1
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Multiple-H-bonded-zwitterionic tetramer structure for L-(+)-2-chlorophenylglycine, as investigated by UV, IR and Raman spectroscopy and electronic structure calculations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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2
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Chakraborty D, Eckermann L, Carmichael I, Ptasińska S. Dissociative electron attachment to amide bond containing molecules: N-ethylformamide and N-ethylacetamide. J Chem Phys 2020; 153:224306. [PMID: 33317314 DOI: 10.1063/5.0029614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
To advance our quest to understand the role of low energy electrons in biomolecular systems, we performed investigations on dissociative electron attachment (DEA) to gas-phase N-ethylformamide (NEF) and N-ethylacetamide (NEA) molecules. Both molecules contain the amide bond, which is the linkage between two consecutive amino acid residues in proteins. Thus, their electron-induced dissociation can imitate the resonant behavior of the DEA process in more complex biostructures. Our experimental results indicate that in these two molecules, the dissociation of the amide bond results in a double resonant structure with peaks at ∼5 eV and 9 eV. We also determined the energy position of resonant states for several negative ions, i.e., the other dissociation products from NEF and NEA. Our predictions of dissociation channels were supported by density functional theory calculations of the corresponding threshold energies. Our results and those previously reported for small amides and peptides imply the fundamental nature for breakage of the amide bond through the DEA process.
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Affiliation(s)
- Dipayan Chakraborty
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Lauren Eckermann
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sylwia Ptasińska
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, USA
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3
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Loupas A, Gorfinkiel JD. Shape and core-excited resonances in electron scattering from alanine. J Chem Phys 2019; 150:064307. [PMID: 30769999 DOI: 10.1063/1.5081813] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present detailed ab initio scattering calculations using the R-matrix method for electron collisions with the most stable conformer of α-alanine. The shape resonances that we identify are in good agreement with earlier calculations and experiments. Core-excited and mixed-character resonances are identified and characterized computationally for the first time. Dissociative electron attachment results are discussed in relation to the resonances identified.
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Affiliation(s)
- Alexandra Loupas
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, Lisboa 2829-516, Portugal
| | - Jimena D Gorfinkiel
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
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4
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Nunes FB, Bettega MHF, Sanchez SD. Positron and electron scattering by glycine and alanine: Shape resonances and methylation effect. J Chem Phys 2018; 145:214313. [PMID: 28799345 DOI: 10.1063/1.4968602] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We report integral cross sections (ICSs) for both positron and electron scattering by glycine and alanine amino acids. These molecules differ only by a methyl group. We computed the scattering cross sections using the Schwinger multichannel method for both glycine and alanine in different levels of approximation for both projectiles. The alanine ICSs are greater in magnitude than the glycine ICSs for both positron and electron scattering, probably due to the larger size of the molecule. In electron scattering calculations, we found two resonances for each molecule. Glycine presents one at 1.8 eV, and another centered at around 8.5 eV, in the static-exchange plus polarization (SEP) approximation. The ICS for alanine shows one resonance at 2.5 eV and another at around 9.5 eV, also in SEP approximation. The results are in good agreement with most of the data present in the literature. The comparison of the electron scattering ICSs for both molecules indicates that the methylation of glycine destabilizes the resonances, shifting them to higher energies.
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Affiliation(s)
- Fernanda B Nunes
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
| | - Márcio H F Bettega
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
| | - Sergio d'Almeida Sanchez
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
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5
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Zawadzki M, Ranković M, Kočišek J, Fedor J. Dissociative electron attachment and anion-induced dimerization in pyruvic acid. Phys Chem Chem Phys 2018; 20:6838-6844. [PMID: 29350234 DOI: 10.1039/c7cp07472g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report partial cross sections for the dissociative electron attachment to pyruvic acid. A rich fragmentation dynamics is observed. Electronic structure calculations facilitate the identification of complex rearrangement reactions that occur during the dissociation. Furthermore, a number of fragment anions produced at electron energies close to 0 eV are observed, that cannot originate from single electron-molecule collisions. We ascribe their production to secondary reactions of the transient anions with neutral molecules. Such reactions turn out to be unusually efficient; the most probable reason for this is that they proceed via the formation of a double-hydrogen-bonded complex followed by an ultrafast proton transfer between the reaction partners.
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Affiliation(s)
- M Zawadzki
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic.
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6
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Ovejas V, Fernández-Fernández M, Montero R, Castaño F, Longarte A. Ultrafast Nonradiative Relaxation Channels of Tryptophan. J Phys Chem Lett 2013; 4:1928-1932. [PMID: 26283130 DOI: 10.1021/jz400810j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The nonradiative relaxation channels of gas-phase tryptophan excited along the S1-S4 excited states (287-217 nm) have been tracked by femtosecond time-resolved ionization. In the low-energy region, λ ≥ 240 nm, the measured transient signals reflect nonadiabatic interactions between the two bright La and Lb states of ππ* character and the dark dissociative πσ* state of the indole NH. The observed dynamical behavior is interpreted in terms of the ultrafast conversion of the prepared La state, which simultaneously populates the fluorescent Lb> and the dissociative πσ* states. At higher energies, after excitation of the S4 state, the tryptophan dynamics diverges from that observed in indole, pointing to the opening of a relaxation channel that could involve states of the amino acid part. The work provides a detailed picture of the processes and electronic states involved in the relaxation of the molecule, after photoexcitation in the near part of its UV absorption spectrum.
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Affiliation(s)
- Virginia Ovejas
- Departamento de Quı́mica-Fı́sica, Facultad de Ciencia y Tecnologı́a, Universidad del Paı́s Vasco (UPV/EHU). Apart. 644, 48080 Bilbao, Spain
| | - Marta Fernández-Fernández
- Departamento de Quı́mica-Fı́sica, Facultad de Ciencia y Tecnologı́a, Universidad del Paı́s Vasco (UPV/EHU). Apart. 644, 48080 Bilbao, Spain
| | - Raúl Montero
- Departamento de Quı́mica-Fı́sica, Facultad de Ciencia y Tecnologı́a, Universidad del Paı́s Vasco (UPV/EHU). Apart. 644, 48080 Bilbao, Spain
| | - Fernando Castaño
- Departamento de Quı́mica-Fı́sica, Facultad de Ciencia y Tecnologı́a, Universidad del Paı́s Vasco (UPV/EHU). Apart. 644, 48080 Bilbao, Spain
| | - Asier Longarte
- Departamento de Quı́mica-Fı́sica, Facultad de Ciencia y Tecnologı́a, Universidad del Paı́s Vasco (UPV/EHU). Apart. 644, 48080 Bilbao, Spain
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7
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Goto T, Ikehata A, Morisawa Y, Ozaki Y. Electronic Transitions of Protonated and Deprotonated Amino Acids in Aqueous Solution in the Region 145–300 nm Studied by Attenuated Total Reflection Far-Ultraviolet Spectroscopy. J Phys Chem A 2013; 117:2517-28. [DOI: 10.1021/jp4008416] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Takeyoshi Goto
- National Food Research Institute, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Akifumi Ikehata
- National Food Research Institute, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Yusuke Morisawa
- Department of Chemistry, School of Science
and Engineering, Kinki University, Higashiosaka,
Osaka 577-8502, Japan
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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Gschliesser D, Vizcaino V, Probst M, Scheier P, Denifl S. Formation and decay of the dehydrogenated parent anion upon electron attachment to dialanine. Chemistry 2012; 18:4613-9. [PMID: 22374822 PMCID: PMC3482929 DOI: 10.1002/chem.201102433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Indexed: 11/24/2022]
Abstract
The dehydrogenated parent anion [M-H](-) is one of the most dominant anions formed in dissociative electron attachment to various small biomolecules like nucleobases and single amino acids. In the present study, we investigate the [M-H](-) channel for the dipeptide dialanine by utilizing an electron monochromator and a two-sector-field mass spectrometer. At electron energies below 2 eV, the measured high-resolution ion-efficiency curve has a different shape to that for the single amino acid alanine, which is explained by the altered threshold energies for formation of [M-H](-) determined in quantum chemical calculations. Moreover, the structure of the formed [M-H](-) anion is further studied by investigating the unimolecular and collision-induced decay of this anion. Trajectory calculations have been carried out to aid the interpretation of the experimentally observed fragmentation patterns.
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Affiliation(s)
- David Gschliesser
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck, Leopold-Franzens-Universität Innsbruck, Technikerstrasse 256020 Innsbruck (Austria)
| | - Violaine Vizcaino
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck, Leopold-Franzens-Universität Innsbruck, Technikerstrasse 256020 Innsbruck (Austria)
| | - Michael Probst
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck, Leopold-Franzens-Universität Innsbruck, Technikerstrasse 256020 Innsbruck (Austria)
| | - Paul Scheier
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck, Leopold-Franzens-Universität Innsbruck, Technikerstrasse 256020 Innsbruck (Austria)
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center for Molecular Biosciences Innsbruck, Leopold-Franzens-Universität Innsbruck, Technikerstrasse 256020 Innsbruck (Austria)
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9
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Santos JSD, da Costa RF, Varella MTDN. Low-energy electron collisions with glycine. J Chem Phys 2012; 136:084307. [DOI: 10.1063/1.3687345] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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10
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The Role of Secondary Electrons in Radiation Damage. RADIATION DAMAGE IN BIOMOLECULAR SYSTEMS 2012. [DOI: 10.1007/978-94-007-2564-5_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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11
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Alizadeh E, Gschliesser D, Bartl P, Hager M, Edtbauer A, Vizcaino V, Mauracher A, Probst M, Märk TD, Ptasińska S, Mason NJ, Denifl S, Scheier P. Bond dissociation of the dipeptide dialanine and its derivative alanine anhydride induced by low energy electrons. J Chem Phys 2011; 134:054305. [PMID: 21303118 DOI: 10.1063/1.3544217] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Dissociative electron attachment to dialanine and alanine anhydride has been studied in the gas phase utilizing a double focusing two sector field mass spectrometer. We show that low-energy electrons (i.e., electrons with kinetic energies from near zero up to 13 eV) attach to these molecules and subsequently dissociate to form a number of anionic fragments. Anion efficiency curves are recorded for the most abundant anions by measuring the ion yield as a function of the incident electron energy. The present experiments show that as for single amino acids (M), e.g., glycine, alanine, valine, and proline, the dehydrogenated closed shell anion (M-H)(-) is the most dominant reaction product. The interpretation of the experiments is aided by quantum chemical calculations based on density functional theory, by which the electrostatic potential and molecular orbitals are calculated and the initial electron attachment process prior to dissociation is investigated.
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Affiliation(s)
- Elahe Alizadeh
- Institut für Ionenphysik and Angewandte Physik, and Center of Molecular Biosciences Innsbruck, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
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12
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Vizcaino V, Bartl P, Gschliesser D, Huber SE, Probst M, Märk TD, Scheier P, Denifl S. Dissociative electron attachment to β-alanine. Chemphyschem 2011; 12:1272-9. [PMID: 21509925 DOI: 10.1002/cphc.201001014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Indexed: 11/08/2022]
Abstract
A detailed study on dissociative electron attachment (DEA) to β-alanine (βA) in the gas phase is presented. Ion yields as a function of the incident electron energy from about 0 to 15 eV have been measured for most of the fragments. As for all α-amino acids, the main reaction corresponds to the loss of a hydrogen atom, although many other fragments have been observed that involved more complex bond cleavages. Threshold energies have been calculated by using the G4(MP2) method for various decomposition reactions. Fragmentation pathways were also investigated to measure metastable decays of the intermediate fragment anion (βA-H)(-) by using the mass-analyzed ion kinetic energy (MIKE) scan technique. Comparisons with α-alanine and other amino acids are made when relevant.
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Affiliation(s)
- Violaine Vizcaino
- Institut für Ionenphysik and Angewandte Physik, Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria.
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13
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Modelli A, Burrow PD. Electron Attachment to Dye-Sensitized Solar Cell Components: Cyanoacetic Acid. J Phys Chem A 2011; 115:1100-7. [DOI: 10.1021/jp110813f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alberto Modelli
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, via Selmi 2, 40126 Bologna, Italy, and Centro Interdipartimentale di Ricerca in Scienze Ambientali, Università di Bologna, via S. Alberto 163, 48123 Ravenna, Italy
| | - Paul D. Burrow
- Department of Physics and Astronomy, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0111, United States
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Ptasińska S, Li Z, Mason NJ, Sanche L. Damage to amino acid-nucleotide pairs induced by 1 eV electrons. Phys Chem Chem Phys 2010; 12:9367-72. [PMID: 20563347 PMCID: PMC3828173 DOI: 10.1039/b926267a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the role of two selected amino acids, glycine and arginine, on damage induced to a short chain of single stranded DNA, the tetramer GCAT, during 1 eV electron exposure. At this energy, DNA has a high cross section for DNA damage via exclusively dissociative electron attachment. Surprisingly, at low ratios of glycine:GCAT, an increase in the total fragmentation yield is observed, whilst at higher ratios, glycine and arginine appear to protect DNA from the direct action of electrons. In addition, binding energies were calculated by molecular modelling of the interactions between these amino acids and either nucleobases or nucleotides. These binding energies appear to be related to the ability of amino acids to protect DNA against low energy electron damage.
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Affiliation(s)
- Sylwia Ptasińska
- Department of Physics & Astronomy, The Open University, Milton Keynes, UK MK7 6AA.
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15
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Shchukin PV, Muftakhov MV, Morré J, Deinzer ML, Vasil’ev YV. High resolution mass analysis of N- and C-terminal negative ions resulting from resonance electron capture by aliphatic amino acids. J Chem Phys 2010; 132:234306. [DOI: 10.1063/1.3436719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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16
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Fabrikant II. Recent progress in the theory of dissociative attachment: From diatomics to biomolecules. ACTA ACUST UNITED AC 2010. [DOI: 10.1088/1742-6596/204/1/012004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Papp P, Shchukin P, Matejčík Š. Specific formation of negative ions from leucine and isoleucine molecules. J Chem Phys 2010; 132:014301. [DOI: 10.1063/1.3270154] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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18
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Kočišek J, Papp P, Mach P, Vasil’ev YV, Deinzer ML, Matejčík Š. Resonance Electron Capture by Serine. J Phys Chem A 2009; 114:1677-83. [DOI: 10.1021/jp906636b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jaroslav Kočišek
- Department of Experimental Physics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Bratislava, Slovak Republic, Departmet of Nuclear Physics and Biophysics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Slovak Republic, Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-7302, and Department of Physics, Bashkir State Agricultural University, 450001, Ufa, Russia
| | - Peter Papp
- Department of Experimental Physics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Bratislava, Slovak Republic, Departmet of Nuclear Physics and Biophysics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Slovak Republic, Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-7302, and Department of Physics, Bashkir State Agricultural University, 450001, Ufa, Russia
| | - Pavel Mach
- Department of Experimental Physics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Bratislava, Slovak Republic, Departmet of Nuclear Physics and Biophysics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Slovak Republic, Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-7302, and Department of Physics, Bashkir State Agricultural University, 450001, Ufa, Russia
| | - Yury V. Vasil’ev
- Department of Experimental Physics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Bratislava, Slovak Republic, Departmet of Nuclear Physics and Biophysics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Slovak Republic, Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-7302, and Department of Physics, Bashkir State Agricultural University, 450001, Ufa, Russia
| | - Max L. Deinzer
- Department of Experimental Physics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Bratislava, Slovak Republic, Departmet of Nuclear Physics and Biophysics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Slovak Republic, Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-7302, and Department of Physics, Bashkir State Agricultural University, 450001, Ufa, Russia
| | - Štefan Matejčík
- Department of Experimental Physics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Bratislava, Slovak Republic, Departmet of Nuclear Physics and Biophysics, Comenius University Bratislava, Mlynská Dolina F2, 84248, Slovak Republic, Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-7302, and Department of Physics, Bashkir State Agricultural University, 450001, Ufa, Russia
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Abdoul-Carime H, König-Lehmann C, Kopyra J, Farizon B, Farizon M, Illenberger E. Dissociative electron attachment to amino-acids: The case of Leucine. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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The Adsorption of Neutral Glycine Molecules on Ice Nanolayers. E-JOURNAL OF SURFACE SCIENCE AND NANOTECHNOLOGY 2009. [DOI: 10.1380/ejssnt.2009.693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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