1
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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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2
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Gate G, Williams A, Boldissar S, Šponer J, Szabla R, de Vries M. The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations. Photochem Photobiol 2024; 100:404-418. [PMID: 38124372 DOI: 10.1111/php.13897] [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: 06/28/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Ann Williams
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc-Holice, Czech Republic
| | - Rafal Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mattanjah de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
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3
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Mayer D, Lever F, Gühr M. Time-resolved x-ray spectroscopy of nucleobases and their thionated analogs. Photochem Photobiol 2024; 100:275-290. [PMID: 38174615 DOI: 10.1111/php.13903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
The photoinduced relaxation dynamics of nucleobases and their thionated analogs have been investigated extensively over the past decades motivated by their crucial role in organisms and their application in medical and biochemical research and treatment. Most of these studies focused on the spectroscopy of valence electrons and fragmentation. The advent of ultrashort x-ray laser sources such as free-electron lasers, however, opens new opportunities for studying the ultrafast molecular relaxation dynamics utilizing the site- and element-selectivity of x-rays. In this review, we want to summarize ultrafast experiments on thymine and 2-thiouracil performed at free-electron lasers. We performed time-resolved x-ray absorption spectroscopy at the oxygen K-edge after UV excitation of thymine. In addition, we investigated the excited state dynamics of 2-tUra via x-ray photoelectron spectroscopy at sulfur. For these methods, we show a strong sensitivity to the electronic state or charge distribution, respectively. We also performed time-resolved Auger-Meitner spectroscopy, which shows spectral shifts associated with internuclear distances close to the probed site. We discuss the complementary aspects of time-resolved x-ray spectroscopy techniques compared to optical and UV spectroscopy for the investigation of ultrafast relaxation processes.
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Affiliation(s)
- Dennis Mayer
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Fabiano Lever
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Markus Gühr
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Institute of Physical Chemistry, University of Hamburg, Hamburg, Germany
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4
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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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5
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Arribas EV, Ibele LM, Lauvergnat D, Maitra NT, Agostini F. Significance of Energy Conservation in Coupled-Trajectory Approaches to Nonadiabatic Dynamics. J Chem Theory Comput 2023; 19:7787-7800. [PMID: 37853509 DOI: 10.1021/acs.jctc.3c00845] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Through approximating electron-nuclear correlation terms in the exact factorization approach, trajectory-based methods have been derived and successfully applied to the dynamics of a variety of light-induced molecular processes, capturing quantum (de)coherence effects rigorously. These terms account for the coupling among the trajectories, recovering the nonlocal nature of quantum nuclear dynamics that is completely overlooked in traditional independent-trajectory algorithms. Nevertheless, some of the approximations introduced in the derivation of some of these methods do not conserve the total energy. We analyze energy conservation in the coupled-trajectory mixed quantum-classical (CTMQC) algorithm and explore the performance of a modified algorithm, CTMQC-E, where some of the terms are redefined to restore energy conservation. A set of molecular models is used as a test, namely, 2-cis-penta-2,4-dienimium cation, bis(methylene) adamantyl radical cation, butatriene cation, uracil radical cation, and neutral pyrazine.
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Affiliation(s)
| | - Lea M Ibele
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, 91405 Orsay, France
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6
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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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7
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Villaseco Arribas E, Vindel-Zandbergen P, Roy S, Maitra NT. Different flavors of exact-factorization-based mixed quantum-classical methods for multistate dynamics. Phys Chem Chem Phys 2023; 25:26380-26395. [PMID: 37750820 DOI: 10.1039/d3cp03464j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The exact factorization approach has led to the development of new mixed quantum-classical methods for simulating coupled electron-ion dynamics. We compare their performance for dynamics when more than two electronic states are occupied at a given time, and analyze: (1) the use of coupled versus auxiliary trajectories in evaluating the electron-nuclear correlation terms, (2) the approximation of using these terms within surface-hopping and Ehrenfest frameworks, and (3) the relevance of the exact conditions of zero population transfer away from nonadiabatic coupling regions and total energy conservation. Dynamics through the three-state conical intersection in the uracil radical cation as well as polaritonic models in one dimension are studied.
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Affiliation(s)
| | - Patricia Vindel-Zandbergen
- Department of Physics, Rutgers University, Newark 07102, New Jersey, USA.
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Saswata Roy
- Department of Physics, Rutgers University, Newark 07102, New Jersey, USA.
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark 07102, New Jersey, USA.
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8
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Ultrafast Photo-Ion Probing of the Relaxation Dynamics in 2-Thiouracil. Molecules 2023; 28:molecules28052354. [PMID: 36903604 PMCID: PMC10005304 DOI: 10.3390/molecules28052354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
In this work, we investigate the relaxation processes of 2-thiouracil after UV photoexcitation to the S2 state through the use of ultrafast, single-colour, pump-probe UV/UV spectroscopy. We place focus on investigating the appearance and subsequent decay signals of ionized fragments. We complement this with VUV-induced dissociative photoionisation studies collected at a synchrotron, allowing us to better understand and assign the ionisation channels involved in the appearance of the fragments. We find that all fragments appear when single photons with energy > 11 eV are used in the VUV experiments and hence appear through 3+ photon-order processes when 266 nm light is used. We also observe three major decays for the fragment ions: a sub-autocorrelation decay (i.e., sub-370 fs), a secondary ultrafast decay on the order of 300-400 fs, and a long decay on the order of 220 to 400 ps (all fragment dependent). These decays agree well with the previously established S2 → S1 → Triplet → Ground decay process. Results from the VUV study also suggest that some of the fragments may be created by dynamics occurring in the excited cationic state.
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9
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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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10
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Jouybari MY, Green JA, Improta R, Santoro F. The Ultrafast Quantum Dynamics of Photoexcited Adenine-Thymine Basepair Investigated with a Fragment-based Diabatization and a Linear Vibronic Coupling Model. J Phys Chem A 2021; 125:8912-8924. [PMID: 34609880 PMCID: PMC9281421 DOI: 10.1021/acs.jpca.1c08132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
this contribution we present a quantum dynamical study of the
photoexcited hydrogen bonded base pair adenine–thymine (AT)
in a Watson–Crick arrangement. To that end, we parametrize
Linear Vibronic Coupling (LVC) models with Time-Dependent Density
Functional Theory (TD-DFT) calculations, exploiting a fragment diabatization
scheme (FrD) we have developed to define diabatic states on the basis
of individual chromophores in a multichromophoric system. Wavepacket
propagations were run with the multilayer extension of the Multiconfiguration
Time-Dependent Hartree method. We considered excitations to the three
lowest bright states, a ππ* state of
thymine and two ππ* states (La and Lb) of adenine, and we found that on the 100 fs time
scale the main decay pathways involve intramonomer population transfers
toward nπ* states of the same nucleobase. In AT this transfer
is less effective than in the isolated nucleobases, because hydrogen
bonding destabilizes the nπ* states. The population transfer
to the A → T charge transfer state is negligible, making the
ultrafast (femtosecond) decay through the proton coupled electron
transfer mechanism unlikely, in line with experimental results in
apolar solvents. The excitation energy transfer is also very small.
We carefully compare the predictions of LVC Hamiltonians obtained
with different sets of diabatic states, defined so to match either
local states of the two separated monomers or the base pair adiabatic
states in the Franck–Condon region. To that end we also extend
the flexibility of the FrD-LVC approach, introducing a new strategy
to define fragments diabatic states that account for the effect of
the rest of the multichromohoric system through a Molecular Mechanics
potential.
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Affiliation(s)
- Martha Yaghoubi Jouybari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
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11
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Robinson MS, Niebuhr M, Lever F, Mayer D, Metje J, Gühr M. Ultrafast Photo-ion Probing of the Ring-Opening Process in Trans-Stilbene Oxide. Chemistry 2021; 27:11418-11427. [PMID: 34037274 PMCID: PMC8453962 DOI: 10.1002/chem.202101343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Indexed: 11/25/2022]
Abstract
The ultrafast photo‐induced ring opening of the oxirane derivative trans‐stilbene oxide has been studied through the use of ultrafast UV/UV pump‐probe spectroscopy by using photo‐ion detection. Single‐ and multiphoton probe paths and final states were identified through comparisons between UV power studies and synchrotron‐based vacuum ultraviolet (VUV) single‐photon ionization studies. Three major time‐dependent features of the parent ion (sub‐450 fs decay, (1.5±0.2) ps, and >100 ps) were observed. These decays are discussed in conjunction with the primary ring‐opening mechanism of stilbene oxide, which occurs through C−C dissociation in the oxirane ring. The appearance of fragments relating to the masses of dehydrogenated diphenylmethane (167 amu) and dehydrogenated methylbenzene (90 amu) were also investigated. The appearance of the 167 amu fragment could suggest an alternative ultrafast ring‐opening pathway via the dissociation of one of the C−O bonds within the oxirane ring.
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Affiliation(s)
- Matthew S Robinson
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Straße 24/25, 14476, Potsdam-Golm, Germany.,Centre for Free Electron Lasers (CFEL) DESY, Notkestraße 85, 22607, Hamburg, Germany
| | - Mario Niebuhr
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Straße 24/25, 14476, Potsdam-Golm, Germany
| | - Fabiano Lever
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Straße 24/25, 14476, Potsdam-Golm, Germany
| | - Dennis Mayer
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Straße 24/25, 14476, Potsdam-Golm, Germany
| | - Jan Metje
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Straße 24/25, 14476, Potsdam-Golm, Germany
| | - Markus Gühr
- Institut für Physik und Astronomie, Universität Potsdam, Karl-Liebknecht-Straße 24/25, 14476, Potsdam-Golm, Germany
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12
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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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13
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Green JA, Jouybari MY, Aranda D, Improta R, Santoro F. Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. Molecules 2021; 26:1743. [PMID: 33804640 PMCID: PMC8003674 DOI: 10.3390/molecules26061743] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 11/16/2022] Open
Abstract
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.
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Affiliation(s)
- James A. Green
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Martha Yaghoubi Jouybari
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Daniel Aranda
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Roberto Improta
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Fabrizio Santoro
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
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14
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Livshits VA, Meshkov BB, Avakyan VG, Titov SV. ESR, STESR, DFT, and MD Study of the Dynamical Structure of Cucurbituril[7]-Spin Probe Guest-Host Complexes. ACS OMEGA 2020; 5:11901-11914. [PMID: 32548369 PMCID: PMC7271031 DOI: 10.1021/acsomega.9b03772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
We study the molecular dynamics and structures of the guest-host complexes of cucurbituril, CB[7], with spin probes through the conventional electron spin resonance (ESR), saturation transfer ESR (STESR), density functional theory (DFT), and molecular dynamics (MD) computations. Protonated TEMPOamine (I), a derivative of TEMPO having a positive charge and an octyl group on the quaternary nitrogen atom (II), and the neutral spin-labeled indole (III) are used as guests. To eliminate the overall complex rotation, the solutions of complexes in a solid CB[7] matrix were prepared. Resultantly, for all of the spin probes, the combined study of the conventional ESR and STESR spectra indicates the librational character of the rotational motion within the CB[7] cavity as opposed to the diffusional rotation over the whole solid angle. The kinetic accessibilities of the reporter NO groups to the paramagnetic complexes in aqueous solutions, determined by Heisenberg exchange broadening of the ESR spectra, together with the environment polarities from the hyperfine interaction values, as well as DFT computation results and MD simulations, were used to estimate the spin probe location relative to CB[7]. Utilizing the concept of the aqueous clusters surrounding the spin probes and CB[7] molecules and MD simulations has allowed the application of DFT to estimate the aqueous environment effects on the complexation energy and spatial structure of the guest-host complexes.
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15
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Balasubramani SG, Chen GP, Coriani S, Diedenhofen M, Frank MS, Franzke YJ, Furche F, Grotjahn R, Harding ME, Hättig C, Hellweg A, Helmich-Paris B, Holzer C, Huniar U, Kaupp M, Marefat Khah A, Karbalaei Khani S, Müller T, Mack F, Nguyen BD, Parker SM, Perlt E, Rappoport D, Reiter K, Roy S, Rückert M, Schmitz G, Sierka M, Tapavicza E, Tew DP, van Wüllen C, Voora VK, Weigend F, Wodyński A, Yu JM. TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations. J Chem Phys 2020; 152:184107. [PMID: 32414256 PMCID: PMC7228783 DOI: 10.1063/5.0004635] [Citation(s) in RCA: 506] [Impact Index Per Article: 126.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 01/30/2023] Open
Abstract
TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy-cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe-Salpeter methods, second-order Møller-Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE's functionality, including excited-state methods, RPA and Green's function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE's current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE's development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.
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Affiliation(s)
- Sree Ganesh Balasubramani
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Guo P Chen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
| | - Michael Diedenhofen
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Marius S Frank
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Yannick J Franzke
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Robin Grotjahn
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Arnim Hellweg
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Christof Holzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Uwe Huniar
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Alireza Marefat Khah
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | | | - Thomas Müller
- Forschungszentrum Jülich, Jülich Supercomputer Centre, Wilhelm-Jonen Straße, 52425 Jülich, Germany
| | - Fabian Mack
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Brian D Nguyen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Shane M Parker
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Eva Perlt
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Dmitrij Rappoport
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kevin Reiter
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Saswata Roy
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Matthias Rückert
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Gunnar Schmitz
- Department of Chemistry, Aarhus Universitet, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Marek Sierka
- TURBOMOLE GmbH, Litzenhardtstraße 19, 76135 Karlsruhe, Germany
| | - Enrico Tapavicza
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, California 90840, USA
| | - David P Tew
- Max Planck Institute for Solid State Research, Heisenbergstaße 1, 70569 Stuttgart, Germany
| | - Christoph van Wüllen
- Fachbereich Chemie and Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, Erwin-Schrödinger-Staße 52, 67663 Kaiserslautern, Germany
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Florian Weigend
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Artur Wodyński
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Jason M Yu
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
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Wolf TJA, Gühr M. Photochemical pathways in nucleobases measured with an X-ray FEL. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20170473. [PMID: 30929626 PMCID: PMC6452046 DOI: 10.1098/rsta.2017.0473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The conversion of light energy into other molecular energetic degrees of freedom is often dominated by ultrafast, non-adiabatic processes. Femtosecond spectroscopy with optical pulses has helped in shaping our understanding of crucial processes in molecular energy-conversion. The advent of new, ultrashort and bright X-ray free electron laser sources opens the possibility to use X-ray-typical element and site sensitivity for ultrafast molecular research. We present two types of spectroscopy, ultrafast Auger and ultrafast X-ray absorption spectroscopy, and discuss their sensitivity to molecular processes. While Auger spectroscopy is able to monitor bond distance changes in the vicinity of an X-ray created core hole, near-edge absorption spectroscopy can deliver high-fidelity information on non-adiabatic transitions involving lone-pair orbitals. We demonstrate these features on the example of the UV-excited nucleobase thymine, investigated at the oxygen K-edge. We find a C-O bond elongation in the Auger data in addition to ππ*/ nπ* non-adiabatic transition in X-ray near-edge absorption. We compare the results from both methods and draw a conclusive scenario of non-adiabatic molecular relaxation after UV excitation. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.
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Affiliation(s)
- Thomas J. A. Wolf
- SLAC National Accelerator Laboratory, PULSE, 2575 Sand Hill Road, Menlo Park 94025, CA, USA
| | - Markus Gühr
- SLAC National Accelerator Laboratory, PULSE, 2575 Sand Hill Road, Menlo Park 94025, CA, USA
- Physics and Astronomy Institute, Universität Potsdam, Karl-Liebknecht-Strasse 24/25, Potsdam 14476, Germany
- e-mail:
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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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18
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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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19
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von Conta A, Tehlar A, Schletter A, Arasaki Y, Takatsuka K, Wörner HJ. Conical-intersection dynamics and ground-state chemistry probed by extreme-ultraviolet time-resolved photoelectron spectroscopy. Nat Commun 2018; 9:3162. [PMID: 30089780 PMCID: PMC6082858 DOI: 10.1038/s41467-018-05292-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/15/2018] [Indexed: 11/09/2022] Open
Abstract
Time-resolved photoelectron spectroscopy (TRPES) is a useful approach to elucidate the coupled electronic-nuclear quantum dynamics underlying chemical processes, but has remained limited by the use of low photon energies. Here, we demonstrate the general advantages of XUV-TRPES through an application to NO2, one of the simplest species displaying the complexity of a non-adiabatic photochemical process. The high photon energy enables ionization from the entire geometrical configuration space, giving access to the true dynamics of the system. Specifically, the technique reveals dynamics through a conical intersection, large-amplitude motion and photodissociation in the electronic ground state. XUV-TRPES simultaneously projects the excited-state wave packet onto many final states, offering a multi-dimensional view of the coupled electronic and nuclear dynamics. Our interpretations are supported by ab initio wavepacket calculations on new global potential-energy surfaces. The presented results contribute to establish XUV-TRPES as a powerful technique providing a complete picture of ultrafast chemical dynamics from photoexcitation to the final products.
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Affiliation(s)
- A von Conta
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093, Zurich, Switzerland
| | - A Tehlar
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093, Zurich, Switzerland
| | - A Schletter
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093, Zurich, Switzerland
| | - Y Arasaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto, 606-8103, Japan
| | - K Takatsuka
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto, 606-8103, Japan
| | - H J Wörner
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093, Zurich, Switzerland.
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20
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Röttger K, Marroux HJB, Böhnke H, Morris DTJ, Voice AT, Temps F, Roberts GM, Orr-Ewing AJ. Probing the excited state relaxation dynamics of pyrimidine nucleosides in chloroform solution. Faraday Discuss 2018; 194:683-708. [PMID: 27711889 DOI: 10.1039/c6fd00068a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ultrafast transient electronic and vibrational absorption spectroscopy (TEAS and TVAS) of 2'-deoxy-cytidine (dC) and 2'-deoxy-thymidine (dT) dissolved in chloroform examines their excited-state dynamics and the recovery of ground electronic state molecules following absorption of ultraviolet light. The chloroform serves as a weakly interacting solvent, allowing comparisons to be drawn with prior experimental studies of the photodynamics of these nucleosides in the gas phase and in polar solvents such as water. The pyrimidine base nucleosides have some propensity to dimerize in aprotic solvents, but the monomer photochemistry can be resolved clearly and is the focus of this study. UV absorption at a wavelength of 260 nm excites a 1ππ* ← S0 transition, but prompt crossing of a significant fraction (50% in dC, 17% in dT) of the 1ππ* population into a nearby 1nπ* state is too fast for the experiments to resolve. The remaining flux on the 1ππ* state leaves the vertical Franck-Condon region and encounters a conical intersection with the ground electronic state of ethylenic twist character. In dC, the 1ππ* state decays to the ground state with a time constant of 1.1 ± 0.1 ps. The lifetime of the 1nπ* state is much longer in the canonical forms of both molecules: recovery of the ground state population from these states occurs with time constants of 18.6 ± 1.1 ps in amino-oxo dC and ∼114 ps in dT, indicating potential energy barriers to the 1nπ*/S0 conical intersections. The small fraction of the imino-oxo tautomer of dC present in solution has a longer-lived 1nπ* state with a lifetime for ground state recovery of 193 ± 55 ps. No evidence is found for photo-induced tautomerization of amino-oxo dC to the imino-oxo form, or for population of low lying triplet states of this nucleoside. In contrast, ∼8% of the UV-excited dT molecules access the long-lived T1 (3ππ*) state through the 1nπ* state. The primary influence of the solvent appears to be the degree to which it destabilizes the states of 1nπ* character, with consequences for the lifetimes of these states as well as the triplet state yields.
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Affiliation(s)
- Katharina Röttger
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Hugo J B Marroux
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Hendrik Böhnke
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - David T J Morris
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Angus T Voice
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Friedrich Temps
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Gareth M Roberts
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Andrew J Orr-Ewing
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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21
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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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22
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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: 58] [Impact Index Per Article: 9.7] [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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23
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Tolosa S, Sánchez J, Sansón J, Hidalgo A. Steered molecular dynamic simulations of the tautomeric equilibria in solution of DNA bases. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.03.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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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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26
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Segarra-Martí J, Garavelli M, Aquilante F. Multiconfigurational Second-Order Perturbation Theory with Frozen Natural Orbitals Extended to the Treatment of Photochemical Problems. J Chem Theory Comput 2016; 11:3772-84. [PMID: 26574459 DOI: 10.1021/acs.jctc.5b00479] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new flavor of the frozen natural orbital complete active space second-order perturbation theory method (FNO-CASPT2, Aquilante et al., J. Chem. Phys. 131, 034113) is proposed herein. In this new implementation, the virtual space in Cholesky decomposition-based CASPT2 computations (CD-CASPT2) is truncated by excluding those orbitals that contribute the least toward preserving a predefined value of the trace of an approximate density matrix, as that represents a measure of the amount of dynamic correlation retained in the model. In this way, the amount of correlation included is practically constant at all nuclear arrangements, thus allowing for the computation of smooth electronic states surfaces and energy gradients-essential requirements for theoretical studies in photochemistry. The method has been benchmarked for a series of relevant biochromophores for which large speed-ups have been recorded while retaining the accuracy achieved in the corresponding CD-CASPT2 calculations. Both vertical excitation energies and gradient calculations have been carried out to establish general guidelines as to how much correlation needs to be retained in the calculation for the results to be consistent with the CD-CASPT2 findings. Our results feature errors within a tenth of an eV for the most difficult cases and have been validated to be used for gradient computations where an up to 3-fold speed-up is observed depending on the size of the system and the basis set employed.
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Affiliation(s)
- Javier Segarra-Martí
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via Selmi 2, IT-40126 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via Selmi 2, IT-40126 Bologna, Italy.,Université de Lyon, CNRS , Institut de Chimie de Lyon, École Normale Supérieure de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France
| | - Francesco Aquilante
- Dipartimento di Chimica "G. Ciamician", Università di Bologna , Via Selmi 2, IT-40126 Bologna, Italy
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27
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 332] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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28
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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.
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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
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29
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Camillis SD, Miles J, Alexander G, Ghafur O, Williams ID, Townsend D, Greenwood JB. Ultrafast non-radiative decay of gas-phase nucleosides. Phys Chem Chem Phys 2015; 17:23643-50. [DOI: 10.1039/c5cp03806e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
De-excitation of DNA nucleosides on picosecond timescales was measured and found to be twice as fast as the equivalent nucleobases.
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Affiliation(s)
- Simone De Camillis
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Jordan Miles
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Grace Alexander
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Omair Ghafur
- Institute of Photonics and Quantum Sciences
- Heriot-Watt University
- Edinburgh EH14 4AS
- UK
| | - Ian D. Williams
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences
- Heriot-Watt University
- Edinburgh EH14 4AS
- UK
- Institute of Chemical Sciences
| | - Jason B. Greenwood
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
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30
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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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31
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McFarland BK, Farrell JP, Miyabe S, Tarantelli F, Aguilar A, Berrah N, Bostedt C, Bozek JD, Bucksbaum PH, Castagna JC, Coffee RN, Cryan JP, Fang L, Feifel R, Gaffney KJ, Glownia JM, Martinez TJ, Mucke M, Murphy B, Natan A, Osipov T, Petrović VS, Schorb S, Schultz T, Spector LS, Swiggers M, Tenney I, Wang S, White JL, White W, Gühr M. Ultrafast X-ray Auger probing of photoexcited molecular dynamics. Nat Commun 2014; 5:4235. [DOI: 10.1038/ncomms5235] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/28/2014] [Indexed: 11/09/2022] Open
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32
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Saed B, Omidyan R. Protonation effect on the electronic properties of 2-pyridone monomer, dimer and its water clusters: a theoretical study. J Chem Phys 2014; 140:024315. [PMID: 24437885 DOI: 10.1063/1.4859255] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The CC2 (second order approximate coupled cluster method) has been applied to investigate protonation effect on electronic transition energies of 2-pyridone (2PY), 2-pyridone dimer, and micro-solvated 2-pyridone (0-2 water molecules). The PE profiles of protonated 2-pyridone (2PYH(+)) as well as monohydrated 2PYH(+) at the different electronic states have been investigated. The (1)πσ∗ state in protonated species (2PYH(+)) is a barrier free and dissociative state along the O-H stretching coordinate. In this reaction coordinate, the lowest lying (1)πσ∗ predissociates the bound S1((1)ππ∗) state, connecting the latter to a conical intersection with the S0 state. These conical intersections lead the (1)ππ∗ state to proceed as predissociative state and finally direct the excited system to the ground state. Furthermore, in presence of water molecule, the (1)πσ∗ state still remains dissociative but the conical intersection between (1)πσ∗ and ground state disappears. In addition, according to the CC2 calculation results, it has been predicted that protonation significantly blue shifts the S1-S0 electronic transition of monomer, dimer, and microhydrated 2-pyridone.
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Affiliation(s)
- Behnaz Saed
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Reza Omidyan
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
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33
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Chatterley AS, West CW, Stavros VG, Verlet JRR. Time-resolved photoelectron imaging of the isolated deprotonated nucleotides. Chem Sci 2014. [DOI: 10.1039/c4sc01493f] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Time-resolved photoelectron spectroscopy of deprotonated nucleotides provides new insights into their relaxation dynamics.
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Affiliation(s)
- Adam S. Chatterley
- Department
- of Chemistry
- University of Durham
- Durham DH1 3LE, United Kingdom
- Department of Chemistry
| | | | - Vasilios G. Stavros
- Department of Chemistry
- University of Warwick
- Coventry CV4 7AL, United Kingdom
| | - Jan R. R. Verlet
- Department
- of Chemistry
- University of Durham
- Durham DH1 3LE, United Kingdom
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34
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Roberts GM, Stavros VG. The role of πσ* states in the photochemistry of heteroaromatic biomolecules and their subunits: insights from gas-phase femtosecond spectroscopy. Chem Sci 2014. [DOI: 10.1039/c3sc53175a] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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35
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Improta R. Photophysics and photochemistry of thymine deoxy-dinucleotide in water: a PCM/TD-DFT quantum mechanical study. J Phys Chem B 2012; 116:14261-74. [PMID: 23134336 DOI: 10.1021/jp3093385] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We here report a fully quantum mechanical study of the main photochemical and photophysical decay routes in aqueous solution of thymine deoxy-dinucleotide (TpT(-) and TpTNa) and of its analogue locked in C3-endo puckering, characterizing five different representative backbone conformers and discussing the chemical physical effects modulating the yield of the different photoproducts. Our approach is based on time-dependent DFT calculations, using the last generation M052X functional, whereas solvent effects are included by means of the polarizable continuum model. Especially when at least one of the sugars adopts C3-endo puckering, a barrierless path on the bright ππ* excitons leads to the S(1)/S(0) crossing region corresponding to the formation of cyclobutane pyrimidine dimer. Charge transfer excited states involving the transfer of an electron from the 5' Thy toward the 3' Thy are involved in the formation of the oxetane intermediate in the path leading to 6-4 pyrimidine pyrimidinone adducts. A non-negligible energy barrier is associated with this latter pathway, which is possible only when one of the two nucleotides adopts C2-endo puckering. Monomer-like decay pathways, involving ππ* or nπ* excited states localized on a single base, are shown to be operative also for loosely stacked bases.
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Affiliation(s)
- Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture Biommagini (IBB-CNR), Via Mezzocannone 16, I-80134 Napoli, Italy.
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36
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Trachsel MA, Lobsiger S, Leutwyler S. Out-of-Plane Low-Frequency Vibrations and Nonradiative Decay in the 1ππ* State of Jet-Cooled 5-Methylcytosine. J Phys Chem B 2012; 116:11081-91. [DOI: 10.1021/jp305688m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria A. Trachsel
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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37
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Pohler L, Kleinschmidt M, Etinski M, Marian CM. In search of the dark state of 5-methyl-2-hydroxypyrimidine using a numerical DFT/MRCI gradient. Mol Phys 2012. [DOI: 10.1080/00268976.2012.695030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Larissa Pohler
- a Institute of Theoretical and Computational Chemistry , Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf , Germany
| | - Martin Kleinschmidt
- a Institute of Theoretical and Computational Chemistry , Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf , Germany
| | - Mihajlo Etinski
- b Faculty of Physical Chemistry , University of Belgrade , Studentski Trg 12-16, 11000 Belgrade , Serbia
| | - Christel M. Marian
- a Institute of Theoretical and Computational Chemistry , Heinrich-Heine-University Düsseldorf , Universitätsstraße 1, 40225 Düsseldorf , Germany
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38
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Picconi D, Lami A, Santoro F. Hierarchical transformation of Hamiltonians with linear and quadratic couplings for nonadiabatic quantum dynamics: Application to the ππ*/nπ* internal conversion in thymine. J Chem Phys 2012; 136:244104. [DOI: 10.1063/1.4729049] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Peralta Conde A, Ovejas V, Montero R, Castaño F, Longarte A. Influence of solvation on the indole photophysics: Ultrafast dynamics of indole–water clusters. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.01.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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40
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Yang ZB, Eriksson LA, Zhang RB. A Theoretical Rationale for Why Azetidine Has a Faster Rate of Formation Than Oxetane in TC(6–4) Photoproducts. J Phys Chem B 2011; 115:9681-6. [DOI: 10.1021/jp204506v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhao bo Yang
- Institute for Chemical Physics, Key Laboratory of Cluster Science, Beijing Institute of Technology, Beijing 100081, China
| | - Leif A. Eriksson
- School of Chemistry, National University of Ireland, Galway, Ireland
| | - Ru bo Zhang
- Institute for Chemical Physics, Key Laboratory of Cluster Science, Beijing Institute of Technology, Beijing 100081, China
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41
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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.
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Affiliation(s)
- Yevgeniy Nosenko
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-str. 7, 60438 Frankfurt/Main, Germany
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42
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Picconi D, Barone V, Lami A, Santoro F, Improta R. The Interplay between ππ*/nπ* Excited States in Gas-Phase Thymine: A Quantum Dynamical Study. Chemphyschem 2011; 12:1957-68. [DOI: 10.1002/cphc.201001080] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/01/2011] [Indexed: 11/10/2022]
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43
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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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44
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Yang ZB, Zhang RB, Eriksson LA. A triplet mechanism for the formation of thymine–thymine (6-4) dimers in UV-irradiated DNA. Phys Chem Chem Phys 2011; 13:8961-6. [DOI: 10.1039/c0cp02830d] [Citation(s) in RCA: 18] [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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45
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Szymczak JJ, Müller T, Lischka H. The effect of hydration on the photo-deactivation pathways of 4-aminopyrimidine. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.07.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Etinski M, Marian CM. Ab initio investigation of the methylation and hydration effects on the electronic spectra of uracil and thymine. Phys Chem Chem Phys 2010; 12:4915-23. [DOI: 10.1039/b925677f] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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47
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Etinski M, Marian CM. Overruling the energy gap law: fast triplet formation in 6-azauracil. Phys Chem Chem Phys 2010; 12:15665-71. [DOI: 10.1039/c0cp00106f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Kosma K, Schröter C, Samoylova E, Hertel IV, Schultz T. Excited-State Dynamics of Cytosine Tautomers. J Am Chem Soc 2009; 131:16939-43. [DOI: 10.1021/ja907355a] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kyriaki Kosma
- Max Born Institute, Max-Born-Strasse 2A, D-12489, Berlin-Adlershof, Germany
| | - Christian Schröter
- Max Born Institute, Max-Born-Strasse 2A, D-12489, Berlin-Adlershof, Germany
| | - Elena Samoylova
- Max Born Institute, Max-Born-Strasse 2A, D-12489, Berlin-Adlershof, Germany
| | | | - Thomas Schultz
- Max Born Institute, Max-Born-Strasse 2A, D-12489, Berlin-Adlershof, Germany
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