1
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Schwickert D, Ruberti M, Kolorenč P, Przystawik A, Skruszewicz S, Sumfleth M, Braune M, Bocklage L, Carretero L, Czwalinna MK, Diaman D, Düsterer S, Kuhlmann M, Palutke S, Röhlsberger R, Rönsch-Schulenburg J, Toleikis S, Usenko S, Viefhaus J, Vorobiov A, Martins M, Kip D, Averbukh V, Marangos JP, Laarmann T. Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:064301. [PMID: 36389279 PMCID: PMC9646253 DOI: 10.1063/4.0000165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
In the present contribution, we use x-rays to monitor charge-induced chemical dynamics in the photoionized amino acid glycine with femtosecond time resolution. The outgoing photoelectron leaves behind the cation in a coherent superposition of quantum mechanical eigenstates. Delayed x-ray pulses track the induced coherence through resonant x-ray absorption that induces Auger decay. Temporal modulation of the Auger electron signal correlated with specific ions is observed, which is governed by the initial electronic coherence and subsequent vibronic coupling to nuclear degrees of freedom. In the time-resolved x-ray absorption measurement, we monitor the time-frequency spectra of the resulting many-body quantum wave packets for a period of 175 fs along different reaction coordinates. Our experiment proves that by measuring specific fragments associated with the glycine dication as a function of the pump-probe delay, one can selectively probe electronic coherences at early times associated with a few distinguishable components of the broad electronic wave packet created initially by the pump pulse in the cation. The corresponding coherent superpositions formed by subsets of electronic eigenstates and evolving along parallel dynamical pathways show different phases and time periods in the range of ( - 0.3 ± 0.1 ) π ≤ ϕ ≤ ( 0.1 ± 0.2 ) π and 18.2 - 1.4 + 1.7 ≤ T ≤ 23.9 - 1.1 + 1.2 fs. Furthermore, for long delays, the data allow us to pinpoint the driving vibrational modes of chemical dynamics mediating charge-induced bond cleavage along different reaction coordinates.
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Affiliation(s)
- David Schwickert
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marco Ruberti
- Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, United Kingdom
| | - Přemysl Kolorenč
- Charles University, Faculty of Mathematics and Physics, V Holesovickach 2, 180 00 Praha 8, Czech Republic
| | - Andreas Przystawik
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Malte Sumfleth
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Markus Braune
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Luis Carretero
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Dian Diaman
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Stefan Düsterer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marion Kuhlmann
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Steffen Palutke
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | | | - Sven Toleikis
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sergey Usenko
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Jens Viefhaus
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Anton Vorobiov
- Faculty of Electrical Engineering, Helmut Schmidt University, Holstenhofweg 85, 22043 Hamburg, Germany
| | - Michael Martins
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Detlef Kip
- Faculty of Electrical Engineering, Helmut Schmidt University, Holstenhofweg 85, 22043 Hamburg, Germany
| | - Vitali Averbukh
- Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, United Kingdom
| | - Jon P. Marangos
- Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, United Kingdom
| | - Tim Laarmann
- Author to whom correspondence should be addressed:
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2
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Bolognesi P, Avaldi L. Photoelectron-photoion(s) coincidence studies of molecules of biological interest. Phys Chem Chem Phys 2022; 24:22356-22370. [PMID: 36124990 DOI: 10.1039/d2cp03079a] [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
Photoelectron-photoion(s) coincidence, PEPICO, experiments with synchrotron radiation have become one of the most powerful tools to investigate dissociative photoionization thanks to their selectivity. In this paper their application to the study of molecular species of biological interest in the gas phase is reviewed. Some applications of PEPICO to the study of potential radiosensitizers, amino acids and small peptides and opportunities offered by the advent of novel methods for the production of beams of these molecules are discussed.
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Affiliation(s)
- P Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 00015 Monterotondo Scalo, Italy.
| | - L Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1, CP 10 00015 Monterotondo Scalo, Italy.
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3
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de Souza GLC, Peterson KA. A high level theory investigation on the lowest-lying ionization potentials of glycine (NH 2CH 2COOH). Phys Chem Chem Phys 2022; 24:17751-17758. [PMID: 35843227 DOI: 10.1039/d2cp02397k] [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
In this work, an investigation on the ionization potentials (IPs) of the glycine molecule (NH2CH2COOH) is presented. IPs ranging up to ∼20 eV were probed for each of the six conformations considered, with the referred threshold being chosen based on both: (i) the observations by recent photoelectron-photoion coincidence (PEPICO) experiments and (ii) the energy range of relevance to the modeling of other photo-induced processes (e.g., photoionization). For computing the IPs, the equation-of-motion ionization potential coupled-cluster with single and double excitations method (EOMIP-CCSD) was employed with large correlation consistent aug-cc-pVXZ and aug-cc-pCVXZ (X = D, T, and Q) basis sets. Extrapolation to the complete basis set limit and consideration of core electron correlation effects were also taken into account. Subsequently, the Feller-Peterson-Dixon (FPD) approach was used for considering all the contributions and to obtain accurate IPs. In addition, coupled-cluster with single and double excitations as well as perturbative triples, CCSD(T), was also used with the aug-cc-pVTZ basis set. When compared to each other, results obtained through the use of these approaches yielded excellent agreement. In general, the outcomes from the present work provide additional information to the insights gathered from the recent PEPICO experiments as well as accurate IPs for all 6 conformations of glycine using an approach based on high levels of theory. Hence, it is expected that other investigations focusing on photo-induced processes originating from NH2CH2COOH (for instance, the computational modeling of its photoionization) will be motivated for study in the future.
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Affiliation(s)
- Gabriel L C de Souza
- Departamento de Química, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, 78060-900, Brazil. .,Department of Chemistry, Washington State University, Pullman, Washington, 99164, USA
| | - Kirk A Peterson
- Department of Chemistry, Washington State University, Pullman, Washington, 99164, USA
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4
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Gopakumar G, Svensson PHW, Grånäs O, Brena B, Schwob L, Unger I, Saak CM, Timm M, Bülow C, Kubin M, Zamudio-Bayer V, Lau JT, von Issendorff B, Abid AR, Lindblad A, Danielsson E, Koerfer E, Caleman C, Björneholm O, Lindblad R. X-ray Induced Fragmentation of Protonated Cystine. J Phys Chem A 2022; 126:1496-1503. [PMID: 35213156 PMCID: PMC8919253 DOI: 10.1021/acs.jpca.1c10158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate site-specific X-ray induced fragmentation across the sulfur L-edge of protonated cystine, the dimer of the amino acid cysteine. Ion yield NEXAFS were performed in the gas phase using electrospray ionization (ESI) in combination with an ion trap. The interpretation of the sulfur L-edge NEXAFS spectrum is supported by Restricted Open-Shell Configuration Interaction (ROCIS) calculations. The fragmentation pathway of triply charged cystine ions was modeled by Molecular Dynamics (MD) simulations. We have deduced a possible pathway of fragmentation upon excitation and ionization of S 2p electrons. The disulfide bridge breaks for resonant excitation at lower photon energies but remains intact upon higher energy resonant excitation and upon ionization of S 2p. The larger fragments initially formed subsequently break into smaller fragments.
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Affiliation(s)
- Geethanjali Gopakumar
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Pamela H W Svensson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Oscar Grånäs
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Barbara Brena
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Lucas Schwob
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Isaak Unger
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Clara-Magdalena Saak
- Department of Physical Chemistry, University of Vienna, Währingerstraßze 42, 1090 Vienna, Austria
| | - Martin Timm
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.,Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, DE-10623 Berlin, Germany
| | - Christine Bülow
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.,Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany
| | - Markus Kubin
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany
| | - Vicente Zamudio-Bayer
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany
| | - J Tobias Lau
- Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.,Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany
| | - Bernd von Issendorff
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, DE-79104 Freiburg, Germany
| | - Abdul R Abid
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.,Nano and Molecular Systems Research Unit, Faculty of Science, University of Oulu, P.O. Box 3000, 90570 Oulu, Finland
| | - Andreas Lindblad
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Emma Danielsson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Ebba Koerfer
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, DE-22607 Hamburg, Germany
| | - Olle Björneholm
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Rebecka Lindblad
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.,Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, DE-12489 Berlin, Germany.,Department of Physics, Lund University, Box 118, SE-22100 Lund, Sweden.,Department of Chemistry - Ångström Laboratory, Uppsala University, Box 538, SE-75121 Uppsala, Sweden
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5
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Khalili F, Vafaee M, Shokri B. Attosecond charge migration following oxygen K-shell ionization in DNA bases and base pairs. Phys Chem Chem Phys 2021; 23:23005-23013. [PMID: 34611693 DOI: 10.1039/d1cp02920g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Core ionization of DNA begins a cascade of events which could lead to cellular inactivation or death. The created core-hole following an impulse inner-shell ionization of molecules naturally decays in the auger timescale. We simulated charge migration (CM) phenomena following an impulsive core ionization of individual DNA bases at the oxygen K-edge which occurs before Auger decay of the oxygen. Our approach is based on real-time time dependent density functional theory (RT-TDDFT). It is shown that the pronounced hole fluctuation observed around bonds of the initial core-hole results in various valence orbital migrations. Also, the same photo-core-ionized dynamics is studied for the related base pairs. We investigate the role of base pairing and H-bonding interactions in the attosecond CM dynamics. In particular, the creation of a core-hole in the oxygen involved in H-bonding leads to an enhancement of charge migration relative to the respective single bases. Importantly, the hole oscillation of the adenine-thymine base pair upon creation of a core-hole at the oxygen, which does not contribute to the donor-acceptor interactions (not H-bonded), decreases compared to the single thymine base. Understanding the detailed dynamics of the localized core-hole initiating CM process would open the way for chemically controlling DNA damage/repair in the future.
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Affiliation(s)
- Fatemeh Khalili
- Department of Physics, Shahid Beheshti University, Velenjak, Tehran 19839, Iran.
| | - Mohsen Vafaee
- Department of Chemistry, Tarbiat Modares University, P. O. Box 14115-175, Tehran, Iran.
| | - Babak Shokri
- Department of Physics, Shahid Beheshti University, Velenjak, Tehran 19839, Iran. .,Laser-Plasma Research Institute, Shahid Beheshti University, Velenjak, Tehran 19839, Iran
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6
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Itälä E, Myllynen H, Niskanen J, González-Vázquez J, Wang Y, Ha DT, Denifl S, Kukk E. Controlling NO Production Upon Valence Ionization of Nitroimidazoles. J Phys Chem A 2019; 123:3074-3079. [PMID: 30807166 DOI: 10.1021/acs.jpca.8b11342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitroimidazole exhibits a remarkable regioselective fragmentation subsequent to valence ionization, which is characterized by ejection of NO. As NO is also considered to be an effective radiosensitizer, we investigated its production efficiency as a function of isomeric composition (the site of the NO2 nitro group). We observe strong dependence in the 8.6-15 eV binding energy range, and moreover, that the production of NO can be effectively suppressed by methylation of nitroimidazole. This behavior can be understood by modification of the valence electronic structure with respect to the dissociation threshold, which gives rise to varying effective density of dissociative states. We find the NO yield to follow the efficiency of the nitroimidazole dervivatives as radiosensitizers, found in preclinical studies.
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Affiliation(s)
- Eero Itälä
- Department of Physics and Astronomy , University of Turku , Turku FI-20014 , Finland
| | - Hanna Myllynen
- Department of Physics and Astronomy , University of Turku , Turku FI-20014 , Finland
| | - Johannes Niskanen
- Department of Physics and Astronomy , University of Turku , Turku FI-20014 , Finland
| | - Jesús González-Vázquez
- Departamento de Química, Módulo 13 , Universidad Autónoma de Madrid , 28049 Madrid , Spain
| | - Yang Wang
- Departamento de Química, Módulo 13 , Universidad Autónoma de Madrid , 28049 Madrid , Spain
| | - Dang Trinh Ha
- Department of Physics and Astronomy , University of Turku , Turku FI-20014 , Finland
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik and Center of Molecular Biosciences , Leopold Franzens Universität Innsbruck , Technikerstrasse 25 , 6020 Innsbruck , Austria
| | - Edwin Kukk
- Department of Physics and Astronomy , University of Turku , Turku FI-20014 , Finland
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7
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Itälä E, Granroth S, Ha D, Kooser K, Levola H, Rachlew E, Tanzer K, Kukk E. Fragmentation of imidazole, pyrimidine and purine induced by core ionization: Significance of small-scale chemical environment. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Takahashi O, Kooser K, Ha DT, Myllynen H, Laksman J, Rachlew E, Kukk E. Site-selective bond scission of methylbenzoate following core excitation. Phys Chem Chem Phys 2018; 20:9591-9599. [DOI: 10.1039/c7cp08428e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Relative ion yield of methylbenzoate depending on photon energy show site-specificity.
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Affiliation(s)
- Osamu Takahashi
- Institute for Sustainable Science and Development
- Hiroshima University
- Higashi-Hiroshima 739-8526
- Japan
| | - Kuno Kooser
- Department of Physics and Astronomy
- University of Turku
- FIN-20014 Turku
- Finland
- Institute of Physics
| | - Dang Trinh Ha
- Institute for Sustainable Science and Development
- Hiroshima University
- Higashi-Hiroshima 739-8526
- Japan
- Department of Physics and Astronomy
| | - Hanna Myllynen
- Department of Physics and Astronomy
- University of Turku
- FIN-20014 Turku
- Finland
| | | | - Elisabeth Rachlew
- Royal Institute of Technology KTH
- Physics Department
- S-10691 Stockholm
- Sweden
| | - Edwin Kukk
- Department of Physics and Astronomy
- University of Turku
- FIN-20014 Turku
- Finland
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9
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Chiarinelli J, Bolognesi P, Domaracka A, Rousseau P, Castrovilli MC, Richter R, Chatterjee S, Wang F, Avaldi L. Insights into the dissociative ionization of glycine by PEPICO experiments. Phys Chem Chem Phys 2018; 20:22841-22848. [PMID: 30151535 DOI: 10.1039/c8cp03473g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fragmentation of glycine (NH2CH2COOH) has been studied by photoelectron–photoion coincidence, PEPICO, experiments at 60 eV photon energy.
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Affiliation(s)
- Jacopo Chiarinelli
- Dipartimento di Scienze, Università di Roma Tre
- Roma
- Italy
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1
- Monterotondo Scalo
| | - Paola Bolognesi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1
- Monterotondo Scalo
- Italy
| | - Alicja Domaracka
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP
- 14000 Caen
- France
| | - Patrick Rousseau
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP
- 14000 Caen
- France
| | | | - Robert Richter
- Molecular Modelling Discovery Laboratory, Department of Chemistry and Biotechnology
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne
- Vic 3122
- Australia
| | | | - Feng Wang
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163.5
- Basovizza
- Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura della Materia, Area della Ricerca di Roma 1
- Monterotondo Scalo
- Italy
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10
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Abstract
Hydrogen bond complexation between glycine and THF and between glycine and water involving four lowest-energy glycine conformers have been studied. The complexes have been investigated in the gas phase at the ab initio molecular orbital theory (MP2) with aug-cc-pVDZ basis set and density functional theory (B3LYP) with aug-cc-pVTZ basis set. Bader’s theory of atoms in molecules (AIM), natural bond orbital (NBO), and symmetry adapted perturbation theory (SAPT) analyses are employed to elucidate the interaction characteristics in the complexes. The premise that the hydrogen bond donor ability of the O–H group of the carboxyl group dominates the interaction between glycine and THF and between glycine and water is confirmed. It is found that in comparison with water, THF binds more strongly to glycine. The quantum studies indicate that contribution of N–H···O and C–H···O hydrogen bonds in the complexes, although lower in magnitude to O–H···O interactions, play an important role in the stability of complexes. The blue and red shifts in the stretching frequencies of the hydrogen bond donors X–H (X = O, C, N) have also been related to stabilization energies. Decomposition of the stabilization energy based on the SAPT method clearly indicates the dominant role of the electrostatic interactions in all the complexes under study; however, induction and dispersion interaction terms are relatively higher in glycine–THF complexes.
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Affiliation(s)
- Damanjit Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
| | - Geetanjali Chopra
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
| | - Rajinder Kaur
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
- Department of Chemistry, Guru Nanak Dev University, Amritsar 143005, India
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11
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Itälä E, Levola H, Ha DT, Kooser K, Rachlew E, Kukk E. Photofragmentation of Serine Following C 1s Core Ionization—Comparison with Cysteine. J Phys Chem A 2016; 120:5419-26. [DOI: 10.1021/acs.jpca.6b02554] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eero Itälä
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Helena Levola
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Dang Trinh Ha
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
- Departamento
de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Kuno Kooser
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
- Institute
of Physics, University of Tartu, 50411, Tartu, Estonia
| | - Elisabeth Rachlew
- Physics
Department, Royal Institute of Technology KTH, S-10691 Stockholm, Sweden
| | - Edwin Kukk
- Department
of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
- Turku University Centre for Materials and Surfaces (MatSurf), FIN-20014 Turku, Finland
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12
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Nhlabatsi ZP, Bhasi P, Sitha S. Possible interstellar formation of glycine through a concerted mechanism: a computational study on the reaction of CH2NH, CO2 and H2. Phys Chem Chem Phys 2016; 18:20109-17. [DOI: 10.1039/c5cp07124k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Computational studies on the reaction of CH2NH, CO2 and H2 show the possible interstellar formation of glycine in both hot-cores and cold interstellar clouds.
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Affiliation(s)
- Zanele P. Nhlabatsi
- Department of Chemistry
- University of Johannesburg
- Auckland Park
- South Africa 2006
| | - Priya Bhasi
- Department of Chemistry
- University of Johannesburg
- Auckland Park
- South Africa 2006
| | - Sanyasi Sitha
- Department of Chemistry
- University of Johannesburg
- Auckland Park
- South Africa 2006
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13
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Li Z, Vendrell O, Santra R. Ultrafast Charge Transfer of a Valence Double Hole in Glycine Driven Exclusively by Nuclear Motion. PHYSICAL REVIEW LETTERS 2015; 115:143002. [PMID: 26551809 DOI: 10.1103/physrevlett.115.143002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Indexed: 06/05/2023]
Abstract
We explore theoretically the ultrafast transfer of a double electron hole between the functional groups of glycine after K-shell ionization and subsequent Auger decay. Although a large energy gap of about 15 eV initially exists between the two electronic states involved and coherent electronic dynamics play no role in the hole transfer, we find that the double hole is transferred within 3 to 4 fs between both functional ends of the glycine molecule driven solely by specific nuclear displacements and non-Born-Oppenheimer effects. The nuclear displacements along specific vibrational modes are of the order of 15% of a typical chemical bond between carbon, oxygen, and nitrogen atoms and about 30% for bonds involving hydrogen atoms. The time required for the hole transfer corresponds to less than half a vibrational period of the involved nuclear modes. This finding challenges the common wisdom that nuclear dynamics of the molecular skeleton are unimportant for charge transfer processes at the few-femtosecond time scale and shows that they can even play a prominent role. It also indicates that in x-ray imaging experiments, in which ionization is unavoidable, valence electron redistribution caused by nuclear dynamics might be much faster than previously anticipated. Thus, non-Born-Oppenheimer effects may affect the apparent electron densities extracted from such measurements.
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Affiliation(s)
- Zheng Li
- Center for Free-Electron Laser Science, DESY, Notkestraß e 85, D-22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Oriol Vendrell
- Center for Free-Electron Laser Science, DESY, Notkestraß e 85, D-22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestraß e 85, D-22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany
- Department of Physics, University of Hamburg, Jungiusstraße 9, D-20355 Hamburg, Germany
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Itälä E, Kooser K, Rachlew E, Levola H, Ha DT, Kukk E. Gas-phase study on uridine: Conformation and X-ray photofragmentation. J Chem Phys 2015; 142:194303. [PMID: 26001457 DOI: 10.1063/1.4919878] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fragmentation of RNA nucleoside uridine, induced by carbon 1s core ionization, has been studied. The measurements by combined electron and ion spectroscopy have been performed in gas phase utilizing synchrotron radiation. As uridine is a combination of d-ribose and uracil, which have been studied earlier with the same method, this study also considers the effect of chemical environment and the relevant functional groups. Furthermore, since in core ionization the initial core hole is always highly localized, charge migration prior to fragmentation has been studied here. This study also demonstrates the destructive nature of core ionization as in most cases the C 1s ionization of uridine leads to concerted explosions producing only small fragments with masses ≤43 amu. In addition to fragmentation patterns, we found out that upon evaporation the sugar part of the uridine molecule attains hexagonal form.
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Affiliation(s)
- Eero Itälä
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Kuno Kooser
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Elisabeth Rachlew
- Royal Institute of Technology KTH, Physics department, S-10691 Stockholm, Sweden
| | - Helena Levola
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Dang Trinh Ha
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
| | - Edwin Kukk
- Department of Physics and Astronomy, University of Turku, FIN-20014 Turku, Finland
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15
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Laksman J, Kooser K, Levola H, Itälä E, Ha DT, Rachlew E, Kukk E. Dissociation pathways in the cysteine dication after site-selective core ionization. J Phys Chem B 2014; 118:11688-95. [PMID: 25233490 DOI: 10.1021/jp508161s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A photoelectron-ion-ion coincidence experiment has been carried out on the amino acid molecule cysteine after core-ionization of the O 1s, N 1s, C 1s, and S 2p orbitals. A number of different dissociation channels have been identified. Some of them show strong site-selective dependence that can be attributed to a combination of nuclear motion in the core-ionized state and Auger processes that populate different final electronic states in the dication.
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Affiliation(s)
- J Laksman
- Department of Physics, University of Oulu , P.O. Box 3000, FIN-90014 Oulu, Finland
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