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Brister MM, Gustavsson T, Crespo-Hernández CE. Excited State Lifetimes of Sulfur-Substituted DNA and RNA Monomers Probed Using the Femtosecond Fluorescence Up-Conversion Technique. Molecules 2020; 25:E584. [PMID: 32013184 PMCID: PMC7037914 DOI: 10.3390/molecules25030584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/23/2020] [Accepted: 01/26/2020] [Indexed: 11/16/2022] Open
Abstract
Sulfur-substituted DNA and RNA nucleobase derivatives (a.k.a., thiobases) are an important family of biomolecules. They are used as prodrugs and as chemotherapeutic agents in medical settings, and as photocrosslinker molecules in structural-biology applications. Remarkably, excitation of thiobases with ultraviolet to near-visible light results in the population of long-lived and reactive triplet states on a time scale of hundreds of femtoseconds and with near-unity yields. This efficient nonradiative decay pathway explains the vanishingly small fluorescence yields reported for the thiobases and the scarcity of fluorescence lifetimes in the literature. In this study, we report fluorescence lifetimes for twelve thiobase derivatives, both in aqueous solution at physiological pH and in acetonitrile. Excitation is performed at 267 and 362 nm, while fluorescence emission is detected at 380, 425, 450, 525, or 532 nm. All the investigated thiobases reveal fluorescence lifetimes that decay in a few hundreds of femtoseconds and with magnitudes that depend and are sensitive to the position and degree of sulfur-atom substitution and on the solvent environment. Interestingly, however, three thiopyrimidine derivatives (i.e., 2-thiocytidine, 2-thiouridine, and 4-thiothymidine) also exhibit a small amplitude fluorescence component of a few picoseconds in aqueous solution. Furthermore, the N-glycosylation of thiobases to form DNA or RNA nucleoside analogues is demonstrated as affecting their fluorescence lifetimes. In aqueous solution, the fluorescence decay signals exciting at 267 nm are equal or slower than those collected exciting at 362 nm. In acetonitrile, however, the fluorescence decay signals recorded upon 267 nm excitation are, in all cases, faster than those measured exciting at 362 nm. A comparison to the literature values show that, while both the DNA and RNA nucleobase and thiobase derivatives exhibit sub-picosecond fluorescence lifetimes, the 1ππ* excited-state population in the nucleobase monomers primarily decay back to the ground state, whereas it predominantly populates long-lived and reactive triplet states in thiobase monomers.
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Affiliation(s)
- Matthew M. Brister
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA;
| | - Thomas Gustavsson
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
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Zhang X, Shi Y, Cai L, Zhou Y, Wang CK, Lin L. Solvent effect on the photophysical properties of thermally activated delayed fluorescence molecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 225:117473. [PMID: 31470345 DOI: 10.1016/j.saa.2019.117473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/27/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
As the third-generation organic electroluminescent materials, thermally activated delayed fluorescence (TADF) molecules have become the research focus recently. Significant solvent effect on TADF molecules were found experimentally, while theoretical investigations are quite limited. In this work, the solvent effect on photophysical properties of DCBPy and DTCBPy are investigated with first-principles calculations. The solvent polarity has slight influence on the molecular geometries and orbitals, while it can decrease the energy gap between the first singlet excited state (S1) and first triplet excited state (T1) significantly. Both the oscillator strength and the radiation rates of S1 increase with larger solvent polarity. The large energy gap between S1 and T1 induce negligible intersystem crossing (ISC) and reverse ISC rates between them, which also indicates higher triplet excited states are involved in the up-conversion process. Our results provide valuable information about solvent influence on the light-emitting properties of TADF molecules, which could help one better understand the light-emitting mechanism of them and favor the design of TADF molecules.
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Affiliation(s)
- Xiaotong Zhang
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China
| | - Yurong Shi
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China
| | - Lei Cai
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China
| | - Yong Zhou
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China
| | - Chuan-Kui Wang
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China.
| | - Lili Lin
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China.
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53
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Valadan M, Pomarico E, Della Ventura B, Gesuele F, Velotta R, Amoresano A, Pinto G, Chergui M, Improta R, Altucci C. A multi-scale time-resolved study of photoactivated dynamics in 5-benzyl uracil, a model for DNA/protein interactions. Phys Chem Chem Phys 2019; 21:26301-26310. [PMID: 31686060 DOI: 10.1039/c9cp03839f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We combine fluorescence up-conversion and time correlated single photon counting experiments to investigate the 5-benzyl uracil excited state dynamics in methanol from 100 fs up to several ns. This molecule has been proposed as a model for DNA/protein interactions. Our results show emission bands at about 310 and 350 nm that exhibit bi-exponential sub-ps decays. Calculations, including solvent effects by a mixed discrete-continuum model, indicate that the Franck Condon region is characterized by significant coupling between the excited states of the benzyl and the uracil moieties, mirrored by the short-lived emission at 310 nm. Two main ground state recovery pathways are identified, both contributing to the 350 nm emission. The first 'photophysical' decay path involves a ππ* excited state localized on the uracil and is connected to the ground electronic state by an easily accessible crossing with S0, accounting for the short lifetime component. Simulations indicate that a possible second pathway is characterized by exciplex formation, with partial benzene → uracil charge transfer character, that may lead instead to photocyclization. The relevance of our results is discussed in view of the photoactivated dynamics of DNA/protein complexes, with implications on their interaction mechanisms.
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Affiliation(s)
- Mohammadhassan Valadan
- Department of Physics "Ettore Pancini", University of Naples "Federico II", Naples, 80126, Italy.
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54
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Jeong H, Oh K. Uracil-doped DNA thin solid films: a new way to control optical dispersion of DNA film using a RNA constituent. OPTICS EXPRESS 2019; 27:36075-36087. [PMID: 31873394 DOI: 10.1364/oe.27.036075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
Among five nucleobases, adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U), uracil is a key distinctive constituent existing only in ribonucleic acid (RNA). RNA shares the common A, G, and C with deoxyribonucleic acid (DNA) made of A-T, G-C hydrogen bonding. We explored a new attempt to combine uracil (U) with DNA, successfully realizing U-doped DNA thin solid films for the first time. Impacts of uracil on optical properties of the films were thoroughly investigated. The method was based on optimal spin-coating of an aqueous solution of DNA and uracil over silicon or silica substrates. Optical absorption of both aqueous solution and U-doped DNA thin solid films was characterized in a wide spectral range covering UV-visible-IR. Immobilization of uracil within DNA thin solid films was experimentally confirmed by FTIR spectroscopy studies. By using an ellipsometer, we measured the refractive indices of the films and discovered that U-doping was a very effective means to control optical dispersion DNA thin solid film. We further investigated thermo-optic behavior to find impacts of U-doping in DNA films. Detailed thin film processes and optical characterizations are discussed.
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55
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Erickson BA, Heim ZN, Pieri E, Liu E, Martinez TJ, Neumark DM. Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy. J Phys Chem A 2019; 123:10676-10684. [PMID: 31756106 DOI: 10.1021/acs.jpca.9b08258] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The relaxation dynamics of thymine and its derivatives thymidine and thymidine monophosphate are studied using time-resolved photoelectron spectroscopy applied to a water microjet. Two absorption bands are studied; the first is a bright ππ* state which is populated using tunable-ultraviolet light in the range 4.74-5.17 eV and probed using a 6.20 eV probe pulse. By reversing the order of these pulses, a band containing multiple ππ* states is populated by the 6.20 eV pulse and the lower energy pulse serves as the probe. The lower lying ππ* state is found to decay in ∼400 fs in both thymine and thymidine independent of pump photon energy, while thymidine monophosphate decays vary from 670 to 840 fs with some pump energy dependence. The application of a computational quantum mechanical/molecular mechanical scheme at the XMS-CASPT2//CASSCF/AMBER level of theory suggests that conformational differences existing between thymidine and thymidine monophosphate in solution account for this difference. The higher lying ππ* band is found to decay in ∼600 fs in all three cases, but it is only able to be characterized when the 5.17 eV probe pulse is used. Notably, no long-lived signal from an nπ* state can be identified in either experiment on any of the three molecules.
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Affiliation(s)
- Blake A Erickson
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Zachary N Heim
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Elisa Pieri
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Erica Liu
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Todd J Martinez
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Daniel M Neumark
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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56
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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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57
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Kunin A, McGraw VS, Lunny KG, Neumark DM. Time-resolved dynamics in iodide-uracil-water clusters upon excitation of the nucleobase. J Chem Phys 2019; 151:154304. [PMID: 31640364 DOI: 10.1063/1.5120706] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dynamics of iodide-uracil-water (I-·U·H2O) clusters following π-π* excitation of the nucleobase are probed using time-resolved photoelectron spectroscopy. Photoexcitation of this cluster at 4.77 eV results in electron transfer from the iodide moiety to the uracil, creating a valence-bound anion within the cross correlation of the pump and probe laser pulses. This species can decay by a number of channels, including autodetachment and dissociation to I- or larger anion fragments. Comparison of the energetics of the photoexcited cluster and its decay dynamics with those of the bare iodide-uracil (I-·U) complex provides a sensitive probe of the effects of microhydration on these species.
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Affiliation(s)
- Alice Kunin
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Valerie S McGraw
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Katharine G Lunny
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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58
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Abebe Alemayehu Y, Tewabe Gebeyehu B, Cheng CC. Photosensitive Supramolecular Micelles with Complementary Hydrogen Bonding Motifs To Improve the Efficacy of Cancer Chemotherapy. Biomacromolecules 2019; 20:4535-4545. [DOI: 10.1021/acs.biomac.9b01322] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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59
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Suda K, Sarinastiti A, Arifin, Kimura Y, Yokogawa D. Understanding Structural Changes through Excited-State Intramolecular Proton Transfer in 4′-N,N-Diethylamino-3-hydroxyflavone (DEAHF) in Solution Based on Quantum Chemical Calculations. J Phys Chem B 2019; 123:9872-9881. [DOI: 10.1021/acs.jpcb.9b07549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Kayo Suda
- Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Asri Sarinastiti
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Arifin
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yoshifumi Kimura
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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61
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Cheng CC, Gebeyehu BT, Huang SY, Abebe Alemayehu Y, Sun YT, Lai YC, Chang YH, Lai JY, Lee DJ. Entrapment of an adenine derivative by a photo-irradiated uracil-functionalized micelle confers controlled self-assembly behavior. J Colloid Interface Sci 2019; 552:166-178. [PMID: 31125827 DOI: 10.1016/j.jcis.2019.05.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 11/15/2022]
Abstract
HYPOTHESIS Invoking cooperative assembly of the uracil-functionalized supramolecular polymer BU-PPG [uracil end-capped poly(propylene glycol)] upon association with the nucleobase adenine derivative A-MA [methyl 3-(6-amino-9H-purin-9-yl)propanoate] as a model drug provides a new concept to control and tune the properties of supramolecular complexes and holds significant potential for the development of safer, more effective drug delivery systems. EXPERIMENTS BU-PPG and A-MA were successfully developed and exhibited specific recognition and high affinity, which enabled reversible complementary adenine-uracil (A-U) hydrogen bonding-induced formation of spherical micelles in aqueous solution. The self-assembly and controllable A-MA release behavior of BU-PPG/A-MA micelles were studied using morphological analysis and optical and light scattering techniques to investigate the effect of photoirradiation and temperature on the complementary hydrogen bond interactions between BU-PPG and A-MA. FINDINGS The resulting micelles possess unusual physical properties, including controlled photoreactivity kinetics, controllable self-assembled morphology and low cytotoxicity in vitro, as well as reversible temperature-responsive behavior. Importantly, irradiated micelles exhibited excellent long-term structural stability under normal physiological conditions and serum disturbance. Increasing the temperature triggered rapid release of A-MA by disrupting A-U complexes. These findings represent an entirely new, promising strategy for the development of multi-controlled release drug delivery nanocarriers based on complementary hydrogen bonding interactions.
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Affiliation(s)
- Chih-Chia Cheng
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; Advanced Membrane Materials Research Center, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
| | - Belete Tewabe Gebeyehu
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Shan-You Huang
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Yihalem Abebe Alemayehu
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Ya-Ting Sun
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - You-Cheng Lai
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Yi-Hsuan Chang
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Juin-Yih Lai
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; Advanced Membrane Materials Research Center, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; R&D Center for Membrane Technology, Chung Yuan Christian University, Chungli, Taoyuan 32043, Taiwan
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan; Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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62
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Ostakhov SS, Ovchinnikov MY, Masyagutova GA, Khursan SL. Luminescent and DFT Study of Keto-Enol Tautomers of 5-Fluorouracil and Its Derivatives in Aqueous Solutions. J Phys Chem A 2019; 123:7956-7964. [PMID: 31442039 DOI: 10.1021/acs.jpca.9b04701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence (FL) spectra were recorded and identified for the following 5-fluorouracil (FU) tautomers: 5-fluoropyrimidine-2,4(1H,3H)-dione (A), 5-fluoro-2-hydroxypyrimidine-4(3H)-one (B), and 5-fluoro-4-hydroxypyrimidine-2(1H)-one (D), as well as the corresponding tautomers A and D of 1-(tetrahydrofuranyl-2)-5-fluorouracil and 1-methyl-5-fluorouracil, tautomers A and B of 3-methyl-5-fluorouracil, and the diketo tautomer of 1,3-dimethyl-5-fluorouracil. It was shown that the FL of rare tautomers of FU derivatives occurs by the excitation of uracil homoassociates followed by intramolecular proton transfer (IPT), formation of a pair of rare tautomers, and radiative deactivation of one of them. The FL quantum yields φi were estimated. In the case of rare tautomers, the φi value includes the probability of IPT in the homoassociate, and density functional theory calculations in the TPSSTPSS/6-311+G(d,p) approximation were used to determine the relative energies of tautomers, associated FU forms, and their spectral properties that agree with the observed luminescence pattern.
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Affiliation(s)
- S S Ostakhov
- Ufa Institute of Chemistry , Ufa Federal Research Centre of the Russian Academy of Sciences , 71 Prospect Oktyabrya , 450054 Ufa , Russian Federation
| | - M Yu Ovchinnikov
- Ufa Institute of Chemistry , Ufa Federal Research Centre of the Russian Academy of Sciences , 71 Prospect Oktyabrya , 450054 Ufa , Russian Federation
| | - G A Masyagutova
- Ufa Institute of Chemistry , Ufa Federal Research Centre of the Russian Academy of Sciences , 71 Prospect Oktyabrya , 450054 Ufa , Russian Federation
| | - S L Khursan
- Ufa Institute of Chemistry , Ufa Federal Research Centre of the Russian Academy of Sciences , 71 Prospect Oktyabrya , 450054 Ufa , Russian Federation
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63
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On the impact of a phosphoryl group in the recognition capabilities of 2-aminopyridines toward carboxylic acids. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2496-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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64
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Diekmann J, Gontcharov J, Fröbel S, Torres Ziegenbein C, Zinth W, Gilch P. The Photoaddition of a Psoralen to DNA Proceeds via the Triplet State. J Am Chem Soc 2019; 141:13643-13653. [DOI: 10.1021/jacs.9b06521] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janina Diekmann
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Julia Gontcharov
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich CIPSM, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 München, Germany
| | - Sascha Fröbel
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Christian Torres Ziegenbein
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Wolfgang Zinth
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Center for Integrated Protein Science Munich CIPSM, Ludwig-Maximilians-Universität München, Oettingenstrasse 67, 80538 München, Germany
| | - Peter Gilch
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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65
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Ben Nasr F, Alata I, Scuderi D, Lepère V, Brenner V, Jaïdane NE, Zehnacker A. Effects of complexation with sulfuric acid on the photodissociation of protonated Cinchona alkaloids in the gas phase. Phys Chem Chem Phys 2019; 21:15439-15451. [PMID: 31257399 DOI: 10.1039/c9cp01518c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of complexation with sulfuric acid on the photo-dissociation of protonated Cinchona alkaloids, namely cinchonidine (Cd), quinine (Qn) and quinidine (Qd), is studied by combining laser spectroscopy with quantum chemical calculations. The protonated complexes are structurally characterized in a room-temperature ion trap by means of infra-red multiple photon dissociation (IRMPD) spectroscopy in the fingerprint and the ν(XH) (X = C, N, O) stretch regions. Comparison with density functional theory calculations including dispersion (DFT-D) unambiguously shows that the complex consists of a doubly protonated Cinchona alkaloid strongly bound to a bisulfate HSO4- anion, which bridges the two protonated sites of the Cinchona alkaloid. UV excitation of the complex does not induce loss of specific photo fragments, in contrast to the protonated monomer or dimer, for which photo-specific fragments were observed. Indeed the UV-induced fragmentation pattern is identical to that observed in collision-induced dissociation experiments. Analysis of the nature of the first electronic transitions at the second order approximate coupled-cluster level (CC2) explains the difference in the behavior of the complex relative to the monomer or dimer towards UV excitation.
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Affiliation(s)
- Feriel Ben Nasr
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France. and Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA) Université de Tunis El Manar, LSAMA, Tunis 1060, Tunisia
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Debora Scuderi
- Univ. Paris-Sud, Laboratoire de Chimie Physique, UMR 8000, and CNRS, Orsay, F-91405, France
| | - Valeria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | | | - Nejm-Eddine Jaïdane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA) Université de Tunis El Manar, LSAMA, Tunis 1060, Tunisia
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
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66
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Duchi M, O'Hagan MP, Kumar R, Bennie SJ, Galan MC, Curchod BFE, Oliver TAA. Exploring ultraviolet photoinduced charge-transfer dynamics in a model dinucleotide of guanine and thymine. Phys Chem Chem Phys 2019; 21:14407-14417. [PMID: 30869082 DOI: 10.1039/c8cp07864e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An understanding of the initial photoexcited states of DNA is essential to unravelling deleterious photoinduced chemical reactions and the intrinsic ultrafast photoprotection of the genetic code for all life. In our combined experimental and theoretical study, we have elucidated the primary non-radiative relaxation dynamics of a model nucleotide of guanine and thymine (2'-deoxyguanosine 3'-monophosphate 5'-thymidine, d(GpT)) in buffered aqueous solution. Experimentally, we unequivocally demonstrate that the Franck-Condon excited states of d(GpT) are significantly delocalised across both nucleobases, and mediate d(G+pT-) exciplex product formation on an ultrafast (<350 fs) timescale. Theoretical studies show that the nature of the vertical excited states is very dependent on the specific geometry of the dinucleotide, and dictate the degree of delocalised, charge-transfer or localised character. Our mechanism for prompt exciplex formation involves a rapid change in electronic structure and includes a diabatic surface crossing very close to the Franck-Condon region mediating fast d(G+pT-) formation. Exciplexes are quickly converted back to neutral ground state molecules on a ∼10 ps timescale with a high quantum yield, ensuring the photostability of the nucleotide sequence.
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Affiliation(s)
- Marta Duchi
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - Michael P O'Hagan
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - Rhea Kumar
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - Simon J Bennie
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - M Carmen Galan
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - Basile F E Curchod
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
| | - Thomas A A Oliver
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
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Gabas F, Di Liberto G, Ceotto M. Vibrational investigation of nucleobases by means of divide and conquer semiclassical dynamics. J Chem Phys 2019; 150:224107. [PMID: 31202241 DOI: 10.1063/1.5100503] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report a computational study of the vibrational features of four different nucleobases employing the divide-and-conquer semiclassical initial value representation molecular dynamics method. Calculations are performed on uracil, cytosine, thymine, and adenine. Results show that the overall accuracy with respect to experiments is within 20 wavenumbers, regardless of the dimensionality of the nucleobase. Vibrational estimates are accurate even in the complex case of cytosine, where two relevant conformers are taken into account. These results are promising in the perspective of future studies on more complex systems, such as nucleotides or nucleobase pairs.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Giovanni Di Liberto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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68
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Fang YG, Peng Q, Fang Q, Fang W, Cui G. MS-CASPT2 Studies on the Photophysics of Selenium-Substituted Guanine Nucleobase. ACS OMEGA 2019; 4:9769-9777. [PMID: 31460068 PMCID: PMC6649137 DOI: 10.1021/acsomega.9b01276] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/23/2019] [Indexed: 05/30/2023]
Abstract
The MS-CASPT2 method has been employed to optimize minimum-energy structures of 6-selenoguanine (6SeGua) and related two- and three-state intersection structures in and between the lowest five electronic states, i.e., S2(1ππ*), S1(1 nπ*), T2(3 nπ*), T1(3ππ*), and S0. In combination with MS-CASPT2 calculated linearly interpolated internal coordinate paths, the photophysical mechanism of 6SeGua has been proposed. The initially populated S2(1ππ*) state decays to either S1(1 nπ*) or T2(3 nπ*) states through a three-state S2/S1/T2 intersection point. The large S2/T2 spin-orbit coupling of 435 cm-1, according to the classical El-Sayed rule, benefits the S2 → T2 intersystem crossing process. The S1(1 nπ*) state that stems from the S2 → S1 internal conversion process at the S2/S1/T2 intersection point can further jump to the T2(3 nπ*) state through the S1 → T2 intersystem crossing process. This process does not comply with the El-Sayed rule, but it is still related to a comparatively large spin-orbit coupling of 39 cm-1 and is expected to occur relatively fast. Finally, the T2(3 nπ*) state, which is populated from the above S2 → T2 and S1 → T2 intersystem crossing processes, decays to the T1(3ππ*) state via an internal conversion process. Because there is merely a small energy barrier of 0.11 eV separating the T1(3ππ*) minimum and an energetically allowed two-state T1/S0 intersection point, the T1(3ππ*) state still can decay to the S0 state quickly, which is also enhanced by a large T1/S0 spin-orbit coupling of 252 cm-1. Our proposed mechanism explains experimentally observed ultrafast intersystem crossing processes in 6SeGua and its 835-fold acceleration of the T1 state decay to the S0 state compared with 6tGua. Finally, we have found that the ground-state electronic structure of 6SeGua has more apparent multireference character.
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69
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Roohi H, Alizadeh P. Fine-tuned dual fluorescence behavior of N-substituted aniline-imidazopyridine based switches: Mechanistic understanding, substituent and solvent effects. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 214:407-428. [PMID: 30802798 DOI: 10.1016/j.saa.2019.02.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/24/2018] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
In order to understand the fine-tuned photo-physical behaviors of the N(X)-H⋯N systems, the excited state intramolecular proton transfer (ESIPT) switching in the N-substituted X1-5-NHIPA molecules (NHIPA = 2-(imidazo[1,2-a]pyridin-2-yl)aniline and X = H, COCH3, CH3C6H4SO2, C6F5SO2, and COCF3) were investigated in detail in gas phase and three solvent media at TD-PBE0/6-311++G(d,p) and TD-M06-2X/6-311++G(d,p) levels of theory. ESIPT reactions at S1 state were approximately without energy barrier, exergonic processes and were quantitatively demonstrated to be mainly sensitive to substituents and solvent media. The X-NHIPA (X = CH3C6H4SO2, C6F5SO2 and CF3CO) compounds were predicted to undergo fast, irreversible proton transfer at S1 state and, in turn, exhibit tautomer emission with anomalous large Stokes shift in the gas phase. In the toluene solvent, except for C6F5SO2-NHIPA that showed exclusively a tautomer emission with a long wavelength, all other X-NHIPA molecules were predicted to involve in the reversible ESIPT and hence exhibit a dual normal and tautomer emissions behavior, in good agreement with the experimental observations. In polar solvents, it is expected that all compounds show dual normal and tautomer emissions. The nearly equal intensities of the normal and tautomer emissions can lead to the generation of the white lights with the potential in lighting applications.
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Affiliation(s)
- Hossein Roohi
- Computational Quantum Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Guilan, Rasht, Iran.
| | - Parvaneh Alizadeh
- Computational Quantum Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Guilan, Rasht, Iran
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70
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Kojima T, Aihara H, Kodashima Y, Makishima H, Nakiri S, Takada S, Shimada H, Ukai M, Ozga C, Holzapfel X, Schmidt P, Küstner-Wetekam C, Otto H, Bloβ D, Knie A, Ehresmann A, Yokoya A, Fujii K, Fukuda Y, Saitoh Y. NOVEL ANALYTICAL STUDY FOR REACTION INTERMEDIATES IN THE PRIMARY RADIATION INTERACTION OF DNA USING A SYNCHROTRON RADIATION-INDUCED LUMINESCENCE SPECTROSCOPY. RADIATION PROTECTION DOSIMETRY 2019; 183:32-35. [PMID: 30753692 DOI: 10.1093/rpd/ncy239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Indexed: 06/09/2023]
Abstract
To identify the precise molecular processes to induce DNA lesions, we attempt a novel spectroscopy of X-ray induced luminescence (XIL) using soft X-ray synchrotron radiation, which is a non-destructive analysis of the reaction intermediates in the elementary reaction pathway of damage induction and self-organized restoration. Using a liquid micro-jet technique to introduce aqueous samples in a vacuum chamber, we measure UV-visible luminescence from nucleotide solution as a function of the soft X-ray energy from the nitrogen to oxygen K-edge region. The XIL intensities for the nucleotide solutions are significantly enhanced in the soft X-ray region (410-530 eV) which is ascribed to the K-shell excitation/ionization of nitrogen atoms in the nucleobases. Furthermore, the XIL spectra do not show any signature of X-ray absorption near-edge structure (XANES) of the nucleobases. This is because the luminescence intensities collected from the integral area of the micro-jet only reflect the quantum yield of luminescence of the absorbed X-ray into UV-visible light irrespective of the absorption cross sections, i.e. of XANES. Thus the present result is the first evidence of luminescence as a result of X-ray absorption of aqueous nucleotides.
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Affiliation(s)
- T Kojima
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - H Aihara
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - Y Kodashima
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - H Makishima
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - S Nakiri
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - S Takada
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - H Shimada
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - M Ukai
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, Japan
| | - C Ozga
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, Heinrich-Plett Str. 40, Kassel, Germany
| | - X Holzapfel
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, Heinrich-Plett Str. 40, Kassel, Germany
| | - Ph Schmidt
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, Heinrich-Plett Str. 40, Kassel, Germany
| | - C Küstner-Wetekam
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, Heinrich-Plett Str. 40, Kassel, Germany
| | - H Otto
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, Heinrich-Plett Str. 40, Kassel, Germany
| | - D Bloβ
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, Heinrich-Plett Str. 40, Kassel, Germany
| | - A Knie
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, Heinrich-Plett Str. 40, Kassel, Germany
| | - A Ehresmann
- Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology, University of Kassel, Heinrich-Plett Str. 40, Kassel, Germany
| | - A Yokoya
- Center of Quantum beam Science, National Institute for Quantum and Radiological Science (QST), Naka-gun, Ibaraki, Japan
| | - K Fujii
- Center of Quantum beam Science, National Institute for Quantum and Radiological Science (QST), Naka-gun, Ibaraki, Japan
| | - Y Fukuda
- Synchrotron Radiation Research Center, Japan Atomic Energy Agency (JAEA), Sayo-gun, Hyougo, Japan
| | - Y Saitoh
- Synchrotron Radiation Research Center, Japan Atomic Energy Agency (JAEA), Sayo-gun, Hyougo, Japan
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71
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Sasidharanpillai S, Loppnow GR. Initial Excited-State Structural Dynamics of dT and dA Oligonucleotide Homopentamers Using Resonance Raman Spectroscopy. J Phys Chem B 2019; 123:3898-3906. [PMID: 30973725 DOI: 10.1021/acs.jpcb.9b01168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photochemical damage of DNA is initiated by absorption of ultraviolet light, and the photoproducts are formed as a result of excited-state structural and electronic dynamics. We have used UV resonance Raman spectroscopy to measure the initial excited-state structural dynamics of homopentamers of adenosine monophosphate (3'-dApdApdApdApdAp-5') and thymidine monophosphate (3'-dTpdTpdTpdTpdTp-5') and compare them to those of the monomeric nucleobases. The resonance Raman spectra of the homopentamers are similar to those of the corresponding monomers. Initial excited-state slopes, homogeneous and inhomogeneous broadening, and other excited-state parameters were extracted by self-consistent simulation of the resonance Raman excitation profiles and absorption spectra with a time-dependent formalism and are also similar to the initial excited-state slopes and broadening in the nucleotide monomers. The lack of differences between the initial excited-state structural dynamics of the nucleotides within the pentamer and the isolated nucleobases is consistent with a model in which the formation of photochemical products in oligonucleotides and DNA is dependent on the formation of the transition-state structure within these polymers, dictated by their large-scale dynamics. These results are discussed in light of the known photochemistry of DNA and the nucleobases.
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Affiliation(s)
| | - Glen R Loppnow
- Department of Chemistry , University of Alberta , Edmonton , Alberta T6G 2G2 , Canada
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72
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Del Galdo S, Chandramouli B, Mancini G, Barone V. Assessment of Multi-Scale Approaches for Computing UV–Vis Spectra in Condensed Phases: Toward an Effective yet Reliable Integration of Variational and Perturbative QM/MM Approaches. J Chem Theory Comput 2019; 15:3170-3184. [DOI: 10.1021/acs.jctc.9b00120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sara Del Galdo
- Istituto di Chimica dei Composti OrganoMetallici (ICCOMCNR), UOS di Pisa, Area della Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Balasubramanian Chandramouli
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163 Genova, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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73
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Semmeq A, Ouaskit S, Monari A, Badawi M. Ionization and fragmentation of uracil upon microhydration. Phys Chem Chem Phys 2019; 21:4810-4821. [PMID: 30773577 DOI: 10.1039/c8cp07452f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study at the DFT level the ionization and the fragmentation of uracil in the presence of zero, one and two water molecules, to unravel the effect of microhydration on the reactivity of this nucleobase. We show that the microhydration lowers the adiabatic and vertical ionization potentials by 0.41 eV and 0.22 eV, respectively. Furthermore, microhydration increases the activation energies of the different dissociation channels up to 0.5 eV and restricts the formation of some fragments, in particular those corresponding to the C5-C6 fragmentation pathway. For the first time, our theoretical study shows new transition states and minima not found for the gas phase, hence indicating a change in the fragmentation mechanisms, as well as a stabilizing effect of microhydration, confirming previous experimental studies.
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Affiliation(s)
- Abderrahmane Semmeq
- Laboratoire Physique et Chimie Théoriques UMR 7019, CNRS - Université de Lorraine, BP239, Boulevard des Aiguillettes, 54 506 Vandoeuvre-lès-Nancy-Cedex, France.
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74
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Tseplin EE, Tseplina SN. Application of polar solvent effects in absorption spectra for determination of lowest electron-excited states of phthalide. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.12.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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75
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Molecular polarity effect on the association constant of cyclodextrin-pyrimidine nucleobases in water. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2018.11.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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76
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Fu F, Liao K, Ma J, Cheng Z, Zheng D, Gao L, Liu C, Li S, Li W. How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases. Phys Chem Chem Phys 2019; 21:4072-4081. [DOI: 10.1039/c8cp06152a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Intermolecular interactions in terms of molecular packing are crucial for the investigation of the absorption spectra of uracil in different environments.
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Affiliation(s)
- Fangjia Fu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Kang Liao
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Jing Ma
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Zheng Cheng
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Dong Zheng
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Liuzhou Gao
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Chungen Liu
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Shuhua Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Wei Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
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77
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Pepino AJ, Segarra-Martí J, Nenov A, Rivalta I, Improta R, Garavelli M. UV-induced long-lived decays in solvated pyrimidine nucleosides resolved at the MS-CASPT2/MM level. Phys Chem Chem Phys 2018; 20:6877-6890. [PMID: 29459916 DOI: 10.1039/c7cp08235e] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most relevant 'dark' electronic excited states in DNA/RNA pyrimidine nucleosides are mapped in water employing hybrid MS-CASPT2/MM optimisations with explicit solvation and including the sugar. Conical intersections (CIs) between initially accessed bright 1ππ* and the lowest energy dark 1nπ* excited states, involving the lone pair localised on the oxygen and/or nitrogen atoms are characterised. They are found in the vicinities of the Franck-Condon (FC) region and are shown to facilitate non-adiabatic population transfer. The excited state population of the 1nOπ* state, localised in the carbonyl moiety on all pyrimidine nucleosides, is predicted to rapidly evolve to its minimum, displaying non-negligible potential energy barriers along its non-radiative decay, and accounting for the ps signal registered in pump-probe experiments as well as for an efficient population of the triplet state. Cytidine displays an additional 1nNπ* state localised in the N3 atom and that leads to its excited state minimum displaying large potential energy barriers in the pathway connecting to the CI with the ground state. Sugar-to-base hydrogen/proton transfer processes are assessed in solution for the first time, displaying a sizable barrier along its decay and thus being competitive with other slow decay channels in the ps and ns timescales. A unified deactivation scheme for the long-lived channels of pyrimidine nucleosides is delivered, where the 1nOπ* state is found to mediate the long-lived decay in the singlet manifold and act as the doorway for triplet population and thus accounting for the recorded phosphorescence and, more generally, for the transient/photoelectron spectral signals registered up to the ns timescale.
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Affiliation(s)
- Ana Julieta Pepino
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy.
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78
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Letrun R, Lang B, Yushchenko O, Wilcken R, Svechkarev D, Kolodieznyi D, Riedle E, Vauthey E. Excited-state dynamics of a molecular dyad with two orthogonally-oriented fluorophores. Phys Chem Chem Phys 2018; 20:30219-30230. [PMID: 30489576 DOI: 10.1039/c8cp05356a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The excited-state dynamics of a T-shaped bichromophoric molecule, consisting of two strong fluorophores, diphenyloxazole and diphenylpyrazoline, directly linked in an orthogonal geometry, was investigated. Despite the weak coupling ensured by this geometry and confirmed by the electronic absorption spectra, this dyad exhibits only weak fluorescence in both apolar and polar solvents, with fluorescence lifetimes ranging from 200 ps in CHX to 10 ps in ACN. Ultrafast spectroscopic measurements reveal that the fluorescence quenching in polar solvents is due to the population of a charge-separated state. In non-polar solvents, this process is energetically not feasible, and a quenching due to an efficient intersystem crossing (ISC) to the triplet manifold is proposed, based on quantum-chemical calculations. This process occurs via the spin-orbit charge-transfer (SOCT) ISC mechanism, which is enabled by the charge-transfer character acquired by the S1 state of the dyad upon structural relaxation and by the orthogonal arrangement of the molecular orbitals involved in the transition. The same mechanism is proposed to explain why the recombination of the charge-separated state is faster in medium than in highly polar solvents, as well as to account for the fast decay of the lowest triplet state to the ground state.
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Affiliation(s)
- Romain Letrun
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
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79
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Lischka H, Barbatti M, Siddique F, Das A, Aquino AJ. The effect of hydrogen bonding on the nonadiabatic dynamics of a thymine-water cluster. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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80
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Wen K, Guo X, Zhang J. Computational prediction on photophysical properties of two excited state intramolecular proton transfer (ESIPT) fluorophores bearing the benzothiazole group. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1542169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Keke Wen
- Department of Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, People’s Republic of China
| | - Xugeng Guo
- Department of Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, People’s Republic of China
| | - Jinglai Zhang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Henan University, Kaifeng, People’s Republic of China
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81
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Miyata S, Tanabe S, Isozaki T, Xu YZ, Suzuki T. Characteristics of the excited triplet states of thiolated guanosine derivatives and singlet oxygen generation. Photochem Photobiol Sci 2018; 17:1469-1476. [PMID: 30280174 DOI: 10.1039/c8pp00240a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Thioguanine is sensitive to UVA light and generates singlet molecular oxygen (1O2*) when exposed to UVA. Three thioguanosine derivatives, 2',3',5'-tri-O-acetyl-6-thioguanosine (ta6TGuo), 2',3',5'-tri-O-acetyl-8-thioguanosine (ta8TGuo), and 2',3',5'-tri-O-acetyl-6,8-dithioguanosine (taDTGuo) were explored photophysically and photochemically. Nanosecond transient absorption and time-resolved near-infrared emission measurements were carried out to investigate the characteristics of their excited triplet states in acetonitrile solution. The quantum yield of intersystem crossing (ΦISC), the intrinsic decay rate constant (k0), the quenching rate constant by 3O2 (kq) and the self-quenching rate constant (kSQ) of their triplet states were all determined. From the precise analysis of the quantum yield of 1O2* generation (ΦΔ) against the concentration of dissolved molecular oxygen, the fraction of the triplet states quenched by dissolved oxygen which gives rise to 1O2* formation (SΔ) was successfully obtained with high accuracy. The ΦΔ values at low oxygen concentrations reveal that these thioguanosines, particularly taDTGuo, can still effectively generate 1O2* at low molecular oxygen concentrations like carcinomatous microenvironments. These findings indicate that taDTGuo would perform well as a potential agent for photo-induced cancer therapies.
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Affiliation(s)
- Shoma Miyata
- Department of Chemistry and Biological Science, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan.
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82
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Ashwood B, Pollum M, Crespo-Hernández CE. Photochemical and Photodynamical Properties of Sulfur-Substituted Nucleic Acid Bases. Photochem Photobiol 2018; 95:33-58. [PMID: 29978490 DOI: 10.1111/php.12975] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 06/28/2018] [Indexed: 12/25/2022]
Abstract
Sulfur-substituted nucleobases (a.k.a., thiobases) are among the world's leading prescriptions for chemotherapy and immunosuppression. Long-term treatment with azathioprine, 6-mercaptopurine and 6-thioguanine has been correlated with the photoinduced formation of carcinomas. Establishing an in-depth understanding of the photochemical properties of these prodrugs may provide a route to overcoming these carcinogenic side effects, or, alternatively, a basis for developing effective compounds for targeted phototherapy. In this review, a broad examination is undertaken, surveying the basic photochemical properties and excited-state dynamics of sulfur-substituted analogs of the canonical DNA and RNA nucleobases. A molecular-level understanding of how sulfur substitution so remarkably perturbs the photochemical properties of the nucleobases is presented by combining experimental results with quantum-chemical calculations. Structure-property relationships demonstrate the impact of site-specific sulfur substitution on the photochemical properties, particularly on the population of the reactive triplet state. The value of fundamental photochemical investigations for driving the development of ultraviolet-A chemotherapeutics is showcased. The most promising photodynamic agents identified thus far have been investigated in various carcinoma cell lines and shown to decrease cell proliferation upon exposure to ultraviolet-A radiation. Overarching principles have been elucidated for the impact that sulfur substitution of the carbonyl oxygen has on the photochemical properties of the nucleobases.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, Case Western Reserve University, Cleveland, OH
| | - Marvin Pollum
- Department of Chemistry, Case Western Reserve University, Cleveland, OH
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83
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Self-assembling behavior of pyrimidine analogues: Unveiling the factors behind morphological diversity. J Colloid Interface Sci 2018; 522:63-73. [DOI: 10.1016/j.jcis.2018.03.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 11/22/2022]
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84
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Conti I, Garavelli M. Evolution of the Excitonic State of DNA Stacked Thymines: Intrabase ππ* → S 0 Decay Paths Account for Ultrafast (Subpicosecond) and Longer (>100 ps) Deactivations. J Phys Chem Lett 2018; 9:2373-2379. [PMID: 29668287 DOI: 10.1021/acs.jpclett.8b00698] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Monomer-like ring puckering decay paths for two stacked quantum mechanical thymines inside a solvated DNA duplex described at the molecular mechanics level are mapped using a hybrid CASPT2//CASSCF/MM protocol that accounts for steric, electronic and electrostatic interactions within the nucleobases native environment. Asymmetric stacking between nucleobases open ups different intrabase ππ* decay paths accounting for distinctive excited state lifetimes, spanning the subps to subns time window.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale "Toso Montanari" , Università di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari" , Università di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
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85
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Lettieri R, D'Abramo M, Stella L, La Bella A, Leonelli F, Giansanti L, Venanzi M, Gatto E. Fluorescence and computational studies of thymidine phosphorylase affinity toward lipidated 5-FU derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 195:84-94. [PMID: 29414586 DOI: 10.1016/j.saa.2018.01.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 06/08/2023]
Abstract
Thymidine phosphorylase (TP) is an enzyme that is up-regulated in a wide variety of solid tumors, including breast and colorectal cancers. It is involved in tumor growth and metastasis, for this reason it is one of the key enzyme to be inhibited, in an attempt to prevent tumor proliferation. However, it also plays an active role in cancer treatment, through its contribution in the conversion of the anti-cancer drug 5-fluorouracil (5-FU) to an irreversible inhibitor of thymidylate synthase (TS), responsible of the inhibition of the DNA synthesis. In this work, the intrinsic TP fluorescence has been investigated for the first time and exploited to study TP binding affinity for the unsubstituted 5-FU and for two 5-FU derivatives, designed to expose this molecule on liposomal membranes. These molecules were obtained by functionalizing the nitrogen atom with a chain consisting of six (1) or seven (2) units of glycol, linked to an alkyl moiety of 12 carbon atoms. Derivatives (1) and (2) exhibited an affinity for TP in the micromolar range, 10 times higher than the parent compound, irrespective of the length of the polyoxyethylenic spacer. This high affinity was maintained also when the compounds were anchored in liposomal membranes. Experimental results were supported by molecular dynamics simulations and docking calculations, supporting a feasible application of the designed supramolecular lipid structure in selective targeting of TP, to be potentially used as a drug delivery system or sensor device.
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Affiliation(s)
- R Lettieri
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - M D'Abramo
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, Roma, Italy
| | - L Stella
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - A La Bella
- Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, Roma, Italy
| | - F Leonelli
- Dipartimento di Biologia Ambientale, Università degli Studi di Roma "La Sapienza", Roma, Italy
| | - L Giansanti
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell'Aquila, Aquila, Italy; CNR, Istituto di Metodologie Chimiche, Monterotondo Scalo, Rome, Italy
| | - M Venanzi
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - E Gatto
- Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, Roma, Italy.
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86
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Yuan H, Feng S, Wen K, Guo X, Zhang J. The excited-state intramolecular proton transfer in NH-type dye molecules with a seven-membered-ring intramolecular hydrogen bond: A theoretical insight. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:421-426. [PMID: 29069638 DOI: 10.1016/j.saa.2017.10.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/09/2017] [Accepted: 10/15/2017] [Indexed: 06/07/2023]
Abstract
Excited-state intramolecular proton transfer (ESIPT) reactions of a series of N(R)H⋯N-type seven-membered-ring hydrogen-bonding compounds were explored by employing density functional theory/time-dependent density functional theory calculations with the PBE0 functional. Our results indicate that the absorption and emission spectra predicted theoretically match very well the experimental findings. Additionally, as the electron-withdrawing strength of R increases, the intramolecular H-bond of the NS1 form gradually enhances, and the forward energy barrier along the ESIPT reaction gradually decreases. For compound 4, its ESIPT reaction is found to be a barrierless process due to the involvement of a strong electron-withdrawing COCF3 group. It is therefore a reasonable presumption that the ESIPT efficiency of these N(R)H⋯N-type seven-membered-ring H-bonding systems can be improved when a strong electron-withdrawing group in R is introduced.
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Affiliation(s)
- Huijuan Yuan
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, PR China
| | - Songyan Feng
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, PR China
| | - Keke Wen
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, PR China
| | - Xugeng Guo
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, PR China.
| | - Jinglai Zhang
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, PR China.
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87
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Taniguchi M, Lindsey JS. Database of Absorption and Fluorescence Spectra of >300 Common Compounds for use in Photochem
CAD. Photochem Photobiol 2018; 94:290-327. [DOI: 10.1111/php.12860] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/22/2017] [Indexed: 12/11/2022]
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88
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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: 69] [Impact Index Per Article: 11.5] [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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89
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Shrivas K, Nirmalkar N, Thakur SS, Kurrey R, Sinha D, Shankar R. Experimental and theoretical approaches for the selective detection of thymine in real samples using gold nanoparticles as a biochemical sensor. RSC Adv 2018; 8:24328-24337. [PMID: 35539214 PMCID: PMC9082146 DOI: 10.1039/c8ra02627k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/15/2018] [Indexed: 12/02/2022] Open
Abstract
We report a simple, selective and cost effective method for the qualitative and quantitative determination of thymine in a DNA standard and urine samples using gold nanoparticles (AuNPs) as a label-free colorimetric biochemical sensor. The mechanism for the detection of thymine is demonstrated via the color change of the AuNPs from pink to blue, followed by the shift of the localized surface plasmon resonance (LSPR) absorption band to a higher wavelength with the introduction of an analyte. The selective detection of thymine was experimentally verified by performing a control experiment with nucleobases, other biomolecules, metal ions and anions. In addition, the computation density functional theory (DFT) and time dependent density functional theory (TD-DFT) using the Gaussian (C.01) program highlighted that the electrostatic potential behavior of the thymine molecule facilitated a non-covalent interaction toward gold for the selective detection of analytes, and the computation was also used to calculate a UV-Vis absorption band as well. The calculated absorption band of the AuNPs with thymine, obtained using TD-DFT, was found to be very close to the experimental data. The omnicapped truncated tetrahedral (ν3-tetrahedral) Au20 cluster structure was considered as the model for the AuNP optimization. The linear range obtained for the quantitative determination of thymine was found to be 10–1200 ng mL−1 with a limit of detection of 3 ng mL−1. The advantages of using the AuNPs as a biochemical sensor are that they provide a facile and low cost method and are selective for the qualitative and quantitative determination of thymine in a DNA standard and in urine samples in comparison to chromatographic and electrochemical methods. We report a simple, selective and cost effective method for the qualitative and quantitative determination of thymine in a DNA standard and in urine samples using gold nanoparticles (AuNPs) as a label-free colorimetric biochemical sensor.![]()
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Affiliation(s)
- Kamlesh Shrivas
- School of Studies in Chemistry
- Pt. Ravishankar Shukla University
- Raipur
- India
- Department of Chemistry
| | - Nidhi Nirmalkar
- Department of Chemistry
- Guru Ghasidas Vishwavidyalaya
- Bilaspur
- India
| | | | - Ramsingh Kurrey
- School of Studies in Chemistry
- Pt. Ravishankar Shukla University
- Raipur
- India
| | - Deepak Sinha
- Department of Chemistry
- Government Nagarjuna Post Graduate College of Science
- Raipur
- India
| | - Ravi Shankar
- Nanoscience and Nanoengineering Program
- South Dakota School of Mines and Technology
- Rapid City
- USA
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90
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Sherin PS, Tsentalovich YP, Vauthey E, Benassi E. Ultrafast excited state decay of natural UV filters: from intermolecular hydrogen bonds to a conical intersection. Phys Chem Chem Phys 2018; 20:15074-15085. [DOI: 10.1039/c8cp02183j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An unsaturated bond in the side chain leads to the ultrafast decay of the excited statesviaa conical intersection independent of solvent properties.
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Affiliation(s)
- Peter S. Sherin
- International Tomography Center SB RAS
- Novosibirsk
- Russia
- Novosibirsk State University
- Novosibirsk
| | - Yuri P. Tsentalovich
- International Tomography Center SB RAS
- Novosibirsk
- Russia
- Novosibirsk State University
- Novosibirsk
| | - Eric Vauthey
- Department of Physical Chemistry
- University of Geneva
- Geneva
- Switzerland
| | - Enrico Benassi
- Novosibirsk State University
- Novosibirsk
- Russia
- School of Science and Technology
- Nazarbayev University
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91
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Pale V, Giedraityte Z, Chen X, Lopez-Acevedo O, Tittonen I, Karppinen M. Excitation-dependent fluorescence from atomic/molecular layer deposited sodium-uracil thin films. Sci Rep 2017; 7:6982. [PMID: 28765548 PMCID: PMC5539323 DOI: 10.1038/s41598-017-07456-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/28/2017] [Indexed: 12/27/2022] Open
Abstract
Atomic/molecular layer deposition (ALD/MLD) offers unique possibilities in the fabrication of inorganic-organic thin films with novel functionalities. Especially, incorporating nucleobases in the thin-film structures could open new avenues in the development of bio-electronic and photonic devices. Here we report an intense blue and widely excitation-dependent fluorescence in the visible region for ALD/MLD fabricated sodium-uracil thin films, where the crystalline network is formed from hydrogen-bonded uracil molecules linked via Na atoms. The excitation-dependent fluorescence is caused by the red-edge excitation shift (REES) effect taking place in the red-edge of the absorption spectrum, where the spectral relaxation occurs in continuous manner as demonstrated by the time-resolved measurements.
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Affiliation(s)
- Ville Pale
- Department of Electronics and Nanoengineering, Aalto University, FI-00076, Aalto, Finland
| | - Zivile Giedraityte
- Department of Chemistry and Materials Science, Aalto University, FI-00076, Aalto, Finland
| | - Xi Chen
- COMP Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, FI-00076, Aalto, Finland
| | - Olga Lopez-Acevedo
- COMP Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, FI-00076, Aalto, Finland
- Departamento de Ciencias Básicas, Universidad de Medellín, Carrera 87 # 30-65, Medellín, Colombia
| | - Ilkka Tittonen
- Department of Electronics and Nanoengineering, Aalto University, FI-00076, Aalto, Finland
| | - Maarit Karppinen
- Department of Chemistry and Materials Science, Aalto University, FI-00076, Aalto, Finland.
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92
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Theoretical study of Au 4 thymine, Au 20 and Ag 20 uracil and thymine complexes for surface enhanced Raman scattering. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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93
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Martínez-Fernández L, Pepino AJ, Segarra-Martí J, Jovaišaitė J, Vaya I, Nenov A, Markovitsi D, Gustavsson T, Banyasz A, Garavelli M, Improta R. Photophysics of Deoxycytidine and 5-Methyldeoxycytidine in Solution: A Comprehensive Picture by Quantum Mechanical Calculations and Femtosecond Fluorescence Spectroscopy. J Am Chem Soc 2017; 139:7780-7791. [DOI: 10.1021/jacs.7b01145] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- L. Martínez-Fernández
- Istituto di Biostrutture e Bioimmagini,
CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - A. J. Pepino
- Dipartimento di Chimica Industriale “T. Montanari”, Università di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - J. Segarra-Martí
- Laboratoire de Chimie UMR 5182, Univ Lyon, ENS de Lyon, CNRS, Université Lyon 1, F-69342 Lyon, France
| | - J. Jovaišaitė
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - I. Vaya
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - A. Nenov
- Dipartimento di Chimica Industriale “T. Montanari”, Università di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - D. Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - T. Gustavsson
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - A. Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - M. Garavelli
- Dipartimento di Chimica Industriale “T. Montanari”, Università di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - R. Improta
- Istituto di Biostrutture e Bioimmagini,
CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
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94
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Pepino AJ, Segarra-Martí J, Nenov A, Improta R, Garavelli M. Resolving Ultrafast Photoinduced Deactivations in Water-Solvated Pyrimidine Nucleosides. J Phys Chem Lett 2017; 8:1777-1783. [PMID: 28346789 DOI: 10.1021/acs.jpclett.7b00316] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
For the first time, ultrafast deactivations of photoexcited water-solvated pyrimidine nucleosides are mapped employing hybrid QM(CASPT2)/MM(AMBER) optimizations that account for explicit solvation, sugar effects, and dynamically correlated potential energy surfaces. Low-energy S1/S0 ring-puckering and ring-opening conical intersections (CIs) are suggested to drive the ballistic coherent subpicosecond (<200 fs) decays observed in each pyrimidine, the energetics controlling this processes correlating with the lifetimes observed. A second bright 1π2π* state, promoting excited-state population branching and leading toward a third CI with the ground state, is proposed to be involved in the slower ultrafast decay component observed in Thd/Cyd. The transient spectroscopic signals of the competitive deactivation channels are computed for the first time. A general unified scheme for ultrafast deactivations, spanning the sub- to few-picosecond time domain, is eventually delivered, with computed data that matches the experiments and elucidates the intrinsic photoprotection mechanism in solvated pyrimidine nucleosides.
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Affiliation(s)
- Ana Julieta Pepino
- Dipartimento di Chimica Industriale "Toso Montanari" Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Javier Segarra-Martí
- Laboratoire de Chimie UMR 5182, Université Lyon, ENS de Lyon, CNRS, Université Lyon 1 , F-69342 Lyon, France
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari" Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini CNR , Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari" Viale del Risorgimento, 4, 40136 Bologna, Italy
- Laboratoire de Chimie UMR 5182, Université Lyon, ENS de Lyon, CNRS, Université Lyon 1 , F-69342 Lyon, France
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95
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Ostakhov SS, Sultanbaev MV, Ovchinnikov MY, Kayumov RR, Khursan SL. Spectral-luminescence and quantum-chemical study of the anionic forms of 5-fluorouracil. HIGH ENERGY CHEMISTRY 2017. [DOI: 10.1134/s0018143917010076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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96
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Luo J, Liu Y, Yang S, Flourat AL, Allais F, Han K. Ultrafast Barrierless Photoisomerization and Strong Ultraviolet Absorption of Photoproducts in Plant Sunscreens. J Phys Chem Lett 2017; 8:1025-1030. [PMID: 28177249 DOI: 10.1021/acs.jpclett.7b00083] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sunscreens are aimed at protecting skin from solar ultraviolet (UV) irradiation. By utilizing femtosecond transient absorption spectroscopy and time-dependent density functional theory, we explain nature's selection of sinapoyl malate rather than sinapic acid as the plant sunscreen molecule. In physiological pH conditions, the two molecules are deprotonated, and their excited ππ* states are found to relax to the ground states in a few tens of picoseconds via a barrierless trans-cis photoisomerization. After the cis-photoproduct is formed, the efficacy of sinapic acid is greatly reduced. In contrast, the efficacy of sinapoyl malate is affected only slightly because the cis-product still absorbs UV light strongly. In addition, protonated sinapic acid is found to be a good potential sunscreen molecule.
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Affiliation(s)
- Jian Luo
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences , 457 Zhongshan Road, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences , Beijing 10049, China
| | - Yan Liu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences , 457 Zhongshan Road, Dalian, Liaoning 116023, China
- University of the Chinese Academy of Sciences , Beijing 10049, China
| | - Songqiu Yang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences , 457 Zhongshan Road, Dalian, Liaoning 116023, China
| | - Amandine L Flourat
- Chaire Agro-Biotechnologies Industrielles (ABI), AgroParisTech , CEBB 3 rue des Rouges Terres, 51110 Pomacle, France
- Institut Jean-Pierre Bourgin, INRA/AgroParisTech/CNRS/Université Paris-Saclay , Route de Saint-Cyr, 78026 Versailles, France
| | - Florent Allais
- Chaire Agro-Biotechnologies Industrielles (ABI), AgroParisTech , CEBB 3 rue des Rouges Terres, 51110 Pomacle, France
- UMR GMPA, INRA/AgroParisTech/CNRS/Université Paris-Saclay , Avenue Lucien Brétignières, 78850 Thiverval-Grignon, France
- Institut Jean-Pierre Bourgin, INRA/AgroParisTech/CNRS/Université Paris-Saclay , Route de Saint-Cyr, 78026 Versailles, France
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics (DICP), Chinese Academy of Sciences , 457 Zhongshan Road, Dalian, Liaoning 116023, China
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97
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Role of base arrangements and intermolecular hydrogen bonding in charge-transfer states of thymine-adenine dinucleotide in aqueous solution. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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98
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Keefer D, Thallmair S, Matsika S, de Vivie-Riedle R. Controlling Photorelaxation in Uracil with Shaped Laser Pulses: A Theoretical Assessment. J Am Chem Soc 2017; 139:5061-5066. [DOI: 10.1021/jacs.6b12033] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Keefer
- Department
Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Sebastian Thallmair
- Department
Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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99
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Effects of hydrogen bonding with H2O on the resonance Raman spectra of uracil and thymine. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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100
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Martinez-Fernandez L, Fahleson T, Norman P, Santoro F, Coriani S, Improta R. Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution. Photochem Photobiol Sci 2017; 16:1415-1423. [DOI: 10.1039/c7pp00105c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The excited electronic states of thiouracils, the analogues of uracil where the carbonyl oxygens are substituted by sulphur atoms, have been investigated by computing the magnetic circular dichroism (MCD) and one-photon absorption (OPA) spectra at the TD-DFT level of theory.
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Affiliation(s)
| | - T. Fahleson
- KTH Royal Institute of Technology
- SE-10044 Stockholm
- Sweden
| | - P. Norman
- KTH Royal Institute of Technology
- SE-10044 Stockholm
- Sweden
| | - F. Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR)
- Area della Ricerca del CNR
- I-56124 Pisa
- Italy
| | - S. Coriani
- Department of Chemistry
- Technical University of Denmark
- Denmark
| | - R. Improta
- Istituto di Biostrutture e Bioimmagini-CNR
- I-80134 Napoli
- Italy
- LIDYL
- CEA
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