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Karak P, Moitra T, Ruud K, Chakrabarti S. Photophysics of uracil: an explicit time-dependent generating function-based method combining both nonadiabatic and spin-orbit coupling effects. Phys Chem Chem Phys 2023; 25:8209-8219. [PMID: 36881024 DOI: 10.1039/d2cp05955j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
We present a composite framework for calculating the rates of non-radiative deactivation processes, namely internal conversion (IC) and intersystem crossing (ISC), on an equal footing by explicitly computing the non-adiabatic coupling (NAC) and spin-orbit coupling (SOC) constants, respectively. The stationary-state approach uses a time-dependent generating function based on Fermi's golden rule. We validate the applicability of the framework by computing the rate of IC for azulene, obtaining comparable rates to experimental and previous theoretical results. Next, we investigate the photophysics associated with the complex photodynamics of the uracil molecule. Interestingly, our simulated rates corroborate experimental observations. Detailed analyses using Duschinsky rotation matrices, displacement vectors and NAC matrix elements are presented to interpret the findings alongside testing the suitability of the approach for such molecular systems. The suitability of the Fermi's golden rule based method is explained qualitatively in terms of single-mode potential energy surfaces.
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Affiliation(s)
- Pijush Karak
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
| | - Torsha Moitra
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway.
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway. .,Norwegian Defence Research Establishment, P.O.Box 25, 2027 Kjeller, Norway
| | - Swapan Chakrabarti
- Department of Chemistry, University of Calcutta, 92 A.P.C Road, Kolkata-700009, West Bengal, India.
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2
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Ultrafast Photo-Ion Probing of the Relaxation Dynamics in 2-Thiouracil. Molecules 2023; 28:molecules28052354. [PMID: 36903604 PMCID: PMC10005304 DOI: 10.3390/molecules28052354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
In this work, we investigate the relaxation processes of 2-thiouracil after UV photoexcitation to the S2 state through the use of ultrafast, single-colour, pump-probe UV/UV spectroscopy. We place focus on investigating the appearance and subsequent decay signals of ionized fragments. We complement this with VUV-induced dissociative photoionisation studies collected at a synchrotron, allowing us to better understand and assign the ionisation channels involved in the appearance of the fragments. We find that all fragments appear when single photons with energy > 11 eV are used in the VUV experiments and hence appear through 3+ photon-order processes when 266 nm light is used. We also observe three major decays for the fragment ions: a sub-autocorrelation decay (i.e., sub-370 fs), a secondary ultrafast decay on the order of 300-400 fs, and a long decay on the order of 220 to 400 ps (all fragment dependent). These decays agree well with the previously established S2 → S1 → Triplet → Ground decay process. Results from the VUV study also suggest that some of the fragments may be created by dynamics occurring in the excited cationic state.
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3
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Huix-Rotllant M, Schwinn K, Pomogaev V, Farmani M, Ferré N, Lee S, Choi CH. Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT. J Chem Theory Comput 2023; 19:147-156. [PMID: 36574493 DOI: 10.1021/acs.jctc.2c01010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.
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Affiliation(s)
| | - Karno Schwinn
- Aix-Marseille Univ, CNRS, ICR, Marseille13013, France
| | - Vladimir Pomogaev
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Maryam Farmani
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, Marseille13013, France
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
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4
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Photoinduced phenomena in water solution of melamine explaining the photostability of the compound. J Mol Model 2021; 27:196. [PMID: 34104983 DOI: 10.1007/s00894-021-04809-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
Two tautomers of melamine (triamino and imino-diamino) were studied at the BLYP/aug-cc-pVDZ theoretical level. It was found that the two tautomers are bridged with the 1πσ* excited-state reaction path. The high photostability of melamine in water solution was explained with the mechanism of ring deformation which occurs along the 1ππ* excited-state reaction path. The two mechanisms are investigated at the TD BLYP level of theory using the linear interpolation in internal coordinates approach.
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5
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Park W, Lee S, Huix-Rotllant M, Filatov M, Choi CH. Impact of the Dynamic Electron Correlation on the Unusually Long Excited-State Lifetime of Thymine. J Phys Chem Lett 2021; 12:4339-4346. [PMID: 33929858 DOI: 10.1021/acs.jpclett.1c00712] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Non-radiative relaxation of the photoexcited thymine in the gas phase shows an unusually long excited-state lifetime, and, over the years, a number of models, i.e., S1-trapping, S2-trapping, and S1&S2-trapping, have been put forward to explain its mechanism. Here, we investigate this mechanism using non-adiabatic molecular dynamics (NAMD) simulations in connection with the recently developed mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) method. We show that the previously predicted S2-trapping model was due to an artifact caused by an insufficient account of the dynamic electron correlation. The current work supports the S1-trapping mechanism with two lifetimes, τ1 = 30 ± 1 fs and τ2 = 6.1 ± 0.035 ps, quantitatively consistent with the recent time-resolved experiments. Upon excitation to the S2 (ππ*) state, thymine undergoes an ultrafast (ca. 30 fs) S2→S1 internal conversion and resides around the minimum on the S1 (nOπ*) surface, slowly decaying to the ground state (ca. 6.1 ps). While the S2→S1 internal conversion is mediated by fast bond length alternation distortion, the subsequent S1→S0 occurs through several conical intersections, involving a slow puckering motion.
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Affiliation(s)
- Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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6
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Balasubramani SG, Chen GP, Coriani S, Diedenhofen M, Frank MS, Franzke YJ, Furche F, Grotjahn R, Harding ME, Hättig C, Hellweg A, Helmich-Paris B, Holzer C, Huniar U, Kaupp M, Marefat Khah A, Karbalaei Khani S, Müller T, Mack F, Nguyen BD, Parker SM, Perlt E, Rappoport D, Reiter K, Roy S, Rückert M, Schmitz G, Sierka M, Tapavicza E, Tew DP, van Wüllen C, Voora VK, Weigend F, Wodyński A, Yu JM. TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations. J Chem Phys 2020; 152:184107. [PMID: 32414256 PMCID: PMC7228783 DOI: 10.1063/5.0004635] [Citation(s) in RCA: 533] [Impact Index Per Article: 133.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 01/30/2023] Open
Abstract
TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy-cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe-Salpeter methods, second-order Møller-Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE's functionality, including excited-state methods, RPA and Green's function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE's current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE's development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.
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Affiliation(s)
- Sree Ganesh Balasubramani
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Guo P Chen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
| | - Michael Diedenhofen
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Marius S Frank
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Yannick J Franzke
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Robin Grotjahn
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Arnim Hellweg
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Christof Holzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Uwe Huniar
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Alireza Marefat Khah
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | | | - Thomas Müller
- Forschungszentrum Jülich, Jülich Supercomputer Centre, Wilhelm-Jonen Straße, 52425 Jülich, Germany
| | - Fabian Mack
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Brian D Nguyen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Shane M Parker
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Eva Perlt
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Dmitrij Rappoport
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kevin Reiter
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Saswata Roy
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Matthias Rückert
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Gunnar Schmitz
- Department of Chemistry, Aarhus Universitet, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Marek Sierka
- TURBOMOLE GmbH, Litzenhardtstraße 19, 76135 Karlsruhe, Germany
| | - Enrico Tapavicza
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, California 90840, USA
| | - David P Tew
- Max Planck Institute for Solid State Research, Heisenbergstaße 1, 70569 Stuttgart, Germany
| | - Christoph van Wüllen
- Fachbereich Chemie and Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, Erwin-Schrödinger-Staße 52, 67663 Kaiserslautern, Germany
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Florian Weigend
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Artur Wodyński
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Jason M Yu
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
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7
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Wohlgemuth M, Mitrić R. Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping. Phys Chem Chem Phys 2020; 22:16536-16551. [DOI: 10.1039/d0cp02255a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Revealing the extended excited state lifetime due to excitation energy transport in DNA by multi-chromophoric field-induced surface-hopping (McFISH).
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Affiliation(s)
- Matthias Wohlgemuth
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie
- Julius-Maximilians-Universität Würzburg
- 97074 Würzburg
- Germany
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8
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Erickson BA, Heim ZN, Pieri E, Liu E, Martinez TJ, Neumark DM. Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy. J Phys Chem A 2019; 123:10676-10684. [PMID: 31756106 DOI: 10.1021/acs.jpca.9b08258] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The relaxation dynamics of thymine and its derivatives thymidine and thymidine monophosphate are studied using time-resolved photoelectron spectroscopy applied to a water microjet. Two absorption bands are studied; the first is a bright ππ* state which is populated using tunable-ultraviolet light in the range 4.74-5.17 eV and probed using a 6.20 eV probe pulse. By reversing the order of these pulses, a band containing multiple ππ* states is populated by the 6.20 eV pulse and the lower energy pulse serves as the probe. The lower lying ππ* state is found to decay in ∼400 fs in both thymine and thymidine independent of pump photon energy, while thymidine monophosphate decays vary from 670 to 840 fs with some pump energy dependence. The application of a computational quantum mechanical/molecular mechanical scheme at the XMS-CASPT2//CASSCF/AMBER level of theory suggests that conformational differences existing between thymidine and thymidine monophosphate in solution account for this difference. The higher lying ππ* band is found to decay in ∼600 fs in all three cases, but it is only able to be characterized when the 5.17 eV probe pulse is used. Notably, no long-lived signal from an nπ* state can be identified in either experiment on any of the three molecules.
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Affiliation(s)
- Blake A Erickson
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Zachary N Heim
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Elisa Pieri
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Erica Liu
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Todd J Martinez
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Daniel M Neumark
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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9
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Parker SM, Roy S, Furche F. Multistate hybrid time-dependent density functional theory with surface hopping accurately captures ultrafast thymine photodeactivation. Phys Chem Chem Phys 2019; 21:18999-19010. [DOI: 10.1039/c9cp03127h] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an efficient analytical implementation of first-order nonadiabatic derivative couplings between arbitrary Born–Oppenheimer states in the hybrid time-dependent density functional theory (TDDFT) framework using atom-centered basis functions.
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Affiliation(s)
- Shane M. Parker
- Department of Chemistry
- University of California, Irvine
- Irvine
- USA
| | - Saswata Roy
- Department of Chemistry
- University of California, Irvine
- Irvine
- USA
| | - Filipp Furche
- Department of Chemistry
- University of California, Irvine
- Irvine
- USA
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10
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Lischka H, Barbatti M, Siddique F, Das A, Aquino AJ. The effect of hydrogen bonding on the nonadiabatic dynamics of a thymine-water cluster. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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11
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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12
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Röttger K, Marroux HJB, Böhnke H, Morris DTJ, Voice AT, Temps F, Roberts GM, Orr-Ewing AJ. Probing the excited state relaxation dynamics of pyrimidine nucleosides in chloroform solution. Faraday Discuss 2018; 194:683-708. [PMID: 27711889 DOI: 10.1039/c6fd00068a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ultrafast transient electronic and vibrational absorption spectroscopy (TEAS and TVAS) of 2'-deoxy-cytidine (dC) and 2'-deoxy-thymidine (dT) dissolved in chloroform examines their excited-state dynamics and the recovery of ground electronic state molecules following absorption of ultraviolet light. The chloroform serves as a weakly interacting solvent, allowing comparisons to be drawn with prior experimental studies of the photodynamics of these nucleosides in the gas phase and in polar solvents such as water. The pyrimidine base nucleosides have some propensity to dimerize in aprotic solvents, but the monomer photochemistry can be resolved clearly and is the focus of this study. UV absorption at a wavelength of 260 nm excites a 1ππ* ← S0 transition, but prompt crossing of a significant fraction (50% in dC, 17% in dT) of the 1ππ* population into a nearby 1nπ* state is too fast for the experiments to resolve. The remaining flux on the 1ππ* state leaves the vertical Franck-Condon region and encounters a conical intersection with the ground electronic state of ethylenic twist character. In dC, the 1ππ* state decays to the ground state with a time constant of 1.1 ± 0.1 ps. The lifetime of the 1nπ* state is much longer in the canonical forms of both molecules: recovery of the ground state population from these states occurs with time constants of 18.6 ± 1.1 ps in amino-oxo dC and ∼114 ps in dT, indicating potential energy barriers to the 1nπ*/S0 conical intersections. The small fraction of the imino-oxo tautomer of dC present in solution has a longer-lived 1nπ* state with a lifetime for ground state recovery of 193 ± 55 ps. No evidence is found for photo-induced tautomerization of amino-oxo dC to the imino-oxo form, or for population of low lying triplet states of this nucleoside. In contrast, ∼8% of the UV-excited dT molecules access the long-lived T1 (3ππ*) state through the 1nπ* state. The primary influence of the solvent appears to be the degree to which it destabilizes the states of 1nπ* character, with consequences for the lifetimes of these states as well as the triplet state yields.
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Affiliation(s)
- Katharina Röttger
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Hugo J B Marroux
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Hendrik Böhnke
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - David T J Morris
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Angus T Voice
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Friedrich Temps
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Gareth M Roberts
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Andrew J Orr-Ewing
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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13
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Marchetti B, Karsili TNV, Ashfold MNR, Domcke W. A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs. Phys Chem Chem Phys 2018; 18:20007-27. [PMID: 26980149 DOI: 10.1039/c6cp00165c] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.
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Affiliation(s)
- Barbara Marchetti
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Tolga N V Karsili
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Michael N R Ashfold
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
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14
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Manae MA, Hazra A. Interplay between Conjugation and Size-Driven Delocalization Leads to Characteristic Properties of Substituted Thymines. J Phys Chem A 2017; 121:8147-8153. [PMID: 28960980 DOI: 10.1021/acs.jpca.7b08566] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Meghna A. Manae
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha
Road, Pune 411008, Maharashtra, India
| | - Anirban Hazra
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha
Road, Pune 411008, Maharashtra, India
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15
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Wolf TJA, Myhre RH, Cryan JP, Coriani S, Squibb RJ, Battistoni A, Berrah N, Bostedt C, Bucksbaum P, Coslovich G, Feifel R, Gaffney KJ, Grilj J, Martinez TJ, Miyabe S, Moeller SP, Mucke M, Natan A, Obaid R, Osipov T, Plekan O, Wang S, Koch H, Gühr M. Probing ultrafast ππ*/nπ* internal conversion in organic chromophores via K-edge resonant absorption. Nat Commun 2017; 8:29. [PMID: 28642477 PMCID: PMC5481431 DOI: 10.1038/s41467-017-00069-7] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/28/2017] [Indexed: 11/09/2022] Open
Abstract
Many photoinduced processes including photosynthesis and human vision happen in organic molecules and involve coupled femtosecond dynamics of nuclei and electrons. Organic molecules with heteroatoms often possess an important excited-state relaxation channel from an optically allowed ππ* to a dark nπ* state. The ππ*/nπ* internal conversion is difficult to investigate, as most spectroscopic methods are not exclusively sensitive to changes in the excited-state electronic structure. Here, we report achieving the required sensitivity by exploiting the element and site specificity of near-edge soft X-ray absorption spectroscopy. As a hole forms in the n orbital during ππ*/nπ* internal conversion, the absorption spectrum at the heteroatom K-edge exhibits an additional resonance. We demonstrate the concept using the nucleobase thymine at the oxygen K-edge, and unambiguously show that ππ*/nπ* internal conversion takes place within (60 ± 30) fs. High-level-coupled cluster calculations confirm the method's impressive electronic structure sensitivity for excited-state investigations.Many photo-induced processes such as photosynthesis occur in organic molecules, but their femtosecond excited-state dynamics are difficult to track. Here, the authors exploit the element and site selectivity of soft X-ray absorption to sensitively follow the ultrafast ππ*/nπ* electronic relaxation of hetero-organic molecules.
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Affiliation(s)
- T J A Wolf
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - R H Myhre
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - J P Cryan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - S Coriani
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Piazzale Europa 1, Trieste, IT-34127, Italy
- Department of Chemistry, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - R J Squibb
- Department of Physics, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - A Battistoni
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - N Berrah
- Department of Physics, University of Connecticut, 2152 Hillside Road, Storrs, CT, 06269, USA
| | - C Bostedt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- Argonne National Laboratory, 9700 Cass Avenue, Lemont, IL, 60439, USA
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - P Bucksbaum
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- Department of Physics, Stanford University, 382 Via Pueblo Mall, Stanford, CA, 94305, USA
| | - G Coslovich
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - R Feifel
- Department of Physics, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - K J Gaffney
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - J Grilj
- Laboratory of Ultrafast Spectroscopy, Ecole Polytechnique Federal de Lausanne, Lausanne, CH-1015, Switzerland
| | - T J Martinez
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA, 94305, USA
| | - S Miyabe
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA, 94305, USA
- Laser Technology Laboratory, RIKEN, Wako, Saitama, 351-0198, Japan
| | - S P Moeller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - M Mucke
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
| | - A Natan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - R Obaid
- Department of Physics, University of Connecticut, 2152 Hillside Road, Storrs, CT, 06269, USA
| | - T Osipov
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - O Plekan
- Elettra-Sincrotrone Trieste, Strada Statale 14-km 163,5 AREA Science Park, IT-34149, Basovizza, Trieste, Italy
| | - S Wang
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA
| | - H Koch
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.
- Department of Chemistry, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.
| | - M Gühr
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Straße 24/25, DE-14476, Potsdam, Germany.
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16
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Peccati F, Mai S, González L. Insights into the deactivation of 5-bromouracil after ultraviolet excitation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20160202. [PMID: 28320905 PMCID: PMC5360901 DOI: 10.1098/rsta.2016.0202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/03/2016] [Indexed: 06/06/2023]
Abstract
5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Francesca Peccati
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
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17
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Wu X, Karsili TNV, Domcke W. Role of Electron-Driven Proton-Transfer Processes in the Ultrafast Deactivation of Photoexcited Anionic 8-oxoGuanine-Adenine and 8-oxoGuanine-Cytosine Base Pairs. Molecules 2017; 22:molecules22010135. [PMID: 28098833 PMCID: PMC6155867 DOI: 10.3390/molecules22010135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/28/2016] [Accepted: 01/10/2017] [Indexed: 11/16/2022] Open
Abstract
It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G- with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S₁/S₀ conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G- nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G--A and 8-oxo-G--C base pairs are likely too short-lived to be efficient electron-transfer repair agents.
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Affiliation(s)
- Xiuxiu Wu
- Department of Chemistry, Technische Universitat Munchen, Lichtenbergstr. 4, Garching D-85747, Germany.
| | - Tolga N V Karsili
- Department of Chemistry, Temple University, 130 Beury Hall, 1901 N. 13th St., Philadelphia, PA 19122, USA.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universitat Munchen, Lichtenbergstr. 4, Garching D-85747, Germany.
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18
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19
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Segarra-Martí J, Francés-Monerris A, Roca-Sanjuán D, Merchán M. Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2. Molecules 2016; 21:molecules21121666. [PMID: 27918489 PMCID: PMC6274573 DOI: 10.3390/molecules21121666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/16/2022] Open
Abstract
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.
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Affiliation(s)
- Javier Segarra-Martí
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
- Present Address: Laboratoire de Chimie UMR 5182, École Normale Supérieure de Lyon, CNRS, Université de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France.
| | - Antonio Francés-Monerris
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Manuela Merchán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
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20
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Stojanović L, Bai S, Nagesh J, Izmaylov AF, Crespo-Otero R, Lischka H, Barbatti M. New Insights into the State Trapping of UV-Excited Thymine. Molecules 2016; 21:E1603. [PMID: 27886099 PMCID: PMC6273395 DOI: 10.3390/molecules21111603] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 11/23/2022] Open
Abstract
After UV excitation, gas phase thymine returns to a ground state in 5 to 7 ps, showing multiple time constants. There is no consensus on the assignment of these processes, with a dispute between models claiming that thymine is trapped either in the first (S₁) or in the second (S₂) excited states. In the present study, a nonadiabatic dynamics simulation of thymine is performed on the basis of ADC(2) surfaces, to understand the role of dynamic electron correlation on the deactivation pathways. The results show that trapping in S₂ is strongly reduced in comparison to previous simulations considering only non-dynamic electron correlation on CASSCF surfaces. The reason for the difference is traced back to the energetic cost for formation of a CO π bond in S₂.
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Affiliation(s)
| | - Shuming Bai
- Aix Marseille Univ., CNRS, ICR, Marseille, France.
| | - Jayashree Nagesh
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Artur F Izmaylov
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Rachel Crespo-Otero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA.
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21
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 338] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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22
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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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23
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Minezawa N. Optimizing minimum free-energy crossing points in solution: Linear-response free energy/spin-flip density functional theory approach. J Chem Phys 2014; 141:164118. [DOI: 10.1063/1.4899049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Noriyuki Minezawa
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto 606-8103, Japan
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24
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Maeda S, Harabuchi Y, Taketsugu T, Morokuma K. Systematic Exploration of Minimum Energy Conical Intersection Structures near the Franck–Condon Region. J Phys Chem A 2014; 118:12050-8. [DOI: 10.1021/jp507698m] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Satoshi Maeda
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yu Harabuchi
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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25
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Cui G, Thiel W. Intersystem Crossing Enables 4-Thiothymidine to Act as a Photosensitizer in Photodynamic Therapy: An Ab Initio QM/MM Study. J Phys Chem Lett 2014; 5:2682-7. [PMID: 26277963 DOI: 10.1021/jz501159j] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Motivated by its potential use as a photosensitizer in photodynamic therapy, we report the first ab initio quantum mechanics/molecular mechanics (QM/MM) study of 4-thiothymidine in aqueous solution. The core chromophore 4-thiothymine was described using the multiconfigurational CASSCF and CASPT2 QM methods, while the ribose and the solvent water molecules were treated at the MM level (CHARMM and TIP3P, respectively). The minima of the five lowest electronic states (S0, S1, S2, T1, and T2) and six minimum-energy intersections were fully optimized at the QM(CASSCF)/MM level, and their energies were further refined by single-point QM(CASPT2)/MM and CASPT2 calculations. The relevant spin-orbit couplings were also computed. We find that (1) there are three efficient photophysical pathways that account for the experimentally observed ultrafast formation of the lowest triplet state with a quantum yield of nearly unity, (2) the striking qualitative differences in the photophysical behavior of 4-thiothymine and thymine originate from the different electronic structure of their S1 states, and (3) environmental effects play an important role. The present QM/MM calculations provide mechanistic insight that may guide the design of improved photosensitizers for photodynamic therapy.
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Affiliation(s)
- Ganglong Cui
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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26
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Barbatti M. Computational reference data for the photochemistry of cyclobutane pyrimidine dimers. Chemphyschem 2014; 15:3342-54. [PMID: 25044616 DOI: 10.1002/cphc.201402302] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 01/19/2023]
Abstract
The cis-syn cyclobutane pyrimidine dimer is one of the major classes of carcinogenic UV-induced DNA photoproducts. In this work, diverse high-level quantum-chemical methods were used to determine the spectroscopic properties of neutral (singlet and triplet) and charged (cation and anion) species of thymine dimers. Maps of potential energy, charge distribution, electron affinity, and ionization potential of the thymidine dimers were computed along the two dimerization coordinates for neutral and charged species, as well as for the singlet excited state. This set of data aims at providing consistent results computed with the same methods as for photodamage and repair. Based on these results, several different photo-, heat-, and charge-induced mechanisms of dimerization and repair are characterized and discussed. Additionally, a new stable dimer with methylmethylidene-hexahydropyrimidine structure was found in the S0 state.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany).
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27
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Nakayama A, Arai G, Yamazaki S, Taketsugu T. Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: excited-state QM/MM molecular dynamics simulations. J Chem Phys 2014; 139:214304. [PMID: 24320377 DOI: 10.1063/1.4833563] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
On-the-fly excited-state quantum mechanics/molecular mechanics molecular dynamics (QM/MM-MD) simulations of thymine in aqueous solution are performed to investigate the role of solvent water molecules on the nonradiative deactivation process. The complete active space second-order perturbation theory (CASPT2) method is employed for a thymine molecule as the QM part in order to provide a reliable description of the excited-state potential energies. It is found that, in addition to the previously reported deactivation pathway involving the twisting of the C-C double bond in the pyrimidine ring, another efficient deactivation pathway leading to conical intersections that accompanies the out-of-plane displacement of the carbonyl group is observed in aqueous solution. Decay through this pathway is not observed in the gas phase simulations, and our analysis indicates that the hydrogen bonds with solvent water molecules play a key role in stabilizing the potential energies of thymine in this additional decay pathway.
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Affiliation(s)
- Akira Nakayama
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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28
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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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29
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Abstract
Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany,
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30
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Cui G, Fang WH. State-specific heavy-atom effect on intersystem crossing processes in 2-thiothymine: a potential photodynamic therapy photosensitizer. J Chem Phys 2013; 138:044315. [PMID: 23387592 DOI: 10.1063/1.4776261] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Thiothymidine has a potential application as a photosensitizer in cancer photodynamic therapy (PDT). As the chromophore of thiothymidine, 2-thiothymine exhibits ultrahigh quantum yield of intersystem crossing to the lowest triplet state T(1) (ca. 100%), which contrasts with the excited-state behavior of the natural thymine that dissipates excess electronic energy via ultrafast internal conversion to the ground state. In this work, we employed high-level complete-active space self-consistent field and its second-order perturbation methods to explore the photophysical mechanism of a 2-thiothymine model. We have optimized the minimum energy structures in the low-lying seven electronic states, as well as ten intersection points. On the basis of the computed potential energy profiles and spin-orbit couplings, we proposed three competitive, efficient nonadiabatic pathways to the lowest triplet state T(1) from the initially populated singlet state S(2). The suggested mechanistic scenario explains well the recent experimental phenomena. The origin responsible for the distinct photophysical behaviors between thymine and 2-thiothymine is ascribed to the heavy-atom effect, which is significantly enhanced in the latter. Additionally, this heavy-atom effect is found to be state-specific, which could in principle be used to tune the photophysics of 2-thiothymine. The present high-level electronic structure calculations also contribute to understand the working mechanism of thiothymidine in PDT.
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Affiliation(s)
- Ganglong Cui
- Chemistry College, Beijing Normal University, Beijing 100875, People's Republic of China.
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31
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Gobbo JP, Borin AC. On The Population of Triplet Excited States of 6-Aza-2-Thiothymine. J Phys Chem A 2013; 117:5589-96. [DOI: 10.1021/jp403508v] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- João Paulo Gobbo
- Instituto
de Química, Universidade de São Paulo, and NAP-PhotoTech, the USP Consortium for Photochemical Technology, Av. Prof. Lineu
Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
| | - Antonio Carlos Borin
- Instituto
de Química, Universidade de São Paulo, and NAP-PhotoTech, the USP Consortium for Photochemical Technology, Av. Prof. Lineu
Prestes 748, 05508-900 São Paulo, São Paulo, Brazil
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32
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33
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Gedik M, Brown A. Computational study of the excited state properties of modified RNA nucleobases. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2013.02.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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34
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Excitation of Nucleobases from a Computational Perspective I: Reaction Paths. Top Curr Chem (Cham) 2013; 355:57-97. [DOI: 10.1007/128_2013_501] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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35
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Barbatti M, Lan Z, Crespo-Otero R, Szymczak JJ, Lischka H, Thiel W. Critical appraisal of excited state nonadiabatic dynamics simulations of 9H-adenine. J Chem Phys 2012; 137:22A503. [DOI: 10.1063/1.4731649] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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36
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Szalay PG, Watson T, Perera A, Lotrich VF, Bartlett RJ. Benchmark Studies on the Building Blocks of DNA. 1. Superiority of Coupled Cluster Methods in Describing the Excited States of Nucleobases in the Franck–Condon Region. J Phys Chem A 2012; 116:6702-10. [DOI: 10.1021/jp300977a] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Péter G. Szalay
- Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518
Budapest, Hungary
| | - Thomas Watson
- Quantum
Theory Project, University of Florida,
Gainesville, Florida 32611-8435,
United States
| | - Ajith Perera
- Quantum
Theory Project, University of Florida,
Gainesville, Florida 32611-8435,
United States
| | - Victor F. Lotrich
- Quantum
Theory Project, University of Florida,
Gainesville, Florida 32611-8435,
United States
| | - Rodney J. Bartlett
- Quantum
Theory Project, University of Florida,
Gainesville, Florida 32611-8435,
United States
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37
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38
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Yamazaki S, Taketsugu T. Nonradiative Deactivation Mechanisms of Uracil, Thymine, and 5-Fluorouracil: A Comparative ab Initio Study. J Phys Chem A 2011; 116:491-503. [DOI: 10.1021/jp206546g] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Shohei Yamazaki
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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39
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Nachtigallová D, Aquino AJA, Szymczak JJ, Barbatti M, Hobza P, Lischka H. Nonadiabatic Dynamics of Uracil: Population Split among Different Decay Mechanisms. J Phys Chem A 2011; 115:5247-55. [DOI: 10.1021/jp201327w] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Adélia J. A. Aquino
- Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria
| | - Jaroslaw J. Szymczak
- Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria
| | - Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim, Germany
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Hans Lischka
- Institute of Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A 1090 Vienna, Austria
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40
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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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41
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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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42
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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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43
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Abstract
A comprehensive effort in photodynamical ab initio simulations of the ultrafast deactivation pathways for all five nucleobases adenine, guanine, cytosine, thymine, and uracil is reported. These simulations are based on a complete nonadiabatic surface-hopping approach using extended multiconfigurational wave functions. Even though all five nucleobases share the basic internal conversion mechanisms, the calculations show a distinct grouping into purine and pyrimidine bases as concerns the complexity of the photodynamics. The purine bases adenine and guanine represent the most simple photodeactivation mechanism with the dynamics leading along a diabatic ππ* path directly and without barrier to the conical intersection seam with the ground state. In the case of the pyrimidine bases, the dynamics starts off in much flatter regions of the ππ* energy surface due to coupling of several states. This fact prohibits a clear formation of a single reaction path. Thus, the photodynamics of the pyrimidine bases is much richer and includes also nπ* states with varying importance, depending on the actual nucleobase considered. Trapping in local minima may occur and, therefore, the deactivation time to the ground state is also much longer in these cases. Implications of these findings are discussed (i) for identifying structural possibilities where singlet/triplet transitions can occur because of sufficient retention time during the singlet dynamics and (ii) concerning the flexibility of finding other deactivation pathways in substituted pyrimidines serving as candidates for alternative nucleobases.
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44
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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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45
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Alexandrova AN, Tully JC, Granucci G. Photochemistry of DNA Fragments via Semiclassical Nonadiabatic Dynamics. J Phys Chem B 2010; 114:12116-28. [DOI: 10.1021/jp103322c] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - John C. Tully
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, v. Risorgimento 35, I-56126, Pisa, Italy
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46
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Dou Y, Xiong S, Wu W, Yuan S, Tang H. Photoinduced dissociation of cyclobutane thymine dimer studied by semiclassical dynamics simulation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2010; 101:31-6. [PMID: 20656502 DOI: 10.1016/j.jphotobiol.2010.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 06/15/2010] [Accepted: 06/21/2010] [Indexed: 11/30/2022]
Abstract
Photoinduced dissociation of the thymine dimer is studied in a semiclassical dynamics simulation. The simulation follows excitation of an isolated thymine dimer by a 25 fs fwhm laser pulse, and finds that dissociation proceeds via an asynchronously concerted mechanism, in which the C(5)-C(5)' bond breaks soon after application of the laser pulse, followed by cleavage of the C(6)-C(6)' bond. The dissociation results in two thymine monomers, one in an electronically excited state and the other in the ground state. The former decays to the electronic ground state through an avoided crossing induced by deformation of the pyrimidine ring at the C(5)' and C(6)' sites.
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Affiliation(s)
- Yusheng Dou
- Institute of Computational Chemistry and Molecular Simulation, Chongqing University of Posts and Telecommunications, Chongqing 400065, PR China.
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47
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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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48
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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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49
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Etinski M, Marian CM. Overruling the energy gap law: fast triplet formation in 6-azauracil. Phys Chem Chem Phys 2010; 12:15665-71. [DOI: 10.1039/c0cp00106f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Asturiol D, Lasorne B, Worth GA, Robb MA, Blancafort L. Exploring the sloped-to-peaked S2/S1 seam of intersection of thymine with electronic structure and direct quantum dynamics calculations. Phys Chem Chem Phys 2010; 12:4949-58. [DOI: 10.1039/c001556c] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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