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Bhavsar N, Shastri A, Vinodkumar PC, Vinodkumar M. Electron impact scattering and electronic excitation in glycolaldehyde: The first ever detected sugar in space. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123397. [PMID: 37716041 DOI: 10.1016/j.saa.2023.123397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/16/2023] [Accepted: 09/10/2023] [Indexed: 09/18/2023]
Abstract
Detailed theoretical investigations on structural, spectroscopic and electron scattering cross sections of glycolaldehyde, the first ever detected sugar in space are reported in this work. Spectroscopic calculations are performed on the ground and excited states of glycolaldehyde using density functional theory (DFT) and time-dependent density functional theory (TDDFT), respectively. The optimized geometrical parameters and vibrational spectrum are in good agreement with the earlier reported work. Vertical excited state (VES) energies at the TDDFT/B3LYP/aug-cc-PVQZ level of theory along with detailed assignments are reported up to 30 transitions. The TDDFT predicted Rydberg series energies are compared with the Rydberg series of glycolaldehyde converging to its first IP, computed using the standard Rydberg formula and are found to be in good agreement. In the absence of sufficient experimental data on excited states of glycolaldehyde, the theoretical results are validated by comparison of VES calculations performed at the same level of theory with the available experimental data for an analogous molecule viz. acetaldehyde. Triplet excited-state energies for glycolaldehyde are reported here for the first time. Electron impact cross section calculations in the energy range 0.1 to 20 eV are carried out using ab-initio R-matrix method. We have detected one π* shape resonance in all the three models viz. SE, SEP and CC, which may also lead to a possible fragmentation channel wherein a hydrogen atom is removed from the molecule forming a glycolaldehyde dehydrogenated anionic radical (C2H3O2-). The π* shape resonance is correlated with the corresponding molecular orbital electronic structure calculations. Additionally, differential, electronic excitation, ionization and total cross sections are reported here for the first time.
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Affiliation(s)
- Nirali Bhavsar
- Government Science College, Varachha, Surat 395006, Gujarat, India; V.P. & R.P.T.P. Science College, Vallabh Vidyanagar 388120, Gujarat, India
| | - Aparna Shastri
- Atomic & Molecular Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - P C Vinodkumar
- P. D. Patel Institute of Applied Science, CHARUSAT, Changa 388421, Gujarat, India
| | - Minaxi Vinodkumar
- V.P. & R.P.T.P. Science College, Vallabh Vidyanagar 388120, Gujarat, India.
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2
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Ziegler B, Rauhut G. Localized Normal Coordinates in Accurate Vibrational Structure Calculations: Benchmarks for Small Molecules. J Chem Theory Comput 2019; 15:4187-4196. [DOI: 10.1021/acs.jctc.9b00381] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Ziegler
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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3
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Dargelos A, Karamanis P, Pouchan C. Ab-initio calculations of the IR spectra of dicyanodiacetylene (C6N2) beyond the harmonic approximation. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.03.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Dargelos A, Karamanis P, Pouchan C. Theoretical Investigation of the Infrared Spectrum of 5‐Bromo‐2,4‐pentadiynenitrile from a CCSD(T)/B3LYP Anharmonic Potential. Chemphyschem 2018; 19:822-826. [DOI: 10.1002/cphc.201701322] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/09/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Alain Dargelos
- CNRS/Université Pau & Pays AdourInstitut Des Sciences Analytiques Et De Physico-Chimie Pour L'environnement Et Les Materiaux, Umr5254 64000 Pau France
| | - Panaghiotis Karamanis
- CNRS/Université Pau & Pays AdourInstitut Des Sciences Analytiques Et De Physico-Chimie Pour L'environnement Et Les Materiaux, Umr5254 64000 Pau France
| | - Claude Pouchan
- CNRS/Université Pau & Pays AdourInstitut Des Sciences Analytiques Et De Physico-Chimie Pour L'environnement Et Les Materiaux, Umr5254 64000 Pau France
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5
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Duvernay F, Butscher T, Chiavassa T, Coussan S. IR induced photochemistry of glycolaldehyde in nitrogen matrix. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Baiardi A, Stein CJ, Barone V, Reiher M. Vibrational Density Matrix Renormalization Group. J Chem Theory Comput 2017; 13:3764-3777. [DOI: 10.1021/acs.jctc.7b00329] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alberto Baiardi
- Scuola Normale
Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Christopher J. Stein
- Laboratorium
für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Vincenzo Barone
- Scuola Normale
Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Markus Reiher
- Laboratorium
für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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7
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Wang P, Hu Y, Zhan H, Chen J. Gas-phase conformational preference of the smallest saccharide (glycolaldehyde) and its hydrated complexes with bridged hydrogen bonding. RSC Adv 2017. [DOI: 10.1039/c6ra26965f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Glycoaldehyde (GA, HOCH2CHO) is the simplest sugar unit of the carbohydrates and the only sugar to have been detected in interstellar space to date.
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Affiliation(s)
- Pengchao Wang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Huaqi Zhan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
| | - Jiaxin Chen
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science
- College of Biophotonics
- South China Normal University
- Guangzhou 510631
- P. R. China
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8
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Sibaev M, Crittenden DL. An efficient and numerically stable procedure for generating sextic force fields in normal mode coordinates. J Chem Phys 2016; 144:214107. [DOI: 10.1063/1.4953080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. Sibaev
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - D. L. Crittenden
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand
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9
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Civiš S, Szabla R, Szyja BM, Smykowski D, Ivanek O, Knížek A, Kubelík P, Šponer J, Ferus M, Šponer JE. TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth. Sci Rep 2016; 6:23199. [PMID: 26979666 PMCID: PMC4793247 DOI: 10.1038/srep23199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/24/2016] [Indexed: 01/05/2023] Open
Abstract
Recent synthetic efforts aimed at reconstructing the beginning of life on our planet point at the plausibility of scenarios fueled by extraterrestrial energy sources. In the current work we show that beyond nucleobases the sugar components of the first informational polymers can be synthesized in this way. We demonstrate that a laser-induced high-energy chemistry combined with TiO2 catalysis readily produces a mixture of pentoses, among them ribose, arabinose and xylose. This chemistry might be highly relevant to the Late Heavy Bombardment period of Earth’s history about 4–3.85 billion years ago. In addition, we present an in-depth theoretical analysis of the most challenging step of the reaction pathway, i.e., the TiO2-catalyzed dimerization of formaldehyde leading to glycolaldehyde.
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Affiliation(s)
- Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Bartłomiej M Szyja
- Inorganic Materials Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Division of Fuels Chemistry and Technology, Faculty of Chemistry, Wrocław University of Technology, Gdańska 7/9, 50-344 Wrocław, Poland
| | - Daniel Smykowski
- Faculty of Mechanical and Power Engineering, Wrocław University of Technology, Ul. Wybrzeże Wyspiańskiego 27, 50-370, Wrocław
| | - Ondřej Ivanek
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Antonín Knížek
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Petr Kubelík
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic.,Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21 Prague 8, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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10
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Cuisset A, Gruet S, Pirali O, Chamaillé T, Mouret G. Synchrotron FT-FIR spectroscopy of nitro-derivatives vapors: new spectroscopic signatures of explosive taggants and degradation products. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 132:838-845. [PMID: 24975521 DOI: 10.1016/j.saa.2014.05.083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 04/12/2014] [Accepted: 05/25/2014] [Indexed: 06/03/2023]
Abstract
We report on the first successful rovibrational study of gas phase mononitrotoluene and dinitrotoluene in the TeraHertz/Far-Infrared (THz/FIR) spectral domain. Using the AILES beamline of the synchrotron SOLEIL and a Fourier Transform spectrometer connected to multipass cells, the low-energy vibrational cross-sections of the different isomers of mononitrotoluene have been measured and compared to calculated spectra with the density functional theory including the anharmonic contribution. The active FIR modes of 2,4 and 2,6 dinitrotoluene have been assigned to the vibrational bands measured by Fourier Transform FIR spectroscopy of the gas-phase molecular cloud produced in an evaporating/recondensating system. This study highlights the selectivity of gas phase THz/FIR spectroscopy allowing an unambiguous recognition and discrimination of nitro-aromatic compounds used as explosive taggants.
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Affiliation(s)
- Arnaud Cuisset
- Laboratoire de Physico-Chimie de l'Atmosphère, EA-4493, Université du Littoral - Côte d'Opale, 59140 Dunkerque, France.
| | - Sébastien Gruet
- Synchrotron SOLEIL, L'orme des Merisiers, Saint-Aubin - BP48, 91192 Gif-sur-Yvette, France
| | - Olivier Pirali
- Synchrotron SOLEIL, L'orme des Merisiers, Saint-Aubin - BP48, 91192 Gif-sur-Yvette, France; Institut des Sciences Moléculaires d'Orsay, UMR-8214 CNRS, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Thierry Chamaillé
- Institut des Sciences Moléculaires d'Orsay, UMR-8214 CNRS, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Gaël Mouret
- Laboratoire de Physico-Chimie de l'Atmosphère, EA-4493, Université du Littoral - Côte d'Opale, 59140 Dunkerque, France
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11
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Chin W, Chevalier M, Thon R, Pollet R, Ceponkus J, Crépin C. Photochemistry of glycolaldehyde in cryogenic matrices. J Chem Phys 2014; 140:224319. [DOI: 10.1063/1.4881605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Mizukami W, Tew DP. A second-order multi-reference perturbation method for molecular vibrations. J Chem Phys 2013; 139:194108. [DOI: 10.1063/1.4830100] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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13
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Gamboa A, Rapacioli M, Spiegelman F. Automatic Differentiation of the Energy within Self-consistent Tight-Binding Methods. J Chem Theory Comput 2013; 9:3900-7. [PMID: 26592385 DOI: 10.1021/ct400214b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We present and implement the calculation of analytical n-order geometric derivatives of the energy obtained within the framework of the density functional based tight binding approach. The use of automatic differentiation techniques allows a unique implementation for the calculation of derivatives up to any order providing that the computational facilities are sufficient. As first applications, the derivatives are used to build an analytical potential energy surface around the optimized geometry of acetylene. We also discuss the relevant anharmonic contributions that have to be considered when building such an analytical potential energy surface for acetylene, ethylene, ethane, benzene, and naphtalene.
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Affiliation(s)
- Antonio Gamboa
- Université de Toulouse , UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, 118 Route de Narbonne, F-31062 Toulouse, France.,CNRS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC , F-31062 Toulouse, France
| | - Mathias Rapacioli
- Université de Toulouse , UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, 118 Route de Narbonne, F-31062 Toulouse, France.,CNRS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC , F-31062 Toulouse, France
| | - Fernand Spiegelman
- Université de Toulouse , UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, 118 Route de Narbonne, F-31062 Toulouse, France.,CNRS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC , F-31062 Toulouse, France
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14
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Benidar A, Georges R, Guillemin J, Mó O, Yáñez M. Infrared Spectra of Cyanoacetaldehyde (NCCH
2
CHO): A Potential Prebiotic Compound of Astrochemical Interest. Chemphyschem 2013; 14:2764-71. [DOI: 10.1002/cphc.201300354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Abdessamad Benidar
- Institut de Physique de Rennes, CNRS UMR 6251, Université de Rennes 1, 35042 Rennes (France)
| | - Robert Georges
- Institut de Physique de Rennes, CNRS UMR 6251, Université de Rennes 1, 35042 Rennes (France)
| | - Jean‐Claude Guillemin
- Institut des Sciences Chimiques de Rennes, École Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7 (France)
| | - Otilia Mó
- Departamento de Quimica, Modulo 13, Universidad Autonoma de Madrid, Campus de Excelencia UAM‐CSIC, Cantoblanco, 28049‐Madrid (Spain)
| | - Manuel Yáñez
- Departamento de Quimica, Modulo 13, Universidad Autonoma de Madrid, Campus de Excelencia UAM‐CSIC, Cantoblanco, 28049‐Madrid (Spain)
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Altnöder J, Lee JJ, Otto KE, Suhm MA. Molecular recognition in glycolaldehyde, the simplest sugar: two isolated hydrogen bonds win over one cooperative pair. ChemistryOpen 2012; 1:269-75. [PMID: 24551516 PMCID: PMC3922484 DOI: 10.1002/open.201200031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Indexed: 11/19/2022] Open
Abstract
Carbohydrates are used in nature as molecular recognition tools. Understanding their conformational behavior upon aggregation helps in rationalizing the way in which cells and bacteria use sugars to communicate. Here, the simplest α-hydroxy carbonyl compound, glycolaldehyde, was used as a model system. It was shown to form compact polar C2-symmetric dimers with intermolecular O–H⋅⋅⋅O=C bonds, while sacrificing the corresponding intramolecular hydrogen bonds. Supersonic jet infrared (IR) and Raman spectra combined with high-level quantum chemical calculations provide a consistent picture for the preference over more typical hydrogen bond insertion and addition patterns. Experimental evidence for at least one metastable dimer is presented. A rotational spectroscopy investigation of these dimers is encouraged, also in view of astrophysical searches. The binding motif competition of aldehydic sugars might play a role in chirality recognition phenomena of more complex derivatives in the gas phase.
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Affiliation(s)
- Jonas Altnöder
- Institut für Physikalische Chemie, Universität Göttingen Tammannstr. 6, 37077 Göttingen (Germany) E-mail:
| | - Juhyon J Lee
- Institut für Physikalische Chemie, Universität Göttingen Tammannstr. 6, 37077 Göttingen (Germany) E-mail:
| | - Katharina E Otto
- Institut für Physikalische Chemie, Universität Göttingen Tammannstr. 6, 37077 Göttingen (Germany) E-mail:
| | - Martin A Suhm
- Institut für Physikalische Chemie, Universität Göttingen Tammannstr. 6, 37077 Göttingen (Germany) E-mail:
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