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Lozano AI, Kumar S, Pereira PJS, Kerkeni B, García G, Limão-Vieira P. Low-lying Negative Ion States Probed in Potassium - Ethanol Collisions. Chemphyschem 2024; 25:e202400314. [PMID: 38630012 DOI: 10.1002/cphc.202400314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/17/2024] [Indexed: 05/23/2024]
Abstract
Dissociative electron transfer in collisions between neutral potassium atoms and neutral ethanol molecules yields mainly OH-, followed by C2H5O-, O-, CH3 - and CH2 -. The dynamics of negative ions have been investigated by recording time-of-flight mass spectra in a wide range of collision energies from 17.5 to 350 eV in the lab frame, where the branching ratios show a relevant energy dependence for low/intermediate collision energies. The dominant fragmentation channel in the whole energy range investigated has been assigned to the hydroxyl anion in contrast to oxygen anion from dissociative electron attachment (DEA) experiments. This result shows the relevant role of the electron donor in the vicinity of the temporary negative ion formed allowing access to reactions which are not thermodynamically attained in DEA experiments. The electronic state spectroscopy of such negative ions, was obtained from potassium cation energy loss spectra in the forward scattering direction at 205 eV impact energy, showing a prevalent Feshbach resonance at 9.36±0.10 eV withσ O H * / σ C H * ${{\sigma }_{OH}^{^{\ast}}/{\sigma }_{CH}^{^{\ast}}}$ character, while a less pronouncedσ O H * ${{\sigma }_{OH}^{^{\ast}}}$ contribution assigned to a shape resonance has been obtained at 3.16±0.10 eV. Quantum chemical calculations for the lowest-lying unoccupied molecular orbitals in the presence of a potassium atom have been performed to support the experimental findings.
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Affiliation(s)
- Ana Isabel Lozano
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- Institut de Recherche en Astrophysique et Planétologie (IRAP), Université Toulouse III - Paul Sabatier, CNRS, CNES, 9 Avenue du Colonel Roche, 31028 Toulouse, France
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, 94720, California, USA
| | - Sarvesh Kumar
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- Institut de Recherche en Astrophysique et Planétologie (IRAP), Université Toulouse III - Paul Sabatier, CNRS, CNES, 9 Avenue du Colonel Roche, 31028 Toulouse, France
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, 94720, California, USA
| | - Pedro J S Pereira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- Institut de Recherche en Astrophysique et Planétologie (IRAP), Université Toulouse III - Paul Sabatier, CNRS, CNES, 9 Avenue du Colonel Roche, 31028 Toulouse, France
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, 94720, California, USA
- Department of Mathematics, Instituto Superior de Engenharia de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007, Lisboa, Portugal
| | - Boutheïna Kerkeni
- ISAMM, Université de la Manouba, La Manouba, 2010, Tunisia
- Département de Physique, LPMC, Faculté des Sciences de Tunis, Université de Tunis el Manar, Tunis, 2092, Tunisia
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006, Madrid, Spain
| | - Paulo Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
- Institut de Recherche en Astrophysique et Planétologie (IRAP), Université Toulouse III - Paul Sabatier, CNRS, CNES, 9 Avenue du Colonel Roche, 31028 Toulouse, France
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, 94720, California, USA
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Electron Attachment to 5-Fluorouracil: The Role of Hydrogen Fluoride in Dissociation Chemistry. Int J Mol Sci 2022; 23:ijms23158325. [PMID: 35955461 PMCID: PMC9369043 DOI: 10.3390/ijms23158325] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 12/03/2022] Open
Abstract
We investigate dissociative electron attachment to 5-fluorouracil (5-FU) employing a crossed electron-molecular beam experiment and quantum chemical calculations. Upon the formation of the 5-FU- anion, 12 different fragmentation products are observed, the most probable dissociation channel being H loss. The parent anion, 5-FU-, is not stable on the experimental timescale (~140 µs), most probably due to the low electron affinity of FU; simple HF loss and F- formation are seen only with a rather weak abundance. The initial dynamics upon electron attachment seems to be governed by hydrogen atom pre-dissociation followed by either its full dissociation or roaming in the vicinity of the molecule, recombining eventually into the HF molecule. When the HF molecule is formed, the released energy might be used for various ring cleavage reactions. Our results show that higher yields of the fluorine anion are most probably prevented through both faster dissociation of an H atom and recombination of F- with a proton to form HF. Resonance calculations indicate that F- is formed upon shape as well as core-excited resonances.
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Sensing the ortho Positions in C6Cl6 and C6H4Cl2 from Cl2− Formation upon Molecular Reduction. Molecules 2022; 27:molecules27154820. [PMID: 35956769 PMCID: PMC9369944 DOI: 10.3390/molecules27154820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
The geometrical effect of chlorine atom positions in polyatomic molecules after capturing a low-energy electron is shown to be a prevalent mechanism yielding Cl2−. In this work, we investigated hexachlorobenzene reduction in electron transfer experiments to determine the role of chlorine atom positions around the aromatic ring, and compared our results with those using ortho-, meta- and para-dichlorobenzene molecules. This was achieved by combining gas-phase experiments to determine the reaction threshold by means of mass spectrometry together with quantum chemical calculations. We also observed that Cl2− formation can only occur in 1,2-C6H4Cl2, where the two closest C–Cl bonds are cleaved while the chlorine atoms are brought together within the ring framework due to excess energy dissipation. These results show that a strong coupling between electronic and C–Cl bending motion is responsible for a positional isomeric effect, where molecular recognition is a determining factor in chlorine anion formation.
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Kumar S, Ben Chouikha I, Kerkeni B, García G, Limão-Vieira P. Bound Electron Enhanced Radiosensitisation of Nimorazole upon Charge Transfer. Molecules 2022; 27:molecules27134134. [PMID: 35807379 PMCID: PMC9268075 DOI: 10.3390/molecules27134134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 02/01/2023] Open
Abstract
This novel work reports nimorazole (NIMO) radiosensitizer reduction upon electron transfer in collisions with neutral potassium (K) atoms in the lab frame energy range of 10–400 eV. The negative ions formed in this energy range were time-of-flight mass analyzed and branching ratios were obtained. Assignment of different anions showed that more than 80% was due to the formation of the non-dissociated parent anion NIMO•− at 226 u and nitrogen dioxide anion NO2− at 46 u. The rich fragmentation pattern revealed that significant collision induced the decomposition of the 4-nitroimidazole ring, as well as other complex internal reactions within the temporary negative ion formed after electron transfer to neutral NIMO. Other fragment anions were only responsible for less than 20% of the total ion yield. Additional information on the electronic state spectroscopy of nimorazole was obtained by recording a K+ energy loss spectrum in the forward scattering direction (θ ≈ 0°), allowing us to determine the most accessible electronic states within the temporary negative ion. Quantum chemical calculations on the electronic structure of NIMO in the presence of a potassium atom were performed to help assign the most significant lowest unoccupied molecular orbitals participating in the collision process. Electron transfer was shown to be a relevant process for nimorazole radiosensitisation through efficient and prevalent non-dissociated parent anion formation.
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Affiliation(s)
- Sarvesh Kumar
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal;
| | - Islem Ben Chouikha
- Département de Physique, LPMC, Faculté des Sciences de Tunis, Université de Tunis el Manar, Tunis 2092, Tunisia;
| | - Boutheïna Kerkeni
- Département de Physique, LPMC, Faculté des Sciences de Tunis, Université de Tunis el Manar, Tunis 2092, Tunisia;
- ISAMM, Université de La Manouba, La Manouba 2010, Tunisia
- Correspondence: (B.K.); (P.L.-V.)
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 113-bis, 28006 Madrid, Spain;
| | - Paulo Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal;
- Correspondence: (B.K.); (P.L.-V.)
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Ziegler P, Pelc A, Arthur-Baidoo E, Ameixa J, Ončák M, Denifl S. Negative ion formation and fragmentation upon dissociative electron attachment to the nicotinamide molecule. RSC Adv 2021; 11:32425-32434. [PMID: 35495526 PMCID: PMC9041917 DOI: 10.1039/d1ra06083j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Nicotinamide (C6H6N2O) is a biologically relevant molecule. This compound has several important roles related to the anabolic and metabolic processes that take place in living organisms. It is also used as a radiosensitizer in tumor therapy. As a result of the interaction of high-energy radiation with matter, low-energy electrons are also released, which can also interact with other molecules, forming several types of ions. In the present investigation, dissociative electron attachment to C6H6N2O has been studied in a crossed electron-molecular beams experiment in the electron energy range of about 0-15 eV. In the experiment, six anionic species were detected: C6H5N2O-, C5H4N-, NCO-, O-/NH2 -, and CN-, with NCO- being the most prominent anion. We also provide detailed computational results regarding the energetic thresholds and pathways of the respective dissociative electron attachment (DEA) channels. The experimental results are compared with the theoretical ones and on this basis, the possible DEA reactions for the formation of anions at a given resonance energy were assigned as well as the generation of neutrals fragments such as pyridine and its several derivatives and radicals are predicted. The pyridine ring seems to stay intact during the DEA process.
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Affiliation(s)
- Patrick Ziegler
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
| | - Andrzej Pelc
- Maria Curie-Skłodowska University, Department of Biophysics, Mass Spectrometry Laboratory Pl. M. C.-Skłodowskiej 1 20-031 Lublin Poland
| | - Eugene Arthur-Baidoo
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
| | - Joao Ameixa
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria .,Centre of Physics and Technological Research, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Milan Ončák
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
| | - Stephan Denifl
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
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Sedmidubská B, Luxford TFM, Kočišek J. Electron attachment to isolated and microhydrated favipiravir. Phys Chem Chem Phys 2021; 23:21501-21511. [PMID: 34382983 DOI: 10.1039/d1cp02686k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Electron attachment and its equivalent in complex environments, single-electron reduction, are important in many biological processes. Here, we experimentally study the electron attachment to favipiravir, a well-known antiviral agent. Electron attachment spectroscopy is used to explore the energetics of associative (AEA) and dissociative (DEA) electron attachment to isolated favipiravir. AEA dominates the interaction and the yields of the fragment anions after DEA are an order of magnitude lower than that of the parent anion. DEA primary proceeds via decomposition of the CONH2 functional group, which is supported by reaction threshold calculations using ab initio methods. Mass spectrometry of small favipiravir-water clusters demonstrates that a lot of energy is transferred to the solvent upon electron attachment. The energy gained upon electron attachment, and the high stability of the parent anion were previously suggested as important properties for the action of several electron-affinic radiosensitizers. If any of these mechanisms cause synergism in chemo-radiation therapy, favipiravir could be repurposed as a radiosensitizer.
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Affiliation(s)
- Barbora Sedmidubská
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic. and Department of Nuclear Chemistry, Faculty of Nuclear Sciences and Physical Engineering, Břehová 7, 11519 Prague, Czech Republic
| | - Thomas F M Luxford
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic.
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic.
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Kopyra J, Wierzbicka P, Tulwin A, Thiam G, Bald I, Rabilloud F, Abdoul-Carime H. Experimental and Theoretical Studies of Dissociative Electron Attachment to Metabolites Oxaloacetic and Citric Acids. Int J Mol Sci 2021; 22:ijms22147676. [PMID: 34299296 PMCID: PMC8303309 DOI: 10.3390/ijms22147676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
In this contribution the dissociative electron attachment to metabolites found in aerobic organisms, namely oxaloacetic and citric acids, was studied both experimentally by means of a crossed-beam setup and theoretically through density functional theory calculations. Prominent negative ion resonances from both compounds are observed peaking below 0.5 eV resulting in intense formation of fragment anions associated with a decomposition of the carboxyl groups. In addition, resonances at higher energies (3-9 eV) are observed exclusively from the decomposition of the oxaloacetic acid. These fragments are generated with considerably smaller intensities. The striking findings of our calculations indicate the different mechanism by which the near 0 eV electron is trapped by the precursor molecule to form the transitory negative ion prior to dissociation. For the oxaloacetic acid, the transitory anion arises from the capture of the electron directly into some valence states, while, for the citric acid, dipole- or multipole-bound states mediate the transition into the valence states. What is also of high importance is that both compounds while undergoing DEA reactions generate highly reactive neutral species that can lead to severe cell damage in a biological environment.
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Affiliation(s)
- Janina Kopyra
- Faculty of Exact and Natural Sciences, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland; (P.W.); (A.T.)
- Correspondence: (J.K.); (I.B.)
| | - Paulina Wierzbicka
- Faculty of Exact and Natural Sciences, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland; (P.W.); (A.T.)
| | - Adrian Tulwin
- Faculty of Exact and Natural Sciences, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland; (P.W.); (A.T.)
| | - Guillaume Thiam
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, F-69622 Villeurbanne, France; (G.T.); (F.R.)
| | - Ilko Bald
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Correspondence: (J.K.); (I.B.)
| | - Franck Rabilloud
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, F-69622 Villeurbanne, France; (G.T.); (F.R.)
| | - Hassan Abdoul-Carime
- Institut de Physique des 2 Infinis, Université Lyon 1, Université de Lyon, CNRS/IN2P3, UMR5822, F-69003 Lyon, France;
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Mendes M, Kossoski F, Lozano AI, Pereira-da-Silva J, Rodrigues R, Ameixa J, Jones NC, Hoffmann SV, Ferreira da Silva F. Excited States of Bromopyrimidines Probed by VUV Photoabsorption Spectroscopy and Theoretical Calculations. Int J Mol Sci 2021; 22:6460. [PMID: 34208711 PMCID: PMC8235550 DOI: 10.3390/ijms22126460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 11/16/2022] Open
Abstract
We report absolute photoabsorption cross sections for gas-phase 2- and 5-bromopyrimidine in the 3.7-10.8 eV energy range, in a joint theoretical and experimental study. The measurements were carried out using high-resolution vacuum ultraviolet synchrotron radiation, with quantum chemical calculations performed through the nuclear ensemble approach in combination with time-dependent density functional theory, along with additional Franck-Condon Herzberg-Teller calculations for the first absorption band (3.7-4.6 eV). The cross sections of both bromopyrimidines are very similar below 7.3 eV, deviating more substantially from each other at higher energies. In the 7.3-9.0 eV range where the maximum cross-section is found, a single and broad band is observed for 5-bromopyrimidine, while more discernible features appear in the case of 2-bromopyrimidine. Several π* ← π transitions account for the most intense bands, while weaker ones are assigned to transitions involving the nitrogen and bromine lone pairs, the antibonding σ*Br orbital, and the lower-lying Rydberg states. A detailed comparison with the available photo-absorption data of bromobenzene is also reported. We have found significant differences regarding the main absorption band, which is more peaked in bromobenzene, becoming broader and shifting to higher energies in both bromopyrimidines. In addition, there is a significant suppression of vibrational structures and of Rydberg states in the pair of isomers, most noticeably for 2-bromopyrimidine.
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Affiliation(s)
- Mónica Mendes
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - Fábris Kossoski
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, CEDEX 09, 31062 Toulouse, France
| | - Ana I. Lozano
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - João Pereira-da-Silva
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - Rodrigo Rodrigues
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - João Ameixa
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Søren V. Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Filipe Ferreira da Silva
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; (A.I.L.); (J.P.-d.-S.); (R.R.); (J.A.); (F.F.d.S.)
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da Silva FF, Cunha T, Rebelo A, Gil A, Calhorda MJ, García G, Ingólfsson O, Limão-Vieira P. Electron-Transfer-Induced Side-Chain Cleavage in Tryptophan Facilitated through Potassium-Induced Transition-State Stabilization in the Gas Phase. J Phys Chem A 2021; 125:2324-2333. [DOI: 10.1021/acs.jpca.1c00690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Filipe Ferreira da Silva
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Tiago Cunha
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Andre Rebelo
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Adrià Gil
- BioISI -Biosystems & Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- CIC nanoGUNE BRTA, Tolosa Hiribidea, 76, E-20018 Donostia − San Sebastián, Euskadi, Spain
| | - Maria José Calhorda
- BioISI -Biosystems & Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain
| | - Oddur Ingólfsson
- Chemistry and Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Paulo Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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Suarez-Moreno HA, Eckermann L, Zappa F, Arthur-Baidoo E, Ptasińska S, Denifl S. Electron ionization of clusters containing the formamide molecule. THE EUROPEAN PHYSICAL JOURNAL. D, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 2021; 75:274. [PMID: 34744506 PMCID: PMC8528779 DOI: 10.1140/epjd/s10053-021-00281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/27/2021] [Indexed: 05/15/2023]
Abstract
Studies on electron interactions with formamide (FA) clusters promote scientific interest as a model system to understand phenomena relevant to astrophysical, prebiotic, and radiobiological processes. In this work, mass spectrometric detection of cationic species for both small bare and microhydrated formamide clusters was performed at an electron ionization of 70 eV. Furthermore, a comparative analysis of the cluster spectra with the literature-reported gas-phase spectra is presented and discussed, revealing different reaction channels affected by the cluster environment. This study is essential in developing our understanding of both low-energy electron phenomena in clusters that can bridge the complexity gap between gas and realistic systems and the effect of hydration on electron-induced processes.
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Affiliation(s)
- Harvey-Andres Suarez-Moreno
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Lauren Eckermann
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556 USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Fabio Zappa
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Eugene Arthur-Baidoo
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Sylwia Ptasińska
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556 USA
- Department of Physics, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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Lozano AI, Maioli LS, Pamplona B, Romero J, Mendes M, Ferreira da Silva F, Kossoski F, Probst M, Süβ D, Bettega MHF, García G, Limão-Vieira P. Selective bond breaking of halothane induced by electron transfer in potassium collisions. Phys Chem Chem Phys 2020; 22:23837-23846. [PMID: 33073277 DOI: 10.1039/d0cp02570d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present novel experimental results of negative ion formation of halothane (C2HBrClF3) upon electron transfer from hyperthermal neutral potassium atoms (K°) in the collision energy range of 8-1000 eV. The experiments were performed in a crossed molecular beam setup allowing a comprehensive analysis of the time-of-flight (TOF) mass negative ions fragmentation pattern and a detailed knowledge of the collision dynamics in the energy range investigated. Such TOF mass spectra data show that the only negative ions formed are Br-, Cl- and F-, with a strong energy dependence in the low-energy collision region, with the bromine anion being the most abundant and sole fragment at the lowest collision energy probed. In addition, potassium cation (K+) energy loss spectra in the forward scattering direction were obtained in a hemispherical energy analyser at different K° impact energies. In order to support our experimental findings, ab initio quantum chemical calculations have been performed to help interpret the role of the electronic structure of halothane. Potential energy curves were obtained along the C-X (X = Br, Cl) coordinate to lend support to the dissociation processes yielding anion formation.
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Affiliation(s)
- A I Lozano
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
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12
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Spisz P, Zdrowowicz M, Kozak W, Chomicz-Mańka L, Falkiewicz K, Makurat S, Sikorski A, Wyrzykowski D, Rak J, Arthur-Baidoo E, Ziegler P, Rodrigues Costa MS, Denifl S. Uracil-5-yl O-Sulfamate: An Illusive Radiosensitizer. Pitfalls in Modeling the Radiosensitizing Derivatives of Nucleobases. J Phys Chem B 2020; 124:5600-5613. [PMID: 32539395 PMCID: PMC7356320 DOI: 10.1021/acs.jpcb.0c03844] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/12/2020] [Indexed: 12/16/2022]
Abstract
Efficient radiotherapy requires the concomitant use of ionizing radiation (IR) and a radiosensitizer. In the present work uracil-5-yl O-sulfamate (SU) is tested against its radiosensitizing potential. The compound possesses appropriate dissociative electron attachment (DEA) characteristics calculated at the M06-2X/6-31++G(d,p) level. Crossed electron-molecular beam experiments in the gas phase demonstrate that SU undergoes efficient DEA processes, and the single C-O or S-O bond dissociations account for the majority of fragments induced by electron attachment. Most DEAs proceed already for electrons with kinetic energies of ∼0 eV, which is supported by the exothermic thresholds calculated at the M06-2X/aug-cc-pVTZ level. However, in water solution under reductive conditions and physiological pH, SU does not undergo radiolysis, which demonstrates the crucial influence of aqueous environment on the radiosensitizing properties of modified nucleosides.
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Affiliation(s)
- Paulina Spisz
- Group
of Biological Sensitizers, Physical Chemistry Department, Faculty
of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Magdalena Zdrowowicz
- Group
of Biological Sensitizers, Physical Chemistry Department, Faculty
of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Witold Kozak
- Group
of Biological Sensitizers, Physical Chemistry Department, Faculty
of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Lidia Chomicz-Mańka
- Group
of Biological Sensitizers, Physical Chemistry Department, Faculty
of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Karina Falkiewicz
- Group
of Biological Sensitizers, Physical Chemistry Department, Faculty
of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Samanta Makurat
- Group
of Biological Sensitizers, Physical Chemistry Department, Faculty
of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Artur Sikorski
- Group
of Crystallochemistry, Physical Chemistry Department, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Dariusz Wyrzykowski
- Group
of Physicochemistry and Complex Compounds, General and Inorganic Chemistry
Department, Faculty of Chemistry, University
of Gdańsk, 80-308 Gdańsk, Poland
| | - Janusz Rak
- Group
of Biological Sensitizers, Physical Chemistry Department, Faculty
of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Eugene Arthur-Baidoo
- Institut
für Ionenphysik und Angewandte Physik and Center for Biomolecular
Sciences Innsbruck, Leopold-Franzens Universität
Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Patrick Ziegler
- Institut
für Ionenphysik und Angewandte Physik and Center for Biomolecular
Sciences Innsbruck, Leopold-Franzens Universität
Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Mateus Salomao Rodrigues Costa
- Institut
für Ionenphysik und Angewandte Physik and Center for Biomolecular
Sciences Innsbruck, Leopold-Franzens Universität
Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - 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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13
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Khatymov RV, Shchukin PV, Muftakhov MV, Yakushchenko IK, Yarmolenko OV, Pankratyev EY. A unified statistical RRKM approach to the fragmentation and autoneutralization of metastable molecular negative ions of hexaazatrinaphthylenes. Phys Chem Chem Phys 2020; 22:3073-3088. [PMID: 31965122 DOI: 10.1039/c9cp05397b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For the compounds promising for use as n-type semiconductors in organic electronics and energy storage devices, hexaazatrinaphthylene (HATNA) and its derivative hexamethoxy-hexaazatrinaphthylene (HMHATA), the monomolecular processes occurring under the exposure of molecules to low-energy (0-15 eV) free electrons were studied by means of resonant electron capture negative ion mass spectrometry. Resonant electron attachment results in the formation of eminently long-lived molecular negative ions (MNIs) in an abnormally wide range of incident electron energy (Ee) from 0 to 5-7 eV. For both compounds, this observation serves as an indication of the strong electron-accepting properties and high stability of MNIs against electron autodetachment. A weak yield of the only fragment NIs, dehydrogenated anions, was detected for HATNA at Ee > 6 eV. MNIs of HMHATA are less stable to dissociative decay because of the presence of weakly bound terminal substituents. This is evidenced by the mass spectral observation of intense fragmentation occurring above Ee≈ 1 eV and leading to a loss of up to 3 methyl groups as the Ee increases. A series of metastable NI peaks observed in the mass spectra testify to the delayed and sequential nature of fragmentation. Based on the principles of statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory, the theoretical model of dissociative decay of NIs was developed and then adopted to quantify the rates of ground-state anion decay via electron autodetachment. The experimentally measured electron autodetachment lifetimes and fragmentation rates were best reproduced by the model at molecular adiabatic electron affinities preset to 2.15 eV for HATNA and 1.88 eV for HMHATA, in reasonable agreement with the quantum chemical DFT PBE/3ζ predictions.
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Affiliation(s)
- Rustem V Khatymov
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450075, Russia.
| | - Pavel V Shchukin
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450075, Russia.
| | - Mars V Muftakhov
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450075, Russia.
| | - Igor K Yakushchenko
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region 142432, Russia
| | - Ol'ga V Yarmolenko
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region 142432, Russia
| | - Evgeniy Yu Pankratyev
- Institute of Molecule and Crystal Physics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450075, Russia.
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14
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Thodika M, Fennimore M, Karsili TNV, Matsika S. Comparative study of methodologies for calculating metastable states of small to medium-sized molecules. J Chem Phys 2019; 151:244104. [DOI: 10.1063/1.5134700] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Mushir Thodika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Mark Fennimore
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Tolga N. V. Karsili
- Department of Chemistry, University of Louisiana, Lafayette, Louisiana 70504, USA
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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15
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Reactions in the Radiosensitizer Misonidazole Induced by Low-Energy (0-10 eV) Electrons. Int J Mol Sci 2019; 20:ijms20143496. [PMID: 31315268 PMCID: PMC6678818 DOI: 10.3390/ijms20143496] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 11/17/2022] Open
Abstract
Misonidazole (MISO) was considered as radiosensitizer for the treatment of hypoxic tumors. A prerequisite for entering a hypoxic cell is reduction of the drug, which may occur in the early physical-chemical stage of radiation damage. Here we study electron attachment to MISO and find that it very effectively captures low energy electrons to form the non-decomposed molecular anion. This associative attachment (AA) process is exclusively operative within a very narrow resonance right at threshold (zero electron energy). In addition, a variety of negatively charged fragments are observed in the electron energy range 0-10 eV arising from dissociative electron attachment (DEA) processes. The observed DEA reactions include single bond cleavages (formation of NO2-), multiple bond cleavages (excision of CN-) as well as complex reactions associated with rearrangement in the transitory anion and formation of new molecules (loss of a neutral H2O unit). While any of these AA and DEA processes represent a reduction of the MISO molecule, the radicals formed in the course of the DEA reactions may play an important role in the action of MISO as radiosensitizer inside the hypoxic cell. The present results may thus reveal details of the molecular description of the action of MISO in hypoxic cells.
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16
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Mendes M, Pamplona B, Kumar S, da Silva FF, Aguilar A, García G, Bacchus-Montabonel MC, Limao-Vieira P. Ion-Pair Formation in Neutral Potassium-Neutral Pyrimidine Collisions: Electron Transfer Experiments. Front Chem 2019; 7:264. [PMID: 31058139 PMCID: PMC6482480 DOI: 10.3389/fchem.2019.00264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
We report novel data on ion-pair formation in hyperthermal (30–800 eV) neutral potassium collisions with neutral pyrimidine (Pyr, C4H4N2) molecules. In this collision regime, negative ions formed by electron transfer from the alkali atom to the target molecule were time-of-flight mass analyzed and the fragmentation patterns and branching ratios have been obtained. The most abundant product anions have been assigned to CN− and C2H− and the electron transfer mechanisms are comprehensively discussed. Particular importance is also given to the efficient loss of integrity of the pyrimidine ring in the presence of an extra electron, which is in contrast to dissociative electron attachment experiments yielding the dehydrogenated parent anion. Theoretical calculations were performed for pyrimidine in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process. In order to further our knowledge about the collision dynamics, potassium cation (K+) energy loss spectrum has been obtained and within this context, we also discuss the role of the accessible electronic states. A vertical electron affinity of (−5.69 ± 0.20) eV was obtained and may be assigned to a π3*(b1) state that leads to CN− formation.
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Affiliation(s)
- Mónica Mendes
- Atomic and Molecular Collisions Laboratory, Centre of Physics and Technological Research (CEFITEC), Department of Physics, Universidade NOVA de Lisboa, Costa de Caparica, Portugal.,Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Beatriz Pamplona
- Atomic and Molecular Collisions Laboratory, Centre of Physics and Technological Research (CEFITEC), Department of Physics, Universidade NOVA de Lisboa, Costa de Caparica, Portugal
| | - Sarvesh Kumar
- Atomic and Molecular Collisions Laboratory, Centre of Physics and Technological Research (CEFITEC), Department of Physics, Universidade NOVA de Lisboa, Costa de Caparica, Portugal
| | - Filipe Ferreira da Silva
- Atomic and Molecular Collisions Laboratory, Centre of Physics and Technological Research (CEFITEC), Department of Physics, Universidade NOVA de Lisboa, Costa de Caparica, Portugal
| | - Antonio Aguilar
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Barcelona, Spain
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | | | - Paulo Limao-Vieira
- Atomic and Molecular Collisions Laboratory, Centre of Physics and Technological Research (CEFITEC), Department of Physics, Universidade NOVA de Lisboa, Costa de Caparica, Portugal
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17
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Biodegradable waterborne polyurethane grafted with gelatin hydrolysate via solvent-free copolymerization for potential porous scaffold material. J Mech Behav Biomed Mater 2019; 92:79-89. [PMID: 30660031 DOI: 10.1016/j.jmbbm.2019.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 01/22/2023]
Abstract
One potential porous scaffold material based on polyester waterborne polyurethane (PEUR) grafted with modified gelatin hydrolysate (GH) has been investigated in this research. First, the GH was modified with a silane coupling agent (KH550), and then the modified GH was mixed with pre-polymer emulsion of PEUR to obtain the PEUR grafted GH emulsion (PEUR-g-GH). The synthesized PEUR-g-GH emulsions were characterized by stability analysis and viscosity test. Moreover, the film-forming property of PEUR-g-GH has also been studied, and the PEUR-g-GH films were characterized regarding the water resistance, solvent resistance, mechanical properties, FTIR, AFM, SEM, DMA, TGA and contact angle testing. Finally, the bioactivity and biodegradation were investigated by soaking PEUR-g-GH scaffolds in simulated body fluid (SBF). The results indicated that the PEUR-g-GH emulsion has good stability, water resisting (the contact angle was over 90o), the PEUR-g-GH showed excellent film-forming, high storage modulus, good structural homogeneity and thermal stability (the temperature of maximum weight loss was over 350 °C). The freeze-dried sample showed porous structure, and the mutual crosslinking of layers can contribute to a good bearing capacity for scaffold. The SBF biodegradability revealed that the biodegradation rate and degree of films gradually increased with the content of GH increased. In addition, the cells on the material were markedly enhanced, and most of cells have proliferated and formed vesicles, which shown a good biocompatibility.
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18
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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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19
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Cunha T, Mendes M, Ferreira da Silva F, Eden S, García G, Bacchus-Montabonel MC, Limão-Vieira P. Electron transfer driven decomposition of adenine and selected analogs as probed by experimental and theoretical methods. J Chem Phys 2018; 148:134301. [PMID: 29626890 DOI: 10.1063/1.5021888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report on a combined experimental and theoretical study of electron-transfer-induced decomposition of adenine (Ad) and a selection of analog molecules in collisions with potassium (K) atoms. Time-of-flight negative ion mass spectra have been obtained in a wide collision energy range (6-68 eV in the centre-of-mass frame), providing a comprehensive investigation of the fragmentation patterns of purine (Pu), adenine (Ad), 9-methyl adenine (9-mAd), 6-dimethyl adenine (6-dimAd), and 2-D adenine (2-DAd). Following our recent communication about selective hydrogen loss from the transient negative ions (TNIs) produced in these collisions [T. Cunha et al., J. Chem. Phys. 148, 021101 (2018)], this work focuses on the production of smaller fragment anions. In the low-energy part of the present range, several dissociation channels that are accessible in free electron attachment experiments are absent from the present mass spectra, notably NH2 loss from adenine and 9-methyl adenine. This can be understood in terms of a relatively long transit time of the K+ cation in the vicinity of the TNI tending to enhance the likelihood of intramolecular electron transfer. In this case, the excess energy can be redistributed through the available degrees of freedom inhibiting fragmentation pathways. Ab initio theoretical calculations were performed for 9-methyl adenine (9-mAd) and adenine (Ad) in the presence of a potassium atom and provided a strong basis for the assignment of the lowest unoccupied molecular orbitals accessed in the collision process.
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Affiliation(s)
- T Cunha
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - M Mendes
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - F Ferreira da Silva
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - S Eden
- School of Physical Sciences, The Open University, Walton Hall, MK7 6AA Milton Keynes, United Kingdom
| | - G García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain
| | - M-C Bacchus-Montabonel
- Institut Lumiére Matiére, Université Lyon, Université Claude Bernard Lyon 1, CNRS, 69622 Villeurbanne, France
| | - P Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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20
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Fennimore MA, Matsika S. Electronic Resonances of Nucleobases Using Stabilization Methods. J Phys Chem A 2018; 122:4048-4057. [DOI: 10.1021/acs.jpca.8b01523] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Mark A. Fennimore
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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21
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Ellis-Gibbings L, Bass AD, Cloutier P, García G, Sanche L. Electron stimulated desorption from condensed pyrimidine and pyridazine. Phys Chem Chem Phys 2018; 19:13038-13048. [PMID: 28484763 DOI: 10.1039/c7cp00715a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Low energy electron (LEE) interactions and the formation of transient negative ions play a dominant role in radiation-induced dissociation of condensed-phase biomolecules (e.g. in radiotherapy). Here we present data on the LEE-induced dissociation and desorption of the DNA/RNA-base and radiosensitizing agent analogues pyrimidine and pyridazine. Vapors of each molecule were condensed on either a Pt or Ar substrate to form a multilayer film or a submonolayer molecular target, respectively. These were irradiated with electrons of 0-80 eV and the desorbing anionic and cationic fragments analysed via time of flight mass spectrometry. The detected cations are the same species seen in gas-phase mass spectra, albeit of differing relative intensity. Anion yield functions exhibit strong maxima, indicating that transient negative ions contribute significantly, via dissociative electron attachment (DEA), to molecular dissociation below 20 eV. For both molecules, the <5 eV shape resonances, seen experimentally and predicted by theory, do not result in fragment desorption. The main anionic fragments are H- and CN- for both molecules, additionally the fragments C-, CH- C2H- and CHN- desorb from pyrimidine and C- and C2H- from pyridazine, with some resonances lying above the ionization limit. Pyrimidine shows higher anion desorption yields than pyridazine for all species except H-. The anion signal also comprises dipolar dissociation (DD), investigated in both anionic and cationic yield functions. From analysis of anion and cation yields, fragmentation pathways are suggested. The direct ionization pathway provides information on the appearance energies for cations and their production processes in condensed phase.
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Affiliation(s)
- L Ellis-Gibbings
- Fundamental Physics Institute, Consejo Superior de Investigaciones Científicas, Serrano 113-bis, 28006 Madrid, Spain.
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22
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Meneses G, Widmann C, Cunha T, Gil A, Ferreira da Silva F, Calhorda MJ, Limão-Vieira P. Unravelling the dissociation pathways of acetic acid upon electron transfer in potassium collisions: experimental and theoretical studies. Phys Chem Chem Phys 2018; 19:1083-1088. [PMID: 27942639 DOI: 10.1039/c6cp06375f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron transfer in alkali-molecule collisions with gas phase acetic acid and its deuterated analogues resulting in OH- formation requires considerable internal rearrangement in the temporary negative ion. At a collision energy well above the threshold of negative ion formation, electron transfer from potassium to CH3COOH/CH3COOD and CD3COOH results not only in H transfer from CH3 to COOH/COOD, but also in H release from COOH and subsequent rearrangement to eliminate OH-. These processes are also investigated by theoretical post-Hartree-Fock and DFT calculations. The combination of both studies reveals that the most favourable intermediate mechanism occurs via diol formation. Such intramolecular H transfer is reported here for the first time in the context of electron transfer induced dissociation experiments in alkali-molecule collisions. A comprehensive fragmentation study is presented and dissociation mechanisms are suggested.
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Affiliation(s)
- G Meneses
- 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.
| | - C Widmann
- 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.
| | - T Cunha
- 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.
| | - A Gil
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - 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.
| | - M J Calhorda
- Centro de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
| | - P Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa Campus de Caparica, 2829-516 Caparica, Portugal.
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23
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Khreis JM, Reitshammer J, Vizcaino V, Klawitter K, Feketeová L, Denifl S. High-energy collision-induced dissociation of histidine ions [His + H] + and [His - H] - and histidine dimer [His 2 + H] . RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:113-120. [PMID: 29108138 DOI: 10.1002/rcm.8027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/05/2017] [Accepted: 10/26/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Histidine (His) is an essential amino acid, whose side group consists of an aromatic imidazole moiety that can bind a proton or metal cation and act as a donor in intermolecular interactions in many biological processes. While the dissociation of His monomer ions is well known, information on the kinetic energy released in the dissociation is missing. METHODS Using a new home-built electrospray ionization (ESI) source adapted to a double-focusing mass spectrometer of BE geometry, we investigated the fragmentation reactions of protonated and deprotonated His, [His + H]+ and [His - H]- , and the protonated His dimer [His2 + H]+ , accelerated to 6 keV in a high-energy collision with helium gas. We evaluated the kinetic energy release (KER) for the observed dissociation channels. RESULTS ESI of His solution in positive mode led to the formation of His clusters [Hisn + H]+ , n = 1-6, with notably enhanced stability of the tetramer. [His + H]+ dissociates predominantly by loss of (H2 O + CO) with a KER of 278 meV, while the dominant dissociation channel of [His - H]- involves loss of NH3 with a high KER of 769 meV. Dissociation of [His2 + H]+ is dominated by loss of the monomer but smaller losses are also observed. CONCLUSIONS The KER for HCOOH loss from both [His + H]+ and [His - H]- is similar at 278 and 249 meV, respectively, which suggests that the collision-induced dissociation takes place via a similar mechanism. The loss of COOH and C2 H5 NO2 from the dimer suggests that the dimer of His binds through a shared proton between the imidazole moieties.
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Affiliation(s)
- Jusuf M Khreis
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Julia Reitshammer
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | | | - Kevin Klawitter
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Linda Feketeová
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
- Université de Lyon, Université Claude Bernard Lyon1, CNRS/IN2P3, UMR5822, Institut de Physique Nucléaire de Lyon, 43 Bd du 11 novembre 1918, 69622, Villeurbanne, France
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Leopold Franzens Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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24
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Li Z, Carmichael I, Ptasińska S. Dissociative electron attachment induced ring opening in five-membered heterocyclic compounds. Phys Chem Chem Phys 2018; 20:18271-18278. [DOI: 10.1039/c8cp02718h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ring opening in five-membered rings induced by gentle impact of low energy electrons.
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Affiliation(s)
- Zhou Li
- Radiation Laboratory
- University of Notre Dame
- Notre Dame
- USA
- Department of Physics
| | - Ian Carmichael
- Radiation Laboratory
- University of Notre Dame
- Notre Dame
- USA
| | - Sylwia Ptasińska
- Radiation Laboratory
- University of Notre Dame
- Notre Dame
- USA
- Department of Physics
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25
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Schürmann R, Tsering T, Tanzer K, Denifl S, Kumar SVK, Bald I. Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low-Energy Electrons (0.5-9 eV). Angew Chem Int Ed Engl 2017; 56:10952-10955. [PMID: 28670830 DOI: 10.1002/anie.201705504] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Indexed: 12/20/2022]
Abstract
Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low-energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross-section for oligonucleotides modified with 8-bromoadenine (8Br A). These results were evaluated against DEA measurements with isolated 8Br A in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks.
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Affiliation(s)
- Robin Schürmann
- Department of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam-Golm, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Strasse 11, 12489, Berlin, Germany
| | - Thupten Tsering
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba Mumbai, 400 005, India
| | - Katrin Tanzer
- Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Stephan Denifl
- Institute of Ion Physics and Applied Physics, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - S V K Kumar
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba Mumbai, 400 005, India
| | - Ilko Bald
- Department of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam-Golm, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Strasse 11, 12489, Berlin, Germany
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26
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Schürmann R, Tsering T, Tanzer K, Denifl S, Kumar SVK, Bald I. Resonante Bildung von Strangbrüchen in sensibilisierten Oligonukleotiden induziert durch niederenergetische Elektronen (0.5-9.0 eV). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Robin Schürmann
- Institut für Chemie - Physikalische Chemie; Universität Potsdam; Karl-Liebknecht-Straße 24-25 14476 Potsdam-Golm Deutschland
- Abteilung 1 - Analytische Chemie und Referenzmaterialien; Bundesanstalt für Materialforschung und -prüfung; Richard-Willstätter Str. 11 12489 Berlin Deutschland
| | - Thupten Tsering
- Tata Institute of Fundamental Research; Homi Bhabha Road Colaba Mumbai 400 005 Indien
| | - Katrin Tanzer
- Institut für Ionenphysik und Angewandte Physik; Universität Innsbruck; Technikerstraße 25 A-6020 Innsbruck Österreich
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik; Universität Innsbruck; Technikerstraße 25 A-6020 Innsbruck Österreich
| | - S. V. K. Kumar
- Tata Institute of Fundamental Research; Homi Bhabha Road Colaba Mumbai 400 005 Indien
| | - Ilko Bald
- Institut für Chemie - Physikalische Chemie; Universität Potsdam; Karl-Liebknecht-Straße 24-25 14476 Potsdam-Golm Deutschland
- Abteilung 1 - Analytische Chemie und Referenzmaterialien; Bundesanstalt für Materialforschung und -prüfung; Richard-Willstätter Str. 11 12489 Berlin Deutschland
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27
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Huber SE, Śmiałek MA, Tanzer K, Denifl S. Dissociative electron attachment to the radiosensitizing chemotherapeutic agent hydroxyurea. J Chem Phys 2017; 144:224309. [PMID: 27306009 DOI: 10.1063/1.4953579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Dissociative electron attachment to hydroxyurea was studied in the gas phase for electron energies ranging from zero to 9 eV in order to probe its radiosensitizing capabilities. The experiments were carried out using a hemispherical electron monochromator coupled with a quadrupole mass spectrometer. Diversified fragmentation of hydroxyurea was observed upon low energy electron attachment and here we highlight the major dissociation channels. Moreover, thermodynamic thresholds for various fragmentation reactions are reported to support the discussion of the experimental findings. The dominant dissociation channel, which was observed over a broad range of energies, is associated with formation of NCO(-), water, and the amidogen (NH2) radical. The second and third most dominant dissociation channels are associated with formation of NCNH(-) and NHCONH2 (-), respectively, which are both directly related to formation of the highly reactive hydroxyl radical. Other ions observed with significant abundance in the mass spectra were NH2 (-)/O(-), OH(-), CN(-), HNOH(-), NCONH2 (-), and ONHCONH2 (-).
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Affiliation(s)
- S E Huber
- Institute for Ion Physics and Applied Physics and Center of Molecular Biosciences Innsbruck, Leopold Franzens University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - M A Śmiałek
- Department of Control and Power Engineering, Faculty of Ocean Engineering and Ship Technology, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - K Tanzer
- Institute for Ion Physics and Applied Physics and Center of Molecular Biosciences Innsbruck, Leopold Franzens University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - S Denifl
- Institute for Ion Physics and Applied Physics and Center of Molecular Biosciences Innsbruck, Leopold Franzens University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
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28
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Khreis JM, Ameixa J, Ferreira da Silva F, Denifl S. Interactions of low-energy electrons with the FEBID precursor chromium hexacarbonyl (Cr(CO) 6). BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2583-2590. [PMID: 29259873 PMCID: PMC5727870 DOI: 10.3762/bjnano.8.258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/08/2017] [Indexed: 05/11/2023]
Abstract
Interactions of low-energy electrons with the FEBID precursor Cr(CO)6 have been investigated in a crossed electron-molecular beam setup coupled with a double focusing mass spectrometer with reverse geometry. Dissociative electron attachment leads to the formation of a series of anions by the loss of CO ligand units. The bare chromium anion is formed by electron capture at an electron energy of about 9 eV. Metastable decays of Cr(CO)5- into Cr(CO)4-, Cr(CO)4- into Cr(CO)3- and Cr(CO)3- into Cr(CO)2- are discussed. Electron-induced dissociation at 70 eV impact energy was found to be in agreement with previous studies. A series of Cr(CO) n C+ (0 ≤ n ≤ 3) cations formed by C-O cleavage is described for the first time. The metastable decay of Cr(CO)6+ into Cr(CO)5+ and collision-induced dissociation leading to bare Cr+, are discussed. In addition, doubly charged cations were identified and the ration between doubly and singly charged fragments was determined and compared with previous studies, showing considerable differences.
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Affiliation(s)
- Jusuf M Khreis
- Institut für Ionenphysik und Angewandte Physik, Leopold Franzens Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - João Ameixa
- Institut für Ionenphysik und Angewandte Physik, Leopold Franzens Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
- 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
| | - Filipe Ferreira da Silva
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik, Leopold Franzens Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
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29
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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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30
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31
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Dawley MM, Tanzer K, Carmichael I, Denifl S, Ptasińska S. Dissociative electron attachment to the gas-phase nucleobase hypoxanthine. J Chem Phys 2015; 142:215101. [DOI: 10.1063/1.4921388] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Michele Dawley
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Katrin Tanzer
- Institut für Ionenphysik und Angewandte Physik, and Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik, and Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck, Austria
| | - 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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32
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Kawarai Y, Weber T, Azuma Y, Winstead C, McKoy V, Belkacem A, Slaughter DS. Dynamics of the Dissociating Uracil Anion Following Resonant Electron Attachment. J Phys Chem Lett 2014; 5:3854-3858. [PMID: 26278760 DOI: 10.1021/jz501907d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report a combined experimental and theoretical investigation of dissociative electron attachment (DEA) to the nucleobase uracil. Using ion momentum imaging experiments employing a DEA reaction microscope we have measured 3-dimensional momentum distributions of specific anionic fragments following DEA to uracil by 6 eV electrons. From the measured anion fragment kinetic energy we determine the possible dissociation pathways and the total kinetic energy release. We employ electronic structure and electron scattering calculations to determine the probability for electron attachment in the molecular frame. Combining these calculations with the imaging measurements, we reveal several key features of the coupled electronic and nuclear dynamics of DEA.
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Affiliation(s)
- Y Kawarai
- †Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1, Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
- ‡Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Th Weber
- ‡Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Y Azuma
- †Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1, Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - C Winstead
- ¶A. A. Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, California 91125, United States
| | - V McKoy
- ¶A. A. Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, California 91125, United States
| | - A Belkacem
- ‡Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - D S Slaughter
- ‡Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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33
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Nyakas A, Eberle RP, Stucki SR, Schürch S. More than charged base loss--revisiting the fragmentation of highly charged oligonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1155-1166. [PMID: 24802162 DOI: 10.1007/s13361-014-0873-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/30/2014] [Accepted: 02/28/2014] [Indexed: 06/03/2023]
Abstract
Tandem mass spectrometry is a well-established analytical tool for rapid and reliable characterization of oligonucleotides (ONs) and their gas-phase dissociation channels. The fragmentation mechanisms of native and modified nucleic acids upon different mass spectrometric activation techniques have been studied extensively, resulting in a comprehensive catalogue of backbone fragments. In this study, the fragmentation behavior of highly charged oligodeoxynucleotides (ODNs) comprising up to 15 nucleobases was investigated. It was found that ODNs exhibiting a charge level (ratio of the actual to the total possible charge) of 100% follow significantly altered dissociation pathways compared with low or medium charge levels if a terminal pyrimidine base (3' or 5') is present. The corresponding product ion spectra gave evidence for the extensive loss of a cyanate anion (NCO(-)), which frequently coincided with the abstraction of water from the 3'- and 5'-end in the presence of a 3'- and 5'-terminal pyrimidine nucleobase, respectively. Subsequent fragmentation of the M-NCO(-) ion by MS(3) revealed a so far unreported consecutive excision of a metaphosphate (PO3 (-))-ion for the investigated sequences. Introduction of a phosphorothioate group allowed pinpointing of PO3 (-) loss to the ultimate phosphate group. Several dissociation mechanisms for the release of NCO(-) and a metaphosphate ion were proposed and the validity of each mechanism was evaluated by the analysis of backbone- or sugar-modified ONs.
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Affiliation(s)
- Adrien Nyakas
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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34
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Almeida D, Bacchus-Montabonel MC, da Silva FF, García G, Limão-Vieira P. Potassium-uracil/thymine ring cleavage enhancement as studied in electron transfer experiments and theoretical calculations. J Phys Chem A 2014; 118:6547-52. [PMID: 24818533 DOI: 10.1021/jp503164a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report experimental and theoretical studies on ring cleavage enhancement in collisions of potassium atoms with uracil/thymine to further increase the understanding of the complex mechanisms yielding such fragmentation pathways. In these electron transfer processes time-of-flight (TOF) negative ion mass spectra were obtained in the collision energy range 13.5-23.0 eV. We note that CNO(-) is the major ring breaking anion formed and its threshold formation is discussed within the collision energy range studied. Such a decomposition process is supported by the first theoretical calculations to clarify how DNA/RNA pyrimidine base fragmentation is enhanced in electron transfer processes yielding ion-pair formation.
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Affiliation(s)
- D Almeida
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
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35
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Cole CA, Wang ZC, Snow TP, Bierbaum VM. Anionic derivatives of uracil: fragmentation and reactivity. Phys Chem Chem Phys 2014; 16:17835-44. [DOI: 10.1039/c4cp02277g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Uracil is an essential biomolecule for terrestrial life, yet its prebiotic formation mechanisms have proven elusive for decades.
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Affiliation(s)
- Callie A. Cole
- Department of Chemistry and Biochemistry
- University of Colorado
- Boulder, USA
| | - Zhe-Chen Wang
- Department of Chemistry and Biochemistry
- University of Colorado
- Boulder, USA
| | - Theodore P. Snow
- Department of Astrophysical and Planetary Sciences
- University of Colorado
- Boulder, USA
- Center for Astrophysics and Space Astronomy
- University of Colorado
| | - Veronica M. Bierbaum
- Department of Chemistry and Biochemistry
- University of Colorado
- Boulder, USA
- Center for Astrophysics and Space Astronomy
- University of Colorado
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36
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Kopyra J, Abdoul-Carime H, Kossoski F, Varella MTDN. Electron driven reactions in sulphur containing analogues of uracil: the case of 2-thiouracil. Phys Chem Chem Phys 2014; 16:25054-61. [DOI: 10.1039/c4cp03544e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron induced fragmentation of 2-thiouracil.
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Affiliation(s)
- J. Kopyra
- Chemistry Department
- Siedlce University
- 08-110 Siedlce, Poland
| | - H. Abdoul-Carime
- Université de Lyon
- Université Lyon 1
- CNRS/IN2P3
- UMR5822
- Institut de Physique Nucléaire de Lyon
| | - F. Kossoski
- Instituto de Fisica
- Universidade de São Paulo
- 05314-970 São Paulo, Brazil
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