1
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Navarrete-Miguel M, Giussani A, Rubio M, Boggio-Pasqua M, Borin AC, Roca-Sanjuán D. Quantum-Chemistry Study of the Photophysical Properties of 4-Thiouracil and Comparisons with 2-Thiouracil. J Phys Chem A 2024; 128:2273-2285. [PMID: 38504122 PMCID: PMC10982997 DOI: 10.1021/acs.jpca.3c06310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/16/2024] [Accepted: 03/03/2024] [Indexed: 03/21/2024]
Abstract
DNA in living beings is constantly damaged by exogenous and endogenous agents. However, in some cases, DNA photodamage can have interesting applications, as it happens in photodynamic therapy. In this work, the current knowledge on the photophysics of 4-thiouracil has been extended by further quantum-chemistry studies to improve the agreement between theory and experiments, to better understand the differences with 2-thiouracil, and, last but not least, to verify its usefulness as a photosensitizer for photodynamic therapy. This study has been carried out by determining the most favorable deactivation paths of UV-vis photoexcited 4-thiouracil by means of the photochemical reaction path approach and an efficient combination of the complete-active-space second-order perturbation theory//complete-active-space self-consistent field (CASPT2//CASSCF), (CASPT2//CASPT2), time-dependent density functional theory (TDDFT), and spin-flip TDDFT (SF-TDDFT) methodologies. By comparing the data computed herein for both 4-thiouracil and 2-thiouracil, a rationale is provided on the relatively higher yields of intersystem crossing, triplet lifetime and singlet oxygen production of 4-thiouracil, and the relatively higher yield of phosphorescence of 2-thiouracil.
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Affiliation(s)
- Miriam Navarrete-Miguel
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Angelo Giussani
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Mercedes Rubio
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
| | - Martial Boggio-Pasqua
- Laboratoire
de Chimie et Physique Quantiques, IRSAMC,
CNRS et Université Toulouse 3, 118 route de Narbonne, 31062 Toulouse, France
| | - Antonio Carlos Borin
- Department
of Fundamental Chemistry, Institute of Chemistry,
University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo CEP 05508-000, Brazil
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain
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2
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Mayer D, Picconi D, Robinson MS, Gühr M. Experimental and theoretical gas-phase absorption spectra of thionated uracils. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Jena S, Tulsiyan KD, Kar RK, Kisan HK, Biswal HS. Doubling Förster Resonance Energy Transfer Efficiency in Proteins with Extrinsic Thioamide Probes: Implications for Thiomodified Nucleobases. Chemistry 2021; 27:4373-4383. [PMID: 33210381 DOI: 10.1002/chem.202004627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Indexed: 12/29/2022]
Abstract
Designing a potential protein-ligand pair is pivotal, not only to track the protein structure dynamics, but also to assist in an atomistic understanding of drug delivery. Herein, the potential of a small model thioamide probe being used to study albumin proteins is reported. By monitoring the Förster resonance energy transfer (FRET) dynamics with the help of fluorescence spectroscopic techniques, a twofold enhancement in the FRET efficiency of 2-thiopyridone (2TPY), relative to that of its amide analogue, is observed. Molecular dynamics simulations depict the relative position of the free energy minimum to be quite stable in the case of 2TPY through noncovalent interactions with sulfur, which help to enhance the FRET efficiency. Finally, its application is shown by pairing thiouracils with protein. It is found that the site-selective sulfur atom substitution approach and noncovalent interactions with sulfur can substantially enhance the FRET efficiency, which could be a potential avenue to explore in the design of FRET probes to study the structure and dynamics of biomolecules.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Hemanta K Kisan
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.,Department of Chemistry, Utkal University, 751004, Bhubaneswar, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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4
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Mohamadzade A, Ullrich S. Internal conversion and intersystem crossing dynamics of uracil upon double thionation: a time-resolved photoelectron spectroscopy study in the gas phase. Phys Chem Chem Phys 2020; 22:15608-15615. [PMID: 32613978 DOI: 10.1039/d0cp02145h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The photophysical properties of 2,4-dithiouracil (2,4-DTU) in the gas phase are studied by time-resolved photoelectron spectroscopy (TRPES) with three different excitation wavelengths in direct extension of previous work on uracil (U), 2-thiouracil (2-TU) and 4-thiouracil (4-TU). Non-radiative deactivation in the canonical nucleobases like uracil mainly occurs via internal conversion (IC) along singlet excited states, although intersystem crossing (ISC) to a long-lived triplet state was confirmed to play a minor role. In thionated uracils, ISC to the triplet state becomes ultrafast and highly efficient with a quantum yield near unity; however, the lifetime of the triplet state is strongly dependent on the position of the sulfur atom. In 2-TU, ISC back to the ground state occurs within a few hundred picoseconds, whereas the population remains trapped in the lowest triplet state in the case of 4-TU. Upon doubling the degree of thionation, ISC remains highly efficient and dominates the photophysics of 2,4-DTU. However, several low-lying excited states contribute to competing IC and ISC pathways and a complex deactivation mechanism, which is evaluated here based on TRPES measurements and discussed in the context of the singly thionated uracils.
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Affiliation(s)
- Abed Mohamadzade
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
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5
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Conformers of 1,2,3,4 –tetrahydroisoquinoline in S0 and S1: An analysis through potential energy surface, hardness principles and vibrational spectroscopy. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127836] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Intersystem crossing dynamics in singly substituted thiouracil studied by time-resolved photoelectron spectroscopy: Micro-environmental effects due to sulfur position. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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7
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Hamlow LA, Zhu Y, Devereaux ZJ, Cunningham NA, Berden G, Oomens J, Rodgers MT. Modified Quadrupole Ion Trap Mass Spectrometer for Infrared Ion Spectroscopy: Application to Protonated Thiated Uridines. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:2125-2137. [PMID: 30136214 DOI: 10.1007/s13361-018-2047-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 05/17/2023]
Abstract
Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s2Urd+H]+, and 4-thiouridine, [s4Urd+H]+. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2'-endo and C3'-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine. Graphical Abstract ᅟ.
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Affiliation(s)
- L A Hamlow
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - Y Zhu
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - Zachary J Devereaux
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - N A Cunningham
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA
| | - G Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - J Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, 5101 Cass Ave., Detroit, MI, 48202, USA.
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8
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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: 66] [Impact Index Per Article: 11.0] [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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9
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Koyama D, Milner MJ, Orr-Ewing AJ. Evidence for a Double Well in the First Triplet Excited State of 2-Thiouracil. J Phys Chem B 2017; 121:9274-9280. [PMID: 28895733 DOI: 10.1021/acs.jpcb.7b06917] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The computationally predicted presence of two structurally distinct minima in the first triplet excited (T1) state of 2-thiouracil (2TU) is substantiated by sub-picosecond transient vibrational absorption spectroscopy (TVAS) in deuterated acetonitrile solution. Following 300 nm ultraviolet excitation to the second singlet excited state of 2TU, a transient infrared absorption band centered at 1643 cm-1 is observed within our minimum time resolution of 0.3 ps. It is assigned either to 2TU molecules in the S1 state or to vibrationally hot T1-state molecules, with the latter assignment more consistent with recent computational and experimental studies. The 1643 cm-1 band decays with a time constant of 7.2 ± 0.8 ps, and there is corresponding growth of several further bands centered at 1234, 1410, 1424, 1443, 1511, 1626, and 1660 cm-1 which show no decline in intensity over the 1 ns time limit of our measurements. These spectral features are assigned to two different conformations of 2TU, corresponding to separate energy minima on the T1-state potential energy surface, on the basis of their extended lifetimes, computed infrared frequencies, and the observed quenching of the bands by addition of styrene. Corresponding measurements for the 4-thiouracil (4TU) isomer show sub-picosecond population of the T1 state, which vibrationally cools with a time constant of 5.2 ± 0.6 ps. However, TVAS measurements in the carbonyl stretching region do not distinguish the two computed T1-state conformers of 4TU because of the similarity of their vibrational frequencies.
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Affiliation(s)
- Daisuke Koyama
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Matthew J Milner
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Andrew J Orr-Ewing
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
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10
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Arslancan S, Martínez-Fernández L, Corral I. Photophysics and Photochemistry of Canonical Nucleobases’ Thioanalogs: From Quantum Mechanical Studies to Time Resolved Experiments. Molecules 2017. [PMCID: PMC6152766 DOI: 10.3390/molecules22060998] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Interest in understanding the photophysics and photochemistry of thiated nucleobases has been awakened because of their possible involvement in primordial RNA or their potential use as photosensitizers in medicinal chemistry. The interpretation of the photodynamics of these systems, conditioned by their intricate potential energy surfaces, requires the powerful interplay between experimental measurements and state of the art molecular simulations. In this review, we provide an overview on the photophysics of natural nucleobases’ thioanalogs, which covers the last 30 years and both experimental and computational contributions. For all the canonical nucleobase’s thioanalogs, we have compiled the main steady state absorption and emission features and their interpretation in terms of theoretical calculations. Then, we revise the main topographical features, including stationary points and interstate crossings, of their potential energy surfaces based on quantum mechanical calculations and we conclude, by combining the outcome of different spectroscopic techniques and molecular dynamics simulations, with the mechanism by which these nucleobase analogs populate their triplet excited states, which are at the origin of their photosensitizing properties.
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Affiliation(s)
- Serra Arslancan
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Madrid 28049, Spain;
| | - Lara Martínez-Fernández
- Istituto Biostrutture e Bioimmagini-Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, Napoli I-80134, Italy
- Correspondence: (L.M.-F.); (I.C.); Tel.: +34-91-497-8471 (I.C.)
| | - Inés Corral
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, Madrid 28049, Spain;
- Institute for Advanced Research in Chemical Sciences (IADCHEM), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Correspondence: (L.M.-F.); (I.C.); Tel.: +34-91-497-8471 (I.C.)
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11
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Excited-State Dynamics of the Thiopurine Prodrug 6-Thioguanine: Can N9-Glycosylation Affect Its Phototoxic Activity? Molecules 2017; 22:molecules22030379. [PMID: 28264514 PMCID: PMC6155220 DOI: 10.3390/molecules22030379] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/15/2017] [Accepted: 02/24/2017] [Indexed: 12/25/2022] Open
Abstract
6-Thioguanine, an immunosuppressant and anticancer prodrug, has been shown to induce DNA damage and cell death following exposure to UVA radiation. Its metabolite, 6-thioguanosine, plays a major role in the prodrug's overall photoreactivity. However, 6-thioguanine itself has proven to be cytotoxic following UVA irradiation, warranting further investigation into its excited-state dynamics. In this contribution, the excited-state dynamics and photochemical properties of 6-thioguanine are studied in aqueous solution following UVA excitation at 345 nm in order to provide mechanistic insight regarding its photochemical reactivity and to scrutinize whether N9-glycosylation modulates its phototoxicity in solution. The experimental results are complemented with time-dependent density functional calculations that include solvent dielectric effects by means of a reaction-field solvation model. UVA excitation results in the initial population of the S₂(ππ*) state, which is followed by ultrafast internal conversion to the S₁(nπ*) state and then intersystem crossing to the triplet manifold within 560 ± 60 fs. A small fraction (ca. 25%) of the population that reaches the S₁(nπ*) state repopulates the ground state. The T₁(ππ*) state decays to the ground state in 1.4 ± 0.2 μs under N₂-purged conditions, using a 0.2 mM concentration of 6-thioguanine, or it can sensitize singlet oxygen in 0.21 ± 0.02 and 0.23 ± 0.02 yields in air- and O₂-saturated solution, respectively. This demonstrates the efficacy of 6-thioguanine to act as a Type II photosensitizer. N9-glycosylation increases the rate of intersystem crossing from the singlet to triplet manifold, as well as from the T₁(ππ*) state to the ground state, which lead to a ca. 40% decrease in the singlet oxygen yield under air-saturated conditions. Enhanced vibronic coupling between the singlet and triplet manifolds due to a higher density of vibrational states is proposed to be responsible for the observed increase in the rates of intersystem crossing in 6-thioguanine upon N9-glycosylation.
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Sánchez-Rodríguez JA, Mohamadzade A, Mai S, Ashwood B, Pollum M, Marquetand P, González L, Crespo-Hernández CE, Ullrich S. 2-Thiouracil intersystem crossing photodynamics studied by wavelength-dependent photoelectron and transient absorption spectroscopies. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp02258a] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The excitation-wavelength dependence of the intersystem crossing (ISC) dynamics of 2-thiouracil was studied in gas-phase and solution.
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Affiliation(s)
| | - Abed Mohamadzade
- Department of Physics and Astronomy
- University of Georgia
- Athens
- USA
| | - Sebastian Mai
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- Währinger Straße 17
- Austria
| | - Brennan Ashwood
- Department of Chemistry and Center for Chemical Dynamics
- Case Western Reserve University
- 10900 Euclid Avenue
- Cleveland
- USA
| | - Marvin Pollum
- Department of Chemistry and Center for Chemical Dynamics
- Case Western Reserve University
- 10900 Euclid Avenue
- Cleveland
- USA
| | - Philipp Marquetand
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- Währinger Straße 17
- Austria
| | - Leticia González
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- Währinger Straße 17
- Austria
| | - Carlos E. Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics
- Case Western Reserve University
- 10900 Euclid Avenue
- Cleveland
- USA
| | - Susanne Ullrich
- Department of Physics and Astronomy
- University of Georgia
- Athens
- USA
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13
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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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14
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Mai S, Marquetand P, González L. A Static Picture of the Relaxation and Intersystem Crossing Mechanisms of Photoexcited 2-Thiouracil. J Phys Chem A 2015; 119:9524-33. [PMID: 26284285 PMCID: PMC4568544 DOI: 10.1021/acs.jpca.5b06639] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 08/17/2015] [Indexed: 12/02/2022]
Abstract
Accurate excited-state quantum chemical calculations on 2-thiouracil, employing large active spaces and up to quadruple-ζ quality basis sets in multistate complete active space perturbation theory calculations, are reported. The results suggest that the main relaxation path for 2-thiouracil after photoexcitation should be S2 → S1 → T2 → T1, and that this relaxation occurs on a subpicosecond time scale. There are two deactivation pathways from the initially excited bright S2 state to S1, one of which is nearly barrierless and should promote ultrafast internal conversion. After relaxation to the S1 minimum, small singlet-triplet energy gaps and spin-orbit couplings of about 130 cm(-1) are expected to facilitate intersystem crossing to T2, from where very fast internal conversion to T1 occurs. An important finding is that 2-thiouracil shows strong pyramidalization at the carbon atom of the thiocarbonyl group in several excited states.
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Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
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15
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Zou X, Dai X, Liu K, Zhao H, Song D, Su H. Photophysical and Photochemical Properties of 4-Thiouracil: Time-Resolved IR Spectroscopy and DFT Studies. J Phys Chem B 2014; 118:5864-72. [DOI: 10.1021/jp501658a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaoran Zou
- State Key Laboratory of Molecular
Reaction Dynamics, Beijing National Laboratory for Molecular Sciences
(BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaojuan Dai
- State Key Laboratory of Molecular
Reaction Dynamics, Beijing National Laboratory for Molecular Sciences
(BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Kunhui Liu
- State Key Laboratory of Molecular
Reaction Dynamics, Beijing National Laboratory for Molecular Sciences
(BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongmei Zhao
- State Key Laboratory of Molecular
Reaction Dynamics, Beijing National Laboratory for Molecular Sciences
(BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Di Song
- State Key Laboratory of Molecular
Reaction Dynamics, Beijing National Laboratory for Molecular Sciences
(BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongmei Su
- State Key Laboratory of Molecular
Reaction Dynamics, Beijing National Laboratory for Molecular Sciences
(BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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16
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Photochemistry of Nucleic Acid Bases and Their Thio- and Aza-Analogues in Solution. Top Curr Chem (Cham) 2014; 355:245-327. [DOI: 10.1007/128_2014_554] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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17
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18
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Kozłowska J, Wielgus M, Bartkowiak W. TD-DFT study on the charge-transfer excitations of anions possessing double or triple bonds. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Shukla MK, Leszczynski J. Tautomerism in nucleic acid bases and base pairs: a brief overview. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1145] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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20
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Comparative theoretical study of the UV/Vis absorption spectra of styrylpyridine compounds using TD-DFT calculations. J Mol Model 2012; 19:2015-26. [DOI: 10.1007/s00894-012-1602-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 09/21/2012] [Indexed: 10/27/2022]
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GOMZI VJERAN. TDDFT STUDY OF NUCLEOBASE THIOANALOGUES AND OXO-DERIVATIVES EXCITED STATES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s021963360900454x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Thioanalogues of nucleic-acid bases have been shown to be the place of preferential charge or energy localization when incorporated in the system of respective regular bases. Most evidence of such behavior is based on experiments using γ-ray or other ionizing radiation. Here time dependent density functional theory (TDDFT) has been applied to investigate singlet and triplet excited state spectra of thioanalogues and some oxo-derivatives of nucleic-acid bases and compare the spectra to the calculated spectra of the regular bases as well as to the existing experimental data. It has been shown that thioanalogues have lower excitation singlet and triplet energies than are the respective energies in the regular bases. Energy localization on thioanalogues and their spectroscopic properties are related to the effect of sulfur substitution in such systems.
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Affiliation(s)
- VJERAN GOMZI
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10000 Zagreb, Croatia
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Wenska G, Taras-Goślińska K, Łukaszewicz A, Burdziński G, Koput J, Maciejewski A. Mechanism and dynamics of intramolecular triplet state decay of 1-propyl-4-thiouracil and its α-methyl-substituted derivatives studied in perfluoro-1,3-dimethylcyclohexane. Photochem Photobiol Sci 2011; 10:1294-302. [PMID: 21594285 DOI: 10.1039/c1pp05034f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The absorption, phosphorescence and phosphorescence excitation spectra, phosphorescence quantum yields, and T(1) excited state lifetimes of four 4-thiouracil derivatives were measured for the first time in chemically inert and very weakly interacting perfluoro-1,3-dimethylcyclohexane at room temperature. The set of the 4-thiouracil derivatives comprises 1-propyl-4-thiouracil (PTU) and the related compounds having a methyl substituent at the position α to the thiocarbonyl group, namely 1-propyl-4-thiothymine (PTT), 1,3-dimethyl-4-thiouracil (DMTU), and 1-methyl-3-trideuteriomethyl-4-thiouracil ([D(3)]DMTU). Quantitative information on the intramolecular decay of the T(1) excited state of the four 4-thiouracil derivatives is presented, and the mechanism and dynamics of this process are discussed. In the absence of self quenching and solvent induced deactivation, the T(1) decay of the four 4-thiouracil derivatives was dominated by intramolecular nonradiative processes (NR). The values of the rate constant k(NR) in DMTU and [D(3)]DMTU are about 4 times larger than that in PTT and about 3 times larger than that in PTU. The reasons for the enhanced nonradiative rate constant in DMTU are discussed. It is concluded that the faster rate of the nonradiative processes in DMTU is related to a larger contribution from mixing of the T(2) (nπ*) state into the lowest energy T(1) (ππ*) state, as compared to the analogous coupling in PTU and PTT. This conclusion is supported by ab initio calculations performed at the EOM-CC2/aug-cc-pVDZ level of theory. The energy spacing between the T(2) (nπ*) and T(1) (ππ*) states is estimated to be about 500, 1100, and 2000 cm(-1) for DMTU, PTU, and PTT, respectively. Among the three compounds in question, the predicted energy spacing is thus the smallest for DMTU.
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Affiliation(s)
- Grazyna Wenska
- Faculty of Chemistry, Adam Mickiewicz University, 60-780, Poznan, Poland.
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Liu J, Guo Z, Sun J, Liang W. Theoretical studies on electronic spectroscopy and dynamics with the real-time time-dependent density functional theory. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11458-009-0205-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wenska G, Koput J, Burdziński G, Taras-Goslinska K, Maciejewski A. Photophysical and photochemical properties of the T1 excited state of thioinosine. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2009.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Elliott P, Furche F, Burke K. Excited States from Time-Dependent Density Functional Theory. REVIEWS IN COMPUTATIONAL CHEMISTRY 2009. [DOI: 10.1002/9780470399545.ch3] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Jacquemin D, Perpète EA, Scalmani G, Frisch MJ, Assfeld X, Ciofini I, Adamo C. Time-dependent density functional theory investigation of the absorption, fluorescence, and phosphorescence spectra of solvated coumarins. J Chem Phys 2007; 125:164324. [PMID: 17092090 DOI: 10.1063/1.2361290] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Using time-dependent density functional theory (TD-DFT) and the polarizable continuum model, we have computed the electronic transitions of a large panel of coumarin dyes in their enol, keto, cationic, and anionic forms. Several processes have been studied: absorption, fluorescence, 0-0 phosphorescence, and triplet-triplet excitations. For each process, detailed comparison with experimental data has been carried out. Using the PBE06-31+G(d) scheme, it turns out that for a given electronic transition the experimental shifts resulting from the substitution of the coumarin core are nicely reproduced. Indeed, once a simple statistical correction is applied, the mean absolute errors on the absorption and fluorescence wavelengths are limited to 8 nm (0.09 eV) and 9 nm (0.07 eV), respectively. A valuable correlation between the experimental and theoretical phosphorescence auxochromic displacements has also been unravelled. The differences between the wavelengths of the various electronic processes of a given dye tend to be fairly predicted, especially for the fluorescence-phosphoresence shifts that are strongly overestimated by TD-DFT.
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Affiliation(s)
- Denis Jacquemin
- Laboratoire de Chimie Théorique Appliquée, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium.
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Jacquemin D, Wathelet V, Preat J, Perpète EA. Ab initio tools for the accurate prediction of the visible spectra of anthraquinones. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2007; 67:334-41. [PMID: 16959534 DOI: 10.1016/j.saa.2006.07.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 05/25/2006] [Accepted: 07/14/2006] [Indexed: 05/11/2023]
Abstract
The UV/vis absorption spectra of 101 anthraquinones solvated in two protic solvents (methanol and ethanol) has been theoretically predicted using the time-dependent density functional theory (TD-DFT) for the excited state calculations and the polarizable continuum model (PCM) for evaluating bulk solvent effects. Two functionals (B3LYP and PBE0) have been used and they provide similar mean absolute deviations (approximately 0.09 eV) but mean signed errors presenting opposite signs. The errors can be minimized by using simple or multiple linear regression, the latter combining the results of both functionals to reach an optimal estimation of the lambda(max) (mean absolute error 0.06 eV). Specific fittings for the two media have been performed and it turned out that our approach is even more efficient for anthraquinones solvated in ethanol.
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Affiliation(s)
- Denis Jacquemin
- Laboratoire de Chimie Théorique Appliquée, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles 61, B-5000 Namur, Belgium.
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Effects of solvent on initiated reaction of maleic anhydride polymerization. J Mol Liq 2007. [DOI: 10.1016/j.molliq.2006.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Burke K, Werschnik J, Gross EKU. Time-dependent density functional theory: past, present, and future. J Chem Phys 2007; 123:62206. [PMID: 16122292 DOI: 10.1063/1.1904586] [Citation(s) in RCA: 503] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Time-dependent density functional theory (TDDFT) is presently enjoying enormous popularity in quantum chemistry, as a useful tool for extracting electronic excited state energies. This article discusses how TDDFT is much broader in scope, and yields predictions for many more properties. We discuss some of the challenges involved in making accurate predictions for these properties.
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Affiliation(s)
- Kieron Burke
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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Jacquemin D, Assfeld X, Preat J, Perpète EA. Comparison of theoretical approaches for predicting the UV/Vis spectra of anthraquinones. Mol Phys 2007. [DOI: 10.1080/00268970601140974] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Shukla M, Leszczynski J. A theoretical study of hydration of 4-thiouracil in the electronic singlet excited state. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.03.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Jacquemin D, Preat J, Wathelet V, Perpète EA. Time-dependent density functional theory determination of the absorption spectra of naphthoquinones. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2006.07.037] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Ab initio calculations of the colour of closed-ring diarylethenes: TD-DFT estimates for molecular switches. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.08.028] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Wenska G, Taras-Goślińska K, Skalski B, Maciejewski A, Burdziński G, Karolczak J. Putative phototautomerization of 4-thiouridine in the S2 excited state revealed by fluorescence study using picosecond laser spectroscopy. J Photochem Photobiol A Chem 2006. [DOI: 10.1016/j.jphotochem.2005.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Khvorostov A, Lapinski L, Rostkowska H, Nowak MJ. Unimolecular photochemistry of 4-thiouracils. Photochem Photobiol 2006; 81:1205-11. [PMID: 15969615 DOI: 10.1562/2005-05-19-ra-534] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Unimolecular phototautomeric reactions in 4-thiouracil, 1-methyl-4-thiouracil and 6-aza-4-thiouracil were studied using the matrix-isolation technique combined with infrared absorption spectroscopy. For monomers of these compounds, isolated in solid argon at 10 K, an intramolecular proton-transfer photoreaction was observed. Upon UV (lambda > 345 nm) irradiation, the initial oxo-thione forms of 4-thiouracils were converted into the corresponding oxo-thiol tautomers. The photogenerated oxo-thiol isomers were identified by comparing their experimental IR spectra with the spectra theoretically calculated at the DFT(B3LYP)/6-311++G(2d,p) level. Good agreement between the observed and predicted pattern of spectral bands allowed a reliable identification. This is the first report on experimental observation of isomeric forms of 4-thiouracils other than the canonical oxo-thione tautomers.
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Affiliation(s)
- Artem Khvorostov
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
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Jacquemin D, Bouhy M, Perpète EA. Excitation spectra of nitro-diphenylaniline: Accurate time-dependent density functional theory predictions for charge-transfer dyes. J Chem Phys 2006; 124:204321. [PMID: 16774346 DOI: 10.1063/1.2202735] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using time-dependent density functional theory (TD-DFT) and the polarizable continuum model (PCM), we have computed the absorption spectra of nitro-diphenylamine dyes. It turns out that the 6-311+G(2d,p) and 6-311G(d,p) basis sets provide, respectively, almost perfectly converged excitation spectra and geometries. Using the PBE0 hybrid functional, we obtain a valuable correlation between PCM-TD-DFT and experimental lambdamax with mean signed/absolute deviations of -4 nm (0.03 eV)8 nm (0.06 eV) and relatively small extreme discrepancies, although the excitations responsible for the color of this class of dyes present a charge-transfer character. The changes in the electron density upon absorption are analyzed through an orbital picture. In addition, a relationship between the light fastness and a well-identified vibrational frequency is proposed.
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Affiliation(s)
- Denis Jacquemin
- Laboratoire de Chimie Théorique Appliquée, Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles 61, B-5000 Namur, Belgium.
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Jacquemin D, Preat J, Wathelet V, Perpète EA. Substitution and chemical environment effects on the absorption spectrum of indigo. J Chem Phys 2006; 124:74104. [PMID: 16497027 DOI: 10.1063/1.2166018] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The UV/visible spectra of a series of indigo derivatives have been evaluated by using ab initio methods. The combination of the Polarizable continuum model for estimating bulk solvent effects with the TD-B3LYP6-311 + G(2d,p)B3LYP6-311G(d,p) level of approximation, leads to an accurate description of the wavelength of maximum absorption of indigoids compounds. Using this procedure, we have assessed the effects of both the surroundings (solvent and solid state) and the substitution pattern. For the latter, we obtained a mean absolute deviation of only 7 nm (0.02 eV) compared to experiment, for a set of 86 molecules/solvents.
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Affiliation(s)
- Denis Jacquemin
- Laboratoire de Chimie Théorique Appliquée, Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium.
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