1
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Solov'yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov'yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
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Affiliation(s)
- Andrey V Solov'yov
- MBN Research Center, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | | | - Nigel J Mason
- School of Physics and Astronomy, University of Kent, Canterbury CT2 7NH, United Kingdom
| | - Richard A Amos
- Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K
| | - Ilko Bald
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université, CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre for Light Matter Interactions, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Sciences Aschaffenburg, Würzburger Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European Innovation Center, Bořivojova 2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K
| | - Kate Ricketts
- Department of Targeted Intervention, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E H Wheatley
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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2
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Rodrigues R, Bou Debes D, Mendes M, Guerra P, Mestre G, Eden S, Cornetta LM, Ingólfsson O, da Silva FF. Experimental and Theoretical Study on Electron Ionization and Fragmentation of Propylene Oxide─the First Chiral Molecule Detected in the Interstellar Medium. J Phys Chem A 2024; 128:4795-4805. [PMID: 38860325 DOI: 10.1021/acs.jpca.4c02116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Propylene oxide, CH3CHOCH2, is the first chiral molecule detected in space and the third C3 oxide detected toward the Sagittarius B2 (Sgr B2 (N)) molecular cloud, the others being propanal, CH3CH2CHO, and acetone, (CH3)2CO. With homochirality being ubiquitous in the building blocks of living matter, the formation and decay paths of propylene oxide in space are of specific interest. Motivated by the significant role of photo- and secondary electrons in astrochemistry, we have studied electron ionization and fragmentation of propylene oxide. Ion appearance energies are determined and compared to threshold values for the respective processes calculated at the G4MP2 level of theory, and potential reaction pathways are computed at the DFT level of theory. Electron ionization is found to destabilize propylene oxide, leading to barrierless opening of the C1-C2 bond of the epoxy ring, hydrogen transfer, and fragmentation over the methyl vinyl ether or rupture of the C2-O bond of the epoxy ring and fragmentation of the allyl alcohol cation as an intermediate, rather than direct bond ruptures.
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Affiliation(s)
- Rodrigo Rodrigues
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
| | - Daniel Bou Debes
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, U.K
| | - Mónica Mendes
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
| | - Pedro Guerra
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
| | - Gonçalo Mestre
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
| | - Samuel Eden
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, U.K
| | - Lucas M Cornetta
- Instituto de Física da Universidade de São Paulo, Universidade de São Paulo, São Paulo 05508-900, Brazil
| | - Oddur Ingólfsson
- Department of Chemistry and Science Institute, University of Iceland, Dunhagi 3, Reykjavik IS-107, Iceland
| | - F Ferreira da Silva
- CEFITEC, Departamento de Física, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
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3
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Li J, Li Y, Wu B, Xie M, Hu Y. Proton Transfer Processes in 2-Butenenitrile Dimer Cation Studied by Mass-Selective Infrared Spectroscopy. J Phys Chem A 2024; 128:4694-4700. [PMID: 38833155 DOI: 10.1021/acs.jpca.4c01989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
2-Butenenitrile (2-Bu) is a recently discovered crucial interstellar molecule. Herein, an abnormal NH band was observed in the infrared spectrum of the 2-Bu dimer cation, suggestive of a proton transfer reaction within the cluster. Through a comprehensive theoretical analysis of the IR spectrum of (2-Bu)2+, we discovered not only the formation of a new C-N bond through the attachment of one 2-Bu to another but also the occurrence of a proton transfer reaction in the cluster. This proton was identified as originating from the methyl group of the attaching 2-Bu in the cluster based on the analysis of IR spectra of (2-Bu)+ and [2-Bu-acrylonitrile (AN)]+. Furthermore, the detailed reaction process of this ion-molecule reaction is examined with theoretical calculation. This finding contributes significantly to our deeper understanding of ion-molecule reactions in the gas phase and the formation of nitrogen-containing prebiotic molecules in the interstellar medium.
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Affiliation(s)
- Jingyu Li
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yujian Li
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Bingbing Wu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Min Xie
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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4
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Zhang C, Leyva V, Wang J, Turner AM, Mcanally M, Herath A, Meinert C, Young LA, Kaiser RI. Ionizing radiation exposure on Arrokoth shapes a sugar world. Proc Natl Acad Sci U S A 2024; 121:e2320215121. [PMID: 38830103 PMCID: PMC11181085 DOI: 10.1073/pnas.2320215121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/18/2024] [Indexed: 06/05/2024] Open
Abstract
The Kuiper Belt object (KBO) Arrokoth, the farthest object in the Solar System ever visited by a spacecraft, possesses a distinctive reddish surface and is characterized by pronounced spectroscopic features associated with methanol. However, the fundamental processes by which methanol ices are converted into reddish, complex organic molecules on Arrokoth's surface have remained elusive. Here, we combine laboratory simulation experiments with a spectroscopic characterization of methanol ices exposed to proxies of galactic cosmic rays (GCRs). Our findings reveal that the surface exposure of methanol ices at 40 K can replicate the color slopes of Arrokoth. Sugars and their derivatives (acids, alcohols) with up to six carbon atoms, including glucose and ribose-fundamental building block of RNA-were ubiquitously identified. In addition, polycyclic aromatic hydrocarbons (PAHs) with up to six ring units (13C22H12) were also observed. These sugars and their derivatives along with PAHs connected by unsaturated linkers represent key molecules rationalizing the reddish appearance of Arrokoth. The formation of abundant sugar-related molecules dubs Arrokoth as a sugar world and provides a plausible abiotic preparation route for a key class of biorelevant molecules on the surface of KBOs prior to their delivery to prebiotic Earth.
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Affiliation(s)
- Chaojiang Zhang
- Department of Chemistry, University of Hawaii at Mānoa, Honolulu, HI96822
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Mānoa, Honolulu, HI96822
| | - Vanessa Leyva
- Université Côte d’Azur, Institut de Chimie de Nice, UMR 7272 CNRS, 06108Nice, France
| | - Jia Wang
- Department of Chemistry, University of Hawaii at Mānoa, Honolulu, HI96822
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Mānoa, Honolulu, HI96822
| | - Andrew M. Turner
- Department of Chemistry, University of Hawaii at Mānoa, Honolulu, HI96822
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Mānoa, Honolulu, HI96822
| | - Mason Mcanally
- Department of Chemistry, University of Hawaii at Mānoa, Honolulu, HI96822
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Mānoa, Honolulu, HI96822
| | - Ashanie Herath
- Department of Chemistry, University of Hawaii at Mānoa, Honolulu, HI96822
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Mānoa, Honolulu, HI96822
| | - Cornelia Meinert
- Université Côte d’Azur, Institut de Chimie de Nice, UMR 7272 CNRS, 06108Nice, France
| | - Leslie A. Young
- Department of Space Studies, Southwest Research Institute, Boulder, CO80302
| | - Ralf I. Kaiser
- Department of Chemistry, University of Hawaii at Mānoa, Honolulu, HI96822
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Mānoa, Honolulu, HI96822
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5
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Danho A, Mardyukov A, Schreiner PR. The enol of isobutyric acid. Chem Commun (Camb) 2024; 60:5161-5164. [PMID: 38639644 PMCID: PMC11080965 DOI: 10.1039/d4cc01140f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
We present the gas-phase synthesis of 2-methyl-prop-1-ene-1,1-diol, an unreported higher energy tautomer of isobutyric acid. The enol was captured in an argon matrix at 3.5 K, characterized spectroscopically and by DFT computations. The enol rearranges likely photochemically to isobutyric acid and dimethylketene. We also identified propene, likely photochemically formed from dimethylketene.
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Affiliation(s)
- Akkad Danho
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany.
| | - Artur Mardyukov
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany.
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany.
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6
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Guerra C, Rodríguez-Núñez YA, Ensuncho AE. Role of Triplet States in the Photolysis of Proteogenic Amino Acids. Chemphyschem 2024; 25:e202300655. [PMID: 38057134 DOI: 10.1002/cphc.202300655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/19/2023] [Indexed: 12/08/2023]
Abstract
This investigation delves into the UV photodissociation of pivotal amino acids (Alanine, Glycine, Leucine, Proline, and Serine) at 213 nm, providing insights into triplet-state deactivation pathways. Utilizing a comprehensive approach involving time-dependent density functional calculations (TD-DFT), multi-configurational methods, and ab-initio molecular dynamics (AIMD) simulations, we scrutinize the excited electronic states (T1 , T2 , and S1 ) subsequent to 213 nm excitation. Our findings demonstrate that α-carbonyl C-C bond-breaking in triplet states exhibits markedly lower barriers than in singlet states (below 5.0 kcal mol-1 ). AIMD simulations corroborate the potential involvement of triplet states in amino acid fragmentation, underscoring the significance of accounting for these states in photochemistry. Chemical bonding analyses unveil distinctive patterns for S1 and T1 states, with the asymmetric redistribution of electron density characterizing the C-C breaking in triplet states, in contrast to the symmetric breaking observed in singlet states. This research complements recent experimental discoveries, enhancing our comprehension of amino acid reactions in the interstellar medium.
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Affiliation(s)
- Cristian Guerra
- Universidad Andrés Bello, Centro de Química Teórica y Computacional (CQTC), Facultad de Ciencias Exactas, Avenida República 275, 8370146, Santiago de Chile, Chile
- Universidad Autónoma de Chile, Facultad de Ingeniería, Avenida Pedro de Valdivia 425, 7500912, Santiago de Chile, Chile
- Universidad de Córdoba, Grupo de Química Computacional, Facultad de Ciencias Básicas, Carrera 6 No. 77-305, Montería-Córdoba, Colombia
| | - Yeray A Rodríguez-Núñez
- Universidad Andrés Bello, Centro de Química Teórica y Computacional (CQTC), Facultad de Ciencias Exactas, Avenida República 275, 8370146, Santiago de Chile, Chile
| | - Adolfo E Ensuncho
- Universidad de Córdoba, Grupo de Química Computacional, Facultad de Ciencias Básicas, Carrera 6 No. 77-305, Montería-Córdoba, Colombia
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7
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Puzzarini C, Alessandrini S. Interstellar Ices: A Factory of the Origin-of-Life Molecules. ACS CENTRAL SCIENCE 2024; 10:13-15. [PMID: 38292599 PMCID: PMC10823504 DOI: 10.1021/acscentsci.3c01636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Affiliation(s)
- Cristina Puzzarini
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Silvia Alessandrini
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
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8
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Wu QT, Anderson H, Watkins AK, Arora D, Barnes K, Padovani M, Shingledecker CN, Arumainayagam CR, Battat JBR. Role of Low-Energy (<20 eV) Secondary Electrons in the Extraterrestrial Synthesis of Prebiotic Molecules. ACS EARTH & SPACE CHEMISTRY 2024; 8:79-88. [PMID: 38264085 PMCID: PMC10801738 DOI: 10.1021/acsearthspacechem.3c00259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 01/25/2024]
Abstract
We demonstrate for the first time that Galactic cosmic rays with energies as high as ∼1010 eV can trigger a cascade of low-energy (<20 eV) secondary electrons that could be a significant contributor to the interstellar synthesis of prebiotic molecules whose delivery by comets, meteorites, and interplanetary dust particles may have kick-started life on Earth. For the energetic processing of interstellar ice mantles inside dark, dense molecular clouds, we explore the relative importance of low-energy (<20 eV) secondary electrons-agents of radiation chemistry-and low-energy (<10 eV), nonionizing photons-instigators of photochemistry. Our calculations indicate fluxes of ∼102 electrons cm-2 s-1 for low-energy secondary electrons produced within interstellar ices due to attenuated Galactic cosmic-ray protons. Consequently, in certain star-forming regions where internal high-energy radiation sources produce ionization rates that are observed to be a thousand times greater than the typical interstellar Galactic ionization rate, the flux of low-energy secondary electrons should far exceed that of nonionizing photons. Because reaction cross sections can be several orders of magnitude larger for electrons than for photons, even in the absence of such enhancement, our calculations indicate that secondary low-energy (<20 eV) electrons are at least as significant as low-energy (<10 eV) nonionizing photons in the interstellar synthesis of prebiotic molecules. Most importantly, our results demonstrate the pressing need for explicitly incorporating low-energy electrons in current and future astrochemical simulations of cosmic ices. Such models are critically important for interpreting James Webb Space Telescope infrared measurements, which are currently being used to probe the origins of life by studying complex organic molecules found in ices near star-forming regions.
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Affiliation(s)
- Qin Tong Wu
- Department
of Chemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Hannah Anderson
- Department
of Chemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Aurland K. Watkins
- Department
of Chemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Devyani Arora
- Department
of Chemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Kennedy Barnes
- Department
of Chemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Marco Padovani
- INAF—Osservatorio
Astrofisico di Arcetri, Largo E. Fermi, 5, 50125 Firenze, Italy
| | | | | | - James B. R. Battat
- Department
of Physics & Astronomy, Wellesley College, Wellesley, Massachusetts 02481, United States
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9
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Yusef-Buey M, Mineva T, Talbi D, Rapacioli M. Temperature driven transformations of glycine molecules embedded in interstellar ice. Phys Chem Chem Phys 2024; 26:2414-2425. [PMID: 38168973 DOI: 10.1039/d3cp03575a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The formation of glycine amino acid on ice grains in space raises fundamental questions about glycine chemistry in interstellar media. In this work, we studied glycine conformational space and the related tautomerization mechanisms in water media by means of QM/MM molecular dynamics simulations of four glycine conformational isomers (cc, ct, tc, and tt). Interstellar low density amorphous (LDA) ice and T = 20 K were considered as representative for a cold interstellar ice environment, while temperatures of 250 and 450 K were included to model rapid local heating in the ice. In addition to the LDA environment, water clusters with 4, 17, and 27 H2O molecules were subjected to QM/MM dynamics simulations that allowed glycine tautomerization behaviour to be evaluated in water surface-like environments. The tautomerization processes were found to be strongly dependent on the number of water molecules and specific isomer structure. All the glycine isomers mostly preserve their canonical "neutral" conformations under interstellar conditions.
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Affiliation(s)
- Maysa Yusef-Buey
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Tzonka Mineva
- ICGM, Univ. Montpellier, CNRS, ENSCM, Montpellier, France.
| | - Dahbia Talbi
- LUPM, Univ. Montpellier, CNRS, Montpellier, France.
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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10
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Feldman VI. Astrochemically Relevant Radicals and Radical-Molecule Complexes: A New Insight from Matrix Isolation. Int J Mol Sci 2023; 24:14510. [PMID: 37833965 PMCID: PMC10572415 DOI: 10.3390/ijms241914510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
The reactive open-shell species play a very important role in the radiation-induced molecular evolution occurring in the cold areas of space and presumably leading to the formation of biologically relevant molecules. This review presents an insight into the mechanism of such processes coming from matrix isolation studies with a main focus on the experimental and theoretical studies performed in the author's laboratory during the past decade. The radicals and radical cations produced from astrochemically relevant molecules were characterized by Fourier transform infrared (FTIR) and electron paramagnetic resonance (EPR) spectroscopy. Small organic radicals containing C, O, and N atoms are considered in view of their possible role in the formation of complex organic molecules (COMs) in space, and a comparison with earlier results is given. In addition, the radical-molecule complexes generated from isolated intermolecular complexes in matrices are discussed in connection with their model significance as the building blocks for COMs formed under the conditions of extremely restricted molecular mobility at cryogenic temperatures.
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Affiliation(s)
- Vladimir I Feldman
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
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11
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Tańska N, Bandeira E, Souza Barbosa A, Wójcik K, Dylnicka S, Ptasińska-Denga E, Szmytkowski C, Bettega MHF, Możejko P. Electron Scattering from Methyl Formate (HCOOCH 3): A Joint Theoretical and Experimental Study. J Phys Chem A 2023; 127:7594-7604. [PMID: 37644637 PMCID: PMC10510396 DOI: 10.1021/acs.jpca.3c04636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Elastic low-energy electron collisions with methyl formate have been studied theoretically at the level of various theories. The elastic integral cross section was calculated using Schwinger multichannel and R-matrix methods, in the static-exchange and static-exchange plus polarization levels of approximations for energies up to 15 eV. The absolute total cross section for electron scattering from methyl formate has been measured in a wide energy range (0.2-300 eV) using a 127° electron spectrometer working in the linear transmission configuration. The integral elastic and the absolute total cross sections display a π* shape resonance at around 1.70-1.84 eV, which can be related to the resonance visible for formic acid, and a broad structure located at 7-8 eV, which can be associated to a superposition of σ* shape resonances. Our results were compared with theoretical and experimental results available in the literature and with the results of electron collisions with formic acid. The additivity rule was used to estimate the total cross section of methyl formate and the results agree well with the experimental data.
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Affiliation(s)
- Natalia Tańska
- Institute
of Physics and Applied Computer Science, Faculty of Applied Physics
and Mathematics, Gdańsk University
of Technology, ul. Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Edvaldo Bandeira
- Departamento
de Física, Universidade Federal
do Paraná, Caixa Postal 19044, 81531-980 Curitiba, Paraná, Brazil
| | - Alessandra Souza Barbosa
- Departamento
de Física, Universidade Federal
do Paraná, Caixa Postal 19044, 81531-980 Curitiba, Paraná, Brazil
| | - Kuba Wójcik
- Institute
of Physics and Applied Computer Science, Faculty of Applied Physics
and Mathematics, Gdańsk University
of Technology, ul. Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Sylwia Dylnicka
- Institute
of Physics and Applied Computer Science, Faculty of Applied Physics
and Mathematics, Gdańsk University
of Technology, ul. Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Elżbieta Ptasińska-Denga
- Institute
of Physics and Applied Computer Science, Faculty of Applied Physics
and Mathematics, Gdańsk University
of Technology, ul. Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Czesław Szmytkowski
- Institute
of Physics and Applied Computer Science, Faculty of Applied Physics
and Mathematics, Gdańsk University
of Technology, ul. Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Márcio H. F. Bettega
- Departamento
de Física, Universidade Federal
do Paraná, Caixa Postal 19044, 81531-980 Curitiba, Paraná, Brazil
| | - Paweł Możejko
- Institute
of Physics and Applied Computer Science, Faculty of Applied Physics
and Mathematics, Gdańsk University
of Technology, ul. Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
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12
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Tolu D, Guillaumont D, de la Lande A. Irradiation of Plutonium Tributyl Phosphate Complexes by Ionizing Alpha Particles: A Computational Study. J Phys Chem A 2023; 127:7045-7057. [PMID: 37606197 DOI: 10.1021/acs.jpca.3c02117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The PUREX solvent extraction process, widely used for recovering uranium and plutonium from spent nuclear fuel, utilizes an organic solvent composed of tributyl phosphate (TBP). The emission of ionizing particles such as alpha particles, resulting from the decay of plutonium, makes the organic solvent vulnerable to degradation. Here, we study the ultrashort time alpha irradiation of tributylphosphate (TBP) and Pu(NO3)4(TBP)2 complex formed in the PUREX process. Electron dynamics is propagated by Real-Time-Dependent Auxiliary Density Functional Theory (RT-TD-ADFT). We investigate the use of previously proposed absorption boundary conditions (ABC) in the molecular orbital space to treat secondary electron emission. Basis set and exchange correlation functional effects with ABC are reported as well as a detailed analysis of the ABC parametrization. Preliminary results on the water molecule and then on TBP show that the phenomenological nature of the ABC parameters necessitates selecting appropriate values for each system under study. Irradiation of free and complexed TBP shows an influence of the ligands on the variation of atomic charges on the femtosecond time scale. An accumulation of atomic charges in the alkyl chains of TBP is observed in the case where the nitrate groups are predominantly irradiated. In addition, we find that the Pu atom regains its electric charge very rapidly after being hit by the projectile, with the coordination sphere serving as an electron reservoir to preserve its formal redox state. This study paves the road toward a full understanding of the degradation of organic extracants employed in the nuclear industry.
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Affiliation(s)
- Damien Tolu
- CEA, DES, ISEC, DMRC, Université Montpellier, Marcoule, 30207 Bagnols sur Cèze, France
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, Paris, 91405, France
| | - Dominique Guillaumont
- CEA, DES, ISEC, DMRC, Université Montpellier, Marcoule, 30207 Bagnols sur Cèze, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS, Université Paris Saclay, 15 Avenue Jean Perrin, Paris, 91405, France
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13
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Zasimov PV, Sanochkina EV, Tyurin DA, Feldman VI. Radiation-induced transformations of matrix-isolated ethanol molecules at cryogenic temperatures: an FTIR study. Phys Chem Chem Phys 2023; 25:21883-21896. [PMID: 37566409 DOI: 10.1039/d3cp02834h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Ethanol (C2H5OH) is one of the most common alcohol molecules observed in various space media (molecular clouds, star formation regions, and, highly likely, interstellar ices), where it is exposed to light and ionizing radiation, leading to more complex organic molecules and eventually to the biologically important species. To better understand the radiation-induced evolution of ethanol molecules in icy media, we have examined the transformations of isolated C2H5OH and C2D5OH under the action of X-rays and vacuum ultraviolet (VUV) radiation in solid inert matrices (Ne, Ar, Kr, and Xe) at 4.4 K using Fourier transform infrared (FTIR) spectroscopy. The results obtained with X-ray irradiation demonstrate the formation of a variety of radiolysis products corresponding to dehydrogenation (CH3CHOH˙, CH3CHO, CH2CHOH, CH3CO˙, H2CCO-H2, H2CCO, HCCO˙, CCO) and C-C bond rupture (H2CO, HCO˙, CO, CH4, and CH3˙). The absorptions of the CH3CHOH˙ radical related to the CCO stretching (the bands at 1249.1, 1247.0, 1246.2, and 1245.1 cm-1, in Ne, Ar, Kr, and Xe, respectively) were first tentatively characterized on the basis of comparison with available computational data. In addition, the C2H2⋯H2O complex, which corresponds to dehydrogenation, was found followed by C-O bond cleavage. The results were confirmed by experiments with isotopic substitution. It was found that dehydrogenation strongly predominated in a xenon matrix, while skeleton bond rupture is more feasible in neon and argon. The matrix effect was attributed to a significant role of "hot" reaction channels in neon and argon, which are efficiently quenched due to relaxation in more polarizable xenon. The VUV photolysis (185 nm) in Ar and Xe matrices yields a similar set of products, except for CH3CHOH˙ and CH2CHOH, which were not found (the nonobservation of the former species may be explained by its efficient secondary photolysis). The plausible mechanisms of product formation and astrochemical implications of the results are discussed.
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Affiliation(s)
- Pavel V Zasimov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
| | | | - Daniil A Tyurin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Vladimir I Feldman
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
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14
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Marks JH, Wang J, Kleimeier NF, Turner AM, Eckhardt AK, Kaiser RI. Prebiotic Synthesis and Isomerization in Interstellar Analog Ice: Glycinal, Acetamide, and Their Enol Tautomers. Angew Chem Int Ed Engl 2023; 62:e202218645. [PMID: 36702757 DOI: 10.1002/anie.202218645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023]
Abstract
Glycinal (HCOCH2 NH2 ) and acetamide (CH3 CONH2 ) are simple molecular building blocks of biomolecules in prebiotic chemistry, though their origin on early Earth and formation in interstellar media remain a mystery. These molecules are formed with their tautomers in low temperature interstellar model ices upon interaction with simulated galactic cosmic rays. Glycinal and acetamide are accessed via barrierless radical-radical reactions of vinoxy (⋅CH2 CHO) and acetyl (⋅C(O)CH3 ), and then undergo keto-enol tautomerization. Exploiting tunable photoionization reflectron time-of-flight mass spectroscopy and photoionization efficiency (PIE) curves, these results demonstrate fundamental reaction pathways for the formation of complex organics through non-equilibrium ice reactions in cold molecular cloud environments. These molecules demonstrate an unconventional starting point for abiotic synthesis of organics relevant to contemporary biomolecules like polypeptides and cell membranes in deep space.
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Affiliation(s)
- Joshua H Marks
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA.,W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Jia Wang
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA.,W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - N Fabian Kleimeier
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA.,W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Andrew M Turner
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA.,W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - André K Eckhardt
- Lehrstuhl für Organische Chemie II, Ruhr-Universität Bochum, 44801, Bochum, Germany
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA.,W. M. Keck Research Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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15
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Mardyukov A, Wende RC, Schreiner PR. Matrix isolation and photorearrangement of cis- and trans-1,2-ethenediol to glycolaldehyde. Chem Commun (Camb) 2023; 59:2596-2599. [PMID: 36753323 DOI: 10.1039/d2cc06331j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
1,2-Ethenediols are deemed key intermediates in prebiotic and interstellar syntheses of carbohydrates. Here we present the gas-phase synthesis of these enediols, the high-energy tautomers of glycolaldehyde, trapped in cryogenic argon matrices. Importantly, upon photolysis at λ = 180-254 nm, the enols rearrange to the simplest sugar glycolaldehyde.
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Affiliation(s)
- Artur Mardyukov
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany.
| | - Raffael C Wende
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany.
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, Giessen 35392, Germany.
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16
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Abdoul-Carime H, Kopyra J. Reactions in CCl4 films deposited onto a cold gold substrate induced by charge transfer vs. (0-5) eV free electrons. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Saha A, Yi R, Fahrenbach AC, Wang A, Jia TZ. A Physicochemical Consideration of Prebiotic Microenvironments for Self-Assembly and Prebiotic Chemistry. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101595. [PMID: 36295030 PMCID: PMC9604842 DOI: 10.3390/life12101595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
The origin of life on Earth required myriads of chemical and physical processes. These include the formation of the planet and its geological structures, the formation of the first primitive chemicals, reaction, and assembly of these primitive chemicals to form more complex or functional products and assemblies, and finally the formation of the first cells (or protocells) on early Earth, which eventually evolved into modern cells. Each of these processes presumably occurred within specific prebiotic reaction environments, which could have been diverse in physical and chemical properties. While there are resources that describe prebiotically plausible environments or nutrient availability, here, we attempt to aggregate the literature for the various physicochemical properties of different prebiotic reaction microenvironments on early Earth. We introduce a handful of properties that can be quantified through physical or chemical techniques. The values for these physicochemical properties, if they are known, are then presented for each reaction environment, giving the reader a sense of the environmental variability of such properties. Such a resource may be useful for prebiotic chemists to understand the range of conditions in each reaction environment, or to select the medium most applicable for their targeted reaction of interest for exploratory studies.
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Affiliation(s)
- Arpita Saha
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Amity Institute of Applied Sciences, Amity University, Kolkata 700135, India
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Albert C. Fahrenbach
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Anna Wang
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: (A.W.); (T.Z.J.)
| | - Tony Z. Jia
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Correspondence: (A.W.); (T.Z.J.)
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18
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Robertson PA, Heathcote D, Milešević D, Vallance C. Imaging the Dynamics of the Electron Ionization of C 2F 6. J Phys Chem A 2022; 126:7221-7229. [PMID: 36194389 PMCID: PMC9574930 DOI: 10.1021/acs.jpca.2c05606] [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] [Indexed: 11/29/2022]
Abstract
![]()
The dissociation of C2F6 following
electron
ionization at 100 eV has been studied using multimass velocity-map
ion imaging and covariance-map imaging analysis. Single ionization
events form parent C2F6+ cations
in an ensemble of electronic states, which follow a multiplex of relaxation
pathways to eventually dissociate into ionic and neutral fragment
products. We observe CF3+, CF2+, CF+, C+, F+, C2F5+, C2F4+, C2F2+, and C2F+ ions, all of which can reasonably be formed from singly charged
parent ions. Dissociation along the C–C bond typically forms
slow-moving, internally excited products, whereas C–F bond
cleavage is rapid and impulsive. Dissociation from the à state
of the cation preferentially forms C2F5+ and neutral F along a purely repulsive surface. No other
electronic state of the ion will form this product pair at the electron
energies studied in this work, nor do we observe any crossing onto
this surface from higher-lying states of the parent ion. Multiply
charged dissociative pathways are also explored, and we note characteristic
high kinetic energy release channels due to Coulombic repulsion between
charged fragments. The most abundant ion pair we observe is (CF2+, CF+), and we also observe ion pair
signals in the covariance maps associated with almost all possible
C–C bond cleavage products as well as between F+ and each of CF3+, CF2+, CF+, and C+. No covariance between F+ and C2F5+ is observed, implying
that any C2F5+ formed with F+ is unstable and undergoes secondary fragmentation. Dissociation
of multiply charged parent ions occurs via a number of mechanisms,
details of which are revealed by recoil-frame covariance-map imaging.
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Affiliation(s)
| | - David Heathcote
- Chemistry Research Laboratory, University of Oxford, OxfordOX1 3TA, U.K
| | - Dennis Milešević
- Chemistry Research Laboratory, University of Oxford, OxfordOX1 3TA, U.K
| | - Claire Vallance
- Chemistry Research Laboratory, University of Oxford, OxfordOX1 3TA, U.K
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19
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Kaiser RI, Zhao L, Lu W, Ahmed M, Evseev MM, Azyazov VN, Mebel AM, Mohamed RK, Fischer FR, Li X. Gas-phase synthesis of racemic helicenes and their potential role in the enantiomeric enrichment of sugars and amino acids in meteorites. Phys Chem Chem Phys 2022; 24:25077-25087. [PMID: 36056687 DOI: 10.1039/d2cp03084e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular origins of homochirality on Earth is not understood well, particularly how enantiomerically enriched molecules of astrobiological significance like sugars and amino acids might have been synthesized on icy grains in space preceding their delivery to Earth. Polycyclic aromatic hydrocarbons (PAHs) identified in carbonaceous chondrites could have been processed in molecular clouds by circularly polarized light prior to the depletion of enantiomerically enriched helicenes onto carbonaceous grains resulting in chiral islands. However, the fundamental low temperature reaction mechanisms leading to racemic helicenes are still unknown. Here, by exploiting synchrotron based molecular beam photoionization mass spectrometry combined with electronic structure calculations, we provide compelling testimony on barrierless, low temperature pathways leading to racemates of [5] and [6]helicene. Astrochemical modeling advocates that gas-phase reactions in molecular clouds lead to racemates of helicenes suggesting a pathway for future astronomical observation and providing a fundamental understanding for the origin of homochirality on early Earth.
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Affiliation(s)
- Ralf I Kaiser
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA.
| | - Long Zhao
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, 96822, USA.
| | - Wenchao Lu
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
| | - Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
| | | | | | - Alexander M Mebel
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, USA.
| | - Rana K Mohamed
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Kavli Energy Nano Sciences Institute at the University of California Berkeley and the Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Felix R Fischer
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Kavli Energy Nano Sciences Institute at the University of California Berkeley and the Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Xiaohu Li
- Xinjiang Astronomical Observatory, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, P. R. China.,Key Laboratory of Radio Astronomy, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, P. R. China.
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20
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Xie M, Sun X, Li W, Guan J, Liang Z, Hu Y. A Facile Route for the Formation of Complex Nitrogen-Containing Prebiotic Molecules in the Interstellar Medium. J Phys Chem Lett 2022; 13:8207-8213. [PMID: 36006401 DOI: 10.1021/acs.jpclett.2c01857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Prebiotic molecules have often been identified in the interstellar medium and meteorite samples. However, we still have only a fragmentary knowledge of the mechanism of the evolutionary process of these prebiotic molecules. With the aid of state-of-the-art vacuum ultraviolet (VUV)-infrared (IR) spectroscopy and ab initio calculations, we reveal a new pathway leading to the formation of the biorelevant molecules carrying amine groups or peptide bonds via the single-photon ionization induced Michael/cyclization reaction of acrylonitrile (AN)-alcohol heterodimer complexes in the gas phase. In the reactions, not only N-H nitrilium cations with H+-N≡C-R Lewis structure but also cyclic amine cations with a peptide bond can be formed when the AN reacts with alcohols of increasing molecular size (such as ethanol, propanol, or butanol). This study suggests the possibility of unsaturated nitriles being reduced by ionized alcohols in space, which can further drive sequential Michael addition/cyclization reactions to form more complex biorelevant molecules.
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Affiliation(s)
- Min Xie
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Xiaonan Sun
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Weixing Li
- Department of Chemistry, Fudan University, Songhu Rd. 2005, 200438 Shanghai, China
| | - Jiwen Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Zhenhao Liang
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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21
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Lozano AI, Kossoski F, Blanco F, Limão-Vieira P, Varella MTDN, García G. Observation of Transient Anions That Do Not Decay through Dissociative Electron Attachment: New Pathways for Radiosensitization. J Phys Chem Lett 2022; 13:7001-7008. [PMID: 35894633 DOI: 10.1021/acs.jpclett.2c01704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Low-energy electrons (LEEs) can very efficiently induce bond breaking via dissociative electron attachment (DEA). While DEA is ubiquitous, the importance of other reactions initiated by LEEs remains much more elusive. Here, we looked into this question by measuring highly accurate total cross sections for electron scattering from 1-methyl-5-nitroimidazole (1M5NI), a model radiosensitizer. The small uncertainty and high energy resolution allow us to identify many resonant features related to the formation of transient anions. In addition to novel insights about DEA reactions through the lower-lying resonances, our key finding is that the higher-lying resonances do not undergo DEA, implying alternative decay channels with significant cross sections. In particular, dissociation into two neutral fragments is probably involved in the case of 1M5NI. This finding has direct implications for the understanding of LEE-induced chemistry, particularly in the fundamental processes underlying the radiosensitization activity.
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Affiliation(s)
- Ana I Lozano
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 113-bis, 28006 Madrid, Spain
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Fábris Kossoski
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Francisco Blanco
- Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Paulo Limão-Vieira
- Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas, Serrano 113-bis, 28006 Madrid, Spain
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong 2522, NSW, Australia
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22
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Mifsud DV, Hailey PA, Herczku P, Sulik B, Juhász Z, Kovács STS, Kaňuchová Z, Ioppolo S, McCullough RW, Paripás B, Mason NJ. Comparative electron irradiations of amorphous and crystalline astrophysical ice analogues. Phys Chem Chem Phys 2022; 24:10974-10984. [PMID: 35466978 DOI: 10.1039/d2cp00886f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Laboratory studies of the radiation chemistry occurring in astrophysical ices have demonstrated the dependence of this chemistry on a number of experimental parameters. One experimental parameter which has received significantly less attention is that of the phase of the solid ice under investigation. In this present study, we have performed systematic 2 keV electron irradiations of the amorphous and crystalline phases of pure CH3OH and N2O astrophysical ice analogues. Radiation-induced decay of these ices and the concomitant formation of products were monitored in situ using FT-IR spectroscopy. A direct comparison between the irradiated amorphous and crystalline CH3OH ices revealed a more rapid decay of the former compared to the latter. Interestingly, a significantly lesser difference was observed when comparing the decay rates of the amorphous and crystalline N2O ices. These observations have been rationalised in terms of the strength and extent of the intermolecular forces present in each ice. The strong and extensive hydrogen-bonding network that exists in crystalline CH3OH (but not in the amorphous phase) is suggested to significantly stabilise this phase against radiation-induced decay. Conversely, although alignment of the dipole moment of N2O is anticipated to be more extensive in the crystalline structure, its weak attractive potential does not significantly stabilise the crystalline phase against radiation-induced decay, hence explaining the smaller difference in decay rates between the amorphous and crystalline phases of N2O compared to those of CH3OH. Our results are relevant to the astrochemistry of interstellar ices and icy Solar System objects, which may experience phase changes due to thermally-induced crystallisation or space radiation-induced amorphisation.
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Affiliation(s)
- Duncan V Mifsud
- Centre for Astrophysics and Planetary Science, School of Physical Sciences, University of Kent, Canterbury CT2 7NH, UK. .,Atomic and Molecular Physics Laboratory, Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Perry A Hailey
- Centre for Astrophysics and Planetary Science, School of Physical Sciences, University of Kent, Canterbury CT2 7NH, UK.
| | - Péter Herczku
- Atomic and Molecular Physics Laboratory, Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Béla Sulik
- Atomic and Molecular Physics Laboratory, Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Zoltán Juhász
- Atomic and Molecular Physics Laboratory, Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Sándor T S Kovács
- Atomic and Molecular Physics Laboratory, Institute for Nuclear Research (Atomki), Debrecen H-4026, Hungary
| | - Zuzana Kaňuchová
- Astronomical Institute, Slovak Academy of Sciences, Tatranska Lomnicá, SK-059 60, Slovakia
| | - Sergio Ioppolo
- School of Electronic Engineering and Computer Science, Queen Mary University of London, London E1 4NS, UK
| | - Robert W McCullough
- Department of Physics and Astronomy, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, UK
| | - Béla Paripás
- Department of Physics, Faculty of Mechanical Engineering and Informatics, University of Miskolc, Miskolc H-3515, Hungary
| | - Nigel J Mason
- Centre for Astrophysics and Planetary Science, School of Physical Sciences, University of Kent, Canterbury CT2 7NH, UK.
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23
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Zasimov PV, Tyurin DA, Ryazantsev SV, Feldman VI. Formation and Evolution of H 2C 3O +• Radical Cations: A Computational and Matrix Isolation Study. J Am Chem Soc 2022; 144:8115-8128. [PMID: 35487219 DOI: 10.1021/jacs.2c00295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The family of isomeric H2C3O+• radical cations is of great interest for physical organic chemistry and chemistry occurring in extraterrestrial media. In this work, we have experimentally examined a unique synthetic route to the generation of H2C3O+• from the C2H2···CO intermolecular complex and also considered the relative stability and monomolecular transformations of the H2C3O+• isomers through high-level ab initio calculations. The structures, energetics, harmonic frequencies, hyperfine coupling constants, and isomerization pathways for several of the most important H2C3O+• isomers were calculated at the UCCSD(T) level of theory. The complementary FTIR and EPR studies in argon matrices at 5 K have demonstrated that the ionized C2H2···CO complex transforms into the E-HCCHCO+• isomer, and this latter species is supposed to be the key intermediate in further chemical transformations, providing a remarkable piece of evidence for kinetic control in low-temperature chemistry. Photolysis of this species at λ = 410-465 nm results in its transformation to the thermodynamically most stable H2CCCO+• isomer. Possible implications of the results and potentiality of the proposed synthetic strategy to the preparation of highly reactive organic radical cations are discussed.
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Affiliation(s)
- Pavel V Zasimov
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Daniil A Tyurin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey V Ryazantsev
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.,Center for Energy Science and Technology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Vladimir I Feldman
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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24
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Sajeev Y, Thodika M, Matsika S. A Unique QP Partitioning and Siegert Width Using Real-Valued Continuum-Remover Potential. J Chem Theory Comput 2022; 18:2863-2874. [DOI: 10.1021/acs.jctc.1c01096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Y. Sajeev
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Mushir Thodika
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122, United States
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25
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Iglesias-Groth S, Cataldo F. Integrated Molar Absorptivity of Mid- and Far-Infrared Spectra of Alanine and a Selection of Other Five Amino Acids of Astrobiological Relevance. ASTROBIOLOGY 2022; 22:462-480. [PMID: 35133882 DOI: 10.1089/ast.2021.0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Alanine and other five proteinogeninc amino acids produced quite easily in exogenous and/or endogenous prebiotic processes, that is, valine, serine, proline, glutamic acid, and aspartic acid (Ala, Val, Ser, Pro, Glu, and Asp, respectively) were studied in the mid- and far-infrared spectral range. This work is an extension of the previous one where other proteinogenic amino acids glycine, isoleucine, phenylalanine, tyrosine, and tryptophan (Gly, Ile, Phe, Tyr, and Trp, respectively) were studied in the mid-infrared and in the far-infrared with the purpose to facilitate the search and identification of these astrobiological and astrochemical relevant molecules in space environments. The molar extinction coefficients (ɛ) of all mid- and far-infrared bands were determined as well as the integrated molar absorptivities (ψ). The mid-infrared spectra of Ala, Val, Ser, Pro, Glu, and Asp were recorded also at three different temperatures from -180°C to nearly ambient temperature and at 200°C. With the reported values of ɛ and ψ, it will be possible to estimate the relative abundance of these molecules in space environments.
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26
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Potapov A, Fulvio D, Krasnokutski S, Jäger C, Henning T. Formation of Complex Organic and Prebiotic Molecules in H 2O:NH 3:CO 2 Ices at Temperatures Relevant to Hot Cores, Protostellar Envelopes, and Planet-Forming Disks. J Phys Chem A 2022; 126:1627-1639. [PMID: 35245052 DOI: 10.1021/acs.jpca.1c10188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photochemistry in H2O:NH3:CO2 cosmic ice analogues was studied at temperatures of 75, 120, and 150 K, relevant to hot cores and warmer regions in protostellar envelopes and planet-forming disks. A combination of two triggers of surface chemistry in cosmic ice analogues, heat and UV irradiation, compared to using either just heat or UV irradiation, leads to a larger variety and an increased production of complex organic molecules, including potential precursors of prebiotic molecules. In addition to complex organic molecules detected in previous studies of H2O:NH3:CO2 ices, ammonium carbamate, carbamic acid, ammonium formate and formamide, we detected acetaldehyde, urea, and, tentatively, glycine, the simplest amino acid. Water ice hampers reactions at low temperature (75 K) but allows the parent molecules, CO2 and NH3, to stay in the solid state and react at higher temperatures (120 and 150 K, above their desorption temperatures). The experiments were performed on the surface of KBr substrates and amorphous silicate grains, analogs of cosmic silicate dust. The production of complex molecules on the silicate surface is decreased compared to KBr. This result suggests that the larger surface area and/or surface properties of the silicate grains play a role in controlling the chemistry, preventing it taking place to the same extent as on the flat KBr substrate. This is further evidence of the fact that cosmic dust grains play an important role in the chemistry taking place on their surface.
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Affiliation(s)
- Alexey Potapov
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 3, 07743 Jena, Germany
| | - Daniele Fulvio
- Osservatorio Astronomico di Capodimonte, Istituto Nazionale di Astrofisica, Salita Moiariello 16, 80131, Naples, Italy.,Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg, Germany
| | - Serge Krasnokutski
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 3, 07743 Jena, Germany
| | - Cornelia Jäger
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 3, 07743 Jena, Germany
| | - Thomas Henning
- Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg, Germany
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27
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Cornetta LM, Martinez TJ, Varella MTDN. Dissociative electron attachment to 5-bromo-uracil: non-adiabatic dynamics on complex-valued potential energy surfaces. Phys Chem Chem Phys 2022; 24:6845-6855. [PMID: 35253036 DOI: 10.1039/d1cp05663h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electron induced dissociation reactions are relevant to many fields, ranging from prebiotic chemistry to cancer treatments. However, the simulation of dissociation electron attachment (DEA) dynamics is very challenging because the auto-ionization widths of the transient negative ions must be accounted for. We propose an adaptation of the ab initio multiple spawning (AIMS) method for complex-valued potential energy surfaces, along the lines of recent developments based on surface hopping dynamics. Our approach combines models for the energy dependence of the auto-ionization widths, obtained from scattering calculations, with survival probabilities computed for the trajectory basis functions employed in the AIMS dynamics. The method is applied to simulate the DEA dynamics of 5-bromo-uracil in full dimensionality, i.e., taking all the vibrational modes into consideration. The propagation starts on the resonance state and describes the formation of Br- anions mediated by non-adiabatic couplings. The potential energies, gradients and non-adiabatic couplings were computed with the fractional-occupancy molecular orbital complete-active-space configuration-interaction method, and the calculated DEA cross section are consistent with the observed DEA intensities.
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Affiliation(s)
- Lucas M Cornetta
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Rua Sérgio Buarque de Holanda, 777 - Cidade Universitária, Campinas, São Paulo, Brazil.
| | - Todd J Martinez
- Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, USA.,SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Marcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508-090, São Paulo, São Paulo, Brazil
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28
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Lozano AI, Kumar S, Kerkeni B, García G, Limão-Vieira P. Methanol Negative Ion Fragmentation Probed in Electron Transfer Experiments. J Phys Chem A 2022; 126:1076-1084. [PMID: 35143199 DOI: 10.1021/acs.jpca.1c07588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this contribution, we report a novel comprehensive investigation on negative ion formation from electron transfer processes mediated by neutral potassium atom collisions with neutral methanol molecules employing experimental and theoretical methodologies. Methanol collision-induced fragmentation yielding anion formation has been obtained by time-of-flight mass spectrometry in the wide energy range of 19 to 275 eV in the lab frame. The negative ions formed in such a collision process have been assigned to CH3O-, OH-, and O-, with a strong energy dependence especially at lower collision energies. The most intense fragment anions in the whole energy range investigated have been assigned to OH- and CH3O-. Additionally, the potassium cation energy loss spectrum in the forward scattering direction at 205 eV impact energy has revealed several features, where the two main electronic states accessible during the collision events have vertical electron affinities of -8.26 ± 0.20 and -10.36 ± 0.2 eV. Quantum chemical calculations have been performed for the lowest-lying unoccupied molecular orbitals of methanol in the presence of a potassium atom, lending strong support to the experimental findings.
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Affiliation(s)
- Ana Isabel Lozano
- Atomic and Molecular Collisions Laboratory, Centro de Física e Investigação Tecnológica, Department of Physics, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal.,Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, Madrid 28006, Spain
| | - Sarvesh Kumar
- Atomic and Molecular Collisions Laboratory, Centro de Física e Investigação Tecnológica, Department of Physics, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
| | - Boutheïna Kerkeni
- Institut Supérieur des Arts Multimédia de la Manouba, Université de la Manouba, La Manouba 2010, Tunisia.,Département de Physique, Laboratoire de recherche: Physique de la matière condensée, Faculté des Sciences de Tunis, Université de Tunis el Manar, Tunis 2092, Tunisia
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, Madrid 28006, Spain
| | - Paulo Limão-Vieira
- Atomic and Molecular Collisions Laboratory, Centro de Física e Investigação Tecnológica, Department of Physics, Universidade NOVA de Lisboa, Caparica 2829-516, Portugal
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29
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Abstract
Electron-induced chemistry is relevant to many processes that occur when ionizing radiation interacts with matter. This includes radiation damage, curing of polymers, and nanofabrication processes but also the formation of complex molecules in molecular ices grown on dust particles in space. High-energy radiation liberates from such materials an abundance of secondary electrons of which most have energies below 20 eV. These electrons efficiently trigger reactions when they attach to molecules or induce electronic excitation and further ionization. This review focuses on the present state of insight regarding the mechanisms of reactions induced by electrons with energies between 0 and 20 eV that lead to formation of larger products in binary ice layers consisting of small molecules (H2O, CO, CH3OH, NH3, CH4, C2H4, CH3CN, C2H6) or some derivatives thereof (C2H5NH2 and (C2H5)2NH, CH2=CHCH3). It summarizes our approach to identify products and quantify their amounts based on thermal desorption spectrometry (TDS) and electron-stimulated desorption (ESD) experiments performed in ultrahigh vacuum (UHV). The overview of the results demonstrates that, although the initial electron-molecule interaction is a non-thermal process, product formation from the resulting reactive species is often governed by subsequent reactions that follow well-known thermal and radical-driven mechanisms of organic chemistry.
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30
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Kleimeier NF, Kaiser RI. Bottom-Up Synthesis of 1,1-Ethenediol (H 2CC(OH) 2)─The Simplest Unsaturated Geminal Diol─In Interstellar Analogue Ices. J Phys Chem Lett 2022; 13:229-235. [PMID: 34967646 DOI: 10.1021/acs.jpclett.1c03515] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Because of their nucleophilic character and high reactivity, enols─reaction intermediates carrying a hydroxyl group connected to a carbon-carbon double bond─play a key role in the formation of complex organic molecules in astrobiology and biochemistry. Here, we report the first bottom-up preparation of 1,1-ethenediol (H2CC(OH)2)─the simplest unsaturated geminal enol of acetic acid (CH3COOH) and potential precursor for the formation of glycine─in interstellar analogue ices of carbon dioxide and methane processed by proxies of galactic cosmic rays. These enols can easily form via nonequilibrium chemistry in low temperature (10 K) interstellar ices at abundances orders of magnitude higher than thermodynamically predicted. These energetically less favorable tautomers remain stable in ice-coated interstellar nanoparticles in molecular clouds and also upon sublimation into the gas phase in star forming regions thus providing the raw material to a complex and exotic organic chemistry under extreme conditions in deep space.
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Affiliation(s)
- N Fabian Kleimeier
- Department of Chemistry, University of Hawai'i at Ma̅noa, Honolulu, Hawaii 96822, United States
- W. M. Keck Laboratory in Astrochemistry, University of Hawai'i at Ma̅noa, Honolulu, Hawaii 96822, United States
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawai'i at Ma̅noa, Honolulu, Hawaii 96822, United States
- W. M. Keck Laboratory in Astrochemistry, University of Hawai'i at Ma̅noa, Honolulu, Hawaii 96822, United States
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31
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Simbizi R, Nduwimana D, Niyoncuti J, Cishahayo P, Gahungu G. On the formation of 2- and 3-cyanofurans and their protonated forms in interstellar medium conditions: quantum chemical evidence. RSC Adv 2022; 12:25332-25341. [PMID: 36199317 PMCID: PMC9446509 DOI: 10.1039/d2ra04351c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/23/2022] [Indexed: 11/21/2022] Open
Abstract
The literature is still poor in theoretical and experimental, including both spectroscopic and thermodynamic data for protonated furan and protonated 2-cyanofuran and 3-cyanofuran (FH+, 2CFH+ and 3CFH+). These data are, however, crucial for astrophysicists and astrochemists in the detection of new species in interstellar medium (ISM), the discovery of these molecular species being not yet reported. It is in this perspective that a computational study based on quantum chemistry on FH+, 2CFH+ and 3CFH+ was undertaken. A series of properties including the proton affinity (PA) of furan and the two cyanofurans, the variations of enthalpy (ΔrH), entropy (ΔrS), and Gibbs free energy (ΔrG) for the reactions yielding cyanofurans (neutral and protonated forms), were studied at different temperatures (5 K, 10 K, 150 K and 298 K) and pressures (P = 1 atm and P = 10−5 atm) based on modern computational models (G2MP2, G3, G4MP2 and G4). While confirming that the protonation favors the α-position for furan, the PA values show that the protonation favors the nitrogen atom in cases of 2CFH+ and 3CFH+. The ΔrH, ΔrS and ΔrG values revealed spontaneous reactions producing these species under ISM conditions of temperature and pressure. In addition quadrupole hyperfine structures and vibrational spectra which are essential tools for the characterization and the identification of interstellar molecular species are predicted, while the region where brightest lines fall for different temperatures is discussed. The results reported in this work are expected to assist astrophysicists and astrochemists, in the search for new chemical species in interstellar environments. The literature is still poor in theoretical and experimental, including both spectroscopic and thermodynamic, data for protonated furan and protonated 2-cyanofuran and 3-cyanofuran (FH+, 2CFH+ and 3CFH+).![]()
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Affiliation(s)
- René Simbizi
- Faculté des Sciences, Département de Physique, Université du Burundi, BP 2700 Bujumbura, Burundi
- Faculté des Sciences, Centre de Recherche en Mathématique & Physique (CRMP), Université du Burundi, BP 2700 Bujumbura, Burundi
| | - Désiré Nduwimana
- Faculté des Sciences, Département de Physique, Université du Burundi, BP 2700 Bujumbura, Burundi
- Faculté des Sciences, Centre de Recherche en Mathématique & Physique (CRMP), Université du Burundi, BP 2700 Bujumbura, Burundi
| | - Joël Niyoncuti
- Faculté des Sciences, Département de Physique, Université du Burundi, BP 2700 Bujumbura, Burundi
- Faculté des Sciences, Centre de Recherche en Mathématique & Physique (CRMP), Université du Burundi, BP 2700 Bujumbura, Burundi
| | - Prosper Cishahayo
- Faculté des Sciences, Département de Chimie, Université du Burundi, BP 2700 Bujumbura, Burundi
- Faculté des Sciences, Centre de Recherche en Sciences Naturelles et Environnementales (CRSNE), Université du Burundi, BP 2700 Bujumbura, Burundi
| | - Godefroid Gahungu
- Faculté des Sciences, Département de Chimie, Université du Burundi, BP 2700 Bujumbura, Burundi
- Faculté des Sciences, Centre de Recherche en Sciences Naturelles et Environnementales (CRSNE), Université du Burundi, BP 2700 Bujumbura, Burundi
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32
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Abstract
Water is the cellular milieu, drives all biochemistry within Earth's biosphere and facilitates microbe-mediated decay processes. Instead of reviewing these topics, the current article focuses on the activities of water as a preservative-its capacity to maintain the long-term integrity and viability of microbial cells-and identifies the mechanisms by which this occurs. Water provides for, and maintains, cellular structures; buffers against thermodynamic extremes, at various scales; can mitigate events that are traumatic to the cell membrane, such as desiccation-rehydration, freeze-thawing and thermal shock; prevents microbial dehydration that can otherwise exacerbate oxidative damage; mitigates against biocidal factors (in some circumstances reducing ultraviolet radiation and diluting solute stressors or toxic substances); and is effective at electrostatic screening so prevents damage to the cell by the intense electrostatic fields of some ions. In addition, the water retained in desiccated cells (historically referred to as 'bound' water) plays key roles in biomacromolecular structures and their interactions even for fully hydrated cells. Assuming that the components of the cell membrane are chemically stable or at least repairable, and the environment is fairly constant, water molecules can apparently maintain membrane geometries over very long periods provided these configurations represent thermodynamically stable states. The spores and vegetative cells of many microbes survive longer in the presence of vapour-phase water (at moderate-to-high relative humidities) than under more-arid conditions. There are several mechanisms by which large bodies of water, when cooled during subzero weather conditions remain in a liquid state thus preventing potentially dangerous (freeze-thaw) transitions for their microbiome. Microbial life can be preserved in pure water, freshwater systems, seawater, brines, ice/permafrost, sugar-rich aqueous milieux and vapour-phase water according to laboratory-based studies carried out over periods of years to decades and some natural environments that have yielded cells that are apparently thousands, or even (for hypersaline fluid inclusions of mineralized NaCl) hundreds of millions, of years old. The term preservative has often been restricted to those substances used to extend the shelf life of foods (e.g. sodium benzoate, nitrites and sulphites) or those used to conserve dead organisms, such as ethanol or formaldehyde. For living microorganisms however, the ultimate preservative may actually be water. Implications of this role are discussed with reference to the ecology of halophiles, human pathogens and other microbes; food science; biotechnology; biosignatures for life and other aspects of astrobiology; and the large-scale release/reactivation of preserved microbes caused by global climate change.
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Affiliation(s)
- John E. Hallsworth
- Institute for Global Food SecuritySchool of Biological SciencesQueen’s University Belfast19 Chlorine GardensBelfastBT9 5DLUK
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33
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El-Sharkawy YH, Elbasuney S, Radwan SM, Askar MA, El-Sayyad GS. Total RNA nonlinear polarization: towards facile early diagnosis of breast cancer. RSC Adv 2021; 11:33319-33325. [PMID: 35497529 PMCID: PMC9042301 DOI: 10.1039/d1ra05599b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/23/2021] [Indexed: 12/16/2022] Open
Abstract
Different cancers are caused by accumulation of numerous genetic and epigenetic changes. Recently, nonlinear polarization has been considered as a marvelous tool for several medical applications. The capability of nonlinear polarization, to monitor any changes in RNA's spectral signature due to breast cancer (BC) was evaluated. Blood samples, from healthy controls and BC patients, were collected for whole blood preparation for genomic total RNA purification. Total RNA samples were stimulated with a light-emitting diode (LED) source of 565 nm; the resonance frequency of investigated RNA samples was captured and processed via hyperspectral imaging. Resonance frequency signatures were processed using fast Fourier transform in an attempt to differentiate between RNA (control) and RNA (BC) via frequency response. RNA (BC) demonstrated a characteristic signal at 0.02 GHz, as well as a phase shift at 0.031, and 0.070 GHZ from RNA (control). These features could offer early BC diagnosis. This is the first time to describe an optical methodology based on nonlinear polarization as a facile principle to distinguish and identify RNA alterations in BC by their characteristic fingerprint spectral signature. Nonlinear polarization has been considered as a marvelous tool for several medical applications, and the capability to monitor any changes in RNA's spectral signature due to breast cancer was evaluated by hyperspectral camera.![]()
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Affiliation(s)
- Yasser H El-Sharkawy
- Head of Biomedical Engineering Department, Military Technical College Cairo Egypt
| | - Sherif Elbasuney
- Head of Nanotechnology Research Center, Military Technical College Cairo Egypt
| | - Sara M Radwan
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University Cairo Egypt
| | - Mostafa A Askar
- Radiation Biology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA) Cairo Egypt
| | - Gharieb S El-Sayyad
- Drug Radiation Research Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA) Cairo Egypt
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34
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Feldman VI, Ryazantsev SV, Kameneva SV. Matrix isolation in laboratory astrochemistry: state-of-the-art, implications and perspective. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Kleimeier NF, Eckhardt AK, Kaiser RI. Identification of Glycolaldehyde Enol (HOHC═CHOH) in Interstellar Analogue Ices. J Am Chem Soc 2021; 143:14009-14018. [PMID: 34407613 DOI: 10.1021/jacs.1c07978] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Glycolaldehyde is considered the entry point in the aqueous prebiotic formose (Butlerow) reaction although it mainly exists in its unreactive hydrated form in aqueous solution. The characterization of the more reactive nucleophilic enol form under interstellar conditions has remained elusive to date. Here we report on the identification of glycolaldehyde enol (1,2-ethenediol, HOHC═CHOH) in low temperature methanol-bearing ices at temperatures as low as 5 K. Exploiting isotope labeling and isomer-selective photoionization coupled with reflectron time-of-flight mass spectrometry, our results unravel distinct reaction pathways to 1,2-ethenediol, thus demonstrating the kinetic stability, availability for prebiotic sugar formation, and potential detectability in deep space.
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Affiliation(s)
- N Fabian Kleimeier
- Department of Chemistry, University of Hawaii at Ma̅noa, Honolulu, Hawaii 96822, United States.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Ma̅noa, Honolulu, Hawaii 96822, United States
| | - André K Eckhardt
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawaii at Ma̅noa, Honolulu, Hawaii 96822, United States.,W. M. Keck Laboratory in Astrochemistry, University of Hawaii at Ma̅noa, Honolulu, Hawaii 96822, United States
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36
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Khatri J, Roy TK, Chatterjee K, Schwaab G, Havenith M. Vibrational Spectroscopy of Benzonitrile-(Water) 1-2 Clusters in Helium Droplets. J Phys Chem A 2021; 125:6954-6963. [PMID: 34355893 DOI: 10.1021/acs.jpca.1c04553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Polycyclic aromatic hydrocarbons are considered as primary carriers of the unidentified interstellar bands. The recent discovery of the first interstellar aromatic molecule, benzonitrile (C6H5CN), suggests a repository of aromatic hydrocarbons in the outer earth environment. Herein, we report an infrared (IR) study of benzonitrile-(D2O)n clusters using mass-selective detection in helium nanodroplets. In this work, we use isotopically substituted water, D2O, instead of H2O because of our restricted IR frequency range (2565-3100 cm-1). A comparison of the experimental and predicted spectra computed at the MP2/6-311++G(d,p) level of benzonitrile-(water)1-2 clusters reveals the formation of a unique local minimum structure, which was not detected in previous gas-phase molecular beam experiments. Here, the solvent water forms a nearly linear hydrogen bond (H-bond) with the nitrile nitrogen of benzonitrile, while the previously reported most stable cyclic H-bonded isomer is not observed. This can be rationalized by the stepwise aggregation process of precooled monomers. The addition of a second water molecule results in the formation of two different isomers. In one of the observed isomers, a H-bonded water chain binds linearly to the nitrile nitrogen similar to the monohydrated benzonitrile-water complex. In the other observed isomer, the water dimer forms a ring-type structure, where a H-bonded water dimer simultaneously interacts with the nitrile nitrogen and the adjacent ortho CH group. Finally, we compare the water-binding motif in the neutral benzonitrile-water complex with the corresponding positively and negatively charged benzonitrile-water monohydrates to comprehend the charge-induced alteration of the solvent binding motif.
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Affiliation(s)
- Jai Khatri
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Tarun Kumar Roy
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Kuntal Chatterjee
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
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37
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Herczku P, Mifsud DV, Ioppolo S, Juhász Z, Kaňuchová Z, Kovács STS, Traspas Muiña A, Hailey PA, Rajta I, Vajda I, Mason NJ, McCullough RW, Paripás B, Sulik B. The Ice Chamber for Astrophysics-Astrochemistry (ICA): A new experimental facility for ion impact studies of astrophysical ice analogs. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:084501. [PMID: 34470410 DOI: 10.1063/5.0050930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
The Ice Chamber for Astrophysics-Astrochemistry (ICA) is a new laboratory end station located at the Institute for Nuclear Research (Atomki) in Debrecen, Hungary. The ICA has been specifically designed for the study of the physico-chemical properties of astrophysical ice analogs and their chemical evolution when subjected to ionizing radiation and thermal processing. The ICA is an ultra-high-vacuum compatible chamber containing a series of IR-transparent substrates mounted on a copper holder connected to a closed-cycle cryostat capable of being cooled down to 20 K, itself mounted on a 360° rotation stage and a z-linear manipulator. Ices are deposited onto the substrates via background deposition of dosed gases. The ice structure and chemical composition are monitored by means of FTIR absorbance spectroscopy in transmission mode, although the use of reflectance mode is possible by using metallic substrates. Pre-prepared ices may be processed in a variety of ways. A 2 MV Tandetron accelerator is capable of delivering a wide variety of high-energy ions into the ICA, which simulates ice processing by cosmic rays, solar wind, or magnetospheric ions. The ICA is also equipped with an electron gun that may be used for electron impact radiolysis of ices. Thermal processing of both deposited and processed ices may be monitored by means of both FTIR spectroscopy and quadrupole mass spectrometry. In this paper, we provide a detailed description of the ICA setup as well as an overview of the preliminary results obtained and future plans.
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Affiliation(s)
- Péter Herczku
- Institute for Nuclear Research (Atomki), PO Box 51, Debrecen H-4026, Hungary
| | - Duncan V Mifsud
- Institute for Nuclear Research (Atomki), PO Box 51, Debrecen H-4026, Hungary
| | - Sergio Ioppolo
- School of Electronic Engineering and Computer Science, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Zoltán Juhász
- Institute for Nuclear Research (Atomki), PO Box 51, Debrecen H-4026, Hungary
| | - Zuzana Kaňuchová
- Astronomical Institute, Slovak Academy of Sciences, Tatranská Lomnica SK-059 60, Slovakia
| | - Sándor T S Kovács
- Institute for Nuclear Research (Atomki), PO Box 51, Debrecen H-4026, Hungary
| | - Alejandra Traspas Muiña
- School of Electronic Engineering and Computer Science, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Perry A Hailey
- Centre for Astrophysics and Planetary Science, School of Physical Sciences, University of Kent, Canterbury CT2 7NH, United Kingdom
| | - István Rajta
- Institute for Nuclear Research (Atomki), PO Box 51, Debrecen H-4026, Hungary
| | - István Vajda
- Institute for Nuclear Research (Atomki), PO Box 51, Debrecen H-4026, Hungary
| | - Nigel J Mason
- Centre for Astrophysics and Planetary Science, School of Physical Sciences, University of Kent, Canterbury CT2 7NH, United Kingdom
| | - Robert W McCullough
- Department of Physics and Astronomy, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Béla Paripás
- Department of Physics, Faculty of Mechanical Engineering and Informatics, University of Miskolc, Miskolc H-3515, Hungary
| | - Béla Sulik
- Institute for Nuclear Research (Atomki), PO Box 51, Debrecen H-4026, Hungary
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Mardyukov A, Keul F, Schreiner PR. 1,1,2‐Ethenetriol: The Enol of Glycolic Acid, a High‐Energy Prebiotic Molecule. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Artur Mardyukov
- Institute of Organic Chemistry Justus Liebig University Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Felix Keul
- Institute of Organic Chemistry Justus Liebig University Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Peter R. Schreiner
- Institute of Organic Chemistry Justus Liebig University Heinrich-Buff-Ring 17 35392 Giessen Germany
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39
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Fulvio D, Potapov A, He J, Henning T. Astrochemical Pathways to Complex Organic and Prebiotic Molecules: Experimental Perspectives for In Situ Solid-State Studies. Life (Basel) 2021; 11:life11060568. [PMID: 34204233 PMCID: PMC8235774 DOI: 10.3390/life11060568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 02/05/2023] Open
Abstract
A deep understanding of the origin of life requires the physical, chemical, and biological study of prebiotic systems and the comprehension of the mechanisms underlying their evolutionary steps. In this context, great attention is paid to the class of interstellar molecules known as "Complex Organic Molecules" (COMs), considered as possible precursors of prebiotic species. Although COMs have already been detected in different astrophysical environments (such as interstellar clouds, protostars, and protoplanetary disks) and in comets, the physical-chemical mechanisms underlying their formation are not yet fully understood. In this framework, a unique contribution comes from laboratory experiments specifically designed to mimic the conditions found in space. We present a review of experimental studies on the formation and evolution of COMs in the solid state, i.e., within ices of astrophysical interest, devoting special attention to the in situ detection and analysis techniques commonly used in laboratory astrochemistry. We discuss their main strengths and weaknesses and provide a perspective view on novel techniques, which may help in overcoming the current experimental challenges.
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Affiliation(s)
- Daniele Fulvio
- Istituto Nazionale di Astrofisica, Osservatorio Astronomico di Capodimonte, Salita Moiariello 16, 80131 Naples, Italy
- Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg, Germany; (J.H.); (T.H.)
- Correspondence:
| | - Alexey Potapov
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Institute of Solid State Physics, Helmholtzweg 3, 07743 Jena, Germany;
| | - Jiao He
- Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg, Germany; (J.H.); (T.H.)
| | - Thomas Henning
- Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg, Germany; (J.H.); (T.H.)
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40
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Mirsaleh-Kohan N, Esmaili S, Bass AD, Huels MA, Sanche L. Chemical transformation of molecular ices containing N 2O and C 2D 2 by low energy electrons: New chemical species of astronomical interest. J Chem Phys 2021; 154:224706. [PMID: 34241211 DOI: 10.1063/5.0040884] [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
We have employed electron stimulated desorption (ESD) and x-ray photoelectron spectroscopy (XPS) to study the chemical species generated from multilayer films of N2O, C2D2, and mixtures thereof (i.e., N2O/C2D2) by the impact of low energy electrons with energies between 30 and 70 eV. Our ESD results for pure films of N2O show the production of numerous fragment cations and anions, and of larger molecular ions, of sufficient kinetic energy to escape into vacuum, which are likely formed by ion-molecule scattering in the film. Ion-molecule scattering is also responsible for the production of cations from C2D2 films that contain as many as six or seven carbon atoms. Many of the same anions and cations desorb from N2O/C2D2 mixtures, as well as new species, which is the result of ion-molecule scattering in the film. Anion desorption signals further indicate the formation of C-N containing species within the irradiated films. XPS spectra of N1s, C1s, and O1s lines reveal the fragmentation of N-O bonds and gradual formation of molecules containing species containing O-C=O, C=O, and C-O functional groups. A comparison between ESD and XPS findings suggests that species observed in the ESD channel are primarily products of reactions taking place at the film-vacuum interface, while those observed in the XPS derive from reactions occurring within the solid.
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Affiliation(s)
- Nasrin Mirsaleh-Kohan
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Sasan Esmaili
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Andrew D Bass
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Michael A Huels
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Leon Sanche
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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41
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Bocková J, Jones NC, Meierhenrich UJ, Hoffmann SV, Meinert C. Chiroptical activity of hydroxycarboxylic acids with implications for the origin of biological homochirality. Commun Chem 2021; 4:86. [PMID: 36697718 PMCID: PMC9814692 DOI: 10.1038/s42004-021-00524-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/14/2021] [Indexed: 02/05/2023] Open
Abstract
Circularly polarised light (CPL) interacting with interstellar organic molecules might have imparted chiral bias and hence preluded prebiotic evolution of biomolecular homochirality. The L-enrichment of extra-terrestrial amino acids in meteorites, as opposed to no detectable excess in monocarboxylic acids and amines, has previously been attributed to their intrinsic interaction with stellar CPL revealed by substantial differences in their chiroptical signals. Recent analyses of meteoritic hydroxycarboxylic acids (HCAs) - potential co-building blocks of ancestral proto-peptides - indicated a chiral bias toward the L-enantiomer of lactic acid. Here we report on novel anisotropy spectra of several HCAs using a synchrotron radiation electronic circular dichroism spectrophotometer to support the re-evaluation of chiral biomarkers of extra-terrestrial origin in the context of absolute photochirogenesis. We found that irradiation by CPL which would yield L-excess in amino acids would also yield L-excess in aliphatic chain HCAs, including lactic acid and mandelic acid, in the examined conditions. Only tartaric acid would show "unnatural" D-enrichment, which makes it a suitable target compound for further assessing the relevance of the CPL scenario.
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Affiliation(s)
- Jana Bocková
- grid.460782.f0000 0004 4910 6551University Côte d’Azur, CNRS, Institute de Chimie de Nice, UMR 7272, Nice, France
| | - Nykola C. Jones
- grid.7048.b0000 0001 1956 2722ISA, Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Uwe J. Meierhenrich
- grid.460782.f0000 0004 4910 6551University Côte d’Azur, CNRS, Institute de Chimie de Nice, UMR 7272, Nice, France
| | - Søren V. Hoffmann
- grid.7048.b0000 0001 1956 2722ISA, Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Cornelia Meinert
- grid.460782.f0000 0004 4910 6551University Côte d’Azur, CNRS, Institute de Chimie de Nice, UMR 7272, Nice, France
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42
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Mardyukov A, Keul F, Schreiner PR. 1,1,2-Ethenetriol: The Enol of Glycolic Acid, a High-Energy Prebiotic Molecule. Angew Chem Int Ed Engl 2021; 60:15313-15316. [PMID: 33950559 PMCID: PMC8362078 DOI: 10.1002/anie.202104436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/19/2021] [Indexed: 12/13/2022]
Abstract
As low‐temperature conditions (e.g. in space) prohibit reactions requiring large activation energies, an alternative mechanism for follow‐up transformations of highly stable molecules involves the reactions of higher energy isomers that were generated in a different environment. Hence, one working model for the formation of larger organic molecules is their generation from high‐lying isomers of otherwise rather stable molecules. As an example, we present here the synthesis as well as IR and UV/Vis spectroscopic identification of the previously elusive 1,1,2‐ethenetriol, the higher energy enol tautomer of glycolic acid, a rather stable and hence unreactive biological building block. The title compound was generated in the gas phase by flash vacuum pyrolysis of tartronic acid at 400 °C and was subsequently trapped in argon matrices at 10 K. The spectral assignments are supported by B3LYP/6–311++G(2d,2p) computations. Upon photolysis at λ=180–254 nm, 1,1,2‐ethenetriol rearranges to glycolic acid and ketene.
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Affiliation(s)
- Artur Mardyukov
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Felix Keul
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
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43
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Potapov A, McCoustra M. Physics and chemistry on the surface of cosmic dust grains: a laboratory view. INT REV PHYS CHEM 2021. [DOI: 10.1080/0144235x.2021.1918498] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alexey Potapov
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena, Jena, Germany
| | - Martin McCoustra
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, UK
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44
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Pelc A, Ribar Valah A, Huber SE, Marciszuk K, Denifl S. Fragmentation of propionitrile (CH 3CH 2CN) by low energy electrons. J Chem Phys 2021; 154:184301. [PMID: 34241001 DOI: 10.1063/5.0051059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Propionitrile (CH3CH2CN, PN) is a molecule relevant for interstellar chemistry. There is credible evidence that anions, molecules, and radicals that may originate from PN could also be involved in the formation of more complex organic compounds. In the present investigation, dissociative electron attachment to CH3CH2CN has been studied in a crossed electron-molecular beam experiment in the electron energy range of about 0-15 eV. In the experiment, seven anionic species were detected: C3H4N-, C3H3N-, C3H2N-, C2H2N-, C2HN-, C2N-, and CN-. The anion formation is most efficient for CN- and anions originating from the dehydrogenation of the parent molecule. A discussion of possible reaction channels for all measured negative ions is provided. The experimental results are compared with calculations of thermochemical thresholds of the detected anions.
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Affiliation(s)
- A Pelc
- Mass Spectrometry Laboratory, Department of Biophysics, Maria Curie-Skłodowska University, Pl. M. C.-Skłodowskiej 1, 20-031 Lublin, Poland
| | - A Ribar Valah
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - S E Huber
- Department of Basic Sciences in Engineering Sciences, University of Innsbruck, Technikerstraße 13, 6020 Innsbruck, Austria
| | - K Marciszuk
- Mass Spectrometry Laboratory, Department of Biophysics, Maria Curie-Skłodowska University, Pl. M. C.-Skłodowskiej 1, 20-031 Lublin, Poland
| | - S Denifl
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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45
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Iglesias-Groth S, Cataldo F. Integrated Molar Absorptivity of Mid- and Far-Infrared Spectra of Glycine and Other Selected Amino Acids. ASTROBIOLOGY 2021; 21:526-540. [PMID: 33956490 DOI: 10.1089/ast.2020.2307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A selection of five proteinogenic amino acids-glycine, isoleucine, phenylalanine, tyrosine, and tryptophan-were studied in the mid-infrared and in the far-infrared with the purpose to facilitate the search and identification of these astrobiologically and astrochemically relevant molecules in space environments. The molar extinction coefficients (ɛ) of all mid- and far-infrared bands were determined as well as the integrated molar absorptivities (ψ). The mid-infrared spectra of the five selected amino acids were recorded also at three different temperatures from -180°C to ambient temperature to +200°C. We measured the wavelength shift of the infrared bands caused by temperature; and for the most relevant or temperature-sensitive infrared bands, a series of linear equations were determined relating wavelength position with temperature. Such equations may provide estimates of the temperature of these molecules once detected in astrophysical objects; and with the reported values of ɛ and ψ, it will be possible to estimate the relative abundance of these molecules in space environments.
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46
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Thripati S, Ramabhadran RO. Pathways for the Formation of Formamide, a Prebiotic Biomonomer: Metal-Ions in Interstellar Gas-Phase Chemistry. J Phys Chem A 2021; 125:3457-3472. [PMID: 33861935 DOI: 10.1021/acs.jpca.1c02132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The chemistry occurring in the interstellar medium (ISM) is an active area of contemporary research. New aspects of interstellar chemistry are getting unraveled regularly. In this context, the role of metal-ions in the chemistry occurring in the ISM is not well-studied so far. Herein, we highlight the role of metal-ions in interstellar chemistry. For this purpose, we choose the problem of gas-phase formamide formation in interstellar molecular clouds. Formamide is a key biomonomer and contains the simplest peptide [-(C═O)-NH-] linkage. With its two electronegative atoms ("O" and "N"), it provides an excellent platform to probe the role of the metal-ions. The metal-ions chosen are Na+, K+, Al+, Mg+, and Mg2+-all of them present in the ISM. The metal-ions are studied in three different forms as bare positively charged ions, as hydrated metal-ions co-ordinated with a molecule of water, and when the metal-ions are part of a neutral covalent molecule. With the aid of electronic structure calculations [CCSD(T) and DFT methods], we study different gas-phase pathways which result in the generation of interstellar formamide. Throughout our study, we find that metal-ions lower the barriers (with Mg+, Mg++, and Al+ offering maximal stabilization of the transition states) and facilitate the reactions. The chemical factors influencing the reactions, how we consider the putative conditions in the ISM, the astrochemical implications of this study, and its connection with terrestrial prebiotic chemistry and refractory astrochemistry are subsequently presented. Based on our results, we also recommend the detection of two new closed-shell molecules, NH2CH2OH (aminomethanol) and CH2NH2+ (iminium ion), and two open-shell molecules, CONH2 (carbamyl radical) and HCONH (an isomer of carbamyl radical), in the ISM.
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Affiliation(s)
- Sorakayala Thripati
- Department of Chemistry, Indian Institute of Science Education and Research, Tirupati Andhra Pradesh 517507, India.,Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Tirupati, Andhra Pradesh 517507, India
| | - Raghunath O Ramabhadran
- Department of Chemistry, Indian Institute of Science Education and Research, Tirupati Andhra Pradesh 517507, India.,Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Tirupati, Andhra Pradesh 517507, India
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47
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Ramakrishnan S, Sagi R, Akerman M, Asscher M. Same-Energy UV Photons and Low-Energy Electrons Activating Methane and Ammonia Frozen in Amorphous Solid Water. J Phys Chem A 2021; 125:3432-3443. [PMID: 33871255 DOI: 10.1021/acs.jpca.1c00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
UV photons and low-energy electrons play an important role in the evolution of various molecules in the interstellar medium (ISM). Here, we examined the product molecule formation as a result of irradiation of 193 nm photons and 6.4 eV electrons (same energy under identical laboratory conditions) on D2O|CH4 + ND3|D2O sandwiched films deposited on Ru(0001) substrate at 25 K in ultrahigh vacuum as a model for processes in the ISM. Temperature-programmed desorption spectra performed following the irradiation revealed the signature of hydrazine and formamide product molecules. These molecules were, however, formed exclusively following the photons' irradiation. These results were compared with the products obtained from a D2O|CH4|D2O sample without ammonia, where deuterated formaldehyde was the dominant product, formed also by photons only. Our results indicate that the photon-induced activation of the cofrozen molecules within D2O occurs via direct (partial) dissociation of the host and embedded molecules, followed by sample annealing. The electron-induced activation occurs through a direct dissociative electron attachment mechanism. The results presented here suggest possible pathways to generate various C-N, C-O, C-C, N-O, and N-H bonds containing molecules in the ISM.
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Affiliation(s)
- Sujith Ramakrishnan
- Institute of Chemistry, Edmond J. Safra Campus, Givat-Ram The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Roey Sagi
- Institute of Chemistry, Edmond J. Safra Campus, Givat-Ram The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Michelle Akerman
- Institute of Chemistry, Edmond J. Safra Campus, Givat-Ram The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Micha Asscher
- Institute of Chemistry, Edmond J. Safra Campus, Givat-Ram The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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48
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Omar KA, Hasnaoui K, de la Lande A. First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation. Annu Rev Phys Chem 2021; 72:445-465. [PMID: 33878897 DOI: 10.1146/annurev-physchem-101419-013639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ionizing rays cause damage to genomes, proteins, and signaling pathways that normally regulate cell activity, with harmful consequences such as accelerated aging, tumors, and cancers but also with beneficial effects in the context of radiotherapies. While the great pace of research in the twentieth century led to the identification of the molecular mechanisms for chemical lesions on the building blocks of biomacromolecules, the last two decades have brought renewed questions, for example, regarding the formation of clustered damage or the rich chemistry involving the secondary electrons produced by radiolysis. Radiation chemistry is now meeting attosecond science, providing extraordinary opportunities to unravel the very first stages of biological matter radiolysis. This review provides an overview of the recent progress made in this direction, focusing mainly on the atto- to femto- to picosecond timescales. We review promising applications of time-dependent density functional theory in this context.
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Affiliation(s)
- Karwan Ali Omar
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France; .,Department of Chemistry, College of Education, University of Sulaimani, 41005 Kurdistan, Iraq
| | - Karim Hasnaoui
- High Performance Computing User Support Team, Institut du Développement et des Ressources en Informatique Scientifique (IDRIS), 91403 Orsay, France.,Maison de la Simulation, CNRS, Commissariat à l'Energie Atomique et aux Énergies Alternatives (CEA), Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France;
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49
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Jensen ET. Contrasting mechanisms for photodissociation of methyl halides adsorbed on thin films of C 6H 6 and C 6F 6. Phys Chem Chem Phys 2021; 23:3748-3760. [PMID: 33533786 DOI: 10.1039/d0cp05844k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanisms for photodissociation of methyl halides (CH3X, X = Cl, Br, I) have been studied for these molecules when adsorbed on thin films of C6H6 or C6F6 on copper single crystals, using time-of-flight spectroscopy with 248 nm and 193 nm light. For CH3Cl and CH3Br monolayers adsorbed on C6H6, two photodissociation pathways can be identified - neutral photodissociation similar to the gas-phase, and a dissociative electron attachment (DEA) pathway due to photoelectrons from the metal. The same methyl halides adsorbed on a C6F6 thin film display only neutral photodissociation, with the DEA pathway entirely absent due to intermolecular quenching via a LUMO-derived electronic band in the C6F6 thin film. For CH3I adsorbed on a C6F6 thin film, illumination with 248 nm light results in CH3 photofragments departing due to neutral photodissociation via the A-band absorption. When CH3I monolayers on C6H6 thin films are illuminated at the same wavelength, additional new photodissociation pathways are observed that are due to absorption in the molecular film with energy transfer leading to dissociation of the CH3I molecules adsorbed on top. The proposed mechanism for this photodissociation is via a charge-transfer complex for the C6H6 layer and adsorbed CH3I.
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Affiliation(s)
- E T Jensen
- Department of Physics, University of Northern BC, 3333 University Way, Prince George B.C., V2N 4Z9, Canada.
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50
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Barone V, Puzzarini C. Looking for the bricks of the life in the interstellar medium: The fascinating world of astrochemistry. EPJ WEB OF CONFERENCES 2020. [DOI: 10.1051/epjconf/202024600021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The discovery in the interstellar medium of molecules showing a certain degree of complexity, and in particular those with a prebiotic character, has attracted great interest. A complex chemistry takes place in space, but the processes that lead to the production of molecular species are a matter of intense discussion, the knowledge still being at a rather primitive stage. Debate on the origins of interstellar molecules has been further stimulated by the identification of biomolecular building blocks, such as nucleobases and amino acids, in meteorites and comets. Since many of the molecules found in space play a role in the chemistry of life, the issue of their molecular genesis and evolution might be related to the profound question of the origin of life itself. Understanding the underlying chemical processes, including the production, reactions and destruction of compounds, requires the concomitant study of spectroscopy, gas-phase reactivity, and heterogeneous processes on dust-grains. The aim of this contribution is to provide a general view of a complex and multifaceted challenge, while focusing on the role played by molecular spectroscopy and quantum-chemical computations. In particular, the derivation of the molecular spectroscopic features and the investigation of gas-phase formation routes of prebiotic species in the interstellar medium are addressed from a computational point of view.
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