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Hadidi R, Božanić DK, Ganjitabar H, Garcia GA, Powis I, Nahon L. Conformer-dependent vacuum ultraviolet photodynamics and chiral asymmetries in pure enantiomers of gas phase proline. Commun Chem 2021; 4:72. [PMID: 36697576 PMCID: PMC9814706 DOI: 10.1038/s42004-021-00508-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Proline is a unique amino-acid, with a secondary amine fixed within a pyrrolidine ring providing specific structural properties to proline-rich biopolymers. Gas-phase proline possesses four main H-bond stabilized conformers differing by the ring puckering and carboxylic acid orientation. The latter defines two classes of conformation, whose large ionization energy difference allows a unique conformer-class tagging via electron spectroscopy. Photoelectron circular dichroism (PECD) is an intense chiroptical effect sensitive to molecular structures, hence theorized to be highly conformation-dependent. Here, we present experimental evidence of an intense and striking conformer-specific PECD, measured in the vacuum ultraviolet (VUV) photoionization of proline, as well as a conformer-dependent cation fragmentation behavior. This finding, combined with theoretical modeling, allows a refinement of the conformational landscape and energetic ordering, that proves inaccessible to current molecular electronic structure calculations. Additionally, astrochemical implications regarding a possible link of PECD to the origin of life's homochirality are considered in terms of plausible temperature constraints.
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Affiliation(s)
- Rim Hadidi
- Synchrotron SOLEIL, l'Orme des Merisiers, Gif sur Yvette Cedex, France
| | - Dušan K Božanić
- Synchrotron SOLEIL, l'Orme des Merisiers, Gif sur Yvette Cedex, France
- Department of Radiation Chemistry and Physics, "VINČA" Institute of Nuclear Sciences-National Institute of thе Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Hassan Ganjitabar
- School of Chemistry, The University of Nottingham, University Park, Nottingham, UK
| | - Gustavo A Garcia
- Synchrotron SOLEIL, l'Orme des Merisiers, Gif sur Yvette Cedex, France
| | - Ivan Powis
- School of Chemistry, The University of Nottingham, University Park, Nottingham, UK
| | - Laurent Nahon
- Synchrotron SOLEIL, l'Orme des Merisiers, Gif sur Yvette Cedex, France.
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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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Resonant electron capture by Captopril molecules. Russ Chem Bull 2019. [DOI: 10.1007/s11172-019-2611-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Barbosa AS, Freitas TC, Bettega MHF. Low-energy electron collisions with proline and pyrrolidine: A comparative study. J Chem Phys 2018; 148:074304. [PMID: 29471649 DOI: 10.1063/1.5008748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We present a comparative study on the calculated cross sections obtained for the elastic collisions of low-energy electrons with the amino acid proline (C5H9NO2) and its building block pyrrolidine (C4H9N). We employed the Schwinger multichannel method implemented with pseudopotentials to compute integral, differential, and momentum transfer cross sections in the static-exchange plus polarization approximation, for energies up to 15 eV. We report three shape resonances for proline at around 1.7 eV, 6.8 eV, and 10 eV and two shape resonances for pyrrolidine centered at 7 eV and 10.2 eV. The present resonance energies are compared with available experimental data on vertical attachment energies and dissociative electron attachment, where a good agreement is found. From the comparison of the present results with available calculated cross sections for the simplest carboxylic acid, formic acid (HCOOH), and from electronic structure calculations, we found that the first resonance of proline, at 1.7 eV, is due the presence of the carboxylic group, whereas the other two structures, at 6.8 eV and 10 eV, clearly arise from the pyrrolidine ring. A comparison between the differential cross sections for proline and pyrrolidine at some selected energies of the incident electron is also reported in this paper.
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Affiliation(s)
- Alessandra Souza Barbosa
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
| | - Thiago Corrêa Freitas
- Tecnologia em Luteria, Universidade Federal do Paraná, 81520-260 Curitiba, Paraná, Brazil
| | - M H F Bettega
- Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
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Formation of negative ions via resonant low-energy electron capture by cysteine and cystine methyl esters. Russ Chem Bull 2016. [DOI: 10.1007/s11172-016-1352-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Puschnigg B, Huber SE, Probst M, Tanzer K, Vizcaino V, Ferreira da Silva F, Scheier P, Limão-Vieira P, Denifl S. Electron attachment to the dipeptide dialanine: influence of methylation on site selective dissociation reactions. Phys Chem Chem Phys 2013; 15:3834-40. [DOI: 10.1039/c3cp44230f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Alizadeh E, Sanche L. Precursors of solvated electrons in radiobiological physics and chemistry. Chem Rev 2012; 112:5578-602. [PMID: 22724633 DOI: 10.1021/cr300063r] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elahe Alizadeh
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
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Shchukin PV, Muftakhov MV, Pogulay AV. Study of fragmentation pathways of metastable negative ions in aliphatic dipeptides using the statistical theory. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:828-834. [PMID: 22368063 DOI: 10.1002/rcm.6156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE Dipeptide molecules are good model systems for investigation of resonant reactions of low-energy electrons with proteins. The present work is devoted to the study of the processes of formation and fragmentation of negative ions in aliphatic dipeptides glycyl-glycine and glycyl-alanine. The metastable decays of negative ions were detected in these objects, and have been investigated with the aim of clarification of the mechanisms of fragmentation. METHODS The effective yield curves for negative ions as functions of electron energy were obtained using a magnetic sector mass spectrometer rebuilt for generation and detection of negative ions. For analysis of the observed metastable decays statistical and thermochemical approaches have been used. RESULTS The ions structures, the enthalpies of formation of neutral and charged particles, and the rate constants of dissociative reactions have been found. CONCLUSIONS Comparison of the experimental results with theoretical data leads to the conclusion that metastable ion decay proceeds with minimal structural changes avoiding complicated rearrangements and isomerization processes.
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Affiliation(s)
- P V Shchukin
- Institute of Molecules and Crystals Physics, Ufa Research Center of Russian Academy of Sciences, Prospekt Oktyabrya 151, 450075, Ufa, Russia.
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Muftakhov MV, Shchukin PV. Fragmentation of valine and proline in resonant free electron capture reactions. Russ Chem Bull 2011. [DOI: 10.1007/s11172-011-0298-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Chomicz L, Rak J, Paneth P, Sevilla M, Ko YJ, Wang H, Bowen KH. Valence anions of N-acetylproline in the gas phase: computational and anion photoelectron spectroscopic studies. J Chem Phys 2011; 135:114301. [PMID: 21950856 PMCID: PMC3298562 DOI: 10.1063/1.3625957] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 07/28/2011] [Indexed: 11/14/2022] Open
Abstract
We report the photoelectron spectrum of anionic N-acetylproline, (N-AcPro)(-), measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that N-acetylproline forms a valence anion in the gas phase. The neutrals and anions of N-AcPro were also studied computationally at the B3LYP∕6-31++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the π* orbital localized at the acetyl group of N-AcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic N-AcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue.
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Affiliation(s)
- Lidia Chomicz
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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Muftakhov MV, Shchukin PV. Dissociative electron attachment to glycyl-glycine, glycyl-alanine and alanyl-alanine. Phys Chem Chem Phys 2011; 13:4600-6. [PMID: 21279203 DOI: 10.1039/c0cp00940g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- M V Muftakhov
- Institute of Molecular and Crystal Physics, Ufa Research Center, Russian Academy of Sciences, Ufa, Russian Federation, 450075
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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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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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Martin I, Langer J, Illenberger E. Reactions in Fluorinated Acetic Acid Esters Triggered by Slow Electrons: Bond Cleavages, Hydrogen Transfer Reactions and Loss of Halocarbons. Z PHYS CHEM 2009. [DOI: 10.1524/zpch.2008.5382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
Low energy electron induced reactions in the four fluorinated acetic acid esters CF3COOCH3, CF3COOC2H5, CF3COOCH2CF3 and CH3COOCH2CF3 are studied by means of a crossed electron-molecular beam experiment and mass spectrometric detection of the anions. All target molecules exhibit a prominent resonance located near 1 eV which is subjected to a variety of unimolecular reactions. The observation of the carboxylate anion CF3COO–/CH3COO– indicates rupture of the O−R ester bond, which in turn demonstrates that the prominent cleavage of the O−H bond recently observed in trifluoroacetic acid and acetic acid is not blocked when O−H is replaced by O−R (R=−CH3, −C2H5, −CH2CF3). In CF3COOCH3 and CF3COOC2H5 an ion of the form CF2COO– is generated which is identified to arise from a complex reaction involving multiple bond cleavages and substantial rearrangement in the transitory negative ion ultimately generating CH3F and C2H5F, respectively, as neutral counterpart. A fragment ion of the type (M-H)– (M: target molecule), i.e. loss of a neutral hydrogen atom, is only observed in CH3COOCH2CF3 which directly demonstrates that dehydrogenation selectively occurs at the CH3 site.
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Vasil’ev YV, Figard BJ, Barofsky DF, Deinzer ML. Resonant electron capture by some amino acids esters. J Am Chem Soc 2007; 268:106-121. [PMID: 19838328 PMCID: PMC2762707 DOI: 10.1016/j.ijms.2007.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Resonant electron capture by Gly, Ala and Phe esters have shown that the most efficient negative ion (NI) fragmentations are associated with the C-termini. A new mechanism for the negative ion-forming processes at energies lower than those associated with the pi*(OO) shape resonance involves coupling between dipole-bound and valence negative ion states of the same symmetry for amino acid conformers with high permanent dipoles. The interaction avoids crossing of the NI states and instead leads to formation of two adiabatic potential energy surfaces. Underivatized amino acids most effectively fragment from the bottom adiabatic surface via generation of [M-H](-) carboxylate anions by hydrogen-atom tunneling through the barrier; fragmentation of the their esters with formation of analogues [M-X](-) NIs occurs through the upper adiabatic state without penetration of the barrier in which the energy of the valence sigma*OX resonance exceeds the bond dissociation energy of the neutral molecule. Low and high temperature resonant electron capture experiments point to the importance of conformational preferences of the amino acids for optimum dissociation of the parent NIs in the gas phase.
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Affiliation(s)
- Yury V. Vasil’ev
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331
- Department of Physics, Bashkir State Agricultural University, Ufa, Russia
| | - Benjamin J. Figard
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | | | - Max L. Deinzer
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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Vasil'ev YV, Figard BJ, Voinov VG, Barofsky DF, Deinzer ML. Resonant electron capture by some amino acids and their methyl esters. J Am Chem Soc 2007; 128:5506-15. [PMID: 16620124 DOI: 10.1021/ja058464q] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Resonant electron capture mass spectra of aliphatic and aromatic amino acids and their methyl esters show intense [M-H](-) negative ions in the low-energy range. Ion formation results from a predissociation mechanism mediated by the low-energy pi*oo resonant state. Methylation in general has little influence on the electronic structure according to quantum chemical calculations, but the corresponding ions from the methyl esters, [M-Me](-), could be ascertained to arise only at higher resonance energies. Aromatic amino acids are characterized by an additional low-energy fragmentation channel associated with the generation of negative ions with loss of the side chain. The complementary negative ions of the side chains are more efficiently produced at higher energies. The results have significant implications in biological systems as they suggest that amino acids can serve as radiation protectors since they have been found to efficiently thermalize electrons.
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Affiliation(s)
- Yury V Vasil'ev
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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Scheer AM, Mozejko P, Gallup GA, Burrow PD. Total dissociative electron attachment cross sections of selected amino acids. J Chem Phys 2007; 126:174301. [PMID: 17492857 DOI: 10.1063/1.2727460] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Total dissociative electron attachment cross sections are presented for the amino acids, glycine, alanine, proline, phenylalanine, and tryptophan, at energies below the first ionization energy. Cross section magnitudes were determined by observation of positive ion production and normalization to ionization cross sections calculated using the binary-encounter-Bethe method. The prominent 1.2 eV feature in the cross sections of the amino acids and the closely related HCOOH molecule is widely attributed to the attachment into the -COOH pi* orbital. The authors discuss evidence that direct attachment to the lowest sigma* orbital may instead be responsible. A close correlation between the energies of the core-excited anion states of glycine, alanine, and proline and the ionization energies of the neutral molecules is found. A prominent feature in the total dissociative electron attachment cross section of these compounds is absent in previous studies using mass analysis, suggesting that the missing fragment is energetic H-.
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Affiliation(s)
- A M Scheer
- Department of Physics and Astronomy, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0111, USA
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