1
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Martinez-Fernandez L, Improta R. The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study. Photochem Photobiol 2024; 100:314-322. [PMID: 37409732 DOI: 10.1111/php.13832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time-dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady-state infrared and absorption spectra of a protonated cytidine (CH+ ), and predict that an easily accessible non-radiative deactivation route exists for the spectroscopic state, explaining its sub-ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out-of-plane motion of the hydrogen substituents of the CC double bond, the so-called ethylenic conical intersection typical of cytidine and other pyrimidine bases. This deactivation route is operative for the two bases forming an hemiprotonated cytidine base pair, [CH·C]+ , the building blocks of I-motif secondary structures, whereas interbase processes play a minor role. N3 protonation disfavors instead the nπ* transitions, associated with the long-living components of cytidine photoactivated dynamics.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Sciences (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Madrid, Spain
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Naples, Italy
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2
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Molina FL, Jara-Toro RA, Noble JA, Dedonder-Lardeux C, Jouvet C, Pino GA. Photodetachment of Deprotonated R-Mandelic Acid: The Role of Proton Delocalization on the Radical Stability. Chemphyschem 2023; 24:e202200324. [PMID: 36000956 DOI: 10.1002/cphc.202200324] [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: 05/10/2022] [Revised: 08/23/2022] [Indexed: 01/05/2023]
Abstract
The photodetachment and stability of R-Mandelate, the deprotonated form of the R-Mandelic acid, was investigated by observing the neutral species issued from either simple photodetachment or dissociative photodetachment in a cold anions set-up. R-Mandalate has the possibility to form an intramolecular ionic hydrogen-bond between adjacent hydroxyl and carboxylate groups. The potential energy surface along the proton transfer (PT) coordinate between both groups (O- …H+ …- OCO) features a single local minima, with the proton localized on the O- group (OH…- OCO). However, the structure with the proton localized on the - OCO group (O- …HOCO) is also observed because it falls within the extremity of the vibrational wavefunction of the OH…- OCO isomer along the PT coordinate. The stability of the corresponding radicals, produced upon photodetachment, is strongly dependent on the position of the proton in the anion: the radicals produced from the OH…- OCO isomer decarboxylate without barrier, while the radicals produced from the O- …HOCO isomer are stable.
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Affiliation(s)
- Franco L Molina
- INFIQC: Instituto de Investigaciones en Fisicoquímica de Córdoba (CONICET - UNC) -, Haya de la Torre s/n, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba -, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Centro Láser de Ciencias Moleculares -, Universidad Nacional de Córdoba, Haya de la Torre s/n, Pabellón Argentina, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Rafael A Jara-Toro
- INFIQC: Instituto de Investigaciones en Fisicoquímica de Córdoba (CONICET - UNC) -, Haya de la Torre s/n, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba -, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Centro Láser de Ciencias Moleculares -, Universidad Nacional de Córdoba, Haya de la Torre s/n, Pabellón Argentina, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Jennifer A Noble
- Physique des Interactions Ioniques et Moléculaires (PIIM), CNRS, Aix-Marseille Université, 13397, Marseille, France
| | - Claude Dedonder-Lardeux
- Physique des Interactions Ioniques et Moléculaires (PIIM), CNRS, Aix-Marseille Université, 13397, Marseille, France
| | - Christophe Jouvet
- Physique des Interactions Ioniques et Moléculaires (PIIM), CNRS, Aix-Marseille Université, 13397, Marseille, France
| | - Gustavo A Pino
- INFIQC: Instituto de Investigaciones en Fisicoquímica de Córdoba (CONICET - UNC) -, Haya de la Torre s/n, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba -, Haya de la Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.,Centro Láser de Ciencias Moleculares -, Universidad Nacional de Córdoba, Haya de la Torre s/n, Pabellón Argentina, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
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3
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Tureček F. UV-vis spectroscopy of gas-phase ions. MASS SPECTROMETRY REVIEWS 2023; 42:206-226. [PMID: 34392556 DOI: 10.1002/mas.21726] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Photodissociation action spectroscopy has made a great progress in expanding investigations of gas-phase ion structures. This review deals with aspects of gas-phase ion electronic excitations that result in wavelength-dependent dissociation and light emission via fluorescence, chiefly covering the ultraviolet and visible regions of the spectrum. The principles are briefly outlined and a few examples of instrumentation are presented. The main thrust of the review is to collect and selectively present applications of UV-vis action spectroscopy to studies of stable gas-phase ion structures and combinations of spectroscopy with ion mobility, collision-induced dissociation, and ion-ion reactions leading to the generation of reactive intermediates and electronic energy transfer.
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Affiliation(s)
- František Tureček
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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4
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Liu Y, Ma C, Nováková G, Marek A, Tureček F. Charge-Tagged Nucleosides in the Gas Phase: UV-Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals. J Phys Chem A 2021; 125:6096-6108. [PMID: 34240862 DOI: 10.1021/acs.jpca.1c03477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cytidine ribonucleosides were furnished at O5' with fixed-charge 6-trimethylammoniumhexan-1-aminecarbonyl tags and studied by UV-vis photodissociation action spectroscopy in the gas phase to probe isolated nucleobase chromophores in their neutral, protonated, and hydrogen-adduct radical forms. The action spectrum of the doubly charged cytidine conjugate showed bands at 310 and 270 nm that were assigned to the N3- and O2-protonated cytosine tautomers formed by electrospray, respectively. In contrast, cytidine conjugates coordinated to dibenzo-18-crown-6-ether (DBCE) in a noncovalent complex were found to strongly favor protonation at N3, forming a single-ion tautomer. This allowed us to form cytidine N3-H radicals by electron transfer dissociation of the complex and study their action spectra. Cytidine radicals showed only very weak absorption in the visible region of the spectrum for dipole-disallowed transitions to the low (A and B) excited states. The main bands were observed at 360, 300, and 250 nm that were assigned with the help of theoretical vibronic spectra obtained by time-dependent density functional theory calculations of multiple (>300) radical vibrational configurations. Collision-induced dissociations of cytidine radicals proceeded by major cleavage of the N1-C1' glycosidic bond leading to loss of cytosine and competitive loss of N3-hydrogen atom. These dissociations were characterized by calculations of transition-state structures and energies using combined Born-Oppenheimer molecular dynamics and DFT calculations. Overall, cytidine radicals were found to be kinetically and thermodynamically more stable than previously reported analogous adenosine and guanosine radicals.
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Affiliation(s)
- Yue Liu
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Congcong Ma
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - Gabriela Nováková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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5
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Cruz-Ortiz AF, Molina FL, Maitre P, Pino GA. Guanine Tautomerism in Ionic Complexes with Ag + Investigated by IRMPD Spectroscopy and Mass Spectrometry. J Phys Chem B 2021; 125:7137-7146. [PMID: 34165305 DOI: 10.1021/acs.jpcb.1c03796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we present the IRMPD spectra of three ionic complexes between guanine (G) and silver (Ag+): [GAg-H2O]+, [GAgG]+ produced in the electrospray ionization source of the mass spectrometer, and [GAg]+ produced by collision induced dissociation of the [GAgG]+ complex. On the basis of the comparison of theoretically calculated IR spectra, we show that there are two isomers of each complex containing two different keto-amino (KA) tautomers of G (GKA(1,9) and GKA(1,7)). The observed isomers are the most stable structures in aqueous solution, and their experimentally estimated relative populations are in better agreement with the calculated relative populations in solution than in the gas phase, both at 298 K. We concluded that these observations suggest that GKA(1,9) and GKA(1,7) coexist in solution according to previous theoretical reports (Colominas, C.; et al. J. Am. Chem. Soc. 1996, 118, 6811). We were unable to find any evidence of the presence of the GEA(9), GKA(3,7), GKA(3,9), or GKA(7,9), whose relative stabilities in solution are strongly dependent on the theoretical method used to account for the solvent effect (Hanus, M.; et al. J. Am. Chem. Soc. 2003, 125, 7678).
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Affiliation(s)
- Andrés F Cruz-Ortiz
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Franco L Molina
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Philippe Maitre
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - Gustavo A Pino
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
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6
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Cruz‐Ortiz AF, Taccone MI, Maitre P, Rossa M, Pino GA. On the Interaction between Deprotonated Cytosine [C
(−H)
]
−
and Ba
2+
: Infrared Multiphoton Spectroscopy and Dynamics. Chemphyschem 2020; 21:2571-2582. [DOI: 10.1002/cphc.202000696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/21/2020] [Indexed: 01/11/2023]
Affiliation(s)
- Andrés F. Cruz‐Ortiz
- INFIQC (CONICET-UNC) Ciudad Universitaria Pabellón Argentina 5000 Córdoba Argentina
- Departamento de Fisicoquímica Fac. de Ciencias Químicas Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
- Centro Láser de Ciencias Moleculares Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
| | - Martín I. Taccone
- INFIQC (CONICET-UNC) Ciudad Universitaria Pabellón Argentina 5000 Córdoba Argentina
- Departamento de Fisicoquímica Fac. de Ciencias Químicas Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
- Centro Láser de Ciencias Moleculares Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
| | - Philippe Maitre
- Université Paris-Saclay CNRS, Institut de Chimie Physique 91405 Orsay France
| | - Maximiliano Rossa
- INFIQC (CONICET-UNC) Ciudad Universitaria Pabellón Argentina 5000 Córdoba Argentina
- Departamento de Fisicoquímica Fac. de Ciencias Químicas Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
- Centro Láser de Ciencias Moleculares Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
| | - Gustavo A. Pino
- INFIQC (CONICET-UNC) Ciudad Universitaria Pabellón Argentina 5000 Córdoba Argentina
- Departamento de Fisicoquímica Fac. de Ciencias Químicas Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
- Centro Láser de Ciencias Moleculares Universidad Nacional de Córdoba Ciudad Universitaria, Pabellón Argentina X5000HUA Córdoba Argentina
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7
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Omidyan R, Abedini F, Shahrokh L, Azimi G. Excited State Deactivation Mechanism in Protonated Uracil: New Insights from Theoretical Studies. J Phys Chem A 2020; 124:5089-5097. [PMID: 32469520 DOI: 10.1021/acs.jpca.0c02284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have conducted here a theoretical exploration, discussing the distinct excited state lifetimes reported experimentally for the two lowest lying protonated isomers of uracil. In this regard, the first-principal computational levels as well as the nonadiabatic surface hopping dynamics have been employed. It has been revealed that relaxation of the 1ππ* state of enol-enol form (EE+) to the ground is barrier-free via out-of-plane coordinates, resulting in an ultrashort S1 lifetime of this species. For the second most stable isomer (EK+), however, a significant barrier predicted in the CASPT2 S1 potential energy profile along the twisting coordinate has been proposed to explain the relevant long lifetime reported experimentally.
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Affiliation(s)
- Reza Omidyan
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Fatemeh Abedini
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Leila Shahrokh
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Gholamhassan Azimi
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
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8
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Marlton SJP, McKinnon BI, Ucur B, Bezzina JP, Blanksby SJ, Trevitt AJ. Discrimination between Protonation Isomers of Quinazoline by Ion Mobility and UV-Photodissociation Action Spectroscopy. J Phys Chem Lett 2020; 11:4226-4231. [PMID: 32368922 DOI: 10.1021/acs.jpclett.0c01009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The influence of oriented electric fields on chemical reactivity and photochemistry is an area of increasing interest. Within a molecule, different protonation sites offer the opportunity to control the location of charge and thus orientation of electric fields. New techniques are thus needed to discriminate between protonation isomers in order to understand this effect. This investigation reports the UV-photodissociation action spectroscopy of two protonation isomers (protomers) of 1,3-diazanaphthalene (quinazoline) arising from protonation of a nitrogen at either the 1- or 3-position. It is shown that these protomers are separable by field-asymmetric ion mobility spectrometry (FAIMS) with confirmation provided by UV-photodissociation (PD) action spectroscopy. Vibronic features in the UVPD action spectra and computational input allow assignment of the origin transitions to the S1 and S5 states of both protomers. These experiments also provide vital benchmarks for protomer-specific calculations and examination of isomer-resolved reaction kinetics and thermodynamics.
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Affiliation(s)
- Samuel J P Marlton
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Benjamin I McKinnon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Boris Ucur
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - James P Bezzina
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Stephen J Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane 4001, Australia
| | - Adam J Trevitt
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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9
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Taccone MI, Cruz-Ortiz AF, Dezalay J, Soorkia S, Broquier M, Grégoire G, Sánchez CG, Pino GA. UV Photofragmentation of Cold Cytosine–M+ Complexes (M+: Na+, K+, Ag+). J Phys Chem A 2019; 123:7744-7750. [DOI: 10.1021/acs.jpca.9b06495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martín I. Taccone
- INFIQC (CONICET), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria,
Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Andrés F. Cruz-Ortiz
- INFIQC (CONICET), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria,
Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Jordan Dezalay
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Satchin Soorkia
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Michel Broquier
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
- Centre Laser de I’Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Cristián G. Sánchez
- INFIQC (CONICET), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Gustavo A. Pino
- INFIQC (CONICET), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria,
Pabellón Argentina, X5000HUA Córdoba, Argentina
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10
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Marlton SJP, McKinnon BI, Ucur B, Maccarone AT, Donald WA, Blanksby SJ, Trevitt AJ. Selecting and identifying gas-phase protonation isomers of nicotineH+ using combined laser, ion mobility and mass spectrometry techniques. Faraday Discuss 2019; 217:453-475. [DOI: 10.1039/c8fd00212f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protonation isomers of gas-phase nicotineH+ are separated and assigned using a combination of FAIMS and UV photodissociation action spectroscopy.
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Affiliation(s)
| | | | - Boris Ucur
- School of Chemistry
- University of Wollongong
- Wollongong
- Australia
| | | | | | - Stephen J. Blanksby
- Central Analytical Research Facility
- Institute for Future Environments
- Queensland University of Technology
- Brisbane
- Australia
| | - Adam J. Trevitt
- School of Chemistry
- University of Wollongong
- Wollongong
- Australia
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11
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Salehi M, Heidari Z, Omidyan R. Photophysics of Protonated and Microhydrated 2-Aminobenzaldehyde: Theoretical Insights into Photoswitchability of Protonated Systems. J Phys Chem A 2018; 122:8849-8857. [PMID: 30365896 DOI: 10.1021/acs.jpca.8b09930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The photoswitchability of a protonated aromatic compound (2-aminobenzaldehyde, 2ABZH+) in its individual and microhydrated states has been addressed based on the RI-MP2/RI-CC2 theoretical methods. Our calculated results give insight into the ultrafast nonradiative deactivation mechanism of the 2ABZH+, driven by a conical intersection between the S1/ S0 potential energy surfaces. Also, it has been predicted that protonation accompanies a significant blue shift effect on the first 1ππ* excited state of 2ABZ by 0.87 eV (at least 50 nm).
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Affiliation(s)
- Mohammad Salehi
- Department of Chemistry , University of Isfahan , 81746-73441 , Isfahan , Iran
| | - Zahra Heidari
- Department of Chemistry , University of Isfahan , 81746-73441 , Isfahan , Iran
| | - Reza Omidyan
- Department of Chemistry , University of Isfahan , 81746-73441 , Isfahan , Iran
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12
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Cruz-Ortiz AF, Rossa M, Berthias F, Berdakin M, Maitre P, Pino GA. Fingerprints of Both Watson-Crick and Hoogsteen Isomers of the Isolated (Cytosine-Guanine)H + Pair. J Phys Chem Lett 2017; 8:5501-5506. [PMID: 29064704 DOI: 10.1021/acs.jpclett.7b02140] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Gas phase protonated guanine-cytosine (CGH+) pair was generated using an electrospray ionization source from solutions at two different pH (5.8 and 3.2). Consistent evidence from MS/MS fragmentation patterns and differential ion mobility spectra (DIMS) point toward the presence of two isomers of the CGH+ pair, whose relative populations depend strongly on the pH of the solution. Gas phase infrared multiphoton dissociation (IRMPD) spectroscopy in the 900-1900 cm-1 spectral range further confirms that the Watson-Crick isomer is preferentially produced (91%) at pH = 5.8, while the Hoogsteen isomer predominates (66%) at pH = 3.2). These fingerprint signatures are expected to be useful for the development of new analytical methodologies and to trigger isomer selective photochemical studies of protonated DNA base pairs.
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Affiliation(s)
- Andrés F Cruz-Ortiz
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Maximiliano Rossa
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Francis Berthias
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Matías Berdakin
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
| | - Philippe Maitre
- Laboratoire de Chimie Physique, Université Paris-Sud, CNRS, Université Paris-Saclay , F-91405 Orsay, France
| | - Gustavo A Pino
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET - UNC, Ciudad Universitaria , X5000HUA Córdoba, Argentina
- Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria , X5000HUA Córdoba, Argentina
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13
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Bull JN, Coughlan NJA, Bieske EJ. Protomer-Specific Photochemistry Investigated Using Ion Mobility Mass Spectrometry. J Phys Chem A 2017; 121:6021-6027. [DOI: 10.1021/acs.jpca.7b05800] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- James N. Bull
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Evan J. Bieske
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
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14
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Féraud G, Domenianni L, Marceca E, Dedonder-Lardeux C, Jouvet C. Photodissociation Electronic Spectra of Cold Protonated Quinoline and Isoquinoline in the Gas Phase. J Phys Chem A 2017; 121:2580-2587. [DOI: 10.1021/acs.jpca.7b01301] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Géraldine Féraud
- CNRS, Aix-Marseille Université, PIIM UMR 7365, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
| | - Luis Domenianni
- Facultad
de Ciencias Exactas y Naturales, DQIAF, Universidad de Buenos Aires, Ciudad Universitaria, 1er piso, Pab. II, C1428EGA, Buenos Aires, Argentina
- Instituto
de Química Física de los Materiales, Medio Ambiente
y Energía (INQUIMAE), CONICET-UBA, Ciudad Universitaria, 3er piso,
Pab. II, C1428EGA, Buenos Aires, Argentina
| | - Ernesto Marceca
- Facultad
de Ciencias Exactas y Naturales, DQIAF, Universidad de Buenos Aires, Ciudad Universitaria, 1er piso, Pab. II, C1428EGA, Buenos Aires, Argentina
- Instituto
de Química Física de los Materiales, Medio Ambiente
y Energía (INQUIMAE), CONICET-UBA, Ciudad Universitaria, 3er piso,
Pab. II, C1428EGA, Buenos Aires, Argentina
| | - Claude Dedonder-Lardeux
- CNRS, Aix-Marseille Université, PIIM UMR 7365, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
| | - Christophe Jouvet
- CNRS, Aix-Marseille Université, PIIM UMR 7365, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France
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15
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Garcia RL, Nieuwjaer N, Desfrançois C, Lecomte F, Leite SD, Manil B, Broquier M, Grégoire G. Vibronic spectra of protonated hydroxypyridines: contributions of prefulvenic and planar structures. Phys Chem Chem Phys 2017; 19:8258-8268. [DOI: 10.1039/c6cp08623c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The UV photofragmentation spectra of cold protonated hydroxypyridines display well resolved vibrational structures, interpreted with calculations at the CC2 level.
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Affiliation(s)
- R. Lozada Garcia
- Laboratoire de Physique des Lasers
- CNRS
- Université Paris 13
- Sorbonne Paris Cité
- France
| | - N. Nieuwjaer
- Laboratoire de Physique des Lasers
- CNRS
- Université Paris 13
- Sorbonne Paris Cité
- France
| | - C. Desfrançois
- Laboratoire de Physique des Lasers
- CNRS
- Université Paris 13
- Sorbonne Paris Cité
- France
| | - F. Lecomte
- Laboratoire de Physique des Lasers
- CNRS
- Université Paris 13
- Sorbonne Paris Cité
- France
| | - S. D. Leite
- Laboratoire de Physique des Lasers
- CNRS
- Université Paris 13
- Sorbonne Paris Cité
- France
| | - B. Manil
- Laboratoire de Physique des Lasers
- CNRS
- Université Paris 13
- Sorbonne Paris Cité
- France
| | - M. Broquier
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris Sud
- Université Paris-Saclay
- F-91405 Orsay
| | - G. Grégoire
- Institut des Sciences Moléculaires d'Orsay (ISMO)
- CNRS
- Univ. Paris Sud
- Université Paris-Saclay
- F-91405 Orsay
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16
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Pino GA, Feraud G, Broquier M, Grégoire G, Soorkia S, Dedonder C, Jouvet C. Non-radiative processes in protonated diazines, pyrimidine bases and an aromatic azine. Phys Chem Chem Phys 2016; 18:20126-34. [PMID: 27110833 DOI: 10.1039/c6cp01345g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excited state lifetimes of DNA bases are often very short due to very efficient non-radiative processes assigned to the ππ*-nπ* coupling. A set of protonated aromatic diazine molecules (pyridazine, pyrimidine and pyrazine C4H5N2(+)) and protonated pyrimidine DNA bases (cytosine, uracil and thymine), as well as the protonated pyridine (C5H6N(+)), have been investigated. For all these molecules except one tautomer of protonated uracil (enol-keto), electronic spectroscopy exhibits vibrational line broadening. Excited state geometry optimization at the CC2 level has been conducted to find out whether the excited state lifetimes measured from line broadening can be correlated to the calculated ordering of the ππ* and nπ* states and the ππ*-nπ* energy gap. The short lifetimes, observed when one nitrogen atom of the ring is not protonated, can be rationalized by relaxation of the ππ* state to the nπ* state or directly to the electronic ground state through ring puckering.
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Affiliation(s)
- Gustavo A Pino
- Instituto de Investigaciones en Físico Química de Córdoba (INFIQC) CONICET - UNC. Dpto. de Fisicoquímica - Facultad de Ciencias Químicas - Centro Láser de Ciencias Moleculares - Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Géraldine Feraud
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France.
| | - Michel Broquier
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France and Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Gilles Grégoire
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France and Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Satchin Soorkia
- Centre Laser de l'Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France and Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Claude Dedonder
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France.
| | - Christophe Jouvet
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France.
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17
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Stockett MH, Houmøller J, Støchkel K, Svendsen A, Brøndsted Nielsen S. A cylindrical quadrupole ion trap in combination with an electrospray ion source for gas-phase luminescence and absorption spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:053103. [PMID: 27250388 DOI: 10.1063/1.4948316] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A relatively simple setup for collection and detection of light emitted from isolated photo-excited molecular ions has been constructed. It benefits from a high collection efficiency of photons, which is accomplished by using a cylindrical ion trap where one end-cap electrode is a mesh grid combined with an aspheric condenser lens. The geometry permits nearly 10% of the emitted light to be collected and, after transmission losses, approximately 5% to be delivered to the entrance of a grating spectrometer equipped with a detector array. The high collection efficiency enables the use of pulsed tunable lasers with low repetition rates (e.g., 20 Hz) instead of continuous wave (cw) lasers or very high repetition rate (e.g., MHz) lasers that are typically used as light sources for gas-phase fluorescence experiments on molecular ions. A hole has been drilled in the cylinder electrode so that a light pulse can interact with the ion cloud in the center of the trap. Simulations indicate that these modifications to the trap do not significantly affect the storage capability and the overall shape of the ion cloud. The overlap between the ion cloud and the laser light is basically 100%, and experimentally >50% of negatively charged chromophore ions are routinely photodepleted. The performance of the setup is illustrated based on fluorescence spectra of several laser dyes, and the quality of these spectra is comparable to those reported by other groups. Finally, by replacing the optical system with a channeltron detector, we demonstrate that the setup can also be used for gas-phase action spectroscopy where either depletion or fragmentation is monitored to provide an indirect measurement on the absorption spectrum of the ion.
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Affiliation(s)
- Mark H Stockett
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Jørgen Houmøller
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Kristian Støchkel
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Annette Svendsen
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
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18
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Taccone MI, Féraud G, Berdakin M, Dedonder-Lardeux C, Jouvet C, Pino GA. Communication: UV photoionization of cytosine catalyzed by Ag+. J Chem Phys 2015; 143:041103. [DOI: 10.1063/1.4927469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Martín I. Taccone
- INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Geraldine Féraud
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille, France
| | - Matías Berdakin
- INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Claude Dedonder-Lardeux
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille, France
| | - Christophe Jouvet
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille, France
| | - Gustavo A. Pino
- INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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19
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Berdakin M, Steinmetz V, Maitre P, Pino GA. On the Ag+–cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory. Phys Chem Chem Phys 2015; 17:25915-24. [DOI: 10.1039/c5cp02221e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single water molecule hydration stabilizes two quasi-isoenergetic complexes of cytosine⋯Ag+.
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Affiliation(s)
- Matias Berdakin
- INFIQC (CONICET – Universidad Nacional de Córdoba)
- Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- Centro Láser de Ciencias Moleculares
- Universidad Nacional de Córdoba
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique
- Université Paris Sud
- UMR8000 CNRS
- Faculté des Sciences
- 91405 Orsay Cedex
| | - Philippe Maitre
- Laboratoire de Chimie Physique
- Université Paris Sud
- UMR8000 CNRS
- Faculté des Sciences
- 91405 Orsay Cedex
| | - Gustavo A. Pino
- INFIQC (CONICET – Universidad Nacional de Córdoba)
- Dpto. de Fisicoquímica
- Facultad de Ciencias Químicas
- Centro Láser de Ciencias Moleculares
- Universidad Nacional de Córdoba
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20
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Omidyan R, Salehi M, Azimi G. A theoretical exploration of the nonradiative deactivation of hydrogen-bond complexes: isoindole–pyridine and quinoline–pyrrole. RSC Adv 2015. [DOI: 10.1039/c5ra18950k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CC2 potential energy profiles of the ground and excited states of the isoindole–pyridine complex along the proton transfer reaction coordinate are studied.
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Affiliation(s)
- Reza Omidyan
- Department of Chemistry
- University of Isfahan
- 81746-73441 Isfahan
- Iran
| | - Mohammad Salehi
- Department of Chemistry
- University of Isfahan
- 81746-73441 Isfahan
- Iran
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