101
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Tuna D, Domcke W. Excited-state deactivation in 8-oxo-deoxyguanosine: comparison between anionic and neutral forms. Phys Chem Chem Phys 2016; 18:947-55. [DOI: 10.1039/c5cp05804j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ab initio explorations of excited-state potential-energy surfaces show that a radiationless deactivation mechanism via intramolecular excited-state proton transfer is available in neutral 8-oxo-deoxyguanosine, whereas it is not available in the anionic form.
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Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim an der Ruhr
- Germany
| | - Wolfgang Domcke
- Department of Chemistry
- Technische Universität München
- 85747 Garching
- Germany
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102
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Sen A, Matthews EM, Hou GL, Wang XB, Dessent CEH. Photoelectron spectroscopy of hexachloroplatinate-nucleobase complexes: Nucleobase excited state decay observed via delayed electron emission. J Chem Phys 2015; 143:184307. [DOI: 10.1063/1.4935171] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ananya Sen
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Edward M. Matthews
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gao-Lei Hou
- Physical Sciences Division, Pacific Northwest National Laboratory, MS K8-88, P.O. Box 999, Richland, Washington 99352, USA
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, MS K8-88, P.O. Box 999, Richland, Washington 99352, USA
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103
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Brister MM, Crespo-Hernández CE. Direct Observation of Triplet-State Population Dynamics in the RNA Uracil Derivative 1-Cyclohexyluracil. J Phys Chem Lett 2015; 6:4404-9. [PMID: 26538051 DOI: 10.1021/acs.jpclett.5b01901] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Investigation of the excited-state dynamics in nucleic acid monomers is an area of active research due to the crucial role these early events play in DNA and RNA photodamage. The dynamics and rate at which the triplet state is populated are key mechanistic pathways yet to be fully elucidated. Direct spectroscopic evidence is presented in this contribution for intersystem crossing dynamics in a uracil derivative, 1-cyclohexyluracil. It is shown that intersystem crossing to the triplet manifold occurs in one picosecond or less in acetonitrile solution-at least an order of magnitude faster than previously estimated experimentally. Broadband transient absorption measurements also reveal the primary electronic relaxation pathways of the uracil chromophore, including the absorption spectra of the (1)ππ*, (1)nπ*, and (3)ππ* states and the rates of vibrational cooling in the ground and (3)ππ* states. The experimental results are supported by density functional calculations.
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Affiliation(s)
- Matthew M Brister
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Carlos E Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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104
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Nenov A, Segarra-Martí J, Giussani A, Conti I, Rivalta I, Dumont E, Jaiswal VK, Altavilla SF, Mukamel S, Garavelli M. Probing deactivation pathways of DNA nucleobases by two-dimensional electronic spectroscopy: first principles simulations. Faraday Discuss 2015; 177:345-62. [PMID: 25607949 DOI: 10.1039/c4fd00175c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The SOS//QM/MM [Rivalta et al., Int. J. Quant. Chem., 2014, 114, 85] method consists of an arsenal of computational tools allowing accurate simulation of one-dimensional (1D) and bi-dimensional (2D) electronic spectra of monomeric and dimeric systems with unprecedented details and accuracy. Prominent features like doubly excited local and excimer states, accessible in multi-photon processes, as well as charge-transfer states arise naturally through the fully quantum-mechanical description of the aggregates. In this contribution the SOS//QM/MM approach is extended to simulate time-resolved 2D spectra that can be used to characterize ultrafast excited state relaxation dynamics with atomistic details. We demonstrate how critical structures on the excited state potential energy surface, obtained through state-of-the-art quantum chemical computations, can be used as snapshots of the excited state relaxation dynamics to generate spectral fingerprints for different de-excitation channels. The approach is based on high-level multi-configurational wavefunction methods combined with non-linear response theory and incorporates the effects of the solvent/environment through hybrid quantum mechanics/molecular mechanics (QM/MM) techniques. Specifically, the protocol makes use of the second-order Perturbation Theory (CASPT2) on top of Complete Active Space Self Consistent Field (CASSCF) strategy to compute the high-lying excited states that can be accessed in different 2D experimental setups. As an example, the photophysics of the stacked adenine-adenine dimer in a double-stranded DNA is modeled through 2D near-ultraviolet (NUV) spectroscopy.
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
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105
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Nenov A, Giussani A, Segarra-Martí J, Jaiswal VK, Rivalta I, Cerullo G, Mukamel S, Garavelli M. Modeling the high-energy electronic state manifold of adenine: Calibration for nonlinear electronic spectroscopy. J Chem Phys 2015; 142:212443. [PMID: 26049463 DOI: 10.1063/1.4921016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pump-probe electronic spectroscopy using femtosecond laser pulses has evolved into a standard tool for tracking ultrafast excited state dynamics. Its two-dimensional (2D) counterpart is becoming an increasingly available and promising technique for resolving many of the limitations of pump-probe caused by spectral congestion. The ability to simulate pump-probe and 2D spectra from ab initio computations would allow one to link mechanistic observables like molecular motions and the making/breaking of chemical bonds to experimental observables like excited state lifetimes and quantum yields. From a theoretical standpoint, the characterization of the electronic transitions in the visible (Vis)/ultraviolet (UV), which are excited via the interaction of a molecular system with the incoming pump/probe pulses, translates into the determination of a computationally challenging number of excited states (going over 100) even for small/medium sized systems. A protocol is therefore required to evaluate the fluctuations of spectral properties like transition energies and dipole moments as a function of the computational parameters and to estimate the effect of these fluctuations on the transient spectral appearance. In the present contribution such a protocol is presented within the framework of complete and restricted active space self-consistent field theory and its second-order perturbation theory extensions. The electronic excited states of adenine have been carefully characterized through a previously presented computational recipe [Nenov et al., Comput. Theor. Chem. 1040-1041, 295-303 (2014)]. A wise reduction of the level of theory has then been performed in order to obtain a computationally less demanding approach that is still able to reproduce the characteristic features of the reference data. Foreseeing the potentiality of 2D electronic spectroscopy to track polynucleotide ground and excited state dynamics, and in particular its expected ability to provide conformational dependent fingerprints in dimeric systems, the performances of the selected reduced level of calculations have been tested in the construction of 2D electronic spectra for the in vacuo adenine monomer and the unstacked adenine homodimer, thereby exciting the Lb/La transitions with the pump pulse pair and probing in the Vis to near ultraviolet spectral window.
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Affiliation(s)
- Artur Nenov
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Angelo Giussani
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Vishal K Jaiswal
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
| | - Ivan Rivalta
- Université de Lyon, CNRS, Institut de Chimie de Lyon, École Normale Supérieure de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, IFN-CNR, Piazza Leonardo Da Vinci 32, IT-20133 Milano, Italy
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician," Università di Bologna, Via Selmi 2, IT-40126 Bologna, Italy
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106
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Sen A, Hou GL, Wang XB, Dessent CEH. Electron Detachment as a Probe of Intrinsic Nucleobase Dynamics in Dianion-Nucleobase Clusters: Photoelectron Spectroscopy of the Platinum II Cyanide Dianion Bound to Uracil, Thymine, Cytosine, and Adenine. J Phys Chem B 2015; 119:11626-31. [DOI: 10.1021/acs.jpcb.5b07108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ananya Sen
- Department
of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Gao-Lei Hou
- Physical
Sciences Division, Pacific Northwest National Laboratory, MS K8-88, P.O. Box 999, Richland, Washington 99352, United States
| | - Xue-Bin Wang
- Physical
Sciences Division, Pacific Northwest National Laboratory, MS K8-88, P.O. Box 999, Richland, Washington 99352, United States
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107
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Taccone MI, Féraud G, Berdakin M, Dedonder-Lardeux C, Jouvet C, Pino GA. Communication: UV photoionization of cytosine catalyzed by Ag+. J Chem Phys 2015; 143:041103. [DOI: 10.1063/1.4927469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Martín I. Taccone
- INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Geraldine Féraud
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille, France
| | - Matías Berdakin
- INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Claude Dedonder-Lardeux
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille, France
| | - Christophe Jouvet
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille, France
| | - Gustavo A. Pino
- INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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108
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Ligare MR, Rijs AM, Berden G, Kabeláč M, Nachtigallova D, Oomens J, de Vries MS. Resonant Infrared Multiple Photon Dissociation Spectroscopy of Anionic Nucleotide Monophosphate Clusters. J Phys Chem B 2015; 119:7894-901. [PMID: 26004928 DOI: 10.1021/acs.jpcb.5b02222] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report mid-infrared spectra and potential energy surfaces of four anionic, 2'-deoxynucleotide-5'-monophosphates (dNMPs) and the ionic DNA pairs [dGMP-dCMP-H](1-), [dAMP-dTMP-H](1-) with a total charge of the complex equal to -1. We recorded IR action spectra by resonant IR multiple-photon dissociation (IRMPD) using the FELIX free electron laser. The potential energy surface study employed an on-the-fly molecular dynamics quenching method (MD/Q), using a semiempirical AM1 method, followed by an optimization of the most stable structures using density functional theory. By employing infrared multiple-photon dissociation (IRMPD) spectroscopy in combination with high-level computational methods, we aim at a better understanding of the hydrogen bonding competition between the phosphate moieties and the nucleobases. We find that, unlike in multimer double stranded DNA structures, the hydrogen bonds in these isolated nucleotide pairs are predominantly formed between the phosphate groups. This intermolecular interaction appears to exceed the stabilization energy resulting from base pairing and directs the overall cluster structure and alignment.
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Affiliation(s)
- Marshall R Ligare
- †Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Anouk M Rijs
- ‡FELIX Facility, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- ‡FELIX Facility, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Martin Kabeláč
- §Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Dana Nachtigallova
- ∥Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Jos Oomens
- ‡FELIX Facility, Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands.,∥Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic.,⊥van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Mattanjah S de Vries
- †Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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109
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Byskov CS, Jensen F, Jørgensen TJD, Nielsen SB. On the photostability of peptides after selective photoexcitation of the backbone: prompt versus slow dissociation. Phys Chem Chem Phys 2015; 16:15831-8. [PMID: 24945849 DOI: 10.1039/c4cp02015d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vulnerability of biomolecules to ultraviolet radiation is intimately linked to deexcitation pathways: photostability requires fast internal conversion to the electronic ground state, but also intramolecular vibrational redistribution and cooling on a time scale faster than dissociation. Here we present a protocol to disentangle slow and non-hazardous statistical dissociation from prompt cleavage of peptide bonds by 210 nm light based on experiments on protonated peptides isolated in vacuo and tagged by 18-crown-6 ether (CE). The weakest link in the system is between the charged site and CE, which is remote from the initial site of excitation. Hence loss of CE serves as direct proof that energy has reached the charge-site end, leaving the backbone intact. Our work demonstrates that excitation of tertiary amide moieties (proline linkages) results in both prompt dissociation and statistical dissociation after energy randomisation over all vibrational degrees of freedom.
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110
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Szabla R, Sponer JE, Sponer J, Sobolewski AL, Góra RW. Solvent effects on the photochemistry of 4-aminoimidazole-5-carbonitrile, a prebiotically plausible precursor of purines. Phys Chem Chem Phys 2015; 16:17617-26. [PMID: 25026912 DOI: 10.1039/c4cp02074j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
4-Aminoimidazole-5-carbonitrile (AICN) was suggested as a prebiotically plausible precursor of purine nucleobases and nucleotides. Although it can be formed in a sequence of photoreactions, AICN is immune to further irradiation with UV-light. We present state-of-the-art multi-reference quantum-chemical calculations of potential energy surface cuts and conical intersection optimizations to explain the molecular mechanisms underlying the photostability of this compound. We have identified the N-H bond stretching and ring-puckering mechanisms that should be responsible for the photochemistry of AICN in the gas phase. We have further considered the photochemistry of AICN-water clusters, while including up to six explicit water molecules. The calculations reveal charge transfer to solvent followed by formation of an H3O(+) cation, both of which occur on the (1)πσ* hypersurface. Interestingly, a second proton transfer to an adjacent water molecule leads to a (1)πσ*/S0 conical intersection. We suggest that this electron-driven proton relay might be characteristic of low-lying (1)πσ* states in chromophore-water clusters. Owing to its nature, this mechanism might also be responsible for the photostability of analogous organic molecules in bulk water.
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Affiliation(s)
- Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.
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111
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Carbonniere P, Pouchan C, Improta R. Intramolecular vibrational redistribution in the non-radiative excited state decay of uracil in the gas phase: an ab initio molecular dynamics study. Phys Chem Chem Phys 2015; 17:11615-26. [PMID: 25866850 DOI: 10.1039/c4cp05265j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a study of intramolecular vibrational distribution (IVR) occurring in the electronic ground state of uracil (S0) in the gas phase, following photoexcitation in the lowest energy bright excited state (Sπ) and decay through the ethylene-like Sπ/S0 Conical Intersection (CI-0π). To this aim we have performed 20 independent ab initio molecular dynamics simulations starting from CI-0π (ten of them with 1 eV kinetic energy randomly distributed over the different molecular degrees of freedom) and 10 starting from the ground state minimum (Franck-Condon, FC, point), with the excess kinetic energy equal to the energy gap between CI-0π and the FC point. The simulations, exploiting PBE0/6-31G(d) calculations, were performed over an overall period of 10 ps. A thorough statistical analysis of the variation of the geometrical parameters of uracil during the simulation time and of the distribution of the kinetic energy among the different vibrational degrees of freedom provides a consistent picture of the IVR process. In the first 0-200 fs the structural dynamics involve mainly the recovery of the average planarity. In the 200-600 fs time range, a substantial activation of CO and NH degrees of freedom is observed. After 500-600 fs most of the geometrical parameters reach average values similar to those found after 10 ps, though the system cannot be considered to be in equilibrium yet.
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Affiliation(s)
- Philippe Carbonniere
- Université de Pau et des Pays de l'Adour UMR5254, IPREM, Equipe Chimie-Physique Hélioparc, 2 av. Président Angot 64053, Pau Cedex 09, France.
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112
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Altavilla SF, Segarra-Martí J, Nenov A, Conti I, Rivalta I, Garavelli M. Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate. Front Chem 2015; 3:29. [PMID: 25941671 PMCID: PMC4403598 DOI: 10.3389/fchem.2015.00029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/30/2015] [Indexed: 01/17/2023] Open
Abstract
The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ(*) La and Lb states, whereas the energy of the oxygen lone-pair nπ(*) state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ(*) state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region.
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Affiliation(s)
| | | | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Irene Conti
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Ivan Rivalta
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
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113
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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114
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Crespo-Hernández CE, Martínez-Fernández L, Rauer C, Reichardt C, Mai S, Pollum M, Marquetand P, González L, Corral I. Electronic and structural elements that regulate the excited-state dynamics in purine nucleobase derivatives. J Am Chem Soc 2015; 137:4368-81. [PMID: 25763596 PMCID: PMC4410903 DOI: 10.1021/ja512536c] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 12/20/2022]
Abstract
The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited (1)nπ* state. Following vibrational and conformational relaxation, the (1)nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the (1)nπ* state while simultaneously facilitating access to the (1)ππ*(La)/S0 conical intersection, such that population of the (1)nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position.
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Affiliation(s)
- Carlos E. Crespo-Hernández
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Lara Martínez-Fernández
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
| | - Clemens Rauer
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Christian Reichardt
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Marvin Pollum
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Inés Corral
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
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115
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Buchner F, Nakayama A, Yamazaki S, Ritze HH, Lübcke A. Excited-state relaxation of hydrated thymine and thymidine measured by liquid-jet photoelectron spectroscopy: experiment and simulation. J Am Chem Soc 2015; 137:2931-8. [PMID: 25671554 DOI: 10.1021/ja511108u] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Time-resolved photoelectron spectroscopy is performed on thymine and thymidine in aqueous solution to study the excited-state relaxation dynamics of these molecules. We find two contributions with sub-ps lifetimes in line with recent excited-state QM/MM molecular dynamics simulations (J. Chem. Phys. 2013, 139, 214304). The temporal evolution of ionization energies for the excited ππ* state along the QM/MM molecular dynamics trajectories were calculated and are compatible with experimental results, where the two contributions correspond to the relaxation paths in the ππ* state involving different conical intersections with the ground state. Theoretical calculations also show that ionization from the nπ* state is possible at the given photon energies, but we have not found any experimental indication for signal from the nπ* state. In contrast to currently accepted relaxation mechanisms, we suggest that the nπ* state is not involved in the relaxation process of thymine in aqueous solution.
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Affiliation(s)
- Franziska Buchner
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie , Max-Born-Straße 2A, 12489 Berlin, Germany
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116
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Abstract
Ultraviolet (UV) radiation is a leading external hazard to the integrity of DNA. Exposure to UV radiation triggers a cascade of chemical reactions, and many molecular products (photolesions) have been isolated that are potentially dangerous for the cellular system. The early steps that take place after UV absorption by DNA have been studied by ultrafast spectroscopy. The review focuses on the evolution of excited electronic states, the formation of photolesions, and processes suppressing their formation. Emphasis is placed on lesions involving two thymine bases, such as the cyclobutane pyrimidine dimer, the (6-4) lesion, and its Dewar valence isomer.
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Affiliation(s)
- Wolfgang J Schreier
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, 80538 München, Germany;
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117
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Klyne J, Schmies M, Fujii M, Dopfer O. Stepwise Microhydration of Aromatic Amide Cations: Formation of Water Solvation Network Revealed by Infrared Spectra of Formanilide+–(H2O)n Clusters (n ≤ 5). J Phys Chem B 2015; 119:1388-406. [DOI: 10.1021/jp511421h] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Johanna Klyne
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Matthias Schmies
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Masaaki Fujii
- Chemical
Resources Laboratory, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Otto Dopfer
- Institut
für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
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118
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Szabla R, Campos J, Šponer JE, Šponer J, Góra RW, Sutherland JD. Excited-state hydrogen atom abstraction initiates the photochemistry of β-2'-deoxycytidine. Chem Sci 2015; 6:2035-2043. [PMID: 27182431 PMCID: PMC4866440 DOI: 10.1039/c4sc03761h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/07/2015] [Indexed: 11/21/2022] Open
Abstract
Understanding the effects of ultraviolet radiation on nucleotides in solution is an important step towards a comprehensive description of the photochemistry of nucleic acids and their constituents. Apart from having implications for mutagenesis and DNA photoprotection mechanisms, the photochemistry of cytidines is a central element in UV-assisted syntheses of pyrimidine nucleotides under prebiotically plausible conditions. In this contribution, we present UV-irradiation experiments of β-2'-deoxycytidine in aqueous solution involving H-D exchange followed by NMR spectroscopic analysis of the photoproducts. We further elucidate the outcome of these experiments by means of high-level quantum chemical calculations. In particular, we show that prolonged UV-irradiation of cytidine may lead to H-C1' hydrogen atom abstraction by the carbonyl oxygen atom of cytosine. This process may enable photoanomerisation and nucleobase loss, two previously unexplained photoreactions observed in pyrimidine nucleotides.
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Affiliation(s)
- Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.
| | - Jesús Campos
- School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK; Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic. ; CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jiřĺ Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic. ; CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Robert W Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK.
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119
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Camillis SD, Miles J, Alexander G, Ghafur O, Williams ID, Townsend D, Greenwood JB. Ultrafast non-radiative decay of gas-phase nucleosides. Phys Chem Chem Phys 2015; 17:23643-50. [DOI: 10.1039/c5cp03806e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
De-excitation of DNA nucleosides on picosecond timescales was measured and found to be twice as fast as the equivalent nucleobases.
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Affiliation(s)
- Simone De Camillis
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Jordan Miles
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Grace Alexander
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Omair Ghafur
- Institute of Photonics and Quantum Sciences
- Heriot-Watt University
- Edinburgh EH14 4AS
- UK
| | - Ian D. Williams
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences
- Heriot-Watt University
- Edinburgh EH14 4AS
- UK
- Institute of Chemical Sciences
| | - Jason B. Greenwood
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
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120
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Conti I, Nenov A, Höfinger S, Flavio Altavilla S, Rivalta I, Dumont E, Orlandi G, Garavelli M. Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back. Phys Chem Chem Phys 2015; 17:7291-302. [DOI: 10.1039/c4cp05546b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
La and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Siegfried Höfinger
- Zentraler Informatikdienst
- Technische Universität Wien
- 1040 Wien, Austria
- Department of Physics
- Michigan Technological University
| | | | - Ivan Rivalta
- Université de Lyon
- CNRS
- Institut de Chimie de Lyon
- École Normale Supérieure de Lyon
- F-69364 Lyon Cedex 07, France
| | - Elise Dumont
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
- Lyon, France
| | - Giorgio Orlandi
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
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121
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Norman P, Parello J, Polavarapu PL, Linares M. Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory. Phys Chem Chem Phys 2015; 17:21866-79. [DOI: 10.1039/c5cp02481a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles.
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Affiliation(s)
- Patrick Norman
- Department of Physics
- Chemistry and Biology
- Linköping University
- SE-581 83 Linköping
- Sweden
| | - Joseph Parello
- Department of Chemistry
- Vanderbilt University
- Nashville
- USA
| | | | - Mathieu Linares
- Department of Physics
- Chemistry and Biology
- Linköping University
- SE-581 83 Linköping
- Sweden
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122
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Sen A, Dessent CEH. Communication: Photoactivation of nucleobase bound platinumIImetal complexes: Probing the influence of the nucleobase. J Chem Phys 2014; 141:241101. [DOI: 10.1063/1.4904259] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Ananya Sen
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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123
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Richter M, Mai S, Marquetand P, González L. Ultrafast intersystem crossing dynamics in uracil unravelled by ab initio molecular dynamics. Phys Chem Chem Phys 2014; 16:24423-36. [PMID: 25301389 PMCID: PMC4391640 DOI: 10.1039/c4cp04158e] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 10/03/2014] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations have been performed in order to investigate the relaxation dynamics of uracil after UV excitation in gas phase. Intersystem crossing (ISC) has been included for the first time into time-dependent simulations of uracil, allowing the system to relax in the singlet as well as in the triplet states. The results show a qualitatively different picture than similar simulations that include singlet states only. The inclusion of ISC effectively quenches the relaxation to the singlet ground state and instead privileges transitions from the low-lying nπ* state (S1) to a ππ* triplet state (T2) followed by rapid internal conversion to the lowest triplet state.
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Affiliation(s)
- Martin Richter
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| | - Sebastian Mai
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| | - Philipp Marquetand
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| | - Leticia González
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
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124
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Kánnár D, Szalay PG. Benchmarking coupled cluster methods on singlet excited states of nucleobases. J Mol Model 2014; 20:2503. [DOI: 10.1007/s00894-014-2503-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/13/2014] [Indexed: 11/30/2022]
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125
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Roberts GM, Marroux HJB, Grubb MP, Ashfold MNR, Orr-Ewing AJ. On the Participation of Photoinduced N–H Bond Fission in Aqueous Adenine at 266 and 220 nm: A Combined Ultrafast Transient Electronic and Vibrational Absorption Spectroscopy Study. J Phys Chem A 2014; 118:11211-25. [DOI: 10.1021/jp508501w] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gareth M. Roberts
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Hugo J. B. Marroux
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Michael P. Grubb
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Michael N. R. Ashfold
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Andrew J. Orr-Ewing
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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126
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Pollum M, Crespo-Hernández CE. Communication: the dark singlet state as a doorway state in the ultrafast and efficient intersystem crossing dynamics in 2-thiothymine and 2-thiouracil. J Chem Phys 2014; 140:071101. [PMID: 24559331 DOI: 10.1063/1.4866447] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Femtosecond broadband transient absorption experiments are reported for 2-thiothymine and 2-thiouracil in aqueous buffer solution and in acetonitrile. It is shown that the S1(nπ*) state acts as a doorway state in the ultrafast and efficient population of the T1(ππ*) state upon 316 nm excitation. A sequential kinetic model is presented to explain the excited-state dynamics in 2-thiothymine and 2-thiouracil upon UVA excitation: S2(ππ*) → S1(nπ*) → T1(ππ*). The experimental results are also used to scrutinize the excited-state relaxation pathways recently predicted for 2-thiouracil at the CASPT2//CASSCF level of theory [G. Cui and W. Fang, J. Chem. Phys. 138, 044315 (2013)]. The efficient population of the T1(ππ*) state for both 2-thiothymine and 2-thiouracil in a few hundreds of femtoseconds lends further support to the emerging idea that thiobase derivatives exhibit photo-toxic properties that can be effectively harnessed in photo-chemotherapeutic applications.
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Affiliation(s)
- Marvin Pollum
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Carlos E Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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127
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Zhang Y, Improta R, Kohler B. Mode-specific vibrational relaxation of photoexcited guanosine 5'-monophosphate and its acid form: a femtosecond broadband mid-IR transient absorption and theoretical study. Phys Chem Chem Phys 2014; 16:1487-99. [PMID: 24302276 DOI: 10.1039/c3cp53815j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV-pump/broadband-mid-IR-probe transient absorption (TA) experiments and ab initio quantum mechanical (QM) calculations were used to investigate the photophysics in heavy water of the neutral and acid forms of guanosine 5'-monophosphate (GMP and GMPD(+), respectively). Excited GMP undergoes ultrafast internal conversion (IC) and returns to the electronic ground state in less than one picosecond with a large amount of excess vibrational energy. The spectroscopic signals are dominated by vibrational cooling - a process in which the solute dissipates vibrational energy to the solvent. For neutral GMP, cooling proceeds with a time constant of 3 ps. Following IC, at least some medium-frequency modes such as the carbonyl stretch and an in-plane ring vibration are excited, suggesting that the vibrational energy distribution is non-statistical. This is consistent with predicted structural changes upon passage through the S1/S0 conical intersection. GMPD(+) differs from GMP by a single deuteron at the N7 position, but has a dramatically longer lifetime of 200 ps. Vibrational cooling of the S1 state of GMPD(+) was monitored via several medium-frequency modes that were assigned using QM calculations. These medium-frequency modes are also vibrationally excited in a non-statistical fashion. Excitation of these modes is in line with the change in geometry at the S1 minimum of GMPD(+) predicted by QM calculations. Furthermore, these modes relax at different rates, fully consistent with QM calculations, which predict that excited vibrational states of the carbonyl stretch couple strongly to the D2O solvent and thus deactivate via intermolecular energy transfer (IET). In contrast, the ring stretch couples strongly to other ring modes of the guanine chromophore and appears to decay via intramolecular vibrational energy redistribution (IVR).
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Affiliation(s)
- Yuyuan Zhang
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59715, USA.
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128
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Abstract
Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.
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129
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Baranovskii V, Maltsev D. DFT study of potential energy surfaces and conical intersection structures of Rhenium(I) tricarbonyl diimine complexes. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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130
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Féraud G, Berdakin M, Dedonder C, Jouvet C, Pino GA. Excited states of proton-bound DNA/RNA base homodimers: pyrimidines. J Phys Chem B 2014; 119:2219-28. [PMID: 25046334 DOI: 10.1021/jp505756a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We are presenting the electronic photofragment spectra of the protonated pyrimidine DNA base homodimers. Only the thymine dimer exhibits a well structured vibrational progression, while the protonated monomer shows broad vibrational bands. This shows that proton bonding can block some nonradiative processes present in the monomer.
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Affiliation(s)
- Géraldine Féraud
- Physique des Interactions Ioniques et Moléculaires (PIIM), UMR 7345, CNRS, Aix-Marseille Université , 13397 Marseille Cedex 20, France
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131
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Benda Z, Szalay PG. Details of the Excited-State Potential Energy Surfaces of Adenine by Coupled Cluster Techniques. J Phys Chem A 2014; 118:6197-207. [DOI: 10.1021/jp505331s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Zsuzsanna Benda
- Laboratory of Theoretical Chemistry, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest, Hungary
| | - Péter G. Szalay
- Laboratory of Theoretical Chemistry, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest, Hungary
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132
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Tan EMM, Hilbers M, Buma WJ. Excited-State Dynamics of Isolated and Microsolvated Cinnamate-Based UV-B Sunscreens. J Phys Chem Lett 2014; 5:2464-8. [PMID: 26277816 DOI: 10.1021/jz501140b] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sunscreens are aimed at providing protection from solar UV radiation. However, the same mechanism that underlies this protection (absorption of UV radiation) is also responsible for their light-induced adverse effects. Here, high-resolution spectroscopic methods are applied to one of the most commonly used sunscreen chromophores to study the excited-state dynamics that determine the delicate balance between favorable and adverse effects. In contrast to common belief, we find that excitation to the "bright" ππ* state does not directly lead to repopulation of the electronic ground state. Instead, internal conversion to another electronically excited state identified as the "dark" nπ* state is a major decay pathway that impedes fast energy dissipation. Microsolvation studies of sunscreen chromophores with water demonstrate that under such conditions, this bottleneck is no longer present. These observations could be a first step toward the development of sunscreens with improved photochemical properties.
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Affiliation(s)
- Eric M M Tan
- van't Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Michiel Hilbers
- van't Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Wybren J Buma
- van't Hoff Institute for Molecular Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
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133
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Berdakin M, Féraud G, Dedonder-Lardeux C, Jouvet C, Pino GA. Effect of Ag(+) on the Excited-State Properties of a Gas-Phase (Cytosine)2Ag(+) Complex: Electronic Transition and Estimated Lifetime. J Phys Chem Lett 2014; 5:2295-2301. [PMID: 26279549 DOI: 10.1021/jz5009455] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recently, DNA molecules have received great attention because of their potential applications in material science. One interesting example is the production of highly fluorescent and tunable DNA-Agn clusters with cytosine (C)-rich DNA strands. Here, we report the UV photofragmentation spectra of gas-phase cytosine···Ag(+)···cytosine (C2Ag(+)) and cytosine···H(+)···cytosine (C2H(+)) complexes together with theoretical calculations. In both cases, the excitation energy does not differ significantly from that of isolated cytosine or protonated cytosine, indicating that the excitation takes place on the DNA base. However, the excited-state lifetime of the C2H(+) (τ = 85 fs), estimated from the bandwidth of the spectrum, is at least 2 orders of magnitude shorter than that of the C2Ag(+) (τ > 5000 fs). The increased excited-state lifetime upon silver complexation is quite unexpected, and it clearly opens the question about what factors are controlling the nonradiative decay in pyrimidine DNA bases. This is an important result for the expanding field of metal-mediated base pairing and may also be important to the photophysical properties of DNA-templated fluorescent silver clusters.
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Affiliation(s)
- Matias Berdakin
- †INFIQC (CONICET - UNC), Departamento de Fisicoquı́mica, Facultad de Ciencias Quı́micas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Géraldine Féraud
- ‡Physique des Interactions Ioniques et Moléculaires (PIIM), CNRS, Aix Marseille Université: UMR-7345, 13397 Marseille, France
| | - Claude Dedonder-Lardeux
- ‡Physique des Interactions Ioniques et Moléculaires (PIIM), CNRS, Aix Marseille Université: UMR-7345, 13397 Marseille, France
| | - Christophe Jouvet
- ‡Physique des Interactions Ioniques et Moléculaires (PIIM), CNRS, Aix Marseille Université: UMR-7345, 13397 Marseille, France
| | - Gustavo A Pino
- †INFIQC (CONICET - UNC), Departamento de Fisicoquı́mica, Facultad de Ciencias Quı́micas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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134
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Bistafa C, Georg HC, Canuto S. Combining ab initio multiconfigurational and Free Energy Gradient methods to study the π–π* excited state structure and properties of uracil in water. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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135
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Sasidharanpillai S, Loppnow GR. Initial Excited-State Structural Dynamics of 5,6-Dimethyluracil from Resonance Raman Spectroscopy. J Phys Chem A 2014; 118:4680-7. [DOI: 10.1021/jp412747c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Glen R. Loppnow
- Department
of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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136
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Pedersen SØ, Byskov CS, Turecek F, Nielsen SB. Structures of Protonated Thymine and Uracil and Their Monohydrated Gas-Phase Ions from Ultraviolet Action Spectroscopy and Theory. J Phys Chem A 2014; 118:4256-65. [DOI: 10.1021/jp504153p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sara Øvad Pedersen
- Department
of Physics and Astronomy, Aarhus University, DK-8000 Aarhus
C, Denmark
| | | | - Frantisek Turecek
- Department
of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
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137
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Berdakin M, Steinmetz V, Maitre P, Pino GA. Gas Phase Structure of Metal Mediated (Cytosine)2Ag+ Mimics the Hemiprotonated (Cytosine)2H+ Dimer in i-Motif Folding. J Phys Chem A 2014; 118:3804-3809. [DOI: 10.1021/jp5038969] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Matias Berdakin
- INFIQC (CONICET
− Universidad Nacional de Córdoba), Departamento de
Fisicoquímica, Facultad de Ciencias Químicas, Centro
Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Córdoba, Argentina
| | - Vincent Steinmetz
- Laboratoire de Chimie Physique, Université Paris Sud, UMR8000 CNRS, Faculté des Sciences, 91405 Orsay Cedex, France
| | - Philippe Maitre
- Laboratoire de Chimie Physique, Université Paris Sud, UMR8000 CNRS, Faculté des Sciences, 91405 Orsay Cedex, France
| | - Gustavo A. Pino
- INFIQC (CONICET
− Universidad Nacional de Córdoba), Departamento de
Fisicoquímica, Facultad de Ciencias Químicas, Centro
Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Córdoba, Argentina
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138
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Chen J, Kohler B. Base stacking in adenosine dimers revealed by femtosecond transient absorption spectroscopy. J Am Chem Soc 2014; 136:6362-72. [PMID: 24735123 DOI: 10.1021/ja501342b] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Excitons formed in DNA by UV absorption decay via poorly understood pathways that can culminate in mutagenic photoproducts. In order to gain insight into how base stacking influences UV excited states in DNA, five dinucleosides composed of adenosine or 2'-deoxyadenosine units joined by flexible linkers were studied by femtosecond transient absorption spectroscopy. In aqueous solution, transient absorption signals recorded at pump and probe wavelengths of 267 and 250 nm, respectively, show that UV absorption produces excimer states in all dimers that decay orders of magnitude more slowly than excitations in a single adenine nucleotide. Adding methanol as a cosolvent disrupts π-π stacking of the adenine moieties and causes the excimer states in all five dinucleosides to vanish for a methanol concentration of 80% by volume. These observations confirm that base stacking is an essential requirement for the slow decay channel seen in these and other DNA model compounds. This channel appears to be insensitive to the precise stacking conformation at the instant of photon absorption as long as the bases are cofacially stacked. Notably, circular dichroism (CD) spectra of several of the dinucleosides are weak and monomer-like and lack the exciton coupling that has been emphasized in the past as an indicator of base-stacked structure. For these dimers, the coupled transition dipole moments of the two adenines are proposed to adopt left- and right-handed arrangements upon stacking with roughly equal probability. Although the mechanism behind slow nonradiative decay in DNA is still uncertain, these results show that the signature of these states in transient absorption experiments can be a more reliable diagnostic of base stacking than the occurrence of exciton-coupled CD signals. These observations also draw attention to the important role the backbone plays in producing structures with axial (helical) chirality.
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Affiliation(s)
- Jinquan Chen
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717-3400, United States
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139
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Chatterley AS, West CW, Roberts GM, Stavros VG, Verlet JRR. Mapping the Ultrafast Dynamics of Adenine onto Its Nucleotide and Oligonucleotides by Time-Resolved Photoelectron Imaging. J Phys Chem Lett 2014; 5:843-848. [PMID: 26274076 DOI: 10.1021/jz500264c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The intrinsic photophysics of nucleobases and nucleotides following UV absorption presents a key reductionist step toward understanding the complex photodamage mechanisms occurring in DNA. The decay mechanism of adenine in particular has been the focus of intense investigation, as has how these correlate to those of its more biologically relevant nucleotide and oligonucleotides in aqueous solution. Here, we report on time-resolved photoelectron imaging of the deprotonated 3'-deoxy-adenosine-5'-monophosphate nucleotide and the adenosine di- and trinucleotides. Through a comparison of gas- and solution-phase experiments and available theoretical studies, the dynamics of the base are shown to be relatively insensitive to the surrounding environment. The decay mechanism primarily involves internal conversion from the initially populated (1)ππ* states to the ground state. The relaxation dynamics of the adenosine oligonucleotides are similar to those of the nucleobase, in contrast to the aqueous oligonucleotides, where a fraction of the ensemble forms long-lived excimer states.
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Affiliation(s)
- Adam S Chatterley
- †Department of Chemistry, University of Durham, Durham DH1 3LE, United Kingdom
- ‡Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Christopher W West
- †Department of Chemistry, University of Durham, Durham DH1 3LE, United Kingdom
| | - Gareth M Roberts
- ‡Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vasilios G Stavros
- ‡Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jan R R Verlet
- †Department of Chemistry, University of Durham, Durham DH1 3LE, United Kingdom
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140
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Lapinski L, Reva I, Rostkowska H, Fausto R, Nowak MJ. Near-IR-Induced, UV-Induced, and Spontaneous Isomerizations in 5-Methylcytosine and 5-Fluorocytosine. J Phys Chem B 2014; 118:2831-41. [DOI: 10.1021/jp411423c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Leszek Lapinski
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Igor Reva
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Hanna Rostkowska
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Rui Fausto
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Maciej J. Nowak
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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141
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Ohyama K, Goto K, Shinmyozu T, Yamamoto N, Iizumi S, Miyagawa M, Nakata M, Sekiya H. Infrared spectroscopic studies on 4-amino-6-oxopyrimidine in a low-temperature Xe matrix and crystalline polymorphs composed of double hydrogen-bonded ribbons. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.01.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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142
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Yamazaki S, Urashima SH, Saigusa H, Taketsugu T. Ab initio studies on the photophysics of uric acid and its monohydrates: role of the water molecule. J Phys Chem A 2014; 118:1132-41. [PMID: 24446809 DOI: 10.1021/jp411880z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photophysical behavior of three lowest-energy tautomers of uric acid and seven most stable isomers of uric acid monohydrate is comprehensively studied by ab initio calculations. Ground-state energies are calculated with the CCSD(T) method, while excitation and ionization energies as well as excited-state potential energy profiles of photoinduced processes are calculated with the CC2 method. For the (1)ππ* state, it is found that the excitation energy of the monohydrate cluster is significantly lower than that of isolated uric acid when the water molecule is hydrogen-bonded at a specific carbonyl group. The calculated excited-state potential energy profiles suggest that some monohydrate isomers can undergo a migration of the water molecule from one site to another site in the (1)ππ* state with a small energy barrier. It is also found for both uric acid and its monohydrate that nonradiative decay via the NH bond dissociation in the (1)πσ* state is likely to occur at higher excitation energies. On the basis of the computational results, possible mechanisms for the absence of specific isomers of uric acid monohydrate from the resonant two-photon ionization spectrum are discussed.
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Affiliation(s)
- Shohei Yamazaki
- Department of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University , Hirosaki 036-8561, Japan
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143
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Berdakin M, Féraud G, Dedonder-Lardeux C, Jouvet C, Pino GA. Excited states of protonated DNA/RNA bases. Phys Chem Chem Phys 2014; 16:10643-50. [DOI: 10.1039/c4cp00742e] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excited state lifetime of protonated DNA/RNA bases is strongly dependent on the tautomeric form.
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Affiliation(s)
- Matias Berdakin
- INFIQC (CONICET – Universidad Nacional de Córdoba) Dpto. de Fisicoquímica – Facultad de Ciencias Químicas – Centro Láser de Ciencias Moleculares – Universidad Nacional de Córdoba
- Ciudad Universitaria
- X5000HUA Córdoba, Argentina
| | - Géraldine Féraud
- CNRS
- Aix Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR-7345
- 13397 Marseille, France
| | - Claude Dedonder-Lardeux
- CNRS
- Aix Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR-7345
- 13397 Marseille, France
| | - Christophe Jouvet
- CNRS
- Aix Marseille Université
- Physique des Interactions Ioniques et Moléculaires (PIIM): UMR-7345
- 13397 Marseille, France
| | - Gustavo A. Pino
- INFIQC (CONICET – Universidad Nacional de Córdoba) Dpto. de Fisicoquímica – Facultad de Ciencias Químicas – Centro Láser de Ciencias Moleculares – Universidad Nacional de Córdoba
- Ciudad Universitaria
- X5000HUA Córdoba, Argentina
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144
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Chen J, Zhang Y, Kohler B. Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:39-87. [DOI: 10.1007/128_2014_570] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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145
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Ovchinnikov VA, Sundholm D. Coupled-cluster and density functional theory studies of the electronic 0–0 transitions of the DNA bases. Phys Chem Chem Phys 2014; 16:6931-41. [DOI: 10.1039/c3cp55080j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 0–0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations.
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Affiliation(s)
- Vasily A. Ovchinnikov
- University of Helsinki
- 00014 Helsinki, Finland
- Emanuel Institute of Biochemical Physics RAS
- 119334 Moscow, Russia
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146
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Mai S, Richter M, Marquetand P, González L. Excitation of Nucleobases from a Computational Perspective II: Dynamics. Top Curr Chem (Cham) 2014; 355:99-153. [DOI: 10.1007/128_2014_549] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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147
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Chatterley AS, West CW, Stavros VG, Verlet JRR. Time-resolved photoelectron imaging of the isolated deprotonated nucleotides. Chem Sci 2014. [DOI: 10.1039/c4sc01493f] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Time-resolved photoelectron spectroscopy of deprotonated nucleotides provides new insights into their relaxation dynamics.
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Affiliation(s)
- Adam S. Chatterley
- Department
- of Chemistry
- University of Durham
- Durham DH1 3LE, United Kingdom
- Department of Chemistry
| | | | - Vasilios G. Stavros
- Department of Chemistry
- University of Warwick
- Coventry CV4 7AL, United Kingdom
| | - Jan R. R. Verlet
- Department
- of Chemistry
- University of Durham
- Durham DH1 3LE, United Kingdom
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148
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Loquais Y, Gloaguen E, Alauddin M, Brenner V, Tardivel B, Mons M. On the near UV photophysics of a phenylalanine residue: conformation-dependent ππ* state deactivation revealed by laser spectroscopy of isolated neutral dipeptides. Phys Chem Chem Phys 2014; 16:22192-200. [DOI: 10.1039/c4cp03401e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The primary step of the near UV photophysics is investigated in pump–probe R2PI ns experiments carried out on specific conformers of model peptide chains.
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Affiliation(s)
- Yohan Loquais
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- CNRS
- INP
- Laboratoire Francis Perrin
- URA 2453
- 91191 Gif-sur-Yvette, France
| | - Mohammad Alauddin
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Benjamin Tardivel
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA
- IRAMIS
- Laboratoire Interactions
- Dynamique et Lasers
- 91191 Gif-sur-Yvette, France
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149
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Rijs AM, Oomens J. IR Spectroscopic Techniques to Study Isolated Biomolecules. Top Curr Chem (Cham) 2014; 364:1-42. [DOI: 10.1007/128_2014_621] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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150
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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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