201
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Picconi D, Barone V, Lami A, Santoro F, Improta R. The Interplay between ππ*/nπ* Excited States in Gas-Phase Thymine: A Quantum Dynamical Study. Chemphyschem 2011; 12:1957-68. [DOI: 10.1002/cphc.201001080] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/01/2011] [Indexed: 11/10/2022]
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202
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DeFusco A, Ivanic J, Schmidt MW, Gordon MS. Solvent-Induced Shifts in Electronic Spectra of Uracil. J Phys Chem A 2011; 115:4574-82. [DOI: 10.1021/jp112230f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Albert DeFusco
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Joseph Ivanic
- Advanced Biomedical Computing Center, Information Systems Program, SAIC—Frederick, Inc., National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Michael W. Schmidt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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203
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Keane PM, Wojdyla M, Doorley GW, Watson GW, Clark IP, Greetham GM, Parker AW, Towrie M, Kelly JM, Quinn SJ. A comparative picosecond transient infrared study of 1-methylcytosine and 5'-dCMP that sheds further light on the excited states of cytosine derivatives. J Am Chem Soc 2011; 133:4212-5. [PMID: 21384855 DOI: 10.1021/ja1106089] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The role of N1-substitution in controlling the deactivation processes in photoexcited cytosine derivatives has been explored using picosecond time-resolved IR spectroscopy. The simplest N1-substituted derivative, 1-methylcytosine, exhibits relaxation dynamics similar to the cytosine nucleobase and distinct from the biologically relevant nucleotide and nucleoside analogues, which have longer-lived excited-state intermediates. It is suggested that this is the case because the sugar group either facilitates access to the long-lived (1)n(O)π* state or retards its crossover to the ground state.
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Affiliation(s)
- Páraic M Keane
- School of Chemistry and Centre for Synthesis and Chemical Biology, Trinity College, Dublin 2, Ireland
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204
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The shape of the conical intersections of monohydrated pyrimidine bases cytosine, uracil, and thymine: a theoretical study. MONATSHEFTE FUR CHEMIE 2011. [DOI: 10.1007/s00706-011-0447-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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205
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Gustavsson T, Banyasz A, Improta R, Markovitsi D. Femtosecond fluorescence studies of DNA/RNA constituents. ACTA ACUST UNITED AC 2011. [DOI: 10.1088/1742-6596/261/1/012009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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206
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Plaza-Medina EF, Rodríguez-Córdoba W, Morales-Cueto R, Peon J. Primary photochemistry of nitrated aromatic compounds: excited-state dynamics and NO· dissociation from 9-nitroanthracene. J Phys Chem A 2011; 115:577-85. [PMID: 21214230 DOI: 10.1021/jp109041y] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report results of femtosecond-resolved ex-periments which elucidate the time scale for the primary photoinduced events in the model nitroaromatic compound 9-nitroanthracene. Through time-resolved fluorescence measurements, we observed the ultrafast decay of the initially excited singlet state, and through transient absorption experiments, we observed the spectral evolution associated with the formation of the relaxed phosphorescent T(1) state. Additionally, we have detected for the first time the accumulation of the anthryloxy radical which results from the nitro-group rearrangement and NO(•) dissociation from photoexcited 9-nitroanthracene, a photochemical channel which occurs in parallel with the formation of the phosphorescent state. The spectral evolution in this molecule is highly complex since both channels take place in similar time ranges of up to a few picoseconds. Despite this complexity, our experiments provide the general time scales in which the primary products are formed. In addition, we include calculations at the time-dependent density functional level of theory which distinguish the molecular orbitals responsible for the n-π* character of the "receiver" vibronic triplet states that couple with the first singlet state and promote the ultrafast transfer of population between the two manifolds. Comparisons with the isoelectronic compounds anthracene-9-carboxylic acid and its conjugated base, which are highly fluorescent, show that in these two compounds the near-isoenergeticity of the S(1) with an appropriate "receiver" triplet state is disrupted, providing support to the idea that a specific energy coincidence is important for the ultrafast population of the triplet manifold, prevalent in polycyclic nitrated aromatic compounds.
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Affiliation(s)
- Eddy F Plaza-Medina
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, DF, México
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207
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Matsika S, Zhou C, Kotur M, Weinacht TC. Combining dissociative ionization pump–probe spectroscopy and ab initio calculations to interpret dynamics and control through conical intersections. Faraday Discuss 2011; 153:247-60; discussion 293-319. [DOI: 10.1039/c1fd00044f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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208
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Barbatti M, Aquino AJA, Szymczak JJ, Nachtigallová D, Lischka H. Photodynamical simulations of cytosine: characterization of the ultrafast bi-exponential UV deactivation. Phys Chem Chem Phys 2011; 13:6145-55. [DOI: 10.1039/c0cp01327g] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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209
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Bányász Á, Karpati S, Mercier Y, Reguero M, Gustavsson T, Markovitsi D, Improta R. The Peculiar Spectral Properties of Amino-Substituted Uracils: A Combined Theoretical and Experimental Study. J Phys Chem B 2010; 114:12708-19. [DOI: 10.1021/jp105267q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Ákos Bányász
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Szilvia Karpati
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Yannick Mercier
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Mar Reguero
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Thomas Gustavsson
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Dimitra Markovitsi
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Roberto Improta
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM - CNRS URA 2453, 91191 Gif-sur-Yvette, France, Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo, s/n-Campus Sescelades, 43007 Tarragona, Spain, and Istituto Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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210
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Delchev VB, Sobolewski AL, Domcke W. Comparison of the non-radiative decay mechanisms of 4-pyrimidinone and uracil: an ab initio study. Phys Chem Chem Phys 2010; 12:5007-15. [PMID: 20407677 DOI: 10.1039/b922505f] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We performed a comparative theoretical study of the relaxation mechanisms of the excited states of uracil and 4-pyrimidinone with the CASSCF, CASPT2, and CC2 ab initio methods. The calculated vertical excitation energies agree with the experimental UV absorption maxima of the two compounds. Three low-lying conical intersections between the S(0) and S(1) states (one for uracil, two for 4-pyrimidinone) are established. They are accessible from the Franck-Condon region of the 1pipi* state through out-of-plane deformations related to C=C (for uracil) or C=N (for 4-pyrimidinone) torsions of the heterocyclic ring. These conical intersections mediate the radiationless deactivation of the compounds after excitation of the lowest 1pipi* state. The relaxation of the 1pipi* state of 4-pyrimidinone via C=C twisting is hindered by a barrier. The relaxed scan of the C=N double-bond twisting of 4-pyrimidinone indicates that the formation of the Dewar form may represent a photochemical channel in 4-pyrimidinone. This fact is detrimental for the photostability of 4-pyrimidinone, since the Dewar form is separated by a high potential-energy barrier from the canonical form of 4-pyrimidinone on the ground-state potential-energy surface, which prevents a thermal back-reaction. The investigation of the vertical excitation energies and the reaction paths shows that 4-pyrimidinone is less photostable than uracil.
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Affiliation(s)
- Vassil B Delchev
- Department of Chemistry, Technische Universität München, D-85747 Garching, Germany.
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211
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Santhanamoorthi N, Senthilkumar K, Kolandaivel P. Tautomerization and solvent effects on the absorption and emission properties of the Schiff baseN,N′-bis(salicylidene)-p-phenylenediamine – A TDDFT study. Mol Phys 2010. [DOI: 10.1080/00268976.2010.490796] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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212
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Kuramochi H, Kobayashi T, Suzuki T, Ichimura T. Excited-State Dynamics of 6-Aza-2-thiothymine and 2-Thiothymine: Highly Efficient Intersystem Crossing and Singlet Oxygen Photosensitization. J Phys Chem B 2010; 114:8782-9. [DOI: 10.1021/jp102067t] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hikaru Kuramochi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Takashi Kobayashi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Suzuki
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Teijiro Ichimura
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
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213
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214
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Miannay FA, Gustavsson T, Banyasz A, Markovitsi D. Excited-state dynamics of dGMP measured by steady-state and femtosecond fluorescence spectroscopy. J Phys Chem A 2010; 114:3256-63. [PMID: 20085298 DOI: 10.1021/jp909410b] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The room-temperature fluorescence of 2'-deoxyguanosine 5'-monophosphate (dGMP) in aqueous solution is studied by steady-state and time-resolved fluorescence spectroscopy. The steady-state fluorescence spectrum of dGMP shows one band centered at 334 nm but has an extraordinary long red tail, extending beyond 700 nm. Both the fluorescence quantum yield and the relative weight of the 334 nm peak increase with the excitation wavelength. The initial fluorescence anisotropy after excitation at 267 nm is lower than 0.2 for all emission wavelengths, indicating an ultrafast S(2) --> S(1) internal conversion. The fluorescence decays depend strongly on the emission wavelength, getting longer with the wavelength. A rise time of 100-150 fs was observed for wavelengths longer than 450 nm, in accordance with a gradual red shift of the time-resolved spectra. The results are discussed in terms of a relaxation occurring mainly on the lowest excited (1)pi pi*-state surface toward a conical intersection with the ground state, in line with recent theoretical predictions. Our results show that the excited-state population undergoes a substantial "spreading out" before reaching the CI, explaining the complex dynamics observed.
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Affiliation(s)
- Francois-Alexandre Miannay
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM-CNRS URA 2453, CEA Saclay, F-91191 Gif-sur-Yvette, France
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215
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Lim JS, Choi H, Lim IS, Park SB, Lee YS, Kim SK. Photodissociation dynamics of thiophenol-d1: the nature of excited electronic states along the S-D bond dissociation coordinate. J Phys Chem A 2010; 113:10410-6. [PMID: 19728695 DOI: 10.1021/jp9076855] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The S-D bond dissociation dynamics of thiophenol-d1 (C6H5SD) pumped at 266, 243, and 224 nm are examined using the velocity map ion imaging technique. At both 266 and 243 nm, distinct peaks associated with X and A states of the phenylthiyl radical (C6H5S*) are observed in the D+ image at high and low kinetic energy regions, respectively. The partitioning of the available energy into the vibrational energy of the phenylthiyl radical is found to be enhanced much more strongly at 266 nm compared to that at 243 nm. This indicates that the pipi* electronic excitation at 266 nm is accompanied by significant vibrational excitation. Given the relatively large anisotropy parameter of -0.6, the S-D dissociation at 266 nm is prompt and should involve the efficient coupling to the upper-lying n(pi)sigma* repulsive potential energy surface. The optical excitation of thiophenol at 224 nm is tentatively assigned to the pisigma* transition, which leads to the fast dissociation on the repulsive potential energy surface along the S-D coordinate. The nature of the electronic transitions associated with UV absorption bands is investigated with high-level ab initio calculations. Excitations to different electronic states of thiophenol result in unique branching ratios and vibrational excitations for the fragment of the phenylthiyl radical in the two lowest electronic states.
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Affiliation(s)
- Jeong Sik Lim
- Department of Chemistry, KAIST, Daejeon (305-701), Republic of Korea
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216
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Improta R, Santoro F, Barone V, Lami A. Vibronic model for the quantum dynamical study of the competition between bright and charge-transfer excited states in single-strand polynucleotides: the adenine dimer case. J Phys Chem A 2010; 113:15346-54. [PMID: 19821596 DOI: 10.1021/jp906278t] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A simple vibronic model aimed at investigating the interplay between bright excitonic states and dark charge-transfer (CT) states in stacked adenine (Ade) nucleobases is presented. Two orbitals (the HOMO and the LUMO) for each Ade site have been included in the electronic Hamiltonian, whose parameters have been fitted to reproduce the main features of the absorption spectra of two stacked 9-methyladenine (9Me-A) molecules, computed in aqueous solution at the PCM/TD-PBE0 level. Three modes for each adenine unit have been included in the Hamiltonian, to describe the main structural changes among the different excited state minima of the adenine stacked dimer, as described at the TD-DFT level. The developed vibronic Hamiltonian (four electronic states and six nuclear coordinates) has been adopted to perform quantum dynamical calculations of a photoexcited Ade stacked dimer, utilizing the multiconfigurational time-dependent Hartree method. The obtained results indicate that the transfer between the bright excitonic state and the CT state is fast and effective.
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Affiliation(s)
- Roberto Improta
- Dipartimento di Chimica and INSTM, Università Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
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217
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Etinski M, Marian CM. Ab initio investigation of the methylation and hydration effects on the electronic spectra of uracil and thymine. Phys Chem Chem Phys 2010; 12:4915-23. [DOI: 10.1039/b925677f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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218
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Santoro F, Barone V, Lami A, Improta R. The excited electronic states of adenine-guanine stacked dimers in aqueous solution: a PCM/TD-DFT study. Phys Chem Chem Phys 2010; 12:4934-48. [DOI: 10.1039/b925108a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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219
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Barbatti M, Aquino AJA, Lischka H. The UV absorption of nucleobases: semi-classical ab initio spectra simulations. Phys Chem Chem Phys 2010; 12:4959-67. [DOI: 10.1039/b924956g] [Citation(s) in RCA: 188] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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220
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Kistler KA, Matsika S. Photophysical pathways of cytosine in aqueous solution. Phys Chem Chem Phys 2010; 12:5024-31. [DOI: 10.1039/b926125g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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221
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Kobayashi T, Kuramochi H, Suzuki T, Ichimura T. Triplet formation of 6-azauridine and singlet oxygen sensitization with UV light irradiation. Phys Chem Chem Phys 2010; 12:5140-8. [DOI: 10.1039/b921568a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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222
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Olsen JM, Aidas K, Mikkelsen KV, Kongsted J. Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study. J Chem Theory Comput 2009; 6:249-56. [DOI: 10.1021/ct900502s] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jógvan Magnus Olsen
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Kęstutis Aidas
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Kurt V. Mikkelsen
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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223
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Chen X, Xing D, Zhang L, Cukier RI, Bu Y. Effect of metal ions on radical type and proton-coupled electron transfer channel: σ-Radical vs π-radical and σ-channel vs π-channel in the imide units. J Comput Chem 2009; 30:2694-705. [DOI: 10.1002/jcc.21284] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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224
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Improta R, Barone V. PCM/TD-DFT study of the two lowest excited states of uracil derivatives in solution: The effect of the functional and of the cavity model. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.02.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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225
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Santoro F, Barone V, Improta R. Excited States Decay of the A−T DNA: A PCM/TD-DFT Study in Aqueous Solution of the (9-Methyl-adenine)2·(1-methyl-thymine)2 Stacked Tetramer. J Am Chem Soc 2009; 131:15232-45. [DOI: 10.1021/ja904777h] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. Santoro
- Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, Dipartimento di Chimica and INSTM, Università Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini - CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - V. Barone
- Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, Dipartimento di Chimica and INSTM, Università Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini - CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - R. Improta
- Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, Dipartimento di Chimica and INSTM, Università Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini - CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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226
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Kobayashi T, Kuramochi H, Harada Y, Suzuki T, Ichimura T. Intersystem Crossing to Excited Triplet State of Aza Analogues of Nucleic Acid Bases in Acetonitrile. J Phys Chem A 2009; 113:12088-93. [DOI: 10.1021/jp905433s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takashi Kobayashi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hikaru Kuramochi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yosuke Harada
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Suzuki
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Teijiro Ichimura
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
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227
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Improta R, Barone V, Lami A, Santoro F. Quantum Dynamics of the Ultrafast ππ*/nπ* Population Transfer in Uracil and 5-Fluoro-Uracil in Water and Acetonitrile. J Phys Chem B 2009; 113:14491-503. [DOI: 10.1021/jp906524p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto Improta
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Vincenzo Barone
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Alessandro Lami
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
| | - Fabrizio Santoro
- Dipartimento di Chimica and INSTM-Village, Universitá Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy, Scuola Normale Superiore di Pisa, P.zza dei Cavalieri 7, I-56126 Pisa, Italy, and Istituto per i Processi Chimico-Fisici - CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
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228
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Theoretical study of structural and optical properties of regioregular head-to-tail oligo (3-n-octylthiophene) and related star molecules. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.06.023] [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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229
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Mitrić R, Werner U, Wohlgemuth M, Seifert G, Bonačić-Koutecký V. Nonadiabatic Dynamics within Time-Dependent Density Functional Tight Binding Method. J Phys Chem A 2009; 113:12700-5. [DOI: 10.1021/jp905600w] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Roland Mitrić
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany, and Physikalische Chemie, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Ute Werner
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany, and Physikalische Chemie, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Matthias Wohlgemuth
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany, and Physikalische Chemie, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Gotthard Seifert
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany, and Physikalische Chemie, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Vlasta Bonačić-Koutecký
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany, Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany, and Physikalische Chemie, Technische Universität Dresden, D-01062 Dresden, Germany
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230
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Szymczak JJ, Barbatti M, Soo Hoo JT, Adkins JA, Windus TL, Nachtigallová D, Lischka H. Photodynamics Simulations of Thymine: Relaxation into the First Excited Singlet State. J Phys Chem A 2009; 113:12686-93. [DOI: 10.1021/jp905085x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jaroslaw J. Szymczak
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Mario Barbatti
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Jason T. Soo Hoo
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Jaclyn A. Adkins
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Theresa L. Windus
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Dana Nachtigallová
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Waehrinegrstrasse 17, A 1090 Vienna, Austria, Departments of Physics, Siena College, 515 Loudon Road, Loudonville, New York 12211, Department of Chemistry, Northwest Missouri State University, 800 University Drive, Maryville, Missouri 64468, Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610
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231
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Etinski M, Fleig T, Marian CM. Intersystem Crossing and Characterization of Dark States in the Pyrimidine Nucleobases Uracil, Thymine, and 1-Methylthymine. J Phys Chem A 2009; 113:11809-16. [DOI: 10.1021/jp902944a] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Mihajlo Etinski
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Timo Fleig
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christel M. Marian
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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232
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Kobyłecka M, Migani A, Asturiol D, Rak J, Blancafort L. Benign decay vs. photolysis in the photophysics and photochemistry of 5-bromouracil. A computational study. J Phys Chem A 2009; 113:5489-95. [PMID: 19374393 DOI: 10.1021/jp811330v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The excited state potential energy surface of 5-bromouracil has been studied with ab initio CASPT2//CASSCF calculations to rationalize the competition between the benign decay and the photolysis found experimentally. The surface is characterized by an extended region of degeneracy between S(1) and S(0). The access to this region has been studied with minimum energy path calculations from the FC structure, the seam of intersection has been mapped in detail, and the decay paths from different regions of the seam have been characterized. There are two decay paths with low barriers that are limiting cases for the actual decay dynamics. The first path involves the bromine elimination and leads to a region of near degeneracy between the ground and excited states, and the second one leads back to the reactant through a conical intersection between the two states. The conical intersection for benign decay is part of a seam that lies along the C(5)-Br stretching coordinate, and decay at the region of the seam with a stretched C(5)-Br bond leads to photolysis. Thus, the reactivity depends on the point of the seam at which decay to the ground state takes place. The low experimental photolysis quantum yield suggests that the energetically favored decay is the one that regenerates the reactant, while the low barriers computed to access the region of decay are in agreement with the measured picosecond excited state lifetime.
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Affiliation(s)
- Monika Kobyłecka
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, Gdańsk 80- 952, Poland
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233
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Meng S, Jiang J, Wang Y, Ma J. Modulation of electronic structures of thienylene vinylene oligomers by substituents and solvents: ground and excited states. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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234
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Karunakaran V, Kleinermanns K, Improta R, Kovalenko SA. Photoinduced dynamics of guanosine monophosphate in water from broad-band transient absorption spectroscopy and quantum-chemical calculations. J Am Chem Soc 2009; 131:5839-50. [PMID: 19341282 DOI: 10.1021/ja810092k] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Guanosine monophosphate (GMP) in aqueous solutions has been studied with femtosecond broad-band transient absorption spectroscopy and by quantum-mechanical calculations. The sample was excited at 267 or 287 nm and probed between 270 and 1000 nm with 100 fs resolution, for various pH values between 2 and 7. At pH 2, when the guanine ring is ground-state protonated (GMPH(+)), we observe isosbestic behavior indicating state-to-state relaxation. The relaxation is biexponential, tau(1) = 0.4 ps, tau(2) = 2.2 ps, and followed by slower internal conversion with tau(3) = 167 ps. For nonprotonated GMP in the pH range 7-4, we find biexponential decay in the region 400-900 nm (tau(1) = 0.22 ps, tau(2) = 0.9 ps), whereas, between 270 and 400 nm, the behavior is triexponential with one growing, tau(1) = 0.25 ps, and two decaying, tau(2) = 1.0 ps, tau(3) = 2.5 ps, components. The excited-state evolution is interpreted with the help of quantum-chemical calculations, performed at the time-dependent PBE0 level accounting for bulk solvent effects and specific solvation. The computed dynamics involves L(a) and L(b) bright excited states, whereas the n(0)pi* and pisigma* dark excited states play a minor role. Independent of the pH, the photoinduced evolution involves ultrafast L(b)-->L(a) conversion (tau(ba) << 100 fs) and exhibits the presence of a wide planar plateau on L(a). For neutral GMP a barrierless path connects this region to a conical intersection (CI) with the ground state, giving an account of the ultrafast decay of this species. For protonated GMPH(+) the system evolves into a stable minimum L(a min) characterized by out-of-plane displacement of NH and CH groups, which explains the longer (167 ps) fluorescence lifetime.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Chemistry, Humboldt University, Brook-Taylor Street-2, D-12489 Berlin, Germany
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235
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Schreier WJ, Kubon J, Regner N, Haiser K, Schrader TE, Zinth W, Clivio P, Gilch P. Thymine dimerization in DNA model systems: cyclobutane photolesion is predominantly formed via the singlet channel. J Am Chem Soc 2009; 131:5038-9. [PMID: 19309140 DOI: 10.1021/ja900436t] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UV-induced formation of cylcobutane pyrimidine dimers (CPD) in all thymine DNA models have been studied by femtosecond IR spectroscopy. CPDs are shown to form within approximately 1 ps during the decay of the initially excited (1)pi pi * state. The quantum yields phi(D)(ps) determined after the (1)pi pi * decay equal the final yield phi(D)(cw). This gives evidence for a predominance of the singlet channel in CPD formation.
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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 Munchen, Oettingenstr. 67, 80538 Munchen, Germany
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236
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Middleton CT, de La Harpe K, Su C, Law YK, Crespo-Hernández CE, Kohler B. DNA excited-state dynamics: from single bases to the double helix. Annu Rev Phys Chem 2009; 60:217-39. [PMID: 19012538 DOI: 10.1146/annurev.physchem.59.032607.093719] [Citation(s) in RCA: 602] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ultraviolet light is strongly absorbed by DNA, producing excited electronic states that sometimes initiate damaging photochemical reactions. Fully mapping the reactive and nonreactive decay pathways available to excited electronic states in DNA is a decades-old quest. Progress toward this goal has accelerated rapidly in recent years, in large measure because of ultrafast laser experiments. Here we review recent discoveries and controversies concerning the nature and dynamics of excited states in DNA model systems in solution. Nonradiative decay by single, solvated nucleotides occurs primarily on the subpicosecond timescale. Surprisingly, excess electronic energy relaxes one or two orders of magnitude more slowly in DNA oligo- and polynucleotides. Highly efficient nonradiative decay pathways guarantee that most excited states do not lead to deleterious reactions but instead relax back to the electronic ground state. Understanding how the spatial organization of the bases controls the relaxation of excess electronic energy in the double helix and in alternative structures is currently one of the most exciting challenges in the field.
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Affiliation(s)
- Chris T Middleton
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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237
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Kistler KA, Matsika S. Solvatochromic Shifts of Uracil and Cytosine Using a Combined Multireference Configuration Interaction/Molecular Dynamics Approach and the Fragment Molecular Orbital Method. J Phys Chem A 2009; 113:12396-403. [DOI: 10.1021/jp901601u] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Kurt A. Kistler
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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238
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239
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Lan Z, Fabiano E, Thiel W. Photoinduced nonadiabatic dynamics of pyrimidine nucleobases: on-the-fly surface-hopping study with semiempirical methods. J Phys Chem B 2009; 113:3548-55. [PMID: 19239209 DOI: 10.1021/jp809085h] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photoinduced relaxation dynamics of pyrimidine nucleobases (uracil, thymine, and cytosine) was studied using the surface-hopping approach at the semiempirical OM2/MRCI level of theory. The relevant potential energy surfaces were characterized by performing geometry optimizations of the energy minima of the lowest electronic states and of the most important conical intersections and by computing excitation energies at each configuration. Surface-hopping molecular dynamics simulations were performed to describe the nonadiabatic dynamics after excitation into the optically active state. In each of the molecules, the two lowest excited singlet states are involved in the dynamics, and there are competing relaxation paths. The dynamics is dominated by a two-step relaxation mechanism in uracil and thymine, while the direct decay to the ground state is most important in cytosine. For all three molecules, the simulations yield ultrafast S(2)-S(1) deexcitation within 50 fs and internal conversion to the ground state in less than 1 ps, consistent with recent experimental results from time-resolved photoelectron spectroscopy.
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Affiliation(s)
- Zhenggang Lan
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
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240
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Theoretical study on the excited states of heteroarene chromophores: Comparison of calculated and experimental values. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.03.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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241
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Sherin PS, Grilj J, Tsentalovich YP, Vauthey E. Ultrafast Excited-State Dynamics of Kynurenine, a UV Filter of the Human Eye. J Phys Chem B 2009; 113:4953-62. [DOI: 10.1021/jp900541b] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter S. Sherin
- International Tomography Center SB RAS, Institutskaya 3a, 630090 Novosibirsk, Russia, and Department of Physical Chemistry, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Jakob Grilj
- International Tomography Center SB RAS, Institutskaya 3a, 630090 Novosibirsk, Russia, and Department of Physical Chemistry, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Yuri P. Tsentalovich
- International Tomography Center SB RAS, Institutskaya 3a, 630090 Novosibirsk, Russia, and Department of Physical Chemistry, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Eric Vauthey
- International Tomography Center SB RAS, Institutskaya 3a, 630090 Novosibirsk, Russia, and Department of Physical Chemistry, University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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242
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Serrano-Andrés L, Merchán M. Are the five natural DNA/RNA base monomers a good choice from natural selection? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2009. [DOI: 10.1016/j.jphotochemrev.2008.12.001] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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243
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Study of hydrogen bonds in crystalline 5-nitrouracil. Density functional theory calculations of the O-17, N-14, and H-2 nuclear quadrupole resonance parameters. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2009. [DOI: 10.1007/bf03246520] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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244
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Santoro F, Improta R, Barone V. Three-dimensional diabatic models for the ππ* → nπ* excited-state decay of uracil derivatives in solution. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0527-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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245
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Santoro F, Barone V, Improta R. Absorption spectrum of A-T DNA unraveled by quantum mechanical calculations in solution on the (dA)2 x (dT)2 tetramer. Chemphyschem 2009; 9:2531-7. [PMID: 19006164 DOI: 10.1002/cphc.200800617] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The absorption spectrum of A-T DNA is computed for the first time in aqueous solution by means of quantum mechanical calculations performed on realistic models, thereby accounting for both stacking and base pairing interactions and including solvent effects through the polarizable continuum model. The computed and experimental spectra are in close agreement. Our analysis allows the identification of all the electronic transitions hidden in the broad absorption spectrum of A-T DNA, thus determining their most relevant properties and providing an explanation for the most significant experimental features, such as the small blue shift of the band maximum and the appearance of a shoulder on the red wing of the absorption band. The lowest-energy dark excited state corresponds to a charge-transfer state between two stacked adenine bases.
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Affiliation(s)
- Fabrizio Santoro
- Istituto per i Processi Chimico-Fisici-CNR, Area della Ricerca del CNR Via Moruzzi,1 I-56124 Pisa, Italy
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246
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Quantum Mechanical Studies of the Photophysics of DNA and RNA Bases. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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247
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248
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Kobayashi T, Harada Y, Suzuki T, Ichimura T. Excited State Characteristics of 6-Azauracil in Acetonitrile: Drastically Different Relaxation Mechanism from Uracil. J Phys Chem A 2008; 112:13308-15. [DOI: 10.1021/jp803096j] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takashi Kobayashi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yosuke Harada
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Suzuki
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Teijiro Ichimura
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ohokayama, Meguro-ku, Tokyo 152-8551, Japan
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249
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Hudock HR, Martínez TJ. Excited-State Dynamics of Cytosine Reveal Multiple Intrinsic Subpicosecond Pathways. Chemphyschem 2008; 9:2486-90. [DOI: 10.1002/cphc.200800649] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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250
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Zhu XM, Wang HG, Zheng X, Phillips DL. Role of Ribose in the Initial Excited State Structural Dynamics of Thymidine in Water Solution: A Resonance Raman and Density Functional Theory Investigation. J Phys Chem B 2008; 112:15828-36. [DOI: 10.1021/jp806248b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xin-Ming Zhu
- Department of Chemistry and State Key Laboratory of ATMMT(MOE), Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China 310018, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Hui-gang Wang
- Department of Chemistry and State Key Laboratory of ATMMT(MOE), Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China 310018, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - Xuming Zheng
- Department of Chemistry and State Key Laboratory of ATMMT(MOE), Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China 310018, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
| | - David Lee Phillips
- Department of Chemistry and State Key Laboratory of ATMMT(MOE), Zhejiang Sci-Tech University, Hangzhou, People’s Republic of China 310018, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China
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