1
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Schultz T. Correlated rotational alignment spectroscopy: a new tool for high-resolution spectroscopy and the analysis of heterogeneous samples. Phys Chem Chem Phys 2024; 26:25287-25313. [PMID: 39328147 DOI: 10.1039/d4cp00994k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Correlated rotational alignment spectroscopy correlates observables of ultrafast gas-phase spectroscopy with high-resolution, broad-band rotational Raman spectra. This article reviews the measurement principle of CRASY, existing implementations for mass-correlated measurements, and the potential for future developments. New spectroscopic capabilities are discussed in detail: signals for individual sample components can be separated even in highly heterogeneous samples. Isotopologue rotational spectra can be observed at natural isotope abundance. Fragmentation channels are readily assigned in molecular and cluster mass spectra. And finally, rotational Raman spectra can be measured with sub-MHz resolution, an improvement of several orders-of-magnitude as compared to preceding experiments.
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Affiliation(s)
- Thomas Schultz
- UNIST (Ulsan National Institute of Science and Technology), Advanced Materials Research, Building 103-413, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, South Korea.
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2
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Park W, Lashkaripour A, Komarov K, Lee S, Huix-Rotllant M, Choi CH. Toward Consistent Predictions of Core/Valence Ionization Potentials and Valence Excitation Energies by MRSF-TDDFT. J Chem Theory Comput 2024; 20:5679-5694. [PMID: 38902891 DOI: 10.1021/acs.jctc.4c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Optimizing exchange-correlation functionals for both core/valence ionization potentials (cIPs/vIPs) and valence excitation energies (VEEs) at the same time in the framework of MRSF-TDDFT is self-contradictory. To overcome the challenge, within the previous "adaptive exact exchange" or double-tuning strategy on Coulomb-attenuating XC functionals (CAM), a new XC functional specifically for cIPs and vIPs was first developed by enhancing exact exchange to both short- and long-range regions. The resulting DTCAM-XI functional achieved remarkably high accuracy in its predictions with errors of less than half eV. An additional concept of "valence attenuation", where the amount of exact exchange for the frontier orbital regions is selectively suppressed, was introduced to consistently predict both VEEs and IPs at the same time. The second functional, DTCAM-XIV, exhibits consistent overall prediction accuracy at ∼0.64 eV. By preferentially optimizing VEEs within the same "valence attenuation" concept, a third functional, DTCAM-VAEE, was obtained, which exhibits improved performance as compared to that of the previous DTCAM-VEE and DTCAM-AEE in the prediction of VEEs, making it an attractive alternative to BH&HLYP. As the combination of "adaptive exchange" and "valence attenuation" is operative, it would be exciting to explore its potential with a more tunable framework in the future.
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Affiliation(s)
- Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Alireza Lashkaripour
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Konstantin Komarov
- Center for Quantum Dynamics, Pohang University of Science and Technology, Pohang 37673, South Korea
- Department of Chemistry, University of Zürich, Zürich 8057, Switzerland
| | - Seunghoon Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, South Korea
| | | | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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3
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Komarov K, Park W, Lee S, Huix-Rotllant M, Choi CH. Doubly Tuned Exchange-Correlation Functionals for Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory. J Chem Theory Comput 2023; 19:7671-7684. [PMID: 37844129 DOI: 10.1021/acs.jctc.3c00884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
It is demonstrated that significant accuracy improvements in MRSF-TDDFT can be achieved by introducing two different exchange-correlation (XC) functionals for the reference Kohn-Sham DFT and the response part of the calculations, respectively. Accordingly, two new XC functionals of doubly tuned Coulomb attenuated method-vertical excitation energy (DTCAM-VEE) and DTCAM-AEE were developed on the basis of the "adaptive exact exchange (AEE)" concept in the framework of the Coulomb-attenuating XC functionals. The values by DTCAM-VEE are in excellent agreement with those of Thiel's set [mean absolute errors (MAEs) and the interquartile range (IQR) values of 0.218 and 0.327 eV, respectively]. On the other hand, DTCAM-AEE faithfully reproduced the qualitative aspects of conical intersections (CIs) of trans-butadiene and thymine and the nonadiabatic molecular dynamics (NAMD) simulations on thymine. The latter functional also remarkably exhibited the exact 1/R asymptotic behavior of the charge-transfer state of an ethylene-tetrafluoroethylene dimer and the accurate potential energy surfaces (PESs) along the two torsional angles of retinal protonated Schiff base model with six double bonds (rPSB6). Overall, DTCAM-AEE generally performs well, as its MAE (0.237) and IQR (0.41 eV) are much improved as compared to BH&HLYP. The current idea can also be applied to other XC functionals as well as other variants of linear response theories, opening a new way of developing XC functionals.
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Affiliation(s)
- Konstantin Komarov
- Center for Quantum Dynamics, Pohang University of Science and Technology, Pohang 37673, South Korea
| | - Woojin Park
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Seunghoon Lee
- Department of Chemistry, Seoul National University, Seoul, 151-747, South Korea
| | | | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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4
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Park W, Komarov K, Lee S, Choi CH. Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory: Multireference Advantages with the Practicality of Linear Response Theory. J Phys Chem Lett 2023; 14:8896-8908. [PMID: 37767969 PMCID: PMC10561896 DOI: 10.1021/acs.jpclett.3c02296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
The density functional theory (DFT) and linear response (LR) time-dependent (TD)-DFT are of the utmost importance for routine computations. However, the single reference formulation of DFT suffers in the description of open-shell singlet systems such as diradicals and bond-breaking. LR-TDDFT, on the other hand, finds difficulties in the modeling of conical intersections, doubly excited states, and core-level excitations. In this Perspective, we demonstrate that many of these limitations can be overcome by recently developed mixed-reference (MR) spin-flip (SF)-TDDFT, providing an alternative yet accurate route for such challenging situations. Empowered by the practicality of the LR formalism, it is anticipated that MRSF-TDDFT can become one of the major workhorses for general routine tasks.
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Affiliation(s)
- Woojin Park
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Konstantin Komarov
- Center
for Quantum Dynamics, Pohang University
of Science and Technology, Pohang 37673, South Korea
| | - Seunghoon Lee
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Cheol Ho Choi
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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5
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Cherneva TD, Todorova MM, Bakalska RI, Shterev IG, Horkel E, Delchev VB. Experimental and theoretical study of the cytosine tautomerism through excited states. J Mol Model 2023; 29:303. [PMID: 37665380 DOI: 10.1007/s00894-023-05707-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
CONTEXT The irradiation of water solution of cytosine with UV light (λmax = 254 nm) shows oxo-hydroxy tautomerism with a rate constant of 6.297 × 10-3 min-1. The order of the reaction implies a tautomeric conversion. After removing the UV light source, we observed a dark reaction with a rate constant of 1.473 × 10-3 min-1 which leads to a restoration of the initial tautomer as before the irradiation. The mechanism of oxo-hydroxy tautomerism of cytosine in water solution was studied in the excited state. It was found that the transformations occur along the 1πσ* excited-state reaction paths which link the Franck-Condon geometries of the tautomers and the conical intersections S0/S1 connected with the H-detachment processes of the corresponding bonds. Furthermore, we established that the conical intersections S0/S1 are also mutually accessible along the 1πσ* excited-state reaction paths. METHODS The ground-state equilibrium geometries were optimized at the B3LYP/aug-cc-pVDZ level of theory in water environment according to PCM as well as at the CC2/aug-cc-pVDZ level in the gas phase. The TD B3LYP and CC2 methods were applied for the study of the excited states. The tautomerization mechanisms were studied with the use of the linear interpolation in internal coordinates approach using the optimized geometries of tautomers minima and conical intersections S0/S1 at the CASSCF(6,6)/6-31G* level. All calculations were performed with the GAUSSIAN 16 commercial software.
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Affiliation(s)
- Tsvetina D Cherneva
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, 4000, Plovdiv, Bulgaria
| | - Mina M Todorova
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, 4000, Plovdiv, Bulgaria
| | - Rumyana I Bakalska
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, 4000, Plovdiv, Bulgaria
| | - Ivan G Shterev
- Department of Inorganic and Physical Chemistry, University of Food Technologies, 4002, Plovdiv, Bulgaria
| | - Ernst Horkel
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Vassil B Delchev
- Faculty of Chemistry, University of Plovdiv, Tzar Assen 24 Str, 4000, Plovdiv, Bulgaria.
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6
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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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7
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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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8
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Park W, Filatov (Gulak) M, Sadiq S, Gerasimov I, Lee S, Joo T, Choi CH. A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate. J Phys Chem Lett 2022; 13:7072-7080. [PMID: 35900137 PMCID: PMC9358713 DOI: 10.1021/acs.jpclett.2c01694] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/11/2022] [Indexed: 05/28/2023]
Abstract
It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" ground-state mechanisms, its detailed mechanism remains elusive. Here, theoretical nonadiabatic simulations of the uracil photodynamics reveal the formation of a highly energetic but kinetically stable intermediate that features a half-chair puckered pyrimidine ring and a strongly twisted intracyclic double bond. The existence and the kinetic stability of the intermediate are confirmed by a variety of computational chemistry methods. According to the simulations, the unusual intermediate is mainly formed almost immediately (∼50-200 fs) upon photoabsorption and survives long enough to engage in a hydration reaction with a neighboring water. A plausible mechanism of uracil photohydration is proposed on the basis of the modeling of nucleophilic insertion of water into the twisted double bond of the intermediate.
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Affiliation(s)
- Woojin Park
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | | | - Saima Sadiq
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Igor Gerasimov
- 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
| | - Taiha Joo
- Department
of Chemistry, Pohang University of Science
and Technology (POSTECH), Pohang 37673, South Korea
| | - Cheol Ho Choi
- Department
of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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9
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Ray J, Ramesh SG. Excited-state proton transfer in the 2-aminopyridine dimer: A surface hopping study. Phys Chem Chem Phys 2022; 24:7274-7292. [DOI: 10.1039/d1cp05517h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a theoretical investigation of the excited-state intermolecular proton transfer process in the 2-aminopyridine dimer. Prior experimental and theoretical studies on this doubly hydrogen bonded system have attributed an...
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10
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Ullah N, Chen S, Zhang R. Adenine ultrafast photorelaxation via electron-driven proton transfer. Phys Chem Chem Phys 2021; 23:23090-23095. [PMID: 34617085 DOI: 10.1039/d1cp03162g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photorelaxation of adenine in water was reported to be ultrafast (within 180 fs) primarily due to radiationless relaxation. However, in the last two decades, several experimental and theoretical investigations on photoexcitation of adenine have revealed diverse types of decay mechanisms. Using time-dependent density functional excited-state nonadiabatic dynamics simulations we show that it is the water to adenine electron-driven proton transfer (EDPT) barrierless reaction responsible for the ultrafast component of the adenine relaxation, which, however, occurred only in the case of the 7H isomer of adenine with five water molecules. This result reveals a known reaction pathway, however not found in previous simulations, with inference for the ultrafast relaxation mechanisms of adenine reported in experiments. The 9H isomer of adenine with six water molecules relaxing in a water cluster followed the previously known structural distortion (C2) decay pathway. The observations of the adenine EDPT reaction with water provide the origin of the experimental ultrafast adenine decay component and present a possible method to tackle future computational challenges in molecular-level biological processes.
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Affiliation(s)
- Naeem Ullah
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China.
| | - Shunwei Chen
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Ruiqin Zhang
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China. .,Beijing Computational Science Research Center, Beijing 100193, China
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11
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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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12
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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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13
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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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14
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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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15
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Penfold TJ, Gindensperger E, Daniel C, Marian CM. Spin-Vibronic Mechanism for Intersystem Crossing. Chem Rev 2018; 118:6975-7025. [DOI: 10.1021/acs.chemrev.7b00617] [Citation(s) in RCA: 401] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Thomas J. Penfold
- Chemistry - School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon-Tyne NE1 7RU, United Kingdom
| | - Etienne Gindensperger
- Laboratoire de Chimie Quantique, Institut de Chimie UMR-7177, CNRS - Université de Strasbourg, 1 Rue Blaise Pascal 67008 Strasbourg, France
| | - Chantal Daniel
- Laboratoire de Chimie Quantique, Institut de Chimie UMR-7177, CNRS - Université de Strasbourg, 1 Rue Blaise Pascal 67008 Strasbourg, France
| | - Christel M. Marian
- Institut für Theoretische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
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16
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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.
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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.
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17
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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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18
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Rapf RJ, Vaida V. Sunlight as an energetic driver in the synthesis of molecules necessary for life. Phys Chem Chem Phys 2016; 18:20067-84. [DOI: 10.1039/c6cp00980h] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This review considers how photochemistry and sunlight-driven reactions can abiotically generate prebiotic molecules necessary for the evolution of life.
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Affiliation(s)
- Rebecca J. Rapf
- Department of Chemistry and Biochemistry
- CIRES
- University of Colorado at Boulder
- Boulder
- USA
| | - Veronica Vaida
- Department of Chemistry and Biochemistry
- CIRES
- University of Colorado at Boulder
- Boulder
- USA
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19
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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20
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Abstract
Ultraviolet (UV) radiation is a leading external hazard to the integrity of DNA. Exposure to UV radiation triggers a cascade of chemical reactions, and many molecular products (photolesions) have been isolated that are potentially dangerous for the cellular system. The early steps that take place after UV absorption by DNA have been studied by ultrafast spectroscopy. The review focuses on the evolution of excited electronic states, the formation of photolesions, and processes suppressing their formation. Emphasis is placed on lesions involving two thymine bases, such as the cyclobutane pyrimidine dimer, the (6-4) lesion, and its Dewar valence isomer.
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Affiliation(s)
- Wolfgang J Schreier
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, 80538 München, Germany;
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21
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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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22
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23
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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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24
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Staniforth M, Stavros VG. Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond. Proc Math Phys Eng Sci 2013; 469:20130458. [PMID: 24204191 PMCID: PMC3780818 DOI: 10.1098/rspa.2013.0458] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 08/07/2013] [Indexed: 11/23/2022] Open
Abstract
In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach.
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Affiliation(s)
| | - Vasilios G. Stavros
- Department of Chemistry, University of Warwick, Library Road, Coventry CV4 7AL, UK
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25
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Miyazaki M, Kang H, Choi CM, Han NS, Song JK, Kim NJ, Fujii M. MODE-specific deactivation of adenine at the singlet excited states. J Chem Phys 2013; 139:124311. [DOI: 10.1063/1.4821830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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26
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Asami H, Yagi K, Ohba M, Urashima SH, Saigusa H. Stacked base-pair structures of adenine nucleosides stabilized by the formation of hydrogen-bonding network involving the two sugar groups. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.01.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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28
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Röttger K, Schwalb NK, Temps F. Electronic Deactivation of Guanosine in Extended Hydrogen-Bonded Self-Assemblies. J Phys Chem A 2013; 117:2469-78. [DOI: 10.1021/jp3095193] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Katharina Röttger
- Institut für
Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr.
40, D-24098 Kiel, Germany
| | - Nina K. Schwalb
- Institut für
Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr.
40, D-24098 Kiel, Germany
| | - Friedrich Temps
- Institut für
Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr.
40, D-24098 Kiel, Germany
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29
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Lucchini M, Seung Kim K, Calegari F, Kelkensberg F, Siu WK, Sansone G, Vrakking MJ, Hochlaf M, Nisoli M. Ultrafast Relaxation Dynamics of Highly-excited States in N 2Molecules Excited by Femtosecond XUV Pulses. EPJ WEB OF CONFERENCES 2013. [DOI: 10.1051/epjconf/20134102004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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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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31
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Nosenko Y, Kunitski M, Stark T, Göbel M, Tarakeshwar P, Brutschy B. Vibrational signatures of Watson–Crick base pairing in adenine–thymine mimics. Phys Chem Chem Phys 2013; 15:11520-30. [DOI: 10.1039/c3cp50337b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Sauri V, Gobbo JP, Serrano-Pérez JJ, Lundberg M, Coto PB, Serrano-Andrés L, Borin AC, Lindh R, Merchán M, Roca-Sanjuán D. Proton/Hydrogen Transfer Mechanisms in the Guanine–Cytosine Base Pair: Photostability and Tautomerism. J Chem Theory Comput 2012; 9:481-96. [DOI: 10.1021/ct3006166] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vicenta Sauri
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
| | - João P. 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, SP, Brazil
| | - Juan J. Serrano-Pérez
- Department of Chemistry, Imperial
College London, Exhibition Road, London, SW7 2AZ, United Kingdom
| | - Marcus Lundberg
- Department of Chemistry—Ångström,
Theoretical Chemistry Program, Uppsala University, P.O. Box 518, SE-75120
Uppsala, Sweden
| | - Pedro B. Coto
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
- Institut
für Theoretische
Physik, Friedrich-Alexander-Universität Erlangen-Nürnberg,
Staudtstraβe 7, 91058 Erlangen, Germany
- Departamento de Química-Física,
Universidad de Alcalá de Henares, Ctra. Madrid-Barcelona (Autovía
A2) Km. 33.600, 28871 Alcalá de Henares, Spain
| | - Luis Serrano-Andrés
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
| | - Antonio C. 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, SP, Brazil
| | - Roland Lindh
- Department of Chemistry—Ångström,
Theoretical Chemistry Program, Uppsala University, P.O. Box 518, SE-75120
Uppsala, Sweden
| | - Manuela Merchán
- Instituto de Ciencia Molecular,
Universitat de València, P.O. Box 22085, ES-46071 València,
Spain
| | - Daniel Roca-Sanjuán
- Department of Chemistry—Ångström,
Theoretical Chemistry Program, Uppsala University, P.O. Box 518, SE-75120
Uppsala, Sweden
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33
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Yamazaki S, Taketsugu T. Photoreaction channels of the guanine-cytosine base pair explored by long-range corrected TDDFT calculations. Phys Chem Chem Phys 2012; 14:8866-77. [PMID: 22596076 DOI: 10.1039/c2cp23867e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoinduced processes in the Watson-Crick guanine-cytosine base pair are comprehensively studied by means of long-range corrected (LC) TDDFT calculations of potential energy profiles using the LC-BLYP and CAM-B3LYP functionals. The ab initio CC2 method and the conventional TDDFT method with the B3LYP functional are also employed to assess the reliability of the LC-TDDFT method. The present approach allows us to compare the potential energy profiles at the same computational level for excited-state reactions of the base pair, including single and double proton transfer between the bases and nonradiative decay via ring puckering in each base. In particular, long-range correction to the TDDFT method is critical for a qualitatively correct description of the proton transfer reactions. The calculated energy profiles exhibit low barriers for out-of-plane deformation of the guanine moiety in the locally-excited state, which is expected to lead to a conical intersection with the ground state, as well as for single proton transfer from guanine to cytosine with the well-known electron-driven proton transfer mechanism. Thus the present results suggest that both processes can compete in hydrogen-bonded base pairs and play a significant role in the mechanism of photostability.
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Affiliation(s)
- Shohei Yamazaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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34
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Nosenko Y, Kunitski M, Stark T, Göbel M, Tarakeshwar P, Brutschy B. 4-Aminobenzimidazole–1-Methylthymine: A Model for Investigating Hoogsteen Base-Pairing between Adenine and Thymine. J Phys Chem A 2011; 115:11403-11. [DOI: 10.1021/jp205575w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Pilarisetty Tarakeshwar
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
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35
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Kim NJ, Chang J, Kim HM, Kang H, Ahn TK, Heo J, Kim SK. Femtosecond Decay Dynamics of Intact Adenine and Thymine Base Pairs in a Supersonic Jet. Chemphyschem 2011; 12:1935-9. [DOI: 10.1002/cphc.201100091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 04/04/2011] [Indexed: 11/06/2022]
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36
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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]
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37
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Oliver TAA, Zhang Y, Ashfold MNR, Bradforth SE. Linking photochemistry in the gas and solution phase: S–H bond fission in p-methylthiophenol following UV photoexcitation. Faraday Discuss 2011; 150:439-58; discussion 505-32. [DOI: 10.1039/c0fd00031k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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38
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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
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39
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Abstract
The singlet excited electronic states of two pi-stacked thymine molecules and their splittings due to electronic coupling have been investigated with a variety of computational methods. Focus has been given on the effect of intermolecular distance on these energies and couplings. Single-reference methods, CIS, CIS(2), EOM-CCSD, TDDFT, and the multireference method CASSCF, have been used, and their performance has been compared. It is found that the excited-state energies are very sensitive to the applied method but the couplings are not as sensitive. Inclusion of diffuse functions in the basis set also affects the excitation energies significantly but not the couplings. TDDFT is inadequate in describing the states and their coupling, while CIS(2) gives results very similar to EOM-CCSD. Excited states of cytosine and adenine pi-stacked dimers were also obtained and compared with those of thymine dimers to gain a more general picture of excited states in pi-stacked DNA base dimers. The coupling is very sensitive to the relative position and orientation of the bases, indicating great variation in the degree of delocalization of the excited states between stacked bases in natural DNA as it fluctuates.
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40
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Conti I, Altoè P, Stenta M, Garavelli M, Orlandi G. Adenine deactivation in DNA resolved at the CASPT2//CASSCF/AMBER level. Phys Chem Chem Phys 2010; 12:5016-23. [DOI: 10.1039/b926608a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Smolarek S, Rijs AM, Buma WJ, Drabbels M. Absorption spectroscopy of adenine, 9-methyladenine, and 2-aminopurine in helium nanodroplets. Phys Chem Chem Phys 2010; 12:15600-6. [DOI: 10.1039/c0cp00746c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Hassan WMI, Chung WC, Shimakura N, Koseki S, Kono H, Fujimura Y. Ultrafast radiationless transition pathways through conical intersections in photo-excited 9H-adenine. Phys Chem Chem Phys 2010; 12:5317-28. [DOI: 10.1039/b926102h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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43
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Smith VR, Samoylova E, Ritze HH, Radloff W, Schultz T. Excimer states in microhydrated adenine clusters. Phys Chem Chem Phys 2010; 12:9632-6. [DOI: 10.1039/c003967e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Conti I, Garavelli M, Orlandi G. Deciphering Low Energy Deactivation Channels in Adenine. J Am Chem Soc 2009; 131:16108-18. [DOI: 10.1021/ja902311y] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Irene Conti
- Dipartimento di Chimica ‘G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica ‘G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
| | - Giorgio Orlandi
- Dipartimento di Chimica ‘G. Ciamician’, Universita’ di Bologna, Via F. Selmi, 2, 40126 Bologna, Italy, and INSTM, UdR Bologna, Italy
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45
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Etinski M, Fleig T, Marian CM. Intersystem Crossing and Characterization of Dark States in the Pyrimidine Nucleobases Uracil, Thymine, and 1-Methylthymine. J Phys Chem A 2009; 113:11809-16. [DOI: 10.1021/jp902944a] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Mihajlo Etinski
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Timo Fleig
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christel M. Marian
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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46
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47
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Lan Z, Fabiano E, Thiel W. Photoinduced nonadiabatic dynamics of pyrimidine nucleobases: on-the-fly surface-hopping study with semiempirical methods. J Phys Chem B 2009; 113:3548-55. [PMID: 19239209 DOI: 10.1021/jp809085h] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photoinduced relaxation dynamics of pyrimidine nucleobases (uracil, thymine, and cytosine) was studied using the surface-hopping approach at the semiempirical OM2/MRCI level of theory. The relevant potential energy surfaces were characterized by performing geometry optimizations of the energy minima of the lowest electronic states and of the most important conical intersections and by computing excitation energies at each configuration. Surface-hopping molecular dynamics simulations were performed to describe the nonadiabatic dynamics after excitation into the optically active state. In each of the molecules, the two lowest excited singlet states are involved in the dynamics, and there are competing relaxation paths. The dynamics is dominated by a two-step relaxation mechanism in uracil and thymine, while the direct decay to the ground state is most important in cytosine. For all three molecules, the simulations yield ultrafast S(2)-S(1) deexcitation within 50 fs and internal conversion to the ground state in less than 1 ps, consistent with recent experimental results from time-resolved photoelectron spectroscopy.
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Affiliation(s)
- Zhenggang Lan
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
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48
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Serrano-Andrés L, Merchán M. Are the five natural DNA/RNA base monomers a good choice from natural selection? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2009. [DOI: 10.1016/j.jphotochemrev.2008.12.001] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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49
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Wells KL, Perriam G, Stavros VG. Time-resolved velocity map ion imaging study of NH3 photodissociation. J Chem Phys 2009; 130:074308. [DOI: 10.1063/1.3072763] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Quantum Mechanical Studies of the Photophysics of DNA and RNA Bases. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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