1
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Ramanathan K, S. A, Bouwman J, Avaldi L, Vinitha MV, Bolognesi P, Richter R, Kadhane U. Photodissociation of Quinoline Cation: Mapping the Potential Energy Surface. J Chem Phys 2022; 157:064303. [DOI: 10.1063/5.0092161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A detailed exploration of the potential energy surface of quinoline cation (C9H7N ·+) is carried out to extend the present understanding of its fragmentation mechanisms. DFT calculations have been performed to explore new fragmentation mechanisms giving special attention to previously unexplored pathways such as isomerisation and elimination of HNC. The isomerization mechanisms producing 5-7 membered ring intermediates have been described and are found to be a dominant channel both energetically and kinetically. Energetically competing pathways have been established for the astrochemically important HNC-loss channel, which has hitherto never been considered in the context of the loss of a 27 amu fragment from the parent ions. Elimination of acetylene was also studied in great detail. Overall computational results are found to complement the experimental observations from the concurrently conducted PEPICO investigation. These could potentially open the doors for rich and interesting VUV radiation driven chemistry on the planetary atomospheres, meteorites and comets.
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Affiliation(s)
| | - Arun S.
- Physics, Indian Institute of Space Science and Technology, India
| | - Jordy Bouwman
- University of Colorado Boulder Laboratory for Atmospheric and Space Physics, United States of America
| | - Lorenzo Avaldi
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche Area della Ricerca di Roma 1, Italy
| | - M. V. Vinitha
- Indian Institute of Space Science and Technology, India
| | - Paola Bolognesi
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche Area della Ricerca di Roma 1, Italy
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2
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Oba Y, Takano Y, Furukawa Y, Koga T, Glavin DP, Dworkin JP, Naraoka H. Identifying the wide diversity of extraterrestrial purine and pyrimidine nucleobases in carbonaceous meteorites. Nat Commun 2022; 13:2008. [PMID: 35473908 PMCID: PMC9042847 DOI: 10.1038/s41467-022-29612-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
The lack of pyrimidine diversity in meteorites remains a mystery since prebiotic chemical models and laboratory experiments have predicted that these compounds can also be produced from chemical precursors found in meteorites. Here we report the detection of nucleobases in three carbonaceous meteorites using state-of-the-art analytical techniques optimized for small-scale quantification of nucleobases down to the range of parts per trillion (ppt). In addition to previously detected purine nucleobases in meteorites such as guanine and adenine, we identify various pyrimidine nucleobases such as cytosine, uracil, and thymine, and their structural isomers such as isocytosine, imidazole-4-carboxylic acid, and 6-methyluracil, respectively. Given the similarity in the molecular distribution of pyrimidines in meteorites and those in photon-processed interstellar ice analogues, some of these derivatives could have been generated by photochemical reactions prevailing in the interstellar medium and later incorporated into asteroids during solar system formation. This study demonstrates that a diversity of meteoritic nucleobases could serve as building blocks of DNA and RNA on the early Earth.
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Affiliation(s)
- Yasuhiro Oba
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, Hokkaido, 060-0189, Japan.
| | - Yoshinori Takano
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Furukawa
- Department of Earth Science, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Toshiki Koga
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Daniel P Glavin
- Solar System Exploration Division, National Aeronautics and Space Administration (NASA), Goddard Space Flight Center (GSFC), Greenbelt, MD, 20771, USA
| | - Jason P Dworkin
- Solar System Exploration Division, National Aeronautics and Space Administration (NASA), Goddard Space Flight Center (GSFC), Greenbelt, MD, 20771, USA
| | - Hiroshi Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
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3
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Marlton SJP, McKinnon BI, Greißel P, Shiels OJ, Ucur B, Trevitt AJ. Picosecond excited-state lifetimes of protonated indazole and benzimidazole: The role of the N-N bond. J Chem Phys 2021; 155:184302. [PMID: 34773941 DOI: 10.1063/5.0071847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Certain chemical groups give rise to characteristic excited-state deactivation mechanisms. Here, we target the role of a protonated N-N chemical group in the excited-state deactivation of protonated indazole by comparison to its isomer that lacks this group, protonated benzimidazole. Gas-phase protonated indazole and protonated benzimidazole ions are investigated at room temperature using picosecond laser pump-probe photodissociation experiments in a linear ion-trap. Excited state lifetimes are measured across a range of pump energies (4.0-5.4 eV). The 1ππ* lifetimes of protonated indazole range from 390 ± 70 ps using 4.0 eV pump energy to ≤18 ps using 4.6 eV pump energy. The 1ππ* lifetimes of protonated benzimidazole are systematically longer, ranging from 3700 ± 1100 ps at 4.6 eV pump energy to 400 ± 200 ps at 5.4 eV. Based on these experimental results and accompanying quantum chemical calculations and potential energy surfaces, the shorter lifetimes of protonated indazole are attributed to πσ* state mediated elongation of the protonated N-N bond.
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Affiliation(s)
- Samuel J P Marlton
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Benjamin I McKinnon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Phillip Greißel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Oisin J Shiels
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Boris Ucur
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Adam J Trevitt
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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4
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Chatterjee K, Dopfer O. Spectroscopic identification of fragment ions of DNA/RNA building blocks: the case of pyrimidine. Phys Chem Chem Phys 2020; 22:17275-17290. [PMID: 32685941 DOI: 10.1039/d0cp02919j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pyrimidine (Pym, 1,3-diazine, 1,3-diazabenzene) is an important N-heterocyclic building block of nucleobases. Understanding the structures of its fragment and precursor ions provides insight into its prebiotic and abiotic synthetic route. The long-standing controversial debate about the structures of the primary fragment ions of the Pym+ cation (C4H4N2+, m/z 80) resulting from loss of HCN, C3H3N+ (m/z 53), is closed herein with the aid of a combined approach utilizing infrared photodissociation (IRPD) spectroscopy in the CH and NH stretch ranges (νCH/NH) and density functional theory (DFT) calculations. IRPD spectra of cold Ar/N2-tagged fragment ions reveal that the C3H3N+ population is dominated by cis-/trans-HCCHNCH+ ions (∼90%) along with a minor contribution of the most stable H2CCCNH+ and cis-/trans-HCCHCNH+ isomers (∼10%). We also spectroscopically confirm that the secondary fragment resulting from further loss of HCN, C2H2+ (m/z 26), is the acetylene cation (HCCH+). The spectroscopic characterization of the identified C3H3N+ isomers and their hydrogen-bonded dimers with Ar and N2 provides insight into the acidity of their CH and NH groups. Finally, the vibrational properties of Pym+ in the 3 μm range are probed by IRPD of Pym+-(N2)1-2 clusters, which shows a high π-binding affinity of Pym+ toward a nonpolar hydrophobic ligand. Its νCH spectrum confirms the different acidity of the three nonequivalent CH groups.
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Affiliation(s)
- Kuntal Chatterjee
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
| | - Otto Dopfer
- Institut für Optik und Atomare Physik, TU Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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5
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Kerkeni B, Bacchus-Montabonel MC. Proton-Induced Charge Transfer on Imidazole and 2-Aminoimidazole. Role of the Substituent and Influence of Stepwise Hydration. J Phys Chem A 2020; 124:1003-1010. [PMID: 31935089 DOI: 10.1021/acs.jpca.9b10602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The behavior of potential prebiotic species in space is of main concern in the chemistry at the origin of life. Their reactivity or stability in spatial conditions, under strong UV radiations or ion bombardments, remains an open question and needs wide investigations. As protons are by far the most abundant ions in space, we focus presently on proton-induced collisions on imidazole and 2-aminoimidazole evidenced as important prebiotic RNA intermediates. Unconstrained full optimization of the structures was performed with B3LYP/cc-pVTZ model chemistry. The calculations were performed in a wide collision energy range in order to model various astrophysical environments, from eV in the interstellar medium, up to keV for solar winds or supernovae shock-wave protons. Such a study provides for the first time a theoretical insight on the influence of the amino substituent on the proton-induced charge transfer. We evaluated the role of icy grain environments through a cluster approach modeling the effect of a stepwise microhydration on the process. Comparisons with oxygenated and sulfurated analogues address further qualitative trends on the respective stability or reactivity of such heterocycles which may be of tremendous interest in prebiotic chemistry. Charge transfer appears to be quite efficient for imidazole compounds and their sulfurated analogue compared to the oxygenated heterocycle.
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Affiliation(s)
- Boutheïna Kerkeni
- Département de Physique, Laboratoire de Physique de la Matière Condensée, Faculté des Sciences de Tunis , Université de Tunis el Manar , Campus Universitaire , 2092 Tunis , Tunisia.,Institut Supérieur des Arts Multimédia de la Manouba , Université de la Manouba , 2010 La Manouba , Tunisia.,Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière , F-69622 Villeurbanne , France
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6
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Meißner R, Feketeová L, Ribar A, Fink K, Limão-Vieira P, Denifl S. Electron Ionization of Imidazole and Its Derivative 2-Nitroimidazole. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2678-2691. [PMID: 31667709 PMCID: PMC6914720 DOI: 10.1007/s13361-019-02337-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/02/2019] [Accepted: 09/08/2019] [Indexed: 05/09/2023]
Abstract
Imidazole (IMI) is a basic building block of many biologically important compounds. Thus, its electron ionization properties are of major interest and essential for the comparison with other molecular targets containing its elemental structure. 2-Nitroimidazole (2NI) contains the imidazole ring together with nitrogen dioxide bound to the C2 position, making it a radiosensitizing compound in hypoxic tumors. In the present study, we investigated electron ionization of IMI and 2NI and determined the mass spectra, the ionization energies, and appearance energies of the most abundant fragment cations. The experiments were complemented by quantum chemical calculations on the thermodynamic thresholds and potential energy surfaces, with particular attention to the calculated transition states for the most important dissociation reactions. In the case of IMI, substantially lower threshold values (up to ~ 1.5 eV) were obtained in the present work compared to the only available previous electron ionization study. Closer agreement was found with recent photon ionization values, albeit the general trend of slightly higher values for the case of electron ionization. The only exception for imidazole was found in the molecular cation at m/z 40 which is tentatively assigned to the quasi-linear HCCNH+/ HCNCH+. Electron ionization of 2NI leads to analogous fragment cations as in imidazole, yet different dissociation pathways must be operative due to the presence of the NO2 group. Regarding the potential radiosensitization properties of 2NI, electron ionization is characterized by dominant parent cation formation and release of the neutral NO radical.
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Affiliation(s)
- Rebecca Meißner
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Linda Feketeová
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
- Institut de Physique des 2 Infinis de Lyon; CNRS/IN2P3, UMR5822, Université de Lyon, Université Claude Bernard Lyon 1, 43 Bd du 11 novembre 1918, 69622, Villeurbanne, France.
| | - Anita Ribar
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Katharina Fink
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Paulo Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
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7
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Meißner R, Feketeová L, Bayer A, Postler J, Limão‐Vieira P, Denifl S. Positive and negative ions of the amino acid histidine formed in low-energy electron collisions. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:802-816. [PMID: 31410948 PMCID: PMC6916310 DOI: 10.1002/jms.4427] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/29/2019] [Accepted: 08/05/2019] [Indexed: 05/28/2023]
Abstract
Histidine is an aromatic amino acid crucial for the biological functioning of proteins and enzymes. When biological matter is exposed to ionising radiation, highly energetic particles interact with the surrounding tissue which leads to efficient formation of low-energy electrons. In the present study, the interaction of low-energy electrons with gas-phase histidine is studied at a molecular level in order to extend the knowledge of electron-induced reactions with amino acids. We report both on the formation of positive ions formed by electron ionisation and negative ions induced by electron attachment. The experimental data were complemented by quantum chemical calculations. Specifically, the free energies for possible fragmentation reactions were derived for the τ and the π tautomer of histidine to get insight into the structures of the formed ions and the corresponding neutrals. We report the experimental ionisation energy of (8.48 ± 0.03) eV for histidine which is in good agreement with the calculated vertical ionisation energy. In the case of negative ions, the dehydrogenated parent anion is the anion with the highest mass observed upon dissociative electron attachment. The comparison of experimental and computational results was also performed in view of a possible thermal decomposition of histidine during the experiments, since the sample was sublimated in the experiment by resistive heating of an oven. Overall, the present study demonstrates the effects of electrons as secondary particles in the chemical degradation of histidine. The reactions induced by those electrons differ when comparing positive and negative ion formation. While for negative ions, simple bond cleav ages prevail, the observed fragment cations exhibit partly restructuring of the molecule during the dissociation process.
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Affiliation(s)
- Rebecca Meißner
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckTechnikerstraße 256020InnsbruckAustria
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of PhysicsUniversidade NOVA de Lisboa2829‐516CaparicaPortugal
| | - Linda Feketeová
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckTechnikerstraße 256020InnsbruckAustria
- Institut de Physique Nucléaire de Lyon; CNRS/IN2P3, UMR5822Université de Lyon, Université Claude Bernard Lyon 143 Bd du 11 novembre 191869622VilleurbanneFrance
| | - Andreas Bayer
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckTechnikerstraße 256020InnsbruckAustria
| | - Johannes Postler
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckTechnikerstraße 256020InnsbruckAustria
| | - Paulo Limão‐Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of PhysicsUniversidade NOVA de Lisboa2829‐516CaparicaPortugal
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck (CMBI)Universität InnsbruckTechnikerstraße 256020InnsbruckAustria
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8
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Bolognesi P, Carravetta V, Sementa L, Barcaro G, Monti S, Manjari Mishra P, Cartoni A, Castrovilli MC, Chiarinelli J, Tosic S, Marinkovic BP, Richter R, Avaldi L. Core Shell Investigation of 2-nitroimidazole. Front Chem 2019; 7:151. [PMID: 31001511 PMCID: PMC6454003 DOI: 10.3389/fchem.2019.00151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/28/2019] [Indexed: 02/01/2023] Open
Abstract
Tunability and selectivity of synchrotron radiation have been used to study the excitation and ionization of 2-nitroimidazole at the C, N, and O K-edges. The combination of a set of different measurements (X-ray photoelectron spectroscopy, near-edge photoabsorption spectroscopy, Resonant Auger electron spectroscopy, and mass spectrometry) and computational modeling have successfully disclosed local effects due to the chemical environment on both excitation/ionization and fragmentation of the molecule.
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Affiliation(s)
- Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy
| | | | - Luca Sementa
- CNR-Istituto per i Processi Chimico Fisici, Pisa, Italy
| | | | - Susanna Monti
- CNR-Istituto di Chimica dei Composti Organo Metallici, Pisa, Italy
| | - Preeti Manjari Mishra
- Stored and Cooled Ions Division, Max Planck Institute for Nuclear Physics, Heidelberg, Germany
| | - Antonella Cartoni
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy.,Dipartimento di Chimica, Sapienza Università di Roma, Rome, Italy
| | - Mattea C Castrovilli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy.,Dipartimento di Scienze, Università degli Studi di Roma 3, Rome, Italy
| | - Sanja Tosic
- Institute of Physics, University of Belgrade, Belgrade, Serbia
| | | | - Robert Richter
- Elettra Sincrotrone Trieste, Area Science Park, Trieste, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, Montelibretti, Italy
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9
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Cartoni A, Casavola AR, Bolognesi P, Castrovilli MC, Catone D, Chiarinelli J, Richter R, Avaldi L. Insights into 2- and 4(5)-Nitroimidazole Decomposition into Relevant Ions and Molecules Induced by VUV Ionization. J Phys Chem A 2018; 122:4031-4041. [DOI: 10.1021/acs.jpca.8b01144] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Cartoni
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
- Dipartimento di Chimica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Roma, Italy
| | - A. R. Casavola
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
| | - P. Bolognesi
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
| | - M. C. Castrovilli
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
| | - D. Catone
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 2, via del Fosso del Cavaliere 10, 00133, Roma, Italy
| | - J. Chiarinelli
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
| | - R. Richter
- Elettra Sincrotrone Trieste, Area Science
Park, 34149, Basovizza, Trieste, Italy
| | - L. Avaldi
- Istituto di Struttura della Materia (ISM), Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca di Roma 1, via Salaria Km 29,300, Monterotondo Scalo (RM), 00016, Italy
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10
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Itälä E, Granroth S, Ha D, Kooser K, Levola H, Rachlew E, Tanzer K, Kukk E. Fragmentation of imidazole, pyrimidine and purine induced by core ionization: Significance of small-scale chemical environment. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Xu Y, Wu H, Zhang H, Aderinto SO, Yang Z. Synthesis, crystal structures, and DNA-binding studies of two silver(I) complexes with 1,3-bis(1-ethylbenzimidazol-2-yl)-2-thiapropane. J COORD CHEM 2016. [DOI: 10.1080/00958972.2016.1218484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Yuling Xu
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
| | - Huilu Wu
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
| | - Han Zhang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
| | | | - Zaihui Yang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
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12
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Wu H, Aderinto SO, Xu Y, Zhang H, Yang Z. A Three-Coordinate Ag(I) Complex Based on the V-Shaped Ligand 1,3-Bis(1-Ethylbenzimidazol-2-Yl)-2-Thiapropane: Synthesis, Crystal Structure and DNA-Binding Properties. JOURNAL OF CHEMICAL RESEARCH 2016. [DOI: 10.3184/174751916x14665109046089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The complex [Ag(bebt)(cinnamate)] [bebt = 1,3-bis(1-ethylbenzimidazol-2-yl)-2-thiapropane], has been synthesised and characterised by physico-chemical and spectroscopic methods. Single-crystal X-ray diffraction revealed that the coordination environment of the Ag(I) complex can be described as trigonal planar, and the Ag(I) atom is coordinated by one oxygen atom from a cinnamate anion and two nitrogen atoms from ligand bebt. Experimental studies of the DNA-binding properties indicated that the free ligand and the complex bind to DNA via the intercalation mode, and the binding affinity of the complex was found to be greater than that of just bebt.
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Affiliation(s)
- Huilu Wu
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, 730070, P.R. China
| | - Stephen Opeyemi Aderinto
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, 730070, P.R. China
| | - Yuling Xu
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, 730070, P.R. China
| | - Han Zhang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, 730070, P.R. China
| | - Zaihui Yang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, Gansu, 730070, P.R. China
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13
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Nguyen NL, Borghi G, Ferretti A, Marzari N. First-Principles Photoemission Spectroscopy of DNA and RNA Nucleobases from Koopmans-Compliant Functionals. J Chem Theory Comput 2016; 12:3948-58. [DOI: 10.1021/acs.jctc.6b00145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ngoc Linh Nguyen
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Giovanni Borghi
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Centro
S3, CNR−Istituto Nanoscienze, 41125 Modena, Italy
| | | | - Nicola Marzari
- Theory
and Simulations of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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14
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Vacuum ultraviolet photofragmentation of octadecane: photoionization mass spectrometric and theoretical investigation. APPLIED PETROCHEMICAL RESEARCH 2015; 5:305-311. [PMID: 27656346 PMCID: PMC5012363 DOI: 10.1007/s13203-015-0119-9] [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: 05/17/2015] [Accepted: 06/21/2015] [Indexed: 11/15/2022] Open
Abstract
The photoionization and fragmentation of octadecane were investigated with infrared laser desorption/tunable synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry (IRLD/VUV PIMS) and theoretical calculations. Mass spectra of octadecane were measured at various photon energies. The fragment ions were gradually detected with the increase of photon energy. The main fragment ions were assigned to radical ions (CnH2n+1+, n = 4–11) and alkene ions (CnH2n+, n = 5–10). The ionization energy of the precursor and appearance energy of ionic fragments were obtained by measuring the photoionization efficiency spectrum. Possible formation pathways of the fragment ions were discussed with the help of density functional theory calculations.
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15
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Itälä E, Kooser K, Rachlew E, Levola H, Ha DT, Kukk E. Gas-phase study on uridine: Conformation and X-ray photofragmentation. J Chem Phys 2015; 142:194303. [PMID: 26001457 DOI: 10.1063/1.4919878] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fragmentation of RNA nucleoside uridine, induced by carbon 1s core ionization, has been studied. The measurements by combined electron and ion spectroscopy have been performed in gas phase utilizing synchrotron radiation. As uridine is a combination of d-ribose and uracil, which have been studied earlier with the same method, this study also considers the effect of chemical environment and the relevant functional groups. Furthermore, since in core ionization the initial core hole is always highly localized, charge migration prior to fragmentation has been studied here. This study also demonstrates the destructive nature of core ionization as in most cases the C 1s ionization of uridine leads to concerted explosions producing only small fragments with masses ≤43 amu. In addition to fragmentation patterns, we found out that upon evaporation the sugar part of the uridine molecule attains hexagonal form.
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Affiliation(s)
- Eero Itälä
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Kuno Kooser
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Elisabeth Rachlew
- Royal Institute of Technology KTH, Physics department, S-10691 Stockholm, Sweden
| | - Helena Levola
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Dang Trinh Ha
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Edwin Kukk
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
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16
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Tentscher PR, Seidel R, Winter B, Guerard JJ, Arey JS. Exploring the aqueous vertical ionization of organic molecules by molecular simulation and liquid microjet photoelectron spectroscopy. J Phys Chem B 2014; 119:238-56. [PMID: 25516011 DOI: 10.1021/jp508053m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
To study the influence of aqueous solvent on the electronic energy levels of dissolved organic molecules, we conducted liquid microjet photoelectron spectroscopy (PES) measurements of the aqueous vertical ionization energies (VIEaq) of aniline (7.49 eV), veratrole alcohol (7.68 eV), and imidazole (8.51 eV). We also reanalyzed previously reported experimental PES data for phenol, phenolate, thymidine, and protonated imidazolium cation. We then simulated PE spectra by means of QM/MM molecular dynamics and EOM-IP-CCSD calculations with effective fragment potentials, used to describe the aqueous vertical ionization energies for six molecules, including aniline, phenol, veratrole alcohol, imidazole, methoxybenzene, and dimethylsulfide. Experimental and computational data enable us to decompose the VIEaq into elementary processes. For neutral compounds, the shift in VIE upon solvation, ΔVIEaq, was found to range from ≈-0.5 to -0.91 eV. The ΔVIEaq was further explained in terms of the influence of deforming the gas phase solute into its solution phase conformation, the influence of solute hydrogen-bond donor and acceptor interactions with proximate solvent molecules, and the polarization of about 3000 outerlying solvent molecules. Among the neutral compounds, variability in ΔVIEaq appeared largely controlled by differences in solute-solvent hydrogen-bonding interactions. Detailed computational analysis of the flexible molecule veratrole alcohol reveals that the VIE is strongly dependent on molecular conformation in both gas and aqueous phases. Finally, aqueous reorganization energies of the oxidation half-cell ionization reaction were determined from experimental data or estimated from simulation for the six compounds aniline, phenol, phenolate, veratrole alcohol, dimethylsulfide, and methoxybenzene, revealing a surprising constancy of 2.06 to 2.35 eV.
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Affiliation(s)
- Peter R Tentscher
- Environmental Chemistry Modeling Laboratory, GR C2 544, Ecole Polytechnique Fédérale de Lausanne , Station 2, CH-1015 Lausanne, Switzerland
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17
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Wolff W, Luna H, Sigaud L, Tavares AC, Montenegro EC. Absolute total and partial dissociative cross sections of pyrimidine at electron and proton intermediate impact velocities. J Chem Phys 2014; 140:064309. [PMID: 24527917 DOI: 10.1063/1.4864322] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Absolute total non-dissociative and partial dissociative cross sections of pyrimidine were measured for electron impact energies ranging from 70 to 400 eV and for proton impact energies from 125 up to 2500 keV. MOs ionization induced by coulomb interaction were studied by measuring both ionization and partial dissociative cross sections through time of flight mass spectrometry and by obtaining the branching ratios for fragment formation via a model calculation based on the Born approximation. The partial yields and the absolute cross sections measured as a function of the energy combined with the model calculation proved to be a useful tool to determine the vacancy population of the valence MOs from which several sets of fragment ions are produced. It was also a key point to distinguish the dissociation regimes induced by both particles. A comparison with previous experimental results is also presented.
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Affiliation(s)
- Wania Wolff
- Instituto de Física, Universidade Federal do Rio de Janeiro, PO 68528, 21941-972 Rio de Janeiro, RJ, Brazil
| | - Hugo Luna
- Instituto de Física, Universidade Federal do Rio de Janeiro, PO 68528, 21941-972 Rio de Janeiro, RJ, Brazil
| | - Lucas Sigaud
- Instituto de Física, Universidade Federal do Rio de Janeiro, PO 68528, 21941-972 Rio de Janeiro, RJ, Brazil
| | - Andre C Tavares
- Departamento de Física, Pontificia Universidade Católica do Rio de Janeiro, PO 38071, Rua Marquês de São Vicente 225, 22453-900 Rio de Janeiro, RJ, Brazil
| | - Eduardo C Montenegro
- Instituto de Física, Universidade Federal do Rio de Janeiro, PO 68528, 21941-972 Rio de Janeiro, RJ, Brazil
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18
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Castrovilli MC, Bolognesi P, Cartoni A, Catone D, O'Keeffe P, Casavola AR, Turchini S, Zema N, Avaldi L. Photofragmentation of halogenated pyrimidine molecules in the VUV range. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:351-367. [PMID: 24385396 DOI: 10.1007/s13361-013-0783-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 11/11/2013] [Accepted: 11/17/2013] [Indexed: 06/03/2023]
Abstract
In the present work, we studied the photoinduced ion chemistry of the halogenated pyrimidines, a class of prototype radiosensitizing molecules, in the energy region 9-15 eV. The work was stimulated by previous studies on inner shell site-selective fragmentation of the pyrimidine molecule, which have shown that the fragmentation is governed by the population/formation of specific ionic states with a hole in valence orbitals, which in turn correlate to accessible dissociation limits. The combined experimental and theoretical study of the appearance energies of the main fragments provides information on the geometric structure of the products and on the role played by the specific halogen atom and the site of halogenation in the dissociation process. This information can be used to gain new insights on the elementary mechanisms that could possibly explain the enhanced radiation damage to the DNA bases or to the medium in which the bases are embedded, thereby contributing to their radiosensitizing effect.
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19
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Raczyńska ED, Kamińska B. Variations of the tautomeric preferences and π-electron delocalization for the neutral and redox forms of purine when proceeding from the gas phase (DFT) to water (PCM). J Mol Model 2013; 19:3947-60. [PMID: 23832652 PMCID: PMC3744648 DOI: 10.1007/s00894-013-1926-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 06/16/2013] [Indexed: 11/25/2022]
Abstract
Quantum-chemical calculations were performed for all possible nine neutral tautomers of purine and their oxidized and reduced forms in water {PCM//DFT(B3LYP)/6-311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6-311+G(d,p)}. PCM hydration influences geometries, π-electron delocalization, and relative energies of purine tautomers in different ways. Generally, the harmonic oscillator model of electron delocalization (HOMED) indices increase when proceeding from the gas phase to aequeous solution for the neutral and redox forms of purine. Their changes for the neutral and oxidized tautomers are almost parallel to the relative energies showing that aromaticity plays an important role in the tautomeric preferences. Tautomeric stabilities and tautomeric preferences vary when proceeding from the gas phase to water indicating additionally that intra- and intermolecular interactions affect tautomeric equilibria. The tautomeric mixture of neutral purine in the gas phase consists mainly of the N9H tautomer, whereas two tautomers (N9H and N7H) dominate in water. For oxidized purine, N9H is favored in the gas phase, whereas N1H in water. A gain of one electron dramatically changes the relative stabilities of the CH and NH tautomers that C6H and C8H dominate in the tautomeric mixture in the gas phase, whereas N3H in water. These variations show exceptional sensitivity of the tautomeric purine system on environment in the electron-transfer reactions.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Live Science (SGGW), 02-776, Warszawa, Poland.
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20
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Cottin H, Guan YY, Noblet A, Poch O, Saiagh K, Cloix M, Macari F, Jérome M, Coll P, Raulin F, Stalport F, Szopa C, Bertrand M, Chabin A, Westall F, Chaput D, Demets R, Brack A. The PROCESS experiment: an astrochemistry laboratory for solid and gaseous organic samples in low-earth orbit. ASTROBIOLOGY 2012; 12:412-425. [PMID: 22680688 DOI: 10.1089/ast.2011.0773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The PROCESS (PRebiotic Organic ChEmistry on the Space Station) experiment was part of the EXPOSE-E payload outside the European Columbus module of the International Space Station from February 2008 to August 2009. During this interval, organic samples were exposed to space conditions to simulate their evolution in various astrophysical environments. The samples used represent organic species related to the evolution of organic matter on the small bodies of the Solar System (carbonaceous asteroids and comets), the photolysis of methane in the atmosphere of Titan, and the search for organic matter at the surface of Mars. This paper describes the hardware developed for this experiment as well as the results for the glycine solid-phase samples and the gas-phase samples that were used with regard to the atmosphere of Titan. Lessons learned from this experiment are also presented for future low-Earth orbit astrochemistry investigations.
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Affiliation(s)
- Hervé Cottin
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Université Paris Est Créteil et Université Paris Diderot, Institut Pierre Simon Laplace, Créteil, France.
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21
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Yu H, Evans NL, Stavros VG, Ullrich S. Investigation of multiple electronic excited state relaxation pathways following 200 nm photolysis of gas-phase imidazole. Phys Chem Chem Phys 2012; 14:6266-72. [PMID: 22370631 DOI: 10.1039/c2cp23533a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Imidazole acts as a subunit in the DNA base adenine and the amino acid histidine-both important biomolecules which display low fluorescence quantum yields following UV excitation. The low fluorescence quantum yields are attributed to competing non-radiative excited state relaxation pathways that operate on ultrafast timescales. Imidazole is investigated here as a model compound due to its accessibility to high level ab initio calculations and time-resolved gas-phase spectroscopic techniques. Recent non-adiabatic dynamics simulations have identified three non-radiative relaxation mechanisms which are active following 6.0-6.2 eV excitation. Presented herein is a comprehensive investigation of each mechanism using a combination of femtosecond time-resolved ion yield and total kinetic energy release spectroscopies to monitor the formation of associated photoproducts. Relaxation along the (1)πσ state constitutes the predominant deactivation pathway. Timescales for NH-dissociation are extracted and distinguished from alternative H-atom sources based on their kinetic energy distributions. Larger photoproducts are observed to a lesser extent and attributed to ring fragmentation following NH-puckering and CN-stretching relaxation paths.
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Affiliation(s)
- Hui Yu
- Department of Physics and Astronomy, University of Georgia, Athens, Georgia 30602, USA
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22
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Schwell M, Bénilan Y, Fray N, Gazeau MC, Es-Sebbar E, Garcia GA, Nahon L, Champion N, Leach S. VUV photoionization of acetamide studied by electron/ion coincidence spectroscopy in the 8–24 eV photon energy range. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.11.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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23
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Xing X, Zhu X, Li H, Jiang Y, Ni J. Electrochemical oxidation of nitrogen-heterocyclic compounds at boron-doped diamond electrode. CHEMOSPHERE 2012; 86:368-375. [PMID: 22071370 DOI: 10.1016/j.chemosphere.2011.10.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 10/14/2011] [Accepted: 10/14/2011] [Indexed: 05/31/2023]
Abstract
Nitrogen-heterocyclic compounds (NHCs) are toxic and bio-refractory contaminants widely spread in environment. This study investigated electrochemical degradation of NHCs at boron-doped diamond (BDD) anode with particular attention to the effect of different number and position of nitrogen atoms in molecular structure. Five classical NHCs with similar structures including indole (ID), quinoline (QL), isoquinoline (IQL), benzotriazole (BT) and benzimidazole (BM) were selected as the target compounds. Results of bulk electrolysis showed that degradation of all NHCs was fit to a pseudo first-order equation. The five compounds were degraded with the following sequence: ID>QL>IQL>BT>BM in terms of their rates of oxidation. Quantum chemical calculation was combined with experimental results to describe the degradation character of NHCs at BDD anode. A linear relationship between degradation rate and delocalization energy was observed, which demonstrated that electronic charge was redistributed through the conjugation system and accumulated at the active sites under the attack of hydroxyl radicals produced at BDD anode. Moreover, atom charge was calculated by semi empirical PM3 method and active sites of NHCs were identified respectively. Analysis of intermediates by GC-MS showed agreement with calculation results.
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Affiliation(s)
- Xuan Xing
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing100871, China
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24
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Kettunen JA, Niskanen J, Huttula M, Vapa M, Urpelainen S, Aksela H. Electron-ion coincidence study of photofragmentation of the CdCl(2) molecule. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:901-907. [PMID: 21915954 DOI: 10.1002/jms.1967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this work, the photofragmentation subsequent to valence and Cd4d photoionization of cadmium dichloride (CdCl(2)) were studied using He I and synchrotron excitation. The measurements were performed with a photoelectron-photoion coincidence (PEPICO) setup, and the connection between the singly ionized electronic states and cationic fragments was investigated. The valence-ionized states were found to lead to CdCl(2)(+), Cd(+) and CdCl(+). The Cd4d(- 1) states were found to lead only to Cl(+) ions. The observed charge transfer effect between Cd and Cl was concluded to take place due to internal conversion or fluorescence decay to dissociating valence states either directly or through consecutive fragmentation. The fragmentation energetics were investigated with molecular ab initio calculations, and the calculated energies were found to agree with the detected fragment appearances.
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Affiliation(s)
- J A Kettunen
- Department of Physics, University of Oulu, P.O. Box 3000, FIN-90014, University of Oulu, Finland.
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25
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Slavíček P, Fárník M. Photochemistry of hydrogen bonded heterocycles probed by photodissociation experiments and ab initio methods. Phys Chem Chem Phys 2011; 13:12123-37. [DOI: 10.1039/c1cp20674e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Photoionization mass spectrometric studies of N-methyl formamide and N,N′-dimethyl formamide in the 7–18eV photon energy range. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.06.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Itälä E, Ha DT, Kooser K, Rachlew E, Huels MA, Kukk E. Fragmentation patterns of core-ionized thymine and 5-bromouracil. J Chem Phys 2010; 133:154316. [DOI: 10.1063/1.3505140] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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28
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Leach S, Jochims HW, Baumgärtel H. Photoionization mass spectrometric study of the prebiotic species formamide in the 10-20 eV photon energy range. J Phys Chem A 2010; 114:4847-56. [PMID: 20085361 DOI: 10.1021/jp9098182] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A photoion mass spectrometry study of the prebiotic species formamide was carried out using synchrotron radiation over the photon energy range 10-20 eV. Photoion yield curves were measured for the parent ion and seven fragment ions. The ionization energy of formamide was determined as IE (1(2)A') = 10.220 +/- 0.005 eV, in agreement with a value obtained by high resolution photoelectron spectroscopy. The adiabatic energy of the first excited state of the ion, 1(2)A'', was revised to 10.55 eV. A comparison of the ionization energies of related formamides, amino acids, and polypeptides provides useful information on the varied effects of methylation and shows that polymerization does not substantially alter the ionization properties of the amino acid monomer units. Assignments of the fragment ions and the pathways of their formation by dissociative photoionization were made on the basis of ion appearance energies in conjunction with thermochemical data and the results of earlier electron impact mass spectral studies. Some of the dissociation pathways are considered to involve coupling between the 1(2)A' ground state and the low-lying 1(2)A'' excited state of the cation. Heats of formation are derived for all ions detected and are compared with literature values where they exist. Formation of the HNCO(+) ion occurs by two separate paths, one involving H(2) loss, the other H + H. In the conclusion a brief discussion is given of some astrophysical implications of these results.
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Affiliation(s)
- Sydney Leach
- LERMA-UMR 8112, Observatoire de Paris-Meudon, 5, place Jules Janssen, 92195 Meudon, France.
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29
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Bolognesi P, O'Keeffe P, Feyer V, Plekan O, Prince K, Coreno M, Mattioli G, Bonapasta AA, Zhang W, Carravetta V, Ovcharenko Y, Avaldi L. Inner shell excitation, ionization and fragmentation of pyrimidine. ACTA ACUST UNITED AC 2010. [DOI: 10.1088/1742-6596/212/1/012002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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30
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Pan Y, Zhang L, Guo H, Deng L, Qi F. Photoionisation and photodissociation studies of nonvolatile organic molecules by synchrotron VUV photoionisation mass spectrometry and theoretical calculations. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442351003668697] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Guo H, Zhang L, Deng L, Jia L, Pan Y, Qi F. Vacuum Ultraviolet Photofragmentation of Sarcosine: Photoionization Mass Spectrometric and Theoretical Insights. J Phys Chem A 2010; 114:3411-7. [DOI: 10.1021/jp9109095] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Huijun Guo
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, People’s Republic of China
| | - Lidong Zhang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, People’s Republic of China
| | - Liulin Deng
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, People’s Republic of China
| | - Liangyuan Jia
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, People’s Republic of China
| | - Yang Pan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, People’s Republic of China
| | - Fei Qi
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, People’s Republic of China
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32
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Poterya V, Profant V, Fárník M, Šištík L, Slavíček P, Buck U. Photoinduced Processes in Hydrogen Bonded System: Photodissociation of Imidazole Clusters. J Phys Chem A 2009; 113:14583-90. [DOI: 10.1021/jp904145q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | - Udo Buck
- Max-Planck Institut für Dynamik und Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany
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