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Mayer D, Lever F, Gühr M. Time-resolved x-ray spectroscopy of nucleobases and their thionated analogs. Photochem Photobiol 2024; 100:275-290. [PMID: 38174615 DOI: 10.1111/php.13903] [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: 11/06/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
The photoinduced relaxation dynamics of nucleobases and their thionated analogs have been investigated extensively over the past decades motivated by their crucial role in organisms and their application in medical and biochemical research and treatment. Most of these studies focused on the spectroscopy of valence electrons and fragmentation. The advent of ultrashort x-ray laser sources such as free-electron lasers, however, opens new opportunities for studying the ultrafast molecular relaxation dynamics utilizing the site- and element-selectivity of x-rays. In this review, we want to summarize ultrafast experiments on thymine and 2-thiouracil performed at free-electron lasers. We performed time-resolved x-ray absorption spectroscopy at the oxygen K-edge after UV excitation of thymine. In addition, we investigated the excited state dynamics of 2-tUra via x-ray photoelectron spectroscopy at sulfur. For these methods, we show a strong sensitivity to the electronic state or charge distribution, respectively. We also performed time-resolved Auger-Meitner spectroscopy, which shows spectral shifts associated with internuclear distances close to the probed site. We discuss the complementary aspects of time-resolved x-ray spectroscopy techniques compared to optical and UV spectroscopy for the investigation of ultrafast relaxation processes.
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Affiliation(s)
- Dennis Mayer
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Fabiano Lever
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Markus Gühr
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Institute of Physical Chemistry, University of Hamburg, Hamburg, Germany
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2
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Raczyńska ED. On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo. Molecules 2023; 28:7282. [PMID: 37959699 PMCID: PMC10648772 DOI: 10.3390/molecules28217282] [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: 09/25/2023] [Revised: 10/21/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023] Open
Abstract
In this review, the complete tautomeric equilibria are derived for disubstituted pyrimidine nucleic acid bases starting from phenol, aniline, and their model compounds-monosubstituted aromatic azines. The differences in tautomeric preferences for isolated (gaseous) neutral pyrimidine bases and their model compounds are discussed in light of different functional groups, their positions within the six-membered ring, electronic effects, and intramolecular interactions. For the discussion of tautomeric preferences and for the analysis of internal effects, recent quantum-chemical results are taken into account and compared to some experimental ones. For each possible tautomer-rotamer of the title compounds, the bond length alternation, measured by means of the harmonic oscillator model of electron delocalization (HOMED) index, is examined. Significant HOMED similarities exist for mono- and disubstituted derivatives. The lack of parallelism between the geometric (HOMED) and energetic (ΔG) parameters for all possible isomers clearly shows that aromaticity is not the main factor that dictates tautomeric preferences for pyrimidine bases, particularly for uracil and thymine. The effects of one-electron loss (positive ionization) and one-electron gain (negative ionization) on prototropy and bond length alternation are also reviewed for pyrimidine bases and their models.
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Affiliation(s)
- Ewa Daniela Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 159c, 02-776 Warszawa, Poland
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3
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Ultrafast Photo-Ion Probing of the Relaxation Dynamics in 2-Thiouracil. Molecules 2023; 28:molecules28052354. [PMID: 36903604 PMCID: PMC10005304 DOI: 10.3390/molecules28052354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
In this work, we investigate the relaxation processes of 2-thiouracil after UV photoexcitation to the S2 state through the use of ultrafast, single-colour, pump-probe UV/UV spectroscopy. We place focus on investigating the appearance and subsequent decay signals of ionized fragments. We complement this with VUV-induced dissociative photoionisation studies collected at a synchrotron, allowing us to better understand and assign the ionisation channels involved in the appearance of the fragments. We find that all fragments appear when single photons with energy > 11 eV are used in the VUV experiments and hence appear through 3+ photon-order processes when 266 nm light is used. We also observe three major decays for the fragment ions: a sub-autocorrelation decay (i.e., sub-370 fs), a secondary ultrafast decay on the order of 300-400 fs, and a long decay on the order of 220 to 400 ps (all fragment dependent). These decays agree well with the previously established S2 → S1 → Triplet → Ground decay process. Results from the VUV study also suggest that some of the fragments may be created by dynamics occurring in the excited cationic state.
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4
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Following excited-state chemical shifts in molecular ultrafast x-ray photoelectron spectroscopy. Nat Commun 2022; 13:198. [PMID: 35017539 PMCID: PMC8752854 DOI: 10.1038/s41467-021-27908-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/20/2021] [Indexed: 01/08/2023] Open
Abstract
The conversion of photon energy into other energetic forms in molecules is accompanied by charge moving on ultrafast timescales. We directly observe the charge motion at a specific site in an electronically excited molecule using time-resolved x-ray photoelectron spectroscopy (TR-XPS). We extend the concept of static chemical shift from conventional XPS by the excited-state chemical shift (ESCS), which is connected to the charge in the framework of a potential model. This allows us to invert TR-XPS spectra to the dynamic charge at a specific atom. We demonstrate the power of TR-XPS by using sulphur 2p-core-electron-emission probing to study the UV-excited dynamics of 2-thiouracil. The method allows us to discover that a major part of the population relaxes to the molecular ground state within 220–250 fs. In addition, a 250-fs oscillation, visible in the kinetic energy of the TR-XPS, reveals a coherent exchange of population among electronic states. Imaging the charge flow in photoexcited molecules would provide key information on photophysical and photochemical processes. Here the authors demonstrate tracking in real time after photoexcitation the change in charge density at a specific site of 2-thiouracil using time-resolved X-ray photoelectron spectroscopy.
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5
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Jin P, Wang X, Pan H, Chen J. One order of magnitude increase of triplet state lifetime observed in deprotonated form selenium substituted uracil. Phys Chem Chem Phys 2022; 24:875-882. [PMID: 34908064 DOI: 10.1039/d1cp04811b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Selenium nucleic acids possess unique properties and have been demonstrated to have a wide range of applications such as in DNA X-ray crystallography and novel medical therapies. However, as a heavy atom, selenium substitution may easily alter the photophysical properties of a nucleic acid by red-shifting the absorption spectra and introducing effective intersystem crossing to triplet excited states. In present work, the excited state dynamics of a naturally occurring selenium substituted uracil (2-selenuracil, 2SeU) is studied by using femtosecond transient absorption spectroscopy as well as quantum chemistry calculations. Ultrafast intersystem crossing to the lowest triplet state (T1) and effective non-radiative decay of this state to the ground state (S0) are demonstrated in the neutral form 2SeU. However, the triplet lifetime of the deprotonated form 2SeU is found to be almost one order of magnitude longer than that in the neutral one. Quantum chemistry calculations indicate that the short triplet lifetime in 2SeU is due to excited state population decay through a crossing point between T1 and S0. In the deprotonated form, shortening the N1-C2 bond length makes the structural distortion more difficult and brings a larger energy barrier on the pathway to the T1/S0 crossing point, resulting in one order of magnitude increase of the triplet state lifetime. Our study reveals one key factor to regulate the triplet lifetime of 2SeU and sets the stage to further investigate the photophysical and photochemical properties of 2SeU-containing DNA/RNA duplexes.
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Affiliation(s)
- Peipei Jin
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China. .,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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6
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Molecular structure, tautomer's, reactivity and inhibition studies on 6-Methyl-2-thiouracil for mild steel corrosion in aqueous HCl (1.00 M): Experimental and Theoretical Studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130927] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Core-Level Spectroscopy of 2-Thiouracil at the Sulfur L 1- and L 2,3-Edges Utilizing a SASE Free-Electron Laser. Molecules 2021; 26:molecules26216469. [PMID: 34770877 PMCID: PMC8586990 DOI: 10.3390/molecules26216469] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
In this paper, we report X-ray absorption and core-level electron spectra of the nucleobase derivative 2-thiouracil at the sulfur L1- and L2,3-edges. We used soft X-rays from the free-electron laser FLASH2 for the excitation of isolated molecules and dispersed the outgoing electrons with a magnetic bottle spectrometer. We identified photoelectrons from the 2p core orbital, accompanied by an electron correlation satellite, as well as resonant and non-resonant Coster–Kronig and Auger–Meitner emission at the L1- and L2,3-edges, respectively. We used the electron yield to construct X-ray absorption spectra at the two edges. The experimental data obtained are put in the context of the literature currently available on sulfur core-level and 2-thiouracil spectroscopy.
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8
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Quantum-chemical study on the relative stability of sildenafil tautomers. Struct Chem 2021. [DOI: 10.1007/s11224-021-01818-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe tautomeric equilibrium of sildenafil molecule was theoretically studied using B3LYP and M06-2X density functional theory (DFT) methods in connection with aug-cc-pVDZ correlation consistent basis set. Calculations were performed for gas phase and water solution conditions modelled by polarizable continuum model (PCM). Three tautomeric forms are possible. Two keto forms: A — where the tautomeric proton in more distant from carbonyl group and B — where it is closer, and one enol form denoted, C. Both DFT methods qualitatively give similar tautomer stability order: B > A > C. The B tautomer is dominant in gas phase and water environment, whereas the C tautomer is too high in energy to be present in the tautomeric mixture. Regarding the A tautomer, it is not present in the gas phase but is present in small amounts in water solution. According to B3LYP/aug-cc-pVDZ, the relative Gibbs-free energies for A and C relative to B are 10.05 kcal/mol and 11.91 kcal/mol for gas phase and 5.49 kcal/mol and 12.49 kcal/mol for water solution. According to M06-2X/aug-cc-pVDZ, the relative Gibbs-free energies for A and C are 9.12 kcal/mol and 10.60 kcal/mol for gas phase and 4.27 kcal/mol and 10.23 kcal/mol for water solution. Therefore, for in vivo conditions, we expect that the B tautomer is dominant, and there may exist small amounts of the A tautomer. The C enol tautomer is not present at all. This picture is very different from the parent tautomeric system: 4-hydroxypyrimidine/4-pyrimidinone where the C enol tautomer is less stable than keto B only by about 1 kcal/mol in the gas phase and the A keto tautomer is the least stable and not present in the tautomeric mixture. In order to understand these differences, we performed additional calculations for a series of parent molecules starting from 4-hydroxypyrimidine/4-pyrimidinone, going through two in-between model molecules and ending at Sildenafil molecule. We found that the most important reasons of C form destabilization are dearomatization of the 6-membered ring caused by the fusion with pyrazole ring, lack of strong intramolecular hydrogen bond in C form of sildenafil and presence of destabilizing steric interaction of oxygen and nitrogen atoms of two 6-memberd rings in this tautomer.
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9
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Babushkina AA, Egorov DM, Kaskevich KI. Synthesis and Functionalization of 5-Alkyl-6-methyl-2-thiouracils. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220110110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Melandri S, Evangelisti L, Canola S, Sa'adeh H, Calabrese C, Coreno M, Grazioli C, Prince KC, Negri F, Maris A. Chlorination and tautomerism: a computational and UPS/XPS study of 2-hydroxypyridine ⇌ 2-pyridone equilibrium. Phys Chem Chem Phys 2020; 22:13440-13455. [PMID: 32519689 DOI: 10.1039/d0cp02304c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The prototropic tautomeric equilibrium in 2-hydroxypyridine serves as a prototype model for the study of nucleobases' behaviour. The position of such an equilibrium in parent and chlorine monosubstituted 2-hydroxypyridine compounds in the gas phase was determined using synchrotron based techniques. The lactim tautomer is dominant for the 5- and 6-substituted compounds, whereas the parent, 3- and 4-substituted isomers have comparable populations for both tautomers. Information was obtained by measuring valence band and core level photoemission spectra at the chlorine L-edge and carbon, nitrogen, and oxygen K-edges. The effect of chlorine on the core ionization potentials of the atoms in the heterocycle was evaluated and reasonable agreement with a simple model was obtained. Basic considerations of resonance structures correctly predicts the tautomeric equilibrium for the 5- and 6-substituted compounds. The vibrationally resolved structure of the low energy portion of the valence band photoionization spectra is assigned based on quantum-chemical calculations of the neutral and charged species followed by simulation of the vibronic structure. It is shown that the first ionization occurs from a π orbital of similar shape for both tautomers. In addition, the highly distinctive vibronic structure observed just above the first ionization of the lactim, for three of the five species investigated, is assigned to the second ionization of the lactam.
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Affiliation(s)
- Sonia Melandri
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Luca Evangelisti
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Sofia Canola
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Hanan Sa'adeh
- Department of Physics, The University of Jordan, Amman, JO-11942, Jordan
| | - Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Apartado 644, E-48080 Bilbao, Spain and Basque Centre for Biophysics (CSIC, UPV/EHU), Barrio Sarriena, E-48940 Leioa, Spain
| | - Marcello Coreno
- CNR-ISM, Trieste LD2 Unit, Elettra-Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Cesare Grazioli
- CNR-ISM, Trieste LD2 Unit, Elettra-Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Kevin C Prince
- Elettra Sincrotrone Trieste, Area Science Park, I-34149 Basovizza, Trieste, Italy. and Centre for Translational Atomaterials, Swinburne University of Technology, Melbourne, Australia
| | - Fabrizia Negri
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Assimo Maris
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
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11
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Yang D, Liu W, Kong L, Zhang Q, Liu Y. Ultrafast excited state intramolecular proton transfer (ESIPT) mechanism for 2,6-bis(benzothiazolyl-2-yl)phenol: A theoretical investigation. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137226] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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13
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Skotnicki K, Taras-Goslinska K, Janik I, Bobrowski K. Radiation Induced One-Electron Oxidation of 2-Thiouracil in Aqueous Solutions. Molecules 2019; 24:E4402. [PMID: 31810289 PMCID: PMC6930642 DOI: 10.3390/molecules24234402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 11/17/2022] Open
Abstract
Oxidative damage to 2-thiouracil (2-TU) by hydroxyl (•OH) and azide (●N3) radicals produces various primary reactive intermediates. Their optical absorption spectra and kinetic characteristics were studied by pulse radiolysis with UV-vis spectrophotometric and conductivity detection and by time-dependent density functional theory (TD-DFT) method. The transient absorption spectra recorded in the reactions of •OH with 2-TU depend on the concentration of 2-TU, however, only slightly on pH. At low concentrations, they are characterized by a broad absorption band with a weakly pronounced maxima located at λ = 325, 340 and 385 nm, whereas for high concentrations, they are dominated by an absorption band with λmax ≈ 425 nm. Based on calculations using TD-DFT method, the transient absorption spectra at low concentration of 2-TU were assigned to the ●OH-adducts to the double bond at C5 and C6 carbon atoms (3●, 4●) and 2c-3e bonded ●OH adduct to sulfur atom (1…●OH) and at high concentration of 2-TU also to the dimeric 2c-3e S-S-bonded radical in neutral form (2●). The dimeric radical (2●) is formed in the reaction of thiyl-type radical (6●) with 2-TU and both radicals are in an equilibrium with Keq = 4.2 × 103 M-1. Similar equilibrium (with Keq = 4.3 × 103 M-1) was found for pH above the pKa of 2-TU which involves admittedly the same radical (6●) but with the dimeric 2c-3e S-S bonded radical in anionic form (2●-). In turn, ●N3-induced oxidation of 2-TU occurs via radical cation with maximum spin location on the sulfur atom which subsequently undergoes deprotonation at N1 atom leading again to thiyl-type radical (6●). This radical is a direct precursor of dimeric radical (2●).
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Affiliation(s)
- Konrad Skotnicki
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
| | | | - Ireneusz Janik
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Krzysztof Bobrowski
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
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14
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Ghafur O, Crane SW, Ryszka M, Bockova J, Rebelo A, Saalbach L, De Camillis S, Greenwood JB, Eden S, Townsend D. Ultraviolet relaxation dynamics in uracil: Time-resolved photoion yield studies using a laser-based thermal desorption source. J Chem Phys 2018; 149:034301. [DOI: 10.1063/1.5034419] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Omair Ghafur
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Stuart W. Crane
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Michal Ryszka
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Jana Bockova
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Andre Rebelo
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
- CEFITEC, Departamento de Física, FCT–Universidade NOVA de Lisboa, P-2829-516 Caparica, Portugal
| | - Lisa Saalbach
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Simone De Camillis
- School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Jason B. Greenwood
- School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Samuel Eden
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
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15
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Yu H, Sanchez-Rodriguez JA, Pollum M, Crespo-Hernández CE, Mai S, Marquetand P, González L, Ullrich S. Internal conversion and intersystem crossing pathways in UV excited, isolated uracils and their implications in prebiotic chemistry. Phys Chem Chem Phys 2018; 18:20168-76. [PMID: 27189184 DOI: 10.1039/c6cp01790h] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The photodynamic properties of molecules determine their ability to survive in harsh radiation environments. As such, the photostability of heterocyclic aromatic compounds to electromagnetic radiation is expected to have been one of the selection pressures influencing the prebiotic chemistry on early Earth. In the present study, the gas-phase photodynamics of uracil, 5-methyluracil (thymine) and 2-thiouracil-three heterocyclic compounds thought to be present during this era-are assessed in the context of their recently proposed intersystem crossing pathways that compete with internal conversion to the ground state. Specifically, time-resolved photoelectron spectroscopy measurements evidence femtosecond to picosecond timescales for relaxation of the singlet (1)ππ* and (1)nπ* states as well as for intersystem crossing to the triplet manifold. Trapping in the excited triplet state and intersystem crossing back to the ground state are investigated as potential factors contributing to the susceptibility of these molecules to ultraviolet photodamage.
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Affiliation(s)
- Hui Yu
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
| | | | - Marvin Pollum
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Carlos E Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Susanne Ullrich
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
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16
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Marchetti B, Karsili TNV, Ashfold MNR, Domcke W. A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs. Phys Chem Chem Phys 2018; 18:20007-27. [PMID: 26980149 DOI: 10.1039/c6cp00165c] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.
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Affiliation(s)
- Barbara Marchetti
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Tolga N V Karsili
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Michael N R Ashfold
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
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17
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Evangelisti L, Brendel K, Mäder H, Caminati W, Melandri S. Rotational Spectroscopy Probes Water Flipping by Full Fluorination of Benzene. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707155] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Luca Evangelisti
- Dipartimento di Chimica “G. Ciamician”; Università degli Studi di Bologna; Via Selmi 2 40126 Bologna Italy
| | - Kai Brendel
- Institut für Physikalische Chemie; Christian-Albrechts-Universität zu Kiel; Max-Eyth-Strasse 1 24118 Kiel Germany
| | - Heinrich Mäder
- Institut für Physikalische Chemie; Christian-Albrechts-Universität zu Kiel; Max-Eyth-Strasse 1 24118 Kiel Germany
| | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”; Università degli Studi di Bologna; Via Selmi 2 40126 Bologna Italy
| | - Sonia Melandri
- Dipartimento di Chimica “G. Ciamician”; Università degli Studi di Bologna; Via Selmi 2 40126 Bologna Italy
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18
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Evangelisti L, Brendel K, Mäder H, Caminati W, Melandri S. Rotational Spectroscopy Probes Water Flipping by Full Fluorination of Benzene. Angew Chem Int Ed Engl 2017; 56:13699-13703. [DOI: 10.1002/anie.201707155] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Luca Evangelisti
- Dipartimento di Chimica “G. Ciamician”; Università degli Studi di Bologna; Via Selmi 2 40126 Bologna Italy
| | - Kai Brendel
- Institut für Physikalische Chemie; Christian-Albrechts-Universität zu Kiel; Max-Eyth-Strasse 1 24118 Kiel Germany
| | - Heinrich Mäder
- Institut für Physikalische Chemie; Christian-Albrechts-Universität zu Kiel; Max-Eyth-Strasse 1 24118 Kiel Germany
| | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”; Università degli Studi di Bologna; Via Selmi 2 40126 Bologna Italy
| | - Sonia Melandri
- Dipartimento di Chimica “G. Ciamician”; Università degli Studi di Bologna; Via Selmi 2 40126 Bologna Italy
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19
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Hall VM, Bertke JA, Swift JA. Two tautomeric forms of 2-amino-5,6-dimethylpyrimidin-4-one. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2016; 72:460-4. [PMID: 27256693 DOI: 10.1107/s2053229616007403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/03/2016] [Indexed: 11/10/2022]
Abstract
Derivatives of 4-hydroxypyrimidine are an important class of biomolecules. These compounds can undergo keto-enol tautomerization in solution, though a search of the Cambridge Structural Database shows a strong bias toward the 3H-keto tautomer in the solid state. Recrystallization of 2-amino-5,6-dimethyl-4-hydroxypyrimidine, C6H9N3O, from aqueous solution yielded triclinic crystals of the 1H-keto tautomer, denoted form (I). Though not apparent in the X-ray data, the IR spectrum suggests that small amounts of the 4-hydroxy tautomer are also present in the crystal. Monoclinic crystals of form (II), comprised of a 1:1 ratio of both the 1H-keto and the 3H-keto tautomers, were obtained from aqueous solutions containing uric acid. Forms (I) and (II) exhibit one-dimensional and three-dimensional hydrogen-bonding motifs, respectively.
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Affiliation(s)
- Victoria M Hall
- Department of Chemistry, Georgetown University, 37th and O Sts NW, Washington, DC 20057, USA
| | - Jeffery A Bertke
- Department of Chemistry, Georgetown University, 37th and O Sts NW, Washington, DC 20057, USA
| | - Jennifer A Swift
- Department of Chemistry, Georgetown University, 37th and O Sts NW, Washington, DC 20057, USA
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20
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Nuñez A, Lehotay SJ, Lightfield AR. Structural characterization of product ions of regulated veterinary drugs by electrospray ionization and quadrupole time-of-flight mass spectrometry. Part 3: Anthelmintics and thyreostats. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:813-822. [PMID: 26969922 DOI: 10.1002/rcm.7508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/22/2015] [Accepted: 01/10/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE Previously, we have reported a liquid chromatography/tandem mass spectrometry method for the identification and quantification of regulated veterinary drugs in food animals. The method uses three selected transition ions per analyte but structural characterization is also needed. This work is a continuation of two previous publications in which we propose structures of the selected transition ions of 130 veterinary drugs altogether. METHODS In this work, 24 additional veterinary drugs were analyzed by infusion into a high-resolution quadrupole time-of-flight (QTOF) mass spectrometer using electrospray ionization (ESI) in positive or negative mode. The TOF analyzer was calibrated to achieve low error mass accuracy in the MS and MS/MS modes. Also, the MS(2) and MS(3) spectra were obtained by using a Q-Trap mass spectrometer to further determine the possible pathways of ion formation. RESULTS The low error mass spectrometry analysis allowed the elucidation of the ion formulae of selected transition ions for qualitative identification. The rational interpretation of data including a review of the published literature led to the proposed structures of the MS/MS product ions of 24 compounds covering two classes of regulated veterinary drugs (anthelmintics and thyreostats). In addition, the use of MS(2) and MS(3) experiments led to the establishment of fragmentation patterns. CONCLUSIONS The identification and quantification of veterinary drug residues is helpful information for regulatory monitoring programs in defense of regulatory enforcement actions. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Alberto Nuñez
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Steven J Lehotay
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Alan R Lightfield
- US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA
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21
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Plekan O, Feyer V, Cassidy A, Lyamayev V, Tsud N, Ptasińska S, Reiff S, Acres RG, Prince KC. Functionalisation and immobilisation of an Au(110) surface via uracil and 2-thiouracil anchored layer. Phys Chem Chem Phys 2015; 17:15181-92. [PMID: 25990541 DOI: 10.1039/c5cp01886b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study surface functionalisation by uracil and 2-thiouracil, and immobilisation of several DNA moieties on functionalised gold surfaces. The combination of X-ray photoelectron and near-edge X-ray absorption spectroscopy allowed us to obtain a complete understanding of complex interfacial processes, starting from adsorption of biomolecules onto the metallic surface and progressing towards a specific surface functionality for interactions with other biologically related adsorbates. Au(110) surfaces were functionalised by deposition of uracil and 2-thiouracil molecules under vacuum conditions, and then tested for their selectivity by immobilisation of different DNA moieties deposited from aqueous solutions. We observed that adenine, adenosine, and RNA polymer (polyadenylic acid) from saturated solutions were immobilized successfully on the 2-thiouracil, but those from dilute (1%) solutions were not. However, cytosine failed to adsorb even from saturated solution. The chemical states of the biologically related adsorbates were investigated and the geometrical orientation of uracil and 2-thiouracil on the Au(110) surface was determined using both spectroscopic techniques.
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Affiliation(s)
- Oksana Plekan
- Sincrotrone Trieste S.C.p.A., in Area Science Park, Strada Statale 14, km 163.5, I-34149 Basovizza, Trieste, Italy.
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22
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Electron delocalization and relative stabilities for the favored and rare tautomers of hydroxyazines in the gas phase – A comparison with aminoazines. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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Galvão TLP, Rocha IM, Ribeiro da Silva MDMC, Ribeiro da Silva MAV. Energetic study of 4(3H)-pyrimidinone: aromaticity of reactions, hydrogen bond rules, and support for an anomeric effect. J Phys Chem A 2014; 118:3360-6. [PMID: 24741997 DOI: 10.1021/jp502468s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
4(3H)-Pyrimidinone is observed in nature in equilibrium with other tautomeric forms, mimicking the tautomeric equilibrium in pyrimidine nucleobases. In this work, the enthalpy of formation in the gaseous phase of 4(3H)-pyrimidinone was derived from the combination of the enthalpy of formation in the crystalline phase, obtained by static bomb combustion calorimetry, and the enthalpy of sublimation, obtained by Knudsen effusion. The gaseous phase enthalpy of formation of 4(3H)-pyrimidinone was interpreted in terms of isodesmic reactions that consider the enthalpic effects of hydroxypyridines and pyrimidine. After comparison of the experimental and computational results, the same type of isodesmic reactions was used to study the substituent effects of the hydroxyl functional group of 2-, 4-, and 5-hydroxypyrimidines. The influence of aromaticity on the energetics of hydroxypyrimidines was evaluated using the variation of nucleus-independent chemical shifts for several reactions. The influence of intramolecular hydrogen bonds was investigated using the quantum theory of atoms in molecules and the geometric rule of Baker and Hubbard to identify hydrogen bonds. The energetic results obtained were also interpreted in terms of an in plane anomeric effect in the pyrimidine ring.
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Affiliation(s)
- Tiago L P Galvão
- Centro de Investigação em Química, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto , Rua do Campo Alegre, 687, P-4169-007 Porto, Portugal
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25
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Galvão TLP, Rocha IM, Ribeiro da Silva MDMC, Ribeiro da Silva MAV. From 2-Hydroxypyridine to 4(3H)-Pyrimidinone: Computational Study on the Control of the Tautomeric Equilibrium. J Phys Chem A 2013; 117:12668-74. [DOI: 10.1021/jp410004x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tiago L. P. Galvão
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
| | - Inês M. Rocha
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
| | - Maria D. M. C. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
| | - Manuel A. V. Ribeiro da Silva
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007, Porto, Portugal
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Puzzarini C, Biczysko M, Barone V, Peña I, Cabezas C, Alonso JL. Accurate molecular structure and spectroscopic properties of nucleobases: a combined computational-microwave investigation of 2-thiouracil as a case study. Phys Chem Chem Phys 2013; 15:16965-75. [PMID: 24002739 PMCID: PMC4596004 DOI: 10.1039/c3cp52347k] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy.
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27
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Mateo-Marti E, Pradier CM. UV irradiation study of a tripeptide isolated in an argon matrix: a tautomerism process evidenced by infrared and X-ray photoemission spectroscopies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 109:247-252. [PMID: 23542515 DOI: 10.1016/j.saa.2013.02.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 02/14/2013] [Accepted: 02/16/2013] [Indexed: 06/02/2023]
Abstract
Matrix isolation is a powerful tool for studying photochemical processes occurring in isolated molecules. In this way, we characterized the chemical modifications occurring within a tri peptide molecule, IGF, when exposed to the influence of Ultraviolet (UV) irradiation. This paper first describes the successful formation of the tripeptide (IGF) argon matrix under vacuum conditions, followed by the in situ UV irradiation and characterization of the molecular matrix reactivity after UV-irradiation. These studies have been performed by combining two complementary spectroscopic techniques, Fourier-Transform Reflexion Absorption Spectroscopy (FT-IRRAS) and X-ray Photoelectron Spectroscopy (XPS). The IR spectra of the isolated peptide-matrix, before and after UV irradiation, revealed significant differences that could be associated either to a partial deprotonation of the molecule or to a tautomeric conversion of some amide bonds to imide ones on some peptide molecules. XPS analyses undoubtedly confirmed the second hypothesis; the combination of IRRAS and XPS results provide evidence that UV irradiation of peptides induces a chemical reaction, namely a shift of the double bond, meaning partial conversion from amide tautomer into an imidic acid tautomer.
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Affiliation(s)
- E Mateo-Marti
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain.
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Prasanthkumar KP, Suresh CH, Aravindakumar CT. Oxidation reactions of 2-thiouracil: a theoretical and pulse radiolysis study. J Phys Chem A 2012; 116:10712-20. [PMID: 23061532 DOI: 10.1021/jp303808r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction of hydroxyl radical ((•)OH) with the nucleic acid base analogue 2-thiouracil (1) has been studied by pulse radiolysis experiments and DFT. The generic intermediate radicals feasible for the (•)OH reactions with 1, namely, one electron oxidation product (1(•+)), (•)OH-adducts (3(•), 4(•), and 5(•)), and H-abstracted radicals (6(•) and 7(•)), were characterized by interpreting their electronic and structural properties along with calculated energetics and UV-vis spectra. Pulse radiolysis experiments showed that the transient formed in the reaction of (•)OH with 1 in water at pH 6.5 has λ(max) at 430 nm. A bimolecular rate constant, k(2) of 9.6 × 10(9) M(-1) s(-1), is determined for this reaction via competition kinetics with 2-propanol. The experiments suggested that the transient species could be a dimer radical cation 2(•+), formed by the reaction of 1 with the radical cation 1(•+). For this reaction, an equilibrium constant of 4.7 × 10(3) M(-1) was determined. The transient formed in the reaction of 1 with pulse radiolytically produced Br(2)(•-) at pH 6.5 as well as Cl(2)(•-) at pH 1 has also produced λ(max) at 430 nm and suggested the formation of 2(•+). The calculated UV-vis spectra of the transient species (1(•+), 3(•), 4(•), 5(•), 6(•), and 7(•)) showed no resemblance to the experimental spectra, while that of 2(•+) (λ(max) = 420 nm) agreed well with the experimental value and thus confirmed the formation of 2(•+). The 420 nm peak was due to σ → σ* electronic excitation centered on a 2-center-3-electron (2c-3e) sulfur-sulfur bond [-S∴S-]. 2(•+) is the first reported example of a dimer radical cation in a pyrimidine heterocyclic system. Further, 5-C and 6-C substituted (substituents are -F, -Cl, -NH(2), -N(CH(3))(2), -OCH(3), -CF(3), -CH(3), -CH(2)CH(3), n-propyl, phenyl, and benzyl) and 5,6-disubstituted 2-thiouracil systems have been characterized by DFT and found that the reaction (1 + 1(•+) → 2(•+)) is exergonic (1.12-13.63 kcal/mol) for many of them.
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Affiliation(s)
- K P Prasanthkumar
- School of Chemical Sciences, Mahatma Gandhi University, Kottayam 686560, India
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Pinto R, Dias A, Coreno M, de Simone M, Giuliano B, Santos J, Costa M. Tautomerism in 5-methyltetrazole investigated by core-level photoelectron spectroscopy and ΔSCF calculations. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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