1
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Chevalier F, Schlathölter T, Poully JC. Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems. Chembiochem 2023; 24:e202300543. [PMID: 37712497 DOI: 10.1002/cbic.202300543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.
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Affiliation(s)
- François Chevalier
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Groningen (The, Netherlands
- University College Groningen, University of Groningen, Groningen (The, Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
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2
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Zima V, Vlk M, Wan J, Cvačka J, Tureček F. Tracking Isomerizations of High-Energy Adenine Cation Radicals by UV-Vis Action Spectroscopy and Cyclic Ion Mobility Mass Spectrometry. J Phys Chem A 2023. [PMID: 37433135 DOI: 10.1021/acs.jpca.3c03179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
We report experimental and computational studies of protonated adenine C-8 σ-radicals that are presumed yet elusive reactive intermediates of oxidative damage to nucleic acids. The radicals were generated in the gas phase by the collision-induced dissociation of C-8-Br and C-8-I bonds in protonated 8-bromo- and 8-iodoadenine as well as by 8-bromo- and 8-iodo-9-methyladenine. Protonation by electrospray of 8-bromo- and 8-iodoadenine was shown by cyclic-ion mobility mass spectrometry (c-IMS) to form the N-1-H, N-9-H and N-3-H, N-7-H protomers in 85:15 and 81:19 ratios, respectively, in accordance with the equilibrium populations of these protomers in water-solvated ions that were calculated by density functional theory (DFT). Protonation of 8-halogenated 9-methyladenines yielded single N-1-H protomers, which was consistent with their thermodynamic stability. The radicals produced from the 8-bromo and 8-iodo adenine cations were characterized by UV-vis photodissociation action spectroscopy (UVPD) and c-IMS. UVPD revealed the formation of C-8 σ-radicals along with N-3-H, N-7-H-adenine π-radicals that arose as secondary products by hydrogen atom migrations. The isomers were identified by matching their action spectra against the calculated vibronic absorption spectra. Deuterium isotope effects were found to slow the isomerization and increase the population of C-8 σ-radicals. The adenine cation radicals were separated by c-IMS and identified by their collision cross sections, which were measured relative to the canonical N-9-H adenine cation radical that was cogenerated in situ as an internal standard. Ab initio CCSD(T)/CBS calculations of isomer energies showed that the adenine C-8 σ-radicals were local energy minima with relative energies at 76-79 kJ mol-1 above that of the canonical adenine cation radical. Rice-Ramsperger-Kassel-Marcus calculations of unimolecular rate constants for hydrogen and deuterium migrations resulting in exergonic isomerizations showed kinetic shifts of 10-17 kJ mol-1, stabilizing the C-8 σ-radicals. C-8 σ-radicals derived from N-1-protonated 9-methyladenine were also thermodynamically unstable and readily isomerized upon formation.
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Affiliation(s)
- Václav Zima
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Mikuláš Vlk
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Jiahao Wan
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16610 Prague 6, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - František Tureček
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, United States
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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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Shahrokh L, Omidyan R, Azimi G. Excited State Deactivation Mechanisms of Protonated Adenine: a Theoretical study. Phys Chem Chem Phys 2022; 24:14898-14908. [DOI: 10.1039/d2cp00106c] [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
Quantum chemical computational method as well as the adiabatic dynamics simulation have been employed to investigate the non-radiative relaxation mechanism of protonated 9H- and 7H-adenine (AH+). We have located three...
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5
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Heldmaier FV, Coughlan NJA, Haack A, Huard R, Guna M, Schneider BB, Le Blanc JCY, Campbell JL, Nooijen M, Hopkins WS. UVPD spectroscopy of differential mobility-selected prototropic isomers of protonated adenine. Phys Chem Chem Phys 2021; 23:19892-19900. [PMID: 34525152 DOI: 10.1039/d1cp02688g] [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
Two prototropic isomers of adenine are formed in an electrospray ion source and are resolved spatially in a differential mobility spectrometer before detection in a triple quadrupole mass spectrometer. Each isomer is gated in CV space before being trapped in the linear ion trap of the modified mass spectrometer, where they are irradiated by the tuneable output of an optical parametric oscillator and undergo photodissociation to form charged fragments with m/z 119, 109, and 94. The photon-normalised intensity of each fragmentation channel is measured and the action spectra for each DMS-gated tautomer are obtained. Our analysis of the action spectra, aided by calculated vibronic spectra and thermochemical data, allow us to assign the two signals in our measured ionograms to specific tautomers of protonated adenine.
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Affiliation(s)
- Fiorella Villanueva Heldmaier
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Neville J A Coughlan
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Alexander Haack
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Rebecca Huard
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Mircea Guna
- SCIEX, Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
| | | | | | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Bedrock Scientific Inc., Milton, Ontario, Canada
| | - Marcel Nooijen
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.,Centre for Eye and Vision Research, Hong Kong Science Park, New Territories, Hong Kong.,Watermine Innovation, Waterloo, Ontario, Canada
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6
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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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7
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Abedini F, Omidyan R, Salehi M. Theoretical insights on nonradiative deactivation mechanisms of protonated xanthine. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.112067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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8
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Soorkia S, Jouvet C, Grégoire G. UV Photoinduced Dynamics of Conformer-Resolved Aromatic Peptides. Chem Rev 2019; 120:3296-3327. [DOI: 10.1021/acs.chemrev.9b00316] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satchin Soorkia
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Christophe Jouvet
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
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9
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Pitzer M, Ozga C, Küstner-Wetekam C, Reiß P, Knie A, Ehresmann A, Jahnke T, Giuliani A, Nahon L. State-Dependent Fragmentation of Protonated Uracil and Uridine. J Phys Chem A 2019; 123:3551-3557. [PMID: 30943036 DOI: 10.1021/acs.jpca.9b01822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Action spectroscopy using photon excitation in the VUV range (photon energy 4.5-9 eV) was performed on protonated uracil (UraH+) and uridine (UrdH+). The precursor ions with m/ z 113 and m/ z 245, respectively, were produced by an electrospray ionization source and accumulated inside a quadrupole ion trap mass spectrometer. After irradiation with tunable synchrotron radiation, product ion mass spectra were obtained. Fragment yields as a function of excitation energy show several maxima that can be attributed to the photoexcitation into different electronic states. For uracil, vertically excited states were calculated using the equation-of-motion coupled cluster approach and compared to the observed maxima. This allows to establish correlations between electronic states and the resulting fragment masses and can thus help to disentangle the complex de-excitation and fragmentation pathways of nucleic acid building blocks. Photofragmentation of the nucleoside uridine shows a significantly lower variety of fragments, indicating stabilization of the nucleobase by the attached sugar.
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Affiliation(s)
- Martin Pitzer
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel.,Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Christian Ozga
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Catmarna Küstner-Wetekam
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Philipp Reiß
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - André Knie
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Arno Ehresmann
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT) , University of Kassel , 34132 Kassel , Germany
| | - Till Jahnke
- Institute for Nuclear Physics , Goethe-University , 60438 Frankfurt , Germany
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10
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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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11
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Omidyan R, Amanollahi Z, Azimi G. Protonated serotonin: Geometry, electronic structures and photophysical properties. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 182:8-16. [PMID: 28388475 DOI: 10.1016/j.saa.2017.03.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/25/2017] [Accepted: 03/30/2017] [Indexed: 06/07/2023]
Abstract
The geometry and electronic structures of protonated serotonin have been investigated by the aim of MP2 and CC2 methods. The relative stabilities, transition energies and geometry of sixteen different protonated isomers of serotonin have been presented. It has been predicted that protonation does not exhibit essential alteration on the S1←S0 electronic transition energy of serotonin. Instead, more complicated photophysical nature in respect to its neutral analogue is suggested for protonated system owing to radiative and non-radiative deactivation pathways. In addition to hydrogen detachment (HD), hydrogen/proton transfer (H/PT) processes from ammonium to indole ring along the NH+⋯π hydrogen bond have been predicted as the most important photophysical consequences of SERH+ at S1 excited state. The PT processes is suggested to be responsible for fluorescence of SERH+ while the HD driving coordinate is proposed for elucidation of its nonradiative deactivation mechanism.
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Affiliation(s)
- Reza Omidyan
- Department of Chemistry, University of Isfahan, 81746-73441, Isfahan, Iran.
| | - Zohreh Amanollahi
- 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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12
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Wu RR, Rodgers MT. Mechanisms and energetics for N-glycosidic bond cleavage of protonated adenine nucleosides: N3 protonation induces base rotation and enhances N-glycosidic bond stability. Phys Chem Chem Phys 2016; 18:16021-32. [DOI: 10.1039/c6cp01445c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
N3 protonation induces base rotation and stabilizes the syn orientation of the adenine nucleobase of [dAdo+H]+ and [Ado+H]+via formation of a strong intramolecular N3H+⋯O5′ hydrogen-bonding interaction, which in turn influences the mechanisms and energetics for N-glycosidic bond cleavage.
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Affiliation(s)
- R. R. Wu
- Department of Chemistry
- Wayne State University
- Detroit
- USA
| | - M. T. Rodgers
- Department of Chemistry
- Wayne State University
- Detroit
- USA
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13
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Masoodi HR, Bagheri S, Abareghi M. The effects of tautomerization and protonation on the adenine-cytosine mismatches: a density functional theory study. J Biomol Struct Dyn 2015. [PMID: 26198186 DOI: 10.1080/07391102.2015.1072734] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine-cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.
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Affiliation(s)
- Hamid Reza Masoodi
- a Faculty of Science, Department of Chemistry , Vali-e-Asr University of Rafsanjan , P.O. Box 77176, Rafsanjan , Iran
| | - Sotoodeh Bagheri
- a Faculty of Science, Department of Chemistry , Vali-e-Asr University of Rafsanjan , P.O. Box 77176, Rafsanjan , Iran
| | - Mahsa Abareghi
- a Faculty of Science, Department of Chemistry , Vali-e-Asr University of Rafsanjan , P.O. Box 77176, Rafsanjan , Iran
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14
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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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15
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Bauer CA, Grimme S. Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics. J Phys Chem A 2014; 118:11479-84. [DOI: 10.1021/jp5096618] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Alexander Bauer
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
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16
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Pedersen SØ, Byskov CS, Turecek F, Nielsen SB. Structures of Protonated Thymine and Uracil and Their Monohydrated Gas-Phase Ions from Ultraviolet Action Spectroscopy and Theory. J Phys Chem A 2014; 118:4256-65. [DOI: 10.1021/jp504153p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sara Øvad Pedersen
- Department
of Physics and Astronomy, Aarhus University, DK-8000 Aarhus
C, Denmark
| | | | - Frantisek Turecek
- Department
of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
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17
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Saed B, Omidyan R. Protonation effect on the electronic properties of 2-pyridone monomer, dimer and its water clusters: a theoretical study. J Chem Phys 2014; 140:024315. [PMID: 24437885 DOI: 10.1063/1.4859255] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The CC2 (second order approximate coupled cluster method) has been applied to investigate protonation effect on electronic transition energies of 2-pyridone (2PY), 2-pyridone dimer, and micro-solvated 2-pyridone (0-2 water molecules). The PE profiles of protonated 2-pyridone (2PYH(+)) as well as monohydrated 2PYH(+) at the different electronic states have been investigated. The (1)πσ∗ state in protonated species (2PYH(+)) is a barrier free and dissociative state along the O-H stretching coordinate. In this reaction coordinate, the lowest lying (1)πσ∗ predissociates the bound S1((1)ππ∗) state, connecting the latter to a conical intersection with the S0 state. These conical intersections lead the (1)ππ∗ state to proceed as predissociative state and finally direct the excited system to the ground state. Furthermore, in presence of water molecule, the (1)πσ∗ state still remains dissociative but the conical intersection between (1)πσ∗ and ground state disappears. In addition, according to the CC2 calculation results, it has been predicted that protonation significantly blue shifts the S1-S0 electronic transition of monomer, dimer, and microhydrated 2-pyridone.
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Affiliation(s)
- Behnaz Saed
- 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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18
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Berdakin M, Féraud G, Dedonder-Lardeux C, Jouvet C, Pino GA. Excited states of protonated DNA/RNA bases. Phys Chem Chem Phys 2014; 16:10643-50. [DOI: 10.1039/c4cp00742e] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excited state lifetime of protonated DNA/RNA bases is strongly dependent on the tautomeric form.
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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
- Ciudad Universitaria
- X5000HUA Córdoba, Argentina
| | - Géraldine Féraud
- CNRS
- Aix Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR-7345
- 13397 Marseille, France
| | - Claude Dedonder-Lardeux
- CNRS
- Aix Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR-7345
- 13397 Marseille, France
| | - Christophe Jouvet
- CNRS
- Aix Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR-7345
- 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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Pedersen SØ, Støchkel K, Byskov CS, Baggesen LM, Nielsen SB. Gas-phase spectroscopy of protonated adenine, adenosine 5'-monophosphate and monohydrated ions. Phys Chem Chem Phys 2013; 15:19748-52. [PMID: 24141603 DOI: 10.1039/c3cp53742k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Microsolvation of chromophore ions commonly has large effects on their electronic structure and as a result on their optical absorption spectra. Here spectroscopy of protonated adenine (AdeH(+)) and its complex with one water molecule isolated in vacuo was done using a home-built mass spectrometer in combination with a tuneable pulsed laser system. Experiments also included the protonated adenosine 5'-monophosphate nucleotide (AMPH(+)). In the case of bare AdeH(+) ions, one-photon absorption leads to four dominant fragment ions corresponding to ammonium and ions formed after loss of either NH3, HCN, or NH2CN. The yields of these were measured as a function of the wavelength of the light from 210 nm to 300 nm, and they were combined to obtain the total photoinduced dissociation at each wavelength (i.e., action spectrum). A broad band between 230 nm and 290 nm and the tail of a band with maximum below 210 nm (high-energy band) are seen. In the case of AdeH(+)(H2O), the dominant dissociation channel after photoexcitation in the low-energy band was simply loss of H2O while photodissociation of protonated AMP revealed two dominant dissociation channels associated with the formation of either AdeH(+) or loss of H3PO4. The action spectra of AdeH(+), AdeH(+)(H2O), and AMPH(+) are almost identical in the 230-290 nm region, and they resemble the absorption spectrum of protonated adenine in aqueous solution recorded at low pH. Hence from our work it is firmly established that the lowest-energy transitions are independent of the surroundings.
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Affiliation(s)
- Sara Øvad Pedersen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.
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Touboul D, Gaie-Levrel F, Garcia GA, Nahon L, Poisson L, Schwell M, Hochlaf M. VUV photoionization of gas phase adenine and cytosine: A comparison between oven and aerosol vaporization. J Chem Phys 2013; 138:094203. [DOI: 10.1063/1.4793734] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Weber JM, Marcum J, Nielsen SB. UV Photophysics of DNA and RNA Nucleotides In Vacuo: Dissociation Channels, Time Scales, and Electronic Spectra. PHOTOPHYSICS OF IONIC BIOCHROMOPHORES 2013. [DOI: 10.1007/978-3-642-40190-9_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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22
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Alauddin M, Song JK, Choe JC, Park SM. Infrared predissociation of ternary cluster cations: the solvent effects on the branching ratio. Phys Chem Chem Phys 2012; 14:3864-71. [PMID: 22331177 DOI: 10.1039/c2cp23924h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Infrared (IR) predissociation of hydrogen-bonded ternary cluster ions such as aniline-water-ethanol (AWE(+)), aniline-water-isopropanol (AWP(+)), aniline-methanol-ethanol (AME(+)), aniline-water-pyrrole (AWPy(+)), and aniline-water-benzene (AWB(+)) was examined in the region of 2700-4000 cm(-1) to explore the key factors which determine the branching ratios in the concurrent unimolecular dissociation. The smaller solvent molecule was predominantly ejected when the binding energies of the two were not too different. On the other hand, when they were far off, the binding energy also acted significantly on the branching ratio. Besides, mode-selective IR predissociation was observed, while the selectivity was not quite distinct. The IR predissociation of ternary cluster ions bound via hydrogen bonding is considered to occur on a time scale much faster than intramolecular vibrational energy redistribution, which was proved by a statistical transition state theory.
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Affiliation(s)
- Md Alauddin
- Department of Chemistry and Research Center for New Nano Bio Fusion Technology, Kyung Hee University, Seoul, Republic of Korea
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23
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Sarangi MK, Bhattacharyya D, Basu S. Influence of 2′-Deoxy Sugar Moiety on Excited-State Protonation Equilibrium of Adenine and Adenosine with Acridine inside SDS Micelles: A Time-Resolved Study with Quantum Chemical Calculations. Chemphyschem 2012; 13:525-34. [DOI: 10.1002/cphc.201100763] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Indexed: 11/10/2022]
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Kumar SS, Pérot-Taillandier M, Lucas B, Soorkia S, Barat M, Fayeton JA. UV photodissociation dynamics of deprotonated 2'-deoxyadenosine 5'-monophosphate [5'-dAMP-H]-. J Phys Chem A 2011; 115:10383-90. [PMID: 21776981 DOI: 10.1021/jp204738q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The UV photodissociation dynamics of deprotonated 2'-deoxyadenosine 5'-monophosphate ([5'-dAMP-H](-)) has been studied using a unique technique based on the coincident detection of the ion and the neutral fragments. The observed fragment ions are m/z 79 (PO(3)(-)), 97 (H(2)PO(4)(-)), 134 ([A-H](-)), 177 ([dAMP-H-A-H(2)O](-)), and 195 ([dAMP-H-A](-)), where "A" refers to a neutral adenine molecule. The relative abundances are comparable to that found in previous studies on [5'-dAMP-H](-) employing different excitation processes, i.e., collisions and UV photons. The fragmentation times of the major channels have been measured, and are all found to be on the microsecond time scale. The fragmentation mechanisms for all channels have been characterized using velocity correlation plots of the ion and neutral fragment(s). The findings show that none of the dissociation channels of [5'-dAMP-H](-) is UV specific and all proceed via statistical fragmentation on the ground state after internal conversion, a result similar to fragmentations induced by collisions.
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Affiliation(s)
- S Sunil Kumar
- Institut des Science Moléculaires d'Orsay, CNRS UMR 8214, Université Paris Sud 11, F-91405 Orsay Cedex, France
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van Zundert GCP, Jaeqx S, Berden G, Bakker JM, Kleinermanns K, Oomens J, Rijs AM. IR Spectroscopy of Isolated Neutral and Protonated Adenine and 9-Methyladenine. Chemphyschem 2011; 12:1921-7. [DOI: 10.1002/cphc.201100133] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Indexed: 11/11/2022]
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