1
|
Komarov K, Park W, Lee S, Zeng T, Choi CH. Accurate Spin-Orbit Coupling by Relativistic Mixed-Reference Spin-Flip-TDDFT. J Chem Theory Comput 2023; 19:953-964. [PMID: 36655271 DOI: 10.1021/acs.jctc.2c01036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Relativistic mixed-reference spin-flip (MRSF)-TDDFT is developed considering the spin-orbit coupling (SOC) within the mean-field approximation. The resulting SOC-MRSF faithfully reproduces the experiments with very high accuracy, which is also consistent with the values by four-component (4c) relativistic CASSCF and 4c-CASPT2 in the spin-orbit-energy splitting calculations of the C, Si, and Ge atoms. Even for the fifth-row element Sn, the SOC-MRSF yielded accurate splittings (∼ 3 % error). In the SOC calculations of the molecular 4-thiothymine with a third-row element, SOC-MRSF values are in excellent agreement with those of the SO-GMC-QDPT2 level, regardless of geometries and exchange-correlation functionals. The same SOC-MRSF predicted the anticipated chance of S1 (nπ*) → T1 (ππ*) intersystem crossing, even in thymine with only second-row elements. With its accuracy and practicality, thus, SOC-MRSF is a promising electronic structure protocol in challenging situations such as nonadiabatic molecular dynamics (NAMD) incorporating both internal conversions and intersystem crossings in large systems.
Collapse
Affiliation(s)
- Konstantin Komarov
- Center for Quantum Dynamics, Pohang University of Science and Technology, Pohang37673, South Korea
| | - Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California91125, USA
| | - Tao Zeng
- Department of Chemistry, York University, Toronto, ONM3J 1P3, Canada
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu41566, South Korea
| |
Collapse
|
2
|
Allahkaram L, Monari A, Dumont E. The Behavior of Triplet Thymine in a Model B-DNA Strand. Energetics and Spin Density Localization Revealed by ab initio Molecular Dynamics Simulations †. Photochem Photobiol 2021; 98:633-639. [PMID: 34699615 DOI: 10.1111/php.13549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/20/2021] [Indexed: 11/28/2022]
Abstract
Among the naturally occurring nucleobases, thymine presents the lowest triplet state, hence it represents a hotspot for energy transfer and photosensitization. In turn, the population of the triplet state may lead to thymine dimerization and hence to the production of toxic DNA lesions and has been the subject of intensive theoretical and experimental investigations. Relying on QM/MM molecular dynamics simulations, we have sought to situate the energy of the lowest triplet state of thymine embedded in a B-DNA environment. The energy gap varies between 305 and 329 kJ mol-1 when a single thymine is treated at the quantum chemistry level, depending on its position in the model double-stranded 16-bp oligonucleotide. The energy of triplet state decreases up to 300 kJ mol-1 , due to polarization effects, when we consider coupled stacked nucleobases up to the inclusion of four nucleobases. Our value lies in good agreement with the energy inferred experimentally by Miranda and coworkers (270 kJ mol-1 ), and our theoretical exploration opens the door to investigations toward other more complex and biologically relevant environments, such as thymines embedded in nucleosome core particles. Our investigations also provide a reference for further studies using semi-empirical approaches such as density functional-based tight-binding, allowing to further rationalize sequence effects.
Collapse
Affiliation(s)
- Laleh Allahkaram
- Laboratoire de Chimie, CNRS UMR 5182, ENS de Lyon, Univ Lyon, Lyon, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, Nancy, France.,Université de Paris and CNRS, Itodys, Paris, France
| | - Elise Dumont
- Laboratoire de Chimie, CNRS UMR 5182, ENS de Lyon, Univ Lyon, Lyon, France.,Institut Universitaire de France, Paris, France
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Lee W, Matsika S. Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA. Chemistry 2020; 26:14181-14186. [PMID: 32809239 DOI: 10.1002/chem.202002834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/01/2020] [Indexed: 11/08/2022]
Abstract
Cyclobutane pyrimidine dimer (CPD) is a photoproduct formed by two stacked pyrimidine bases through a cycloaddition reaction upon irradiation. Owing to its close association with skin cancer, the mechanism of CPD formation has been studied thoroughly. Among many aspects of CPD, its formation involving 5-methylcytosine (5mC) has been of special interest because the CPD yield is known to increase with C5-methylation of cytosine. In this work, high-level quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine a previously experimentally detected pathway for CPD formation in hetero (thymine-cytosine and thymine-5mC) dipyrimidines, which is facilitated through intersystem crossing in thymine and formation of a triplet biradical intermediate. A DNA duplex model system containing a core sequence TmCG or TCG is used. The stabilization of a radical center in the biradical intermediate by the methyl group of 5mC can lead to increased CPD yield in TmCG compared with its non-methylated counterpart, TCG, thereby suggesting the existence of a new pathway of CPD formation enhanced by 5mC.
Collapse
Affiliation(s)
- Wook Lee
- Department of Biochemistry, Kangwon National University, Chuncheon, 24341, South Korea
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| |
Collapse
|
5
|
Wolf TJA, Parrish RM, Myhre RH, Martínez TJ, Koch H, Gühr M. Observation of Ultrafast Intersystem Crossing in Thymine by Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy. J Phys Chem A 2019; 123:6897-6903. [PMID: 31319031 DOI: 10.1021/acs.jpca.9b05573] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied the photoinduced ultrafast relaxation dynamics of the nucleobase thymine using gas-phase time-resolved photoelectron spectroscopy. By employing extreme ultraviolet pulses from high harmonic generation for photoionization, we substantially extend our spectral observation window with respect to previous studies. This enables us to follow relaxation of the excited state population all the way to low-lying electronic states including the ground state. In thymine, we observe relaxation from the optically bright 1ππ* state of thymine to a dark 1nπ* state within 80 ± 30 fs. The 1nπ* state relaxes further within 3.5 ± 0.3 ps to a low-lying electronic state. By comparison with quantum chemical simulations, we can unambiguously assign its spectroscopic signature to the 3ππ* state. Hence, our study draws a comprehensive picture of the relaxation mechanism of thymine including ultrafast intersystem crossing to the triplet manifold.
Collapse
Affiliation(s)
- Thomas J A Wolf
- Stanford PULSE Institute , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States
| | - Robert M Parrish
- Stanford PULSE Institute , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States.,Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Rolf H Myhre
- Department of Chemistry , Norwegian University of Science and Technology , NO-7491 Trondheim , Norway
| | - Todd J Martínez
- Stanford PULSE Institute , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States.,Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Henrik Koch
- Scuola Normale Superiore , Piazza dei Cavalieri, 7 , 56126 Pisa , PI , Italy
| | - Markus Gühr
- Stanford PULSE Institute , SLAC National Accelerator Laboratory , Menlo Park , California 94025 , United States.,Institut für Physik und Astronomie , Universität Potsdam , 14476 Potsdam , Germany
| |
Collapse
|
6
|
Brister MM, Crespo-Hernández CE. Excited-State Dynamics in the RNA Nucleotide Uridine 5'-Monophosphate Investigated Using Femtosecond Broadband Transient Absorption Spectroscopy. J Phys Chem Lett 2019; 10:2156-2161. [PMID: 30995048 DOI: 10.1021/acs.jpclett.9b00492] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Damage to RNA from ultraviolet radiation induces chemical modifications to the nucleobases. Unraveling the excited states involved in these reactions is essential; however, investigations aimed at understanding the electronic-energy relaxation pathways of the RNA nucleotide uridine 5'-monophosphate (UMP) have not received enough attention. In this Letter, the excited-state dynamics of UMP is investigated in aqueous solution. Excitation at 267 nm results in a trifurcation event that leads to the simultaneous population of the vibrationally excited ground state, a long-lived 1nπ* state, and a receiver triplet state within 200 fs. The receiver state internally converts to the long-lived 3ππ* state in an ultrafast time scale. The results elucidate the electronic relaxation pathways and clarify earlier transient absorption experiments performed for uracil derivatives in solution. This mechanistic information is important because long-lived nπ* and ππ* excited states of both singlet and triplet multiplicities are thought to lead to the formation of harmful photoproducts.
Collapse
Affiliation(s)
- Matthew M Brister
- Department of Chemistry , Case Western Reserve University , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| | - Carlos E Crespo-Hernández
- Department of Chemistry , Case Western Reserve University , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| |
Collapse
|
7
|
Pepino AJ, Segarra-Martí J, Nenov A, Rivalta I, Improta R, Garavelli M. UV-induced long-lived decays in solvated pyrimidine nucleosides resolved at the MS-CASPT2/MM level. Phys Chem Chem Phys 2018; 20:6877-6890. [PMID: 29459916 DOI: 10.1039/c7cp08235e] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most relevant 'dark' electronic excited states in DNA/RNA pyrimidine nucleosides are mapped in water employing hybrid MS-CASPT2/MM optimisations with explicit solvation and including the sugar. Conical intersections (CIs) between initially accessed bright 1ππ* and the lowest energy dark 1nπ* excited states, involving the lone pair localised on the oxygen and/or nitrogen atoms are characterised. They are found in the vicinities of the Franck-Condon (FC) region and are shown to facilitate non-adiabatic population transfer. The excited state population of the 1nOπ* state, localised in the carbonyl moiety on all pyrimidine nucleosides, is predicted to rapidly evolve to its minimum, displaying non-negligible potential energy barriers along its non-radiative decay, and accounting for the ps signal registered in pump-probe experiments as well as for an efficient population of the triplet state. Cytidine displays an additional 1nNπ* state localised in the N3 atom and that leads to its excited state minimum displaying large potential energy barriers in the pathway connecting to the CI with the ground state. Sugar-to-base hydrogen/proton transfer processes are assessed in solution for the first time, displaying a sizable barrier along its decay and thus being competitive with other slow decay channels in the ps and ns timescales. A unified deactivation scheme for the long-lived channels of pyrimidine nucleosides is delivered, where the 1nOπ* state is found to mediate the long-lived decay in the singlet manifold and act as the doorway for triplet population and thus accounting for the recorded phosphorescence and, more generally, for the transient/photoelectron spectral signals registered up to the ns timescale.
Collapse
Affiliation(s)
- Ana Julieta Pepino
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy.
| | | | | | | | | | | |
Collapse
|
8
|
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
| | | |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Yu H, Sanchez-Rodriguez JA, Pollum M, Crespo-Hernández CE, Mai S, Marquetand P, González L, Ullrich S. Internal conversion and intersystem crossing pathways in UV excited, isolated uracils and their implications in prebiotic chemistry. Phys Chem Chem Phys 2018; 18:20168-76. [PMID: 27189184 DOI: 10.1039/c6cp01790h] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The photodynamic properties of molecules determine their ability to survive in harsh radiation environments. As such, the photostability of heterocyclic aromatic compounds to electromagnetic radiation is expected to have been one of the selection pressures influencing the prebiotic chemistry on early Earth. In the present study, the gas-phase photodynamics of uracil, 5-methyluracil (thymine) and 2-thiouracil-three heterocyclic compounds thought to be present during this era-are assessed in the context of their recently proposed intersystem crossing pathways that compete with internal conversion to the ground state. Specifically, time-resolved photoelectron spectroscopy measurements evidence femtosecond to picosecond timescales for relaxation of the singlet (1)ππ* and (1)nπ* states as well as for intersystem crossing to the triplet manifold. Trapping in the excited triplet state and intersystem crossing back to the ground state are investigated as potential factors contributing to the susceptibility of these molecules to ultraviolet photodamage.
Collapse
Affiliation(s)
- Hui Yu
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
| | | | - Marvin Pollum
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Carlos E Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Susanne Ullrich
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
11
|
Giussani A, Conti I, Nenov A, Garavelli M. Photoinduced formation mechanism of the thymine–thymine (6–4) adduct in DNA; a QM(CASPT2//CASSCF):MM(AMBER) study. Faraday Discuss 2018; 207:375-387. [DOI: 10.1039/c7fd00202e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Out-of-plane puckering of the C4′ atom forming a new CC bond seems essential for oxetane formation.
Collapse
Affiliation(s)
- Angelo Giussani
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Irene Conti
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
- Dipartimento di Chimica Industriale “Toso Montanari”
| | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
- Dipartimento di Chimica Industriale “Toso Montanari”
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
- Dipartimento di Chimica Industriale “Toso Montanari”
| |
Collapse
|
12
|
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
| |
Collapse
|
13
|
Pandey R, Ryszka M, da Fonseca Cunha T, Lalande M, Dampc M, Limão-Vieira P, Mason N, Poully J, Eden S. Threshold behavior in metastable dissociation of multi-photon ionized thymine and uracil. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.06.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
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'.
Collapse
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
| |
Collapse
|
16
|
Abstract
Phosphorescence is a phenomenon of delayed luminescence that corresponds to the radiative decay of the molecular triplet state. As a general property of molecules, phosphorescence represents a cornerstone problem of chemical physics due to the spin prohibition of the underlying triplet-singlet emission and because its analysis embraces a deep knowledge of electronic molecular structure. Phosphorescence is the simplest physical process which provides an example of spin-forbidden transformation with a characteristic spin selectivity and magnetic field dependence, being the model also for more complicated chemical reactions and for spin catalysis applications. The bridging of the spin prohibition in phosphorescence is commonly analyzed by perturbation theory, which considers the intensity borrowing from spin-allowed electronic transitions. In this review, we highlight the basic theoretical principles and computational aspects for the estimation of various phosphorescence parameters, like intensity, radiative rate constant, lifetime, polarization, zero-field splitting, and spin sublevel population. Qualitative aspects of the phosphorescence phenomenon are discussed in terms of concepts like structure-activity relationships, donor-acceptor interactions, vibronic activity, and the role of spin-orbit coupling under charge-transfer perturbations. We illustrate the theory and principles of computational phosphorescence by highlighting studies of classical examples like molecular nitrogen and oxygen, benzene, naphthalene and their azaderivatives, porphyrins, as well as by reviewing current research on systems like electrophosphorescent transition metal complexes, nucleobases, and amino acids. We furthermore discuss modern studies of phosphorescence that cover topics of applied relevance, like the design of novel photofunctional materials for organic light-emitting diodes (OLEDs), photovoltaic cells, chemical sensors, and bioimaging.
Collapse
Affiliation(s)
- Gleb Baryshnikov
- Division of Theoretical Chemistry and Biology, Royal Institute of Technology , SE-106 91 Stockholm, Sweden.,Bohdan Khmelnytsky National University , 18031 Cherkasy, Ukraine
| | - Boris Minaev
- Division of Theoretical Chemistry and Biology, Royal Institute of Technology , SE-106 91 Stockholm, Sweden.,Bohdan Khmelnytsky National University , 18031 Cherkasy, Ukraine
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, Royal Institute of Technology , SE-106 91 Stockholm, Sweden.,Institute of Nanotechnology, Spectroscopy and Quantum Chemistry, Siberian Federal University , Svobodny pr. 79, 660041 Krasnoyarsk, Russia
| |
Collapse
|
17
|
|
18
|
How Does Thymine DNA Survive Ultrafast Dimerization Damage? Molecules 2016; 22:molecules22010060. [PMID: 28042858 PMCID: PMC6155609 DOI: 10.3390/molecules22010060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/13/2016] [Accepted: 12/24/2016] [Indexed: 11/16/2022] Open
Abstract
The photodimerization reaction between the two adjacent thymine bases within a single strand has been the subject of numerous studies due to its potential to induce DNA mutagenesis and possible tumorigenesis in human skin cells. It is well established that the cycloaddition photoreaction takes place on a picosecond time scale along barrierless or low barrier singlet/triplet pathways. However, the observed dimerization quantum yield in different thymine multimer is considerable lower than might be expected. A reasonable explanation is required to understand why thymine in DNA is able to survive ultrafast dimerization damage. In this work, accurate quantum calculations based on the combined CASPT2//CASSCF/AMBER method were conducted to map the excited state relaxation pathways of the thymine monomer in aqueous solution and of the thymine oligomer in DNA. A monomer-like decay pathway, induced by the twisting of the methyl group, is found to provide a bypass channel to ensure the photostability of thymine in single-stranded oligomers. This fast relaxation path is regulated by the conical intersection between the bright SCT(¹ππ*) state with the intra-base charge transfer character and the ground state to remove the excess excitation energy, thereby achieving the ground-state recovery with high efficiency.
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
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.
Collapse
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.
| | | |
Collapse
|
21
|
Rauer C, Nogueira JJ, Marquetand P, González L. Cyclobutane Thymine Photodimerization Mechanism Revealed by Nonadiabatic Molecular Dynamics. J Am Chem Soc 2016; 138:15911-15916. [PMID: 27682199 DOI: 10.1021/jacs.6b06701] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of cyclobutane thymine dimers is one of the most important DNA carcinogenic photolesions induced by ultraviolet irradiation. The long debated question whether thymine dimerization after direct light excitation involves singlet or triplet states is investigated here for the first time using nonadiabatic molecular dynamics simulations. We find that the precursor of this [2 + 2] cycloaddition reaction is the singlet doubly π2π*2 excited state, which is spectroscopically rather dark. Excitation to the bright 1ππ* or dark 1nπ* excited states does not lead to thymine dimer formation. In all cases, intersystem crossing to the triplet states is not observed during the simulated time, indicating that ultrafast dimerization occurs in the singlet manifold. The dynamics simulations also show that dimerization takes place only when conformational control happens in the doubly excited state.
Collapse
Affiliation(s)
- Clemens Rauer
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna , Währinger Straße 17, 1090 Vienna, Austria
| | - Juan J Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna , Währinger Straße 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- 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
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
González-Luque R, Climent T, González-Ramírez I, Merchán M, Serrano-Andrés L. Singlet-Triplet States Interaction Regions in DNA/RNA Nucleobase Hypersurfaces. J Chem Theory Comput 2015; 6:2103-14. [PMID: 26615938 DOI: 10.1021/ct100164m] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present study provides new insight into the intrinsic mechanisms for the population of the triplet manifold in DNA nucleobases by determining, at the multiconfigurational CASSCF/CASPT2 level, the singlet-triplet states crossing regions and the main decay paths for their lowest singlet and triplet states after near-UV irradiation. The studied singlet-triplet interacting regions are accessible along the minimum energy path of the initially populated singlet bright (1)ππ* state. In particular, all five natural DNA/RNA nucleobases have, at the end of the main minimum energy path and near a conical intersection of the ground and (1)ππ* states, a low-energy, easily accessible, singlet-triplet crossing region directly connecting the lowest singlet and triplet ππ* excited states. Adenine, thymine, and uracil display additional higher-energy crossing regions related to the presence of low-lying singlet and a triplet nπ* state. These funnels are absent in guanine and cytosine, which have the bright (1)ππ* state lower in energy and less accessible nπ* states. Knowledge of the location and accessibility of these regions, in which the singlet-triplet interaction is related to large spin-orbit coupling elements, may help to understand experimental evidence such as the wavelength dependence measured for the triplet formation quantum yield in nucleobases and the prevalence of adenine and thymine components in the phosphorescence spectra of DNA.
Collapse
Affiliation(s)
- Remedios González-Luque
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain
| | - Teresa Climent
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain
| | - Israel González-Ramírez
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain
| | - Manuela Merchán
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain
| | - Luis Serrano-Andrés
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain
| |
Collapse
|
24
|
Crespo-Hernández CE, Martínez-Fernández L, Rauer C, Reichardt C, Mai S, Pollum M, Marquetand P, González L, Corral I. Electronic and structural elements that regulate the excited-state dynamics in purine nucleobase derivatives. J Am Chem Soc 2015; 137:4368-81. [PMID: 25763596 PMCID: PMC4410903 DOI: 10.1021/ja512536c] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 12/20/2022]
Abstract
The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited (1)nπ* state. Following vibrational and conformational relaxation, the (1)nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the (1)nπ* state while simultaneously facilitating access to the (1)ππ*(La)/S0 conical intersection, such that population of the (1)nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position.
Collapse
Affiliation(s)
- Carlos E. Crespo-Hernández
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Lara Martínez-Fernández
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
| | - Clemens Rauer
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Christian Reichardt
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Marvin Pollum
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Inés Corral
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
25
|
Dumont E, Wibowo M, Roca-Sanjuán D, Garavelli M, Assfeld X, Monari A. Resolving the Benzophenone DNA-Photosensitization Mechanism at QM/MM Level. J Phys Chem Lett 2015; 6:576-80. [PMID: 26262469 DOI: 10.1021/jz502562d] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Benzophenone, the parent of the diarylketone family, is a versatile compound commonly used as a UV blocker. It may also trigger triplet-based DNA photosensitization. Therefore, benzophenone is involved in DNA photodamage induction. In the absence of experimentally resolved structure, the mechanism of DNA damage production remains elusive. Employing a hybrid quantum mechanics/molecular mechanics approach, here we address the spin transfer mechanism between this drug and proximal thymine, that is, the DNA nucleobase most prone to suffer triplet damages.
Collapse
Affiliation(s)
- Elise Dumont
- †Laboratoire de Chimie, UMR 5182 CNRS et Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Meilani Wibowo
- ‡Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46701 València, Spain
| | - Daniel Roca-Sanjuán
- ‡Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46701 València, Spain
| | - Marco Garavelli
- †Laboratoire de Chimie, UMR 5182 CNRS et Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
- §Dipartimento di Chimica G. Ciamician, Università di Bologna, via Selmi 2, Bologna 40126, Italy
| | - Xavier Assfeld
- ∥Université de Lorraine - Nancy, Theory-Modeling-Simulation SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- ⊥CNRS, Theory-Modeling-Simulation SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- ∥Université de Lorraine - Nancy, Theory-Modeling-Simulation SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- ⊥CNRS, Theory-Modeling-Simulation SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| |
Collapse
|
26
|
Esboui M, Jaidane N. Non-radiative deactivation in phenol–pyridine complex: theoretical study. Photochem Photobiol Sci 2015; 14:1127-37. [DOI: 10.1039/c4pp00199k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A comparative theoretical study of the nonradiative decay mechanisms to the ground state of phenol-pyridine complex under Cs symmetry (Pl and Pe conformers) and without symmetry constraints has been performed by ab initio calculations.
Collapse
Affiliation(s)
- Mounir Esboui
- Laboratoire de Spectroscopie Atomique
- Moléculaire et Applications
- Département de Physique
- Faculté des Sciences de Tunis
- 2092 Tunis
| | - Nejmeddine Jaidane
- Laboratoire de Spectroscopie Atomique
- Moléculaire et Applications
- Département de Physique
- Faculté des Sciences de Tunis
- 2092 Tunis
| |
Collapse
|
27
|
Ligare M, Siouri F, Bludsky O, Nachtigallová D, de Vries MS. Characterizing the dark state in thymine and uracil by double resonant spectroscopy and quantum computation. Phys Chem Chem Phys 2015; 17:24336-41. [DOI: 10.1039/c5cp03516c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double resonant spectroscopy characterizes both grounds state and dark excited state of uracil and thymine.
Collapse
Affiliation(s)
- M. Ligare
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - F. Siouri
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - O. Bludsky
- Institute of Organic Chemistry and Biochemistry v.v.i
- AS CR
- 16610 Prague
- Czech Republic
| | - D. Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i
- AS CR
- 16610 Prague
- Czech Republic
| | - M. S. de Vries
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| |
Collapse
|
28
|
Richter M, Mai S, Marquetand P, González L. Ultrafast intersystem crossing dynamics in uracil unravelled by ab initio molecular dynamics. Phys Chem Chem Phys 2014; 16:24423-36. [PMID: 25301389 PMCID: PMC4391640 DOI: 10.1039/c4cp04158e] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 10/03/2014] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations have been performed in order to investigate the relaxation dynamics of uracil after UV excitation in gas phase. Intersystem crossing (ISC) has been included for the first time into time-dependent simulations of uracil, allowing the system to relax in the singlet as well as in the triplet states. The results show a qualitatively different picture than similar simulations that include singlet states only. The inclusion of ISC effectively quenches the relaxation to the singlet ground state and instead privileges transitions from the low-lying nπ* state (S1) to a ππ* triplet state (T2) followed by rapid internal conversion to the lowest triplet state.
Collapse
Affiliation(s)
- Martin Richter
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| | - Sebastian Mai
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| | - Philipp Marquetand
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| | - Leticia González
- Institute of Theoretical Chemistry , Währinger Str. 17 , 1090 Vienna , Austria .
| |
Collapse
|
29
|
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
| |
Collapse
|
30
|
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.
Collapse
Affiliation(s)
- Akira Nakayama
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | | | | | | |
Collapse
|
31
|
Zhao H, Liu K, Song D, Su H. Physical quenching in competition with the formation of cyclobutane pyrimidine dimers in DNA photolesion. J Phys Chem A 2014; 118:9105-12. [PMID: 24964272 DOI: 10.1021/jp504944b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The potential energy profiles toward formation of cyclobutane pyrimidine dimers CPD and the physical quenching after UV excitation were explored for the dinucleotide thymine dinucleoside monophosphate (TpT) using density functional theory (ωB97XD) and the time-dependent density functional theory (TD-ωB97XD). The ωB97XD functional that includes empirical dispersion correction is shown to be an appropriate method to obtain rational results for the current large reaction system of TpT. Photophysical quenching is shown to be predominant over the photochemical CPD formation. Following the initial excitation to the (1)ππ* state, the underlying dark (1)nπ* state bifurcates the excited population to the prevailing IC to S0 and the small ISC to the long-lived triplet state T1 via T4 ((3)ππ*) state that has negligible energy gap with (1)nπ* state. Even for the reactive T1 state, two physical quenching pathways resulting in the conversion back to ground-state reactant via the T1/S0 crossing points are newly located, which are in strong competition with CPD formation. These results provide rationale for the recently observed nanosecond triplet decay rates in the single-stranded (dT)18 and inefficiency of deleterious CPD formation, which allow for a deeper understanding of DNA photostability.
Collapse
Affiliation(s)
- Hongmei Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | | | | | | |
Collapse
|
32
|
Martínez-Fernández L, Corral I, Granucci G, Persico M. Competing ultrafast intersystem crossing and internal conversion: a time resolved picture for the deactivation of 6-thioguanine. Chem Sci 2014. [DOI: 10.1039/c3sc52856a] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
|
33
|
Electronic Excitation Processes in Single-Strand and Double-Strand DNA: A Computational Approach. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:1-37. [DOI: 10.1007/128_2013_517] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
34
|
Ovchinnikov VA, Sundholm D. Coupled-cluster and density functional theory studies of the electronic 0–0 transitions of the DNA bases. Phys Chem Chem Phys 2014; 16:6931-41. [DOI: 10.1039/c3cp55080j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 0–0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations.
Collapse
Affiliation(s)
- Vasily A. Ovchinnikov
- University of Helsinki
- 00014 Helsinki, Finland
- Emanuel Institute of Biochemical Physics RAS
- 119334 Moscow, Russia
| | | |
Collapse
|
35
|
Vendrell-Criado V, Rodríguez-Muñiz GM, Yamaji M, Lhiaubet-Vallet V, Cuquerella MC, Miranda MA. Two-Photon Chemistry from Upper Triplet States of Thymine. J Am Chem Soc 2013; 135:16714-9. [DOI: 10.1021/ja408997j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Victoria Vendrell-Criado
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
| | - Gemma M. Rodríguez-Muñiz
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
| | - Minoru Yamaji
- Division
of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu Gunma 376-8515, Japan
| | - Virginie Lhiaubet-Vallet
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
| | - M. Consuelo Cuquerella
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
| | - Miguel A. Miranda
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
| |
Collapse
|
36
|
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.
Collapse
Affiliation(s)
- Ganglong Cui
- Chemistry College, Beijing Normal University, Beijing 100875, People's Republic of China.
| | | |
Collapse
|
37
|
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
| |
Collapse
|
38
|
Giussani A, Pou-Amérigo R, Serrano-Andrés L, Freire-Corbacho A, Martínez-García C, Fernández P. MI, Sarakha M, Canle L. M, Santaballa JA. Combined Theoretical and Experimental Study of the Photophysics of Asulam. J Phys Chem A 2013; 117:2125-37. [DOI: 10.1021/jp311932z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Angelo Giussani
- Instituto de Ciencia Molecular, Universitat de Valencia, Ap. 22085, ES-46100 Valencia,
Spain
| | - Rosendo Pou-Amérigo
- Instituto de Ciencia Molecular, Universitat de Valencia, Ap. 22085, ES-46100 Valencia,
Spain
| | - Luis Serrano-Andrés
- Instituto de Ciencia Molecular, Universitat de Valencia, Ap. 22085, ES-46100 Valencia,
Spain
| | - Antonio Freire-Corbacho
- Departamento de Química
Física e Enxeñería Química I, Universidade da Coruña, Rúa da Fraga
10, ES-15008 A Coruña, Spain
| | - Cristina Martínez-García
- Departamento de Química
Física e Enxeñería Química I, Universidade da Coruña, Rúa da Fraga
10, ES-15008 A Coruña, Spain
| | - M Isabel Fernández P.
- Departamento de Química
Física e Enxeñería Química I, Universidade da Coruña, Rúa da Fraga
10, ES-15008 A Coruña, Spain
| | - Mohamed Sarakha
- Laboratoire de Photochemie Moléculaire et Macromoléculaire, Université Blaise Pascal, UMR CNRS 6505, F-63177
Aubière Cedex, France
| | - Moisés Canle L.
- Departamento de Química
Física e Enxeñería Química I, Universidade da Coruña, Rúa da Fraga
10, ES-15008 A Coruña, Spain
| | - J. Arturo Santaballa
- Departamento de Química
Física e Enxeñería Química I, Universidade da Coruña, Rúa da Fraga
10, ES-15008 A Coruña, Spain
| |
Collapse
|
39
|
Giussani A, Serrano-Andrés L, Merchán M, Roca-Sanjuán D, Garavelli M. Photoinduced formation mechanism of the thymine-thymine (6-4) adduct. J Phys Chem B 2013; 117:1999-2004. [PMID: 23339629 DOI: 10.1021/jp307200g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet (3)(nπ*) state of thymine. This state, displaying an elongated C(4)═O bond, triggers (6-4) dimer formation by reaction with the C(5)═C(6) double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just one thymine, whose main decay channel (by radiationless repopulation of its ground state) is nonphotochemical, can rationalize the experimentally observed low quantum yield of formation for the thymine-thymine (6-4) adduct.
Collapse
Affiliation(s)
- Angelo Giussani
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain.
| | | | | | | | | |
Collapse
|
40
|
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]
|
41
|
Patwardhan S, Tonzani S, Lewis FD, Siebbeles LDA, Schatz GC, Grozema FC. Effect of Structural Dynamics and Base Pair Sequence on the Nature of Excited States in DNA Hairpins. J Phys Chem B 2012; 116:11447-58. [DOI: 10.1021/jp307146u] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Sameer Patwardhan
- Opto-Electronic Materials Section,
Department of Chemical Engineering, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The
Netherlands
- Department
of Chemistry, Center
for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - Stefano Tonzani
- Department
of Chemistry, Center
for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - Frederick D. Lewis
- Department
of Chemistry, Center
for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - Laurens D. A. Siebbeles
- Opto-Electronic Materials Section,
Department of Chemical Engineering, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The
Netherlands
| | - George C. Schatz
- Department
of Chemistry, Center
for Nanofabrication and Molecular Self-Assembly, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113,
United States
| | - Ferdinand C. Grozema
- Opto-Electronic Materials Section,
Department of Chemical Engineering, Delft University of Technology, Julianalaan 136, 2628 BL, Delft, The
Netherlands
| |
Collapse
|
42
|
Bonancía P, Vayá I, Climent MJ, Gustavsson T, Markovitsi D, Jiménez MC, Miranda MA. Excited-State Interactions in Diastereomeric Flurbiprofen–Thymine Dyads. J Phys Chem A 2012; 116:8807-14. [DOI: 10.1021/jp3063838] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Paula Bonancía
- Chemistry Department/Institute
of Chemical Technology UPV-CSIC, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ignacio Vayá
- Chemistry Department/Institute
of Chemical Technology UPV-CSIC, Universitat Politècnica de València, 46022 Valencia, Spain
| | - M. José Climent
- Chemistry Department/Institute
of Chemical Technology UPV-CSIC, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Thomas Gustavsson
- CNRS, IRAMIS, SPAM, Francis Perrin Laboratory, URA 2453, 91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- CNRS, IRAMIS, SPAM, Francis Perrin Laboratory, URA 2453, 91191 Gif-sur-Yvette, France
| | - M. Consuelo Jiménez
- Chemistry Department/Institute
of Chemical Technology UPV-CSIC, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Miguel A. Miranda
- Chemistry Department/Institute
of Chemical Technology UPV-CSIC, Universitat Politècnica de València, 46022 Valencia, Spain
| |
Collapse
|
43
|
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
| |
Collapse
|
44
|
González L, Escudero D, Serrano-Andrés L. Progress and Challenges in the Calculation of Electronic Excited States. Chemphyschem 2011; 13:28-51. [DOI: 10.1002/cphc.201100200] [Citation(s) in RCA: 310] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 08/05/2011] [Indexed: 11/09/2022]
|
45
|
Nosenko Y, Kunitski M, Brutschy B. Specific photodynamics in thymine clusters: the role of hydrogen bonding. J Phys Chem A 2011; 115:9429-39. [PMID: 21648386 DOI: 10.1021/jp111373t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photoionization detected IR study of thymine and 1-methylthymine monohydrates and of their homodimers was carried out to shed some light on the structure of the thymine clusters whose complex photodynamics has recently been the subject of great interest. Under supersonic jet conditions, thymine forms doubly H-bonded cyclic clusters with water or another base preferentially via its N1-H group and the adjacent carbonyl group. This hydrate is of no biological relevance since the N1-H group is the sugar binding site in thymidine. On the other hand, 1-methylthymine forms the donor H-bonds only via the N3-H group. Hence, properties of the N1-H and the N3-H bound clusters of thymine can be studied using thymine and 1-methylthymine molecules, respectively. No biologically relevant conformations of the dimers and hydrates of thymine, contrary to those of 1-methylthymine, are observed under supersonic jet conditions. Thymine homodimer, which extensively fragments upon UV ionization by formation of a protonated monomer, exhibits two N1-H···O═C2 hydrogen bonds. The photodynamics of hydrated thymines is found to be extremely sensitive to the hydration site: ranging from an ultrafast relaxation in less than 100 fs up to formation of a dark state with the lifetime on the microsecond time scale.
Collapse
Affiliation(s)
- Yevgeniy Nosenko
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-str. 7, 60438 Frankfurt/Main, Germany
| | | | | |
Collapse
|
46
|
Kunitski M, Nosenko Y, Brutschy B. On the Nature of the Long-Lived “Dark” State of Isolated 1-Methylthymine. Chemphyschem 2011; 12:2024-30. [DOI: 10.1002/cphc.201000985] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 02/16/2011] [Indexed: 11/10/2022]
|
47
|
Curutchet C, Voityuk AA. Triplet-Triplet Energy Transfer in DNA: A Process that Occurs on the Nanosecond Timescale. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201004732] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
48
|
Curutchet C, Voityuk AA. Triplet-triplet energy transfer in DNA: a process that occurs on the nanosecond timescale. Angew Chem Int Ed Engl 2011; 50:1820-2. [PMID: 21328647 DOI: 10.1002/anie.201004732] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 11/29/2010] [Indexed: 11/09/2022]
Affiliation(s)
- Carles Curutchet
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain.
| | | |
Collapse
|
49
|
Cuquerella MC, Lhiaubet-Vallet V, Bosca F, Miranda MA. Photosensitised pyrimidine dimerisation in DNA. Chem Sci 2011. [DOI: 10.1039/c1sc00088h] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
50
|
Sauri V, Serrano-Andrés L, Shahi ARM, Gagliardi L, Vancoillie S, Pierloot K. Multiconfigurational Second-Order Perturbation Theory Restricted Active Space (RASPT2) Method for Electronic Excited States: A Benchmark Study. J Chem Theory Comput 2010; 7:153-68. [PMID: 26606229 DOI: 10.1021/ct100478d] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The recently developed second-order perturbation theory restricted active space (RASPT2) method has been benchmarked versus the well-established complete active space (CASPT2) approach. Vertical excitation energies for valence and Rydberg excited states of different groups of organic (polyenes, acenes, heterocycles, azabenzenes, nucleobases, and free base porphin) and inorganic (nickel atom and copper tetrachloride dianion) molecules have been computed at the RASPT2 and multistate (MS) RASPT2 levels using different reference spaces and compared with CASPT2, CCSD, and experimental data in order to set the accuracy of the approach, which extends the applicability of multiconfigurational perturbation theory to much larger and complex systems than previously. Relevant aspects in multiconfigurational excited state quantum chemistry such as the valence-Rydberg mixing problem in organic molecules or the double d-shell effect for first-row transition metals have also been addressed.
Collapse
Affiliation(s)
- Vicenta Sauri
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain, Department of Physical Chemistry, University of Geneva, 30, q. E. Ansermet, 1211 Genève, Switzerland, Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States, and Department of Chemistry, Katholieke Universiteit Leuven, Belgium
| | - Luis Serrano-Andrés
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain, Department of Physical Chemistry, University of Geneva, 30, q. E. Ansermet, 1211 Genève, Switzerland, Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States, and Department of Chemistry, Katholieke Universiteit Leuven, Belgium
| | - Abdul Rehaman Moughal Shahi
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain, Department of Physical Chemistry, University of Geneva, 30, q. E. Ansermet, 1211 Genève, Switzerland, Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States, and Department of Chemistry, Katholieke Universiteit Leuven, Belgium
| | - Laura Gagliardi
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain, Department of Physical Chemistry, University of Geneva, 30, q. E. Ansermet, 1211 Genève, Switzerland, Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States, and Department of Chemistry, Katholieke Universiteit Leuven, Belgium
| | - Steven Vancoillie
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain, Department of Physical Chemistry, University of Geneva, 30, q. E. Ansermet, 1211 Genève, Switzerland, Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States, and Department of Chemistry, Katholieke Universiteit Leuven, Belgium
| | - Kristine Pierloot
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071 Valencia, Spain, Department of Physical Chemistry, University of Geneva, 30, q. E. Ansermet, 1211 Genève, Switzerland, Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States, and Department of Chemistry, Katholieke Universiteit Leuven, Belgium
| |
Collapse
|