
- Research Laboratory of Electronics, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - William P Putnam
- Research Laboratory of Electronics, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
- Department of Physics and Center for Ultrafast Imaging, University of Hamburg , Hamburg, Germany
- Northrop Grumman Corporation, NG Next , Redondo Beach, California 90254, United States
| | - Arya Fallahi
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron , 22607 Hamburg, Germany
| | - Yujia Yang
- Research Laboratory of Electronics, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Franz X Kärtner
- Research Laboratory of Electronics, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
- Department of Physics and Center for Ultrafast Imaging, University of Hamburg , Hamburg, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron , 22607 Hamburg, Germany
| | - Karl K Berggren
- Research Laboratory of Electronics, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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137
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Kohanoff J, McAllister M, Tribello GA, Gu B. Interactions between low energy electrons and DNA: a perspective from first-principles simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:383001. [PMID: 28617676 DOI: 10.1088/1361-648x/aa79e3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts with the interaction of radiation-either photons or swift ions-and the biological medium, which causes electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, and strand breaks in plasmid DNA in particular (Boudaiffa et al 2000 Science 287 1658-60). These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage. In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.
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Affiliation(s)
- Jorge Kohanoff
- Atomistic Simulation Centre, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
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138
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Dong Y, Chen Y, Zhou L, Shao Y, Fu X, Zheng Y. Molecular efficacy of radio- and chemotherapy sequences from direct DNA damage measurements. Int J Radiat Biol 2017; 93:1274-1282. [PMID: 28799445 DOI: 10.1080/09553002.2017.1366673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
PURPOSE To investigate the molecular aspects of the synergy between ionizing radiation and platinum (Pt) chemotherapeutic agents in cancer treatment with chemoradiation therapy (CRT) by measuring damages induced by low-energy electrons (LEE) to DNA bound to cisplatin. LEE are produced abundantly by any type of ionizing radiation and cisplatin represents a typical Pt-chemotherapeutic agents. MATERIALS AND METHODS Our strategy involves two parallel administrations of cisplatin and irradiation with a 4.6 and 9.6 eV electron fluence of 1.1 × 1012: (1) LEE bombardment of supercoiled DNA and its subsequent reaction with cisplatin; (2) the reaction of DNA with cisplatin followed by LEE irradiation. The damage yields for the loss of supercoiled (LS), single-strand breaks (SSB) and double-strand breaks (DSB) were obtained from gel electrophoresis analysis. Base modifications were revealed by treating the samples with Escherichia coli base excision repair endonuclease (Nth and Fpg). RESULTS The yields were deduced from the respective time-response for the reaction of DNA with cisplatin. The results show that binding cisplatin to DNA followed by LEE irradiation, consistently yields more DNA damages than the reverse order. In comparison to non-treated DNA, administration (2) results in an increase of LS and SSB of 1.4-3.3 folds and of DSB by more than an order of magnitude. Furthermore, after enzyme treatment, the yields of DSB rise by factors of 5.3-15.4, indicating a large increase of clustered damages, which should at least partially translate into an increase of lethal damages in cancer cells during the CRT. CONCLUSIONS Our results demonstrate that a strong synergy between radiation and cisplatin can only be achieved at the molecular level, if the drug is present at the time of irradiation. Furthermore, this work confirms the LEE mechanism previously proposed to explain the synergy between radiation and Pt drugs in CRT. It involves chemical sensitization of DNA prior to irradiation, to facilitate strand breaks and clustered damages induced by the highly reactive LEE.
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Affiliation(s)
- Yanfang Dong
- a Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment , Fuzhou University , Fuzhou , P.R. China
| | - Yunfeng Chen
- a Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment , Fuzhou University , Fuzhou , P.R. China
| | - Limei Zhou
- a Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment , Fuzhou University , Fuzhou , P.R. China
| | - Yu Shao
- a Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment , Fuzhou University , Fuzhou , P.R. China
| | - Xianzhi Fu
- a Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment , Fuzhou University , Fuzhou , P.R. China
| | - Yi Zheng
- a Research Institute of Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment , Fuzhou University , Fuzhou , P.R. China
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139
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Zilio P, Dipalo M, Tantussi F, Messina GC, de Angelis F. Hot electrons in water: injection and ponderomotive acceleration by means of plasmonic nanoelectrodes. LIGHT, SCIENCE & APPLICATIONS 2017; 6:e17002. [PMID: 30167264 PMCID: PMC6062236 DOI: 10.1038/lsa.2017.2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 01/10/2017] [Accepted: 01/16/2017] [Indexed: 05/19/2023]
Abstract
We present a theoretical and experimental study of a plasmonic nanoelectrode architecture that is able to inject bunches of hot electrons into an aqueous environment. In this approach, electrons are accelerated in water by ponderomotive forces up to energies capable of exciting or ionizing water molecules. This ability is enabled by the nanoelectrode structure (extruding out of a metal baseplate), which allows for the production of an intense plasmonic hot spot at the apex of the structure while maintaining the electrical connection to a virtually unlimited charge reservoir. The electron injection is experimentally monitored by recording the current transmitted through the water medium, whereas the electron acceleration is confirmed by observation of the bubble generation for a laser power exceeding a proper threshold. An understanding of the complex physics involved is obtained via a numerical approach that explicitly models the electromagnetic hot spot generation, electron-by-electron injection via multiphoton absorption, acceleration by ponderomotive forces and electron-water interaction through random elastic and inelastic scattering. The model predicts a critical electron density for bubble nucleation that nicely matches the experimental findings and reveals that the efficiency of energy transfer from the plasmonic hot spot to the free electron cloud is much more efficient (17 times higher) in water than in a vacuum. Because of their high kinetic energy and large reduction potential, these proposed wet hot electrons may provide new opportunities in photocatalysis, electrochemical processes and hot-electron driven chemistry.
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140
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Hahn MB, Meyer S, Kunte HJ, Solomun T, Sturm H. Measurements and simulations of microscopic damage to DNA in water by 30 keV electrons: A general approach applicable to other radiation sources and biological targets. Phys Rev E 2017; 95:052419. [PMID: 28618479 DOI: 10.1103/physreve.95.052419] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Indexed: 12/28/2022]
Abstract
The determination of the microscopic dose-damage relationship for DNA in an aqueous environment is of a fundamental interest for dosimetry and applications in radiation therapy and protection. We combine geant4 particle-scattering simulations in water with calculations concerning the movement of biomolecules to obtain the energy deposit in the biologically relevant nanoscopic volume. We juxtaposition these results to the experimentally determined damage to obtain the dose-damage relationship at a molecular level. This approach is tested for an experimentally challenging system concerning the direct irradiation of plasmid DNA (pUC19) in water with electrons as primary particles. Here a microscopic target model for the plasmid DNA based on the relation of lineal energy and radiation quality is used to calculate the effective target volume. It was found that on average fewer than two ionizations within a 7.5-nm radius around the sugar-phosphate backbone are sufficient to cause a single strand break, with a corresponding median lethal energy deposit being E_{1/2}=6±4 eV. The presented method is applicable for ionizing radiation (e.g., γ rays, x rays, and electrons) and a variety of targets, such as DNA, proteins, or cells.
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Affiliation(s)
- Marc Benjamin Hahn
- Institut für Experimentalphysik, Freie Universität Berlin, D-14195 Berlin, Germany and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany
| | - Susann Meyer
- Institute of Biochemistry and Biology, University of Potsdam, D-14476 Potsdam, Germany and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany
| | - Hans-Jörg Kunte
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany
| | - Tihomir Solomun
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany
| | - Heinz Sturm
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany and Technical University Berlin, D-10587 Berlin, Germany
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141
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Rezaee M, Hill RP, Jaffray DA. The Exploitation of Low-Energy Electrons in Cancer Treatment. Radiat Res 2017; 188:123-143. [PMID: 28557630 DOI: 10.1667/rr14727.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Given the distinct characteristics of low-energy electrons (LEEs), particularly at energies less than 30 eV, they can be applied to a wide range of therapeutic modalities to improve cancer treatment. LEEs have been shown to efficiently produce complex molecular damage resulting in substantial cellular toxicities. Since LEEs are produced in copious amounts from high-energy radiation beam, including photons, protons and ions; the control of LEE distribution can potentially enhance the therapeutic radio of such beams. LEEs can play a substantial role in the synergistic effect between radiation and chemotherapy, particularly halogenated and platinum-based anticancer drugs. Radiosensitizing entities containing atoms of high atomic number such as gold nanoparticles can be a source of LEE production if high-energy radiation interacts with them. This can provide a high local density of LEEs in a cell and produce cellular toxicity. Auger-electron-emitting radionuclides also create a high number of LEEs in each decay, which can induce lethal damage in a cell. Exploitation of LEEs in cancer treatment, however, faces a few challenges, such as dosimetry of LEEs and selective delivery of radiosensitizing and chemotherapeutic molecules close to cellular targets. This review first discusses the rationale for utilizing LEEs in cancer treatment by explaining their mechanism of action, describes theoretical and experimental studies at the molecular and cellular levels, then discusses strategies for achieving modification of the distribution and effectiveness of LEEs in cancerous tissue and their associated clinical benefit.
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Affiliation(s)
- Mohammad Rezaee
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Ontario Cancer Institute and Campbell Family Institute for Cancer Research and Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Richard P Hill
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Ontario Cancer Institute and Campbell Family Institute for Cancer Research and Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - David A Jaffray
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Ontario Cancer Institute and Campbell Family Institute for Cancer Research and Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
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142
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Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
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143
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Neustetter M, Mahmoodi-Darian M, Denifl S. Study of Electron Ionization and Fragmentation of Non-hydrated and Hydrated Tetrahydrofuran Clusters. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:866-872. [PMID: 28326462 PMCID: PMC5391379 DOI: 10.1007/s13361-017-1634-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 05/28/2023]
Abstract
Mass spectroscopic investigations on tetrahydrofuran (THF, C4H8O), a common model molecule of the DNA-backbone, have been carried out. We irradiated isolated THF and (hydrated) THF clusters with low energy electrons (electron energy ~70 eV) in order to study electron ionization and ionic fragmentation. For elucidation of fragmentation pathways, deuterated TDF (C4D8O) was investigated as well. One major observation is that the cluster environment shows overall a protective behavior on THF. However, also new fragmentation channels open in the cluster. In this context, we were able to solve a discrepancy in the literature about the fragment ion peak at mass 55 u in the electron ionization mass spectrum of THF. We ascribe this ion yield to the fragmentation of ionized THF clusters. Graphical Abstract ᅟ.
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Affiliation(s)
- Michael Neustetter
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences, Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | | | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences, Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
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144
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Luckhaus D, Yamamoto YI, Suzuki T, Signorell R. Genuine binding energy of the hydrated electron. SCIENCE ADVANCES 2017; 3:e1603224. [PMID: 28508051 PMCID: PMC5409453 DOI: 10.1126/sciadv.1603224] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/02/2017] [Indexed: 05/24/2023]
Abstract
The unknown influence of inelastic and elastic scattering of slow electrons in water has made it difficult to clarify the role of the solvated electron in radiation chemistry and biology. We combine accurate scattering simulations with experimental photoemission spectroscopy of the hydrated electron in a liquid water microjet, with the aim of resolving ambiguities regarding the influence of electron scattering on binding energy spectra, photoelectron angular distributions, and probing depths. The scattering parameters used in the simulations are retrieved from independent photoemission experiments of water droplets. For the ground-state hydrated electron, we report genuine values devoid of scattering contributions for the vertical binding energy and the anisotropy parameter of 3.7 ± 0.1 eV and 0.6 ± 0.2, respectively. Our probing depths suggest that even vacuum ultraviolet probing is not particularly surface-selective. Our work demonstrates the importance of quantitative scattering simulations for a detailed analysis of key properties of the hydrated electron.
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Affiliation(s)
- David Luckhaus
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Yo-ichi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Ruth Signorell
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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145
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Fennimore MA, Karsili TNV, Matsika S. Mechanisms of H and CO loss from the uracil nucleobase following low energy electron irradiation. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp01345k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Uracil anion fragments into 1-IM-, H and CO when an electron is attached to the D2 anionic state in a concerted mechanism.
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146
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Tang M, Hu CE, Lv ZL, Chen XR, Cai LC. Ab Initio Study of Ionized Water Radical Cation (H 2O) 8+ in Combination with the Particle Swarm Optimization Method. J Phys Chem A 2016; 120:9489-9499. [PMID: 27934325 DOI: 10.1021/acs.jpca.6b09866] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The structures of cationic water clusters (H2O)8+ have been globally explored by the particle swarm optimization method in combination with quantum chemical calculations. Geometry optimization and vibrational analysis for the 15 most interesting clusters were computed at the MP2/aug-cc-pVDZ level and infrared spectrum calculation at MPW1K/6-311++G** level. Special attention was paid to the relationships between their configurations and energies. Both MP2 and B3LYP-D3 calculations revealed that the cage-like structure is the most stable, which is different from a five-membered ring lowest energy structure but agrees well with a cage-like structure in the literature. Furthermore, our obtained cage-like structure is more stable by 0.87 and 1.23 kcal/mol than the previously reported structures at MP2 and B3LYP-D3 levels, respectively. Interestingly, on the basis of their relative Gibbs free energies and the temperature dependence of populations, the cage-like structure predominates only at very low temperatures, and the most dominating species transforms into a newfound four-membered ring structure from 100 to 400 K, which can contribute greatly to the experimental infrared spectrum. By topological analysis and reduced density gradient analysis, we also investigated the structural characteristics and bonding strengths of these water cluster radical cations.
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Affiliation(s)
- Mei Tang
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University , Chengdu 610065, China
| | - Cui-E Hu
- College of Physics and Electronic Engineering, Chongqing Normal University , Chongqing 400047, China
| | - Zhen-Long Lv
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University , Chengdu 610065, China
| | - Xiang-Rong Chen
- Institute of Atomic and Molecular Physics, College of Physical Science and Technology, Sichuan University , Chengdu 610065, China
| | - Ling-Cang Cai
- National Key Laboratory for Shock Wave and Detonation Physics Research, Institute of Fluid Physics, Chinese Academy of Engineering Physics , Mianyang 621900, China
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147
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Sanche L. Interaction of low energy electrons with DNA: Applications to cancer radiation therapy. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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148
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Choofong S, Cloutier P, Sanche L, Wagner JR. Base Release and Modification in Solid-Phase DNA Exposed to Low-Energy Electrons. Radiat Res 2016; 186:520-530. [PMID: 27802110 DOI: 10.1667/rr14476.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ionization generates a large number of secondary low-energy electrons (LEEs) with a most probable energy of approximately 10 eV, which can break DNA bonds by dissociative electron attachment (DEA) and lead to DNA damage. In this study, we investigated radiation damage to dry DNA induced by X rays (1.5 keV) alone on a glass substrate or X rays combined with extra LEEs (average energy of 5.8 eV) emitted from a tantalum (Ta) substrate under an atmosphere of N2 and standard ambient conditions of temperature and pressure. The targets included calf-thymus DNA and double-stranded synthetic oligonucleotides. We developed analytical methods to measure the release of non-modified DNA bases from DNA and the formation of several base modifications by LC-MS/MS with isotopic dilution for precise quantification. The results show that the yield of non-modified bases as well as base modifications increase by 20-30% when DNA is deposited on a Ta substrate compared to that on a glass substrate. The order of base release (Gua > Ade > Thy ∼ Cyt) agrees well with several theoretical studies indicating that Gua is the most susceptible site toward sugar-phosphate cleavage. The formation of DNA damage by LEEs is explained by DEA leading to the release of non-modified bases involving the initial cleavage of N1-C1', C3'-O3' or C5'-O5' bonds. The yield of base modifications was lower than the release of non-modified bases. The main LEE-induced base modifications include 5,6-dihydrothymine (5,6-dHT), 5,6-dihydrouracil (5-dHU), 5-hydroxymethyluracil (5-HmU) and 5-formyluracil (5-ForU). The formation of base modifications by LEEs can be explained by DEA and cleavage of the C-H bond of the methyl group of Thy (giving 5-HmU and 5-ForU) and by secondary reactions of H atoms and hydride anions that are generated by primary LEE reactions followed by subsequent reaction with Cyt and Thy (giving 5,6-dHU and 5,6-dHT).
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Affiliation(s)
- Surakarn Choofong
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Pierre Cloutier
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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149
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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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