1
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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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2
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Shu Y, Akher FB, Guo H, Truhlar DG. Parametrically Managed Activation Functions for Improved Global Potential Energy Surfaces for Six Coupled 5A' States and Fourteen Coupled 3A' States of O + O 2. J Phys Chem A 2024; 128:1207-1217. [PMID: 38349764 DOI: 10.1021/acs.jpca.3c06823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
We report new potential energy surfaces for six coupled 5A' states and 14 coupled 3A' states of O3. The new surfaces are created by parametrically managed diabatization by deep neural network (PM-DDNN). The PM-DDNN method uses calculated adiabatic potential energy surfaces to discover and fit an underlying adiabatic-equivalent set of diabatic surfaces and their couplings and obtains the fit to the adiabatic surfaces by diagonalization of the diabatic potential energy matrix (DPEM). The procedure yields the adiabatic surfaces and their gradients, as well as the DPEM and its gradient. If desired one can also compute the nonadiabatic coupling due to the transformation. The present work improves on previous work by using a new coordinate to guide the decay of the neural network contribution to the many-body fit to the whole DPEM. The main objective was to obtain smoother potentials than the previous ones with better suitability for dynamics calculations, and this was achieved. Furthermore, we obtained suitably small deviations from the input reference data. For the six coupled 5A' surfaces, the 60,366 data below 10 eV are fit with a mean unsigned error (MUE) of 49 meV, and for the 14 coupled 3A' surfaces, the 76,733 data below 10 eV are fit with an MUE of 28 meV. The data below 5 eV fit even more accurately with MUEs of 37 meV (5A') and 20 meV (3A').
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Affiliation(s)
- Yinan Shu
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Farideh Badichi Akher
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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3
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Valverde D, Mai S, Canuto S, Borin AC, González L. Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water. JACS AU 2022; 2:1699-1711. [PMID: 35911449 PMCID: PMC9327080 DOI: 10.1021/jacsau.2c00250] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rationalizing the photochemistry of nucleobases where an oxygen is replaced by a heavier atom is essential for applications that exploit near-unity triplet quantum yields. Herein, we report on the ultrafast excited-state deactivation mechanism of 6-selenoguanine (6SeGua) in water by combining nonadiabatic trajectory surface-hopping dynamics with an electrostatic embedding quantum mechanics/molecular mechanics (QM/MM) scheme. We find that the predominant relaxation mechanism after irradiation starts on the bright singlet S2 state that converts internally to the dark S1 state, from which the population is transferred to the triplet T2 state via intersystem crossing and finally to the lowest T1 state. This S2 → S1 → T2 → T1 deactivation pathway is similar to that observed for the lighter 6-thioguanine (6tGua) analogue, but counterintuitively, the T1 lifetime of the heavier 6SeGua is shorter than that of 6tGua. This fact is explained by the smaller activation barrier to reach the T1/S0 crossing point and the larger spin-orbit couplings of 6SeGua compared to 6tGua. From the dynamical simulations, we also calculate transient absorption spectra (TAS), which provide two time constants (τ1 = 131 fs and τ2 = 191 fs) that are in excellent agreement with the experimentally reported value (τexp = 130 ± 50 fs) (Farrel et al. J. Am. Chem. Soc. 2018, 140, 11214). Intersystem crossing itself is calculated to occur with a time scale of 452 ± 38 fs, highlighting that the TAS is the result of a complex average of signals coming from different nonradiative processes and not intersystem crossing alone.
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Affiliation(s)
- Danillo Valverde
- Department
of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, São Paulo CEP 05508-000, Brazil
- Institute
of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo CEP 05508-090, Brazil
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Sylvio Canuto
- Institute
of Physics, University of São Paulo, Rua do Matão 1371, São Paulo, São Paulo CEP 05508-090, Brazil
| | - Antonio Carlos Borin
- Department
of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo, São Paulo CEP 05508-000, Brazil
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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4
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Fedotov DA, Paul AC, Koch H, Santoro F, Coriani S, Improta R. Excited state absorption of DNA bases in the gas phase and in chloroform solution: a comparative quantum mechanical study. Phys Chem Chem Phys 2022; 24:4987-5000. [PMID: 35142309 DOI: 10.1039/d1cp04340d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, namely, equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for thymine. In the gas phase, the three methods predict similar One Photon Absorption (OPA) spectra, which are consistent with the experimental results and with the most accurate computational studies available in the literature. The ESA spectra are then computed for the ππ* states (one for pyrimidine, two for purines) associated with the lowest-energy absorption band, and for the close-lying nπ* state. The EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase, TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effects by the polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the nπ* state. Finally, ESA spectra have been computed from the minima of the lowest energy ππ* state, and found in line with the available experimental transient absorption spectra of the nucleosides in solution, providing further validation of our computational approach.
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Affiliation(s)
- Daniil A Fedotov
- DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Alexander C Paul
- Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway.,Scuola Normale Superiore, Piazza dei Cavalieri, 7, I-56126, Pisa, Italy.
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, I-56124 Pisa, Italy.
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark. .,Department of Chemistry, NTNU - Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, I-80134 Napoli, Italy.
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5
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Lizondo-Aranda P, Martínez-Fernández L, Miranda MA, Improta R, Gustavsson T, Lhiaubet-Vallet V. The Excited State Dynamics of a Mutagenic Cytidine Etheno Adduct Investigated by Combining Time-Resolved Spectroscopy and Quantum Mechanical Calculations. J Phys Chem Lett 2022; 13:251-257. [PMID: 34968067 PMCID: PMC9135321 DOI: 10.1021/acs.jpclett.1c03534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Joint femtosecond fluorescence upconversion experiments and theoretical calculations provide a hitherto unattained degree of characterization and understanding of the mutagenic etheno adduct 3,N4-etheno-2'-deoxycytidine (εdC) excited state relaxation. This endogenously formed lesion is attracting great interest because of its ubiquity in human tissues and its highly mutagenic properties. The εdC fluorescence is modified with respect to that of the canonical base dC, with a 3-fold increased lifetime and quantum yield at neutral pH. This behavior is amplified upon protonation of the etheno ring (εdCH+). Quantum mechanical calculations show that the lowest energy state ππ*1 is responsible for the fluorescence and that the main nonradiative decay pathway to the ground state goes through an ethene-like conical intersection, involving the out-of-plane motion of the C5 and C6 substituents. This conical intersection is lower in energy than the ππ* state (ππ*1) minimum, but a sizable energy barrier explains the increase of εdC and εdCH+ fluorescence lifetimes with respect to that of dC.
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Affiliation(s)
- Paloma Lizondo-Aranda
- Instituto
Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avda de los Naranjos s/n, 46022 Valencia, Spain
| | - Lara Martínez-Fernández
- Departamento
de Química, Facultad de Ciencias and IADCHEM (Institute for
Advanced Research in Chemistry) Universidad
Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Miguel A. Miranda
- Instituto
Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avda de los Naranjos s/n, 46022 Valencia, Spain
| | - Roberto Improta
- Istituto
di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Thomas Gustavsson
- Université
Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Virginie Lhiaubet-Vallet
- Instituto
Universitario Mixto de Tecnología Química (UPV-CSIC), Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avda de los Naranjos s/n, 46022 Valencia, Spain
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6
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Jouybari M, 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] [Grants] [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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7
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Valverde D, de Araújo AVS, Borin AC. Photophysical Deactivation Mechanisms of the Pyrimidine Analogue 1-Cyclohexyluracil. Molecules 2021; 26:5191. [PMID: 34500625 PMCID: PMC8434193 DOI: 10.3390/molecules26175191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
The photophysical relaxation mechanisms of 1-cyclohexyluracil, in vacuum and water, were investigated by employing the Multi-State CASPT2 (MS-CASPT2, Multi-State Complete Active-Space Second-Order Perturbation Theory) quantum chemical method and Dunning's cc-pVDZ basis sets. In both environments, our results suggest that the primary photophysical event is the population of the S11(ππ*) bright state. Afterwards, two likely deactivation pathways can take place, which is sustained by linear interpolation in internal coordinates defined via Z-Matrix scans connecting the most important characteristic points. The first one (Route 1) is the same relaxation mechanism observed for uracil, its canonical analogue, i.e., internal conversion to the ground state through an ethylenic-like conical intersection. The other route (Route 2) is the direct population transfer from the S11(ππ*) bright state to the T23(nπ*) triplet state via an intersystem crossing process involving the (S11(ππ*)/T23(nπ*))STCP singlet-triplet crossing point. As the spin-orbit coupling is not too large in either environment, we propose that most of the electronic population initially on the S11(ππ*) state returns to the ground following the same ultrafast deactivation mechanism observed in uracil (Route 1), while a smaller percentage goes to the triplet manifold. The presence of a minimum on the S11(ππ*) potential energy hypersurface in water can help to understand why experimentally it is noticed suppression of the triplet states population in polar protic solvent.
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Affiliation(s)
- Danillo Valverde
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
| | | | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, SP, Brazil;
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8
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Westermayr J, Marquetand P. Machine Learning for Electronically Excited States of Molecules. Chem Rev 2021; 121:9873-9926. [PMID: 33211478 PMCID: PMC8391943 DOI: 10.1021/acs.chemrev.0c00749] [Citation(s) in RCA: 171] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.
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Affiliation(s)
- Julia Westermayr
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Data
Science @ Uni Vienna, University of Vienna, Währinger Strasse 29, 1090 Vienna, Austria
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9
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Felicetti S, Fregoni J, Schnappinger T, Reiter S, de Vivie-Riedle R, Feist J. Photoprotecting Uracil by Coupling with Lossy Nanocavities. J Phys Chem Lett 2020; 11:8810-8818. [PMID: 32914984 PMCID: PMC7569670 DOI: 10.1021/acs.jpclett.0c02236] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/11/2020] [Indexed: 05/08/2023]
Abstract
We analyze how the photorelaxation dynamics of a molecule can be controlled by modifying its electromagnetic environment using a nanocavity mode. In particular, we consider the photorelaxation of the RNA nucleobase uracil, which is the natural mechanism to prevent photodamage. In our theoretical work, we identify the operative conditions in which strong coupling with the cavity mode can open an efficient photoprotective channel, resulting in a relaxation dynamics twice as fast as the natural one. We rely on a state-of-the-art chemically detailed molecular model and a non-Hermitian Hamiltonian propagation approach to perform full-quantum simulations of the system dissipative dynamics. By focusing on the photon decay, our analysis unveils the active role played by cavity-induced dissipative processes in modifying chemical reaction rates, in the context of molecular polaritonics. Remarkably, we find that the photorelaxation efficiency is maximized when an optimal trade-off between light-matter coupling strength and photon decay rate is satisfied. This result is in contrast with the common intuition that increasing the quality factor of nanocavities and plasmonic devices improves their performance. Finally, we use a detailed model of a metal nanoparticle to show that the speedup of the uracil relaxation could be observed via coupling with a nanosphere pseudomode, without requiring the implementation of complex nanophotonic structures.
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Affiliation(s)
- Simone Felicetti
- Istituto
di Fotonica e Nanotecnologie, Consiglio
Nazionale delle Ricerche (IFN-CNR), Milano, Italy
- Departamento
de Física Teórica
de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autonoma de Madrid, Madrid, Spain
| | - Jacopo Fregoni
- Dipartimento
di Scienze Chimiche, University of Padova, Padova, Italy
- Dipartimento
di Scienze Fisiche, Informatiche e Matematiche, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Sebastian Reiter
- Department
Chemie, Ludwig-Maximilians-Universität
München, München, Germany
| | | | - Johannes Feist
- Departamento
de Física Teórica
de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autonoma de Madrid, Madrid, Spain
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10
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Yaghoubi Jouybari M, Liu Y, Improta R, Santoro F. Ultrafast Dynamics of the Two Lowest Bright Excited States of Cytosine and 1-Methylcytosine: A Quantum Dynamical Study. J Chem Theory Comput 2020; 16:5792-5808. [PMID: 32687360 DOI: 10.1021/acs.jctc.0c00455] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The nonadiabatic quantum dynamics (QD) of cytosine and 1-methylcytosine in the gas phase is simulated for 250 fs after a photoexcitation to one of the first two bright states. The nuclear wavepacket is propagated on the coupled diabatic potential energy surfaces of the lowest seven excited states, including ππ*, nπ*, and Rydberg states along all the vibrational degrees of freedom. We focus in particular on the interplay between the bright and the dark nπ* states, not considering the decay to the ground electronic state. To run these simulations, we implemented an automatic general procedure to parametrize linear vibronic coupling (LVC) models with time-dependent density functional theory (DFT) computations and interfaced it with Gaussian package. The wavepacket was propagated with the multilayer version of the multiconfigurational time dependent Hartree method. Two different density functionals, PBE0 and CAM-B3LYP, which provide a different description of the relative stability of the lowest energy dark states, were used to parametrize the LVC Hamiltonian. Part of the photoexcited population on lowest HOMO-LUMO transition (πHπL*) decays within less than 100 fs to a nπ* state which mainly involves a promotion of an electron from the oxygen lone pair to the LUMO (nOπL*). The population of the second ππ* state decays almost completely, in <100 fs, not only to πHπL* and to nOπL* states but also to another nπL* state involving the nitrogen lone pair. The efficiency of the adopted protocol allowed us to check the accuracy of the predictions by repeating the QD simulations with different LVC Hamiltonians parametrized either at the ground-state minimum or at stationary structures of different relevant excited states.
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Affiliation(s)
- 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
| | - Yanli Liu
- School of Physics and Optoelectronics Engineering, Ludong University, 264025 Yantai, Shandong, PR China
| | - 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
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11
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Jaiswal VK, Segarra-Martí J, Marazzi M, Zvereva E, Assfeld X, Monari A, Garavelli M, Rivalta I. First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases. Phys Chem Chem Phys 2020; 22:15496-15508. [DOI: 10.1039/d0cp01823f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
TD-DFT characterization of the high-energy singlet excited state manifold of the canonical DNA/RNA nucleobasesin vacuumis assessed against RASPT2 reference computations for reliable simulations of linear and non-linear electronic spectra.
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Affiliation(s)
- Vishal K. Jaiswal
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Viale del Risorgimento 4
- I-40136 Bologna
- Italy
| | - Javier Segarra-Martí
- Univ Lyon, Ens de Lyon, CNRS
- Université Lyon 1
- Laboratoire de Chimie UMR 5182
- Lyon
- France
| | - Marco Marazzi
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
- CNRS, Laboratoire de Physique et Chimie Théoriques
| | - Elena Zvereva
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
- CNRS, Laboratoire de Physique et Chimie Théoriques
| | - Xavier Assfeld
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
- CNRS, Laboratoire de Physique et Chimie Théoriques
| | - Antonio Monari
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
- CNRS, Laboratoire de Physique et Chimie Théoriques
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Viale del Risorgimento 4
- I-40136 Bologna
- Italy
| | - Ivan Rivalta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Viale del Risorgimento 4
- I-40136 Bologna
- Italy
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12
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Freitag L, Ma Y, Baiardi A, Knecht S, Reiher M. Approximate Analytical Gradients and Nonadiabatic Couplings for the State-Average Density Matrix Renormalization Group Self-Consistent-Field Method. J Chem Theory Comput 2019; 15:6724-6737. [PMID: 31670947 DOI: 10.1021/acs.jctc.9b00969] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present an approximate scheme for analytical gradients and nonadiabatic couplings for calculating state-average density matrix renormalization group self-consistent-field wave function. Our formalism follows closely the state-average complete active space self-consistent-field (SA-CASSCF) ansatz, which employs a Lagrangian, and the corresponding Lagrange multipliers are obtained from a solution of the coupled-perturbed CASSCF (CP-CASSCF) equations. We introduce a definition of the matrix product state (MPS) Lagrange multipliers based on a single-site tensor in a mixed-canonical form of the MPS, such that a sweep procedure is avoided in the solution of the CP-CASSCF equations. We apply our implementation to the optimization of a conical intersection in 1,2-dioxetanone, where we are able to fully reproduce the SA-CASSCF result up to arbitrary accuracy.
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Affiliation(s)
- Leon Freitag
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Yingjin Ma
- Computer Network Information Center , Chinese Academy of Sciences , Beijing 100190 , China.,Center of Scientific Computing Applications & Research, Chinese Academy of Sciences , Beijing 100190 , China
| | - Alberto Baiardi
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Stefan Knecht
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
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13
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Sasidharanpillai S, Friedman AA, Loppnow GR. Initial excited-state structural dynamics of 2′-deoxyadenosine. CAN J CHEM 2019. [DOI: 10.1139/cjc-2018-0409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Purine nucleobases (adenosine and guanosine) are prone to spontaneous breaking of the nucleosidic bond to form abasic sites in both DNA and RNA. However, the purines also undergo photochemical reactions, including oxidation and cycloaddition, to form damage sites, albeit at lower photochemical quantum yields than the pyrimidines. In this study, we use ultraviolet resonance Raman spectroscopy to measure the initial excited-state structural dynamics in the nucleoside, 2′-deoxyadenosine. The resonance Raman-derived initial excited-state structural dynamics throughout the 260 nm La excited electronic state of adenine are found to be smaller in the nucleoside than in the previously reported 9-methyladenine nucleobase derivative, consistent with what is found for the pyrimidines thymine and uracil. Interestingly, resonance-enhanced vibrational modes in this electronic state also contain internal coordinates localized on the sugar, which may represent a different energy dissipation mechanism than in the pyrimidine nucleosides. The results will be discussed in terms of the initial excited-state photophysics and photochemistry of DNA and RNA.
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Affiliation(s)
| | - Adam A. Friedman
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
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14
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Martinez-Fernandez L, Gavvala K, Sharma R, Didier P, Richert L, Segarra Martì J, Mori M, Mely Y, Improta R. Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine. Chemistry 2019; 25:7375-7386. [PMID: 30882930 DOI: 10.1002/chem.201900677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Indexed: 12/27/2022]
Abstract
Thienoguanosine (th G) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, th G exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto-amino tautomers. We herein investigate the photophysics of th G in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5-20.5 and 7-13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of th G, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias, Modúlo13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Krishna Gavvala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Rajhans Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Javier Segarra Martì
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK
| | - Mattia Mori
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto Biostrutture e Bioimmagini, Via Mezzocannone 16, 80134, Napoli, Italy
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15
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Sanches de Araújo AV, Borin AC. Photochemical Relaxation Pathways of 9 H-8-Azaguanine and 8 H-8-Azaguanine. J Phys Chem A 2019; 123:3109-3120. [PMID: 30901221 DOI: 10.1021/acs.jpca.9b01397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The photochemical reaction path approach, the MS-CASPT2 quantum-chemical method, and double-ζ basis sets (cc-pVDZ) were used to study 9 H-8-azaguanine and 8 H-8-azaguanine relaxation pathways. Several potential energy hypersurfaces were characterized by means of equilibrium geometries, surface crossings (conical intersections and singlet-triplet intersystem crossings), minimum energy paths, and linear interpolation in internal coordinates. The 9 H-8-azaguanine main photochemical event begins with the direct population of the 1(ππ* La) state, which evolves toward a conical intersection with the ground state after surmounting a small energy barrier, explaining why it is nonfluorescent. For 8 H-8-azaguanine, two relaxation mechanisms are possible, depending on the excitation energy. If the S1 1(ππ*) state is initially populated (lower-energy region), the system evolves barrierless to the S1 1(ππ*)min region, from where the excess energy is released. If the 1(ππ* La) state is populated (higher-energy radiation), the system will encounter conical intersections with the S2 1(nOπ*) and S1 1(ππ*) states before evolving to the 1(ππ* La)min region, from where a conical intersection with the ground state is accessible, favoring radiationless deactivation to the ground state. However, because a fraction of the population can be transferred from 1(ππ* La) to the S1 1(ππ*) state, emission from the S1 1(ππ*)min region is also expected, although weaker than it would be if the S1 1(ππ*) state were populated directly. Irrespective of the excitation energy, the emissive state is the same and a single fluorescence band is observed, with the strongest emission occurring upon excitation in the lower-energy region, as observed experimentally. Therefore, our computational study corroborates experimental results, attributing the emission of the neutral form of 8-azaguanine in solution to the presence of the minor 8 H-8-azaguanine tautomer, while the 9 H-8-azaguanine major tautomer is nonfluorescent.
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Affiliation(s)
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry , Institute of Chemistry, University of São Paulo , Av. Prof. Lineu Prestes 748 , 05508-000 São Paulo , SP , Brazil
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16
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Mai S, Marquetand P, González L. Nonadiabatic dynamics: The SHARC approach. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2018; 8:e1370. [PMID: 30450129 PMCID: PMC6220962 DOI: 10.1002/wcms.1370] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 12/12/2022]
Abstract
We review the Surface Hopping including ARbitrary Couplings (SHARC) approach for excited-state nonadiabatic dynamics simulations. As a generalization of the popular surface hopping method, SHARC allows simulating the full-dimensional dynamics of molecules including any type of coupling terms beyond nonadiabatic couplings. Examples of these arbitrary couplings include spin-orbit couplings or dipole moment-laser field couplings, such that SHARC can describe ultrafast internal conversion, intersystem crossing, and radiative processes. The key step of the SHARC approach consists of a diagonalization of the Hamiltonian including these couplings, such that the nuclear dynamics is carried out on potential energy surfaces including the effects of the couplings-this is critical in any applications considering, for example, transition metal complexes or strong laser fields. We also give an overview over the new SHARC2.0 dynamics software package, released under the GNU General Public License, which implements the SHARC approach and several analysis tools. The review closes with a brief survey of applications where SHARC was employed to study the nonadiabatic dynamics of a wide range of molecular systems. This article is categorized under: Theoretical and Physical Chemistry > Reaction Dynamics and KineticsSoftware > Simulation MethodsSoftware > Quantum Chemistry.
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Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry University of Vienna Vienna Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry University of Vienna Vienna Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry University of Vienna Vienna Austria
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17
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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18
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Wang X, Zhou Z, Tang Y, Chen J, Zhong D, Jianhua Xu. Excited State Decay Pathways of 2'-Deoxy-5-methylcytidine and Deoxycytidine Revisited in Solution: A Comprehensive Kinetic Study by Femtosecond Transient Absorption. J Phys Chem B 2018; 122:7027-7037. [PMID: 29939745 DOI: 10.1021/acs.jpcb.8b00927] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylated cytosine is proved to have an important role as an epigenetic signal in gene regulation and is often referred to "the fifth base of DNA". A comprehensive understanding of the electronic excited state relaxation in cytosine and its methylated derivatives is crucial for revealing UV-induced photodamage to the biological genome. Because of the existence of multiple closely lying "bright" and "dark" excited states, the decay pathways in these DNA nucleosides are the most complex and the least understood so far. In this study, femtosecond transient absorption with different excitation wavelengths (240-296 nm) was used to study the relaxation of excited electronic states of 5-methylcytosine (5mC) and 2'-deoxy-5-methylcytidine (5mdCyd) in phosphate buffered aqueous solution and in acetonitrile solution. Two distinct nonradiative decay channels were directly observed. The first one is a several picosecond internal conversion channel that involves two bright ππ* states (ππ*2 and ππ*1) when ππ*2 state is initially populated. The second channel contains the lower energy ππ*1 state and a so far experimental unidentified long-lived state which exhibits a several nanosecond lifetime. The long-lived state can only be accessed by the initially excited ππ*1 state. Inspired by this new discovery in 5mC and 5mdCyd, we revisited the decay of excited state of 2'-deoxycytidine (dCyd), revealing very similar decay pathways. Additionally, a well-known dark nOπ* state (carbonyl lone pair) with ∼30 ps lifetime is present in both decay channels in dCyd. With our detailed experimental results, we successfully reconcile the long history debate of cytosine excited state relaxation mechanism by pointing out that the reason for the complex dynamics under traditional 266 nm excitation is mixed signals from the above-mentioned two distinct decay pathways. Our findings lead to a dramatically different and new picture of electronic energy relaxation in 5mdCyd/dCyd and could help to understand photostability as well as UV-induced photodamage of these nucleotides and related DNAs.
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Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China
| | - Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China
| | - Yuankai Tang
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China.,Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy , East China Normal University , Shanghai , 200062 China.,Collaborative Innovation Center of Extreme Optics , Shanxi University , Taiyuan , Shanxi 030006 , China
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19
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Pilles BM, Maerz B, Chen J, Bucher DB, Gilch P, Kohler B, Zinth W, Fingerhut BP, Schreier WJ. Decay Pathways of Thymine Revisited. J Phys Chem A 2018; 122:4819-4828. [PMID: 29747505 DOI: 10.1021/acs.jpca.8b02050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The decay of electronically excited states of thymine (Thy) and thymidine 5'-monophosphate (TMP) was studied by time-resolved UV/vis and IR spectroscopy. In addition to the well-established ultrafast internal conversion to the ground state, a so far unidentified UV-induced species is observed. In D2O, this species decays with a time constant of 300 ps for thymine and of 1 ns for TMP. The species coexists with the lowest triplet state and is formed with a comparably high quantum yield of about 10% independent of the solvent. The experimentally determined spectral signatures are discussed in the light of quantum chemical calculations of the singlet and triplet excited states of thymine.
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Affiliation(s)
- Bert M Pilles
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
| | - Benjamin Maerz
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy , East China Normal University , 3663 North Zhongshan Road , Shanghai 200062 , China
| | - Dominik B Bucher
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
| | - Peter Gilch
- Institut für Physikalische Chemie , Heinrich-Heine-Universität Düsseldorf , Universitätsstrasse 1 , Düsseldorf 40225 , Germany
| | - Bern Kohler
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States
| | - Wolfgang Zinth
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , Max-Born-Strasse 2A , Berlin D-12489 , Germany
| | - Wolfgang J Schreier
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM , Ludwig-Maximilians-Universität München , Oettingenstrasse 67 , München 80538 , Germany
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20
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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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21
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Mai S, Ashwood B, Marquetand P, Crespo-Hernández CE, González L. Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine. J Phys Chem B 2017; 121:5187-5196. [PMID: 28452483 PMCID: PMC5447245 DOI: 10.1021/acs.jpcb.7b02715] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/27/2017] [Indexed: 01/01/2023]
Abstract
The solvatochromic effects of six different solvents on the UV absorption spectrum of 2-thiocytosine have been studied by a combination of experimental and theoretical techniques. The steady-state absorption spectra show significant shifts of the absorption bands, where in more polar solvents the first absorption maximum shifts to higher transition energies and the second maximum to lower energies. The observed solvatochromic shifts have been rationalized using three popular solvatochromic scales and with high-level multireference quantum chemistry calculations including implicit and explicit solvent effects. It has been found that the dipole moments of the excited states account for some general shifts in the excitation energies, whereas the explicit solvent interactions explain the differences in the spectra recorded in the different solvents.
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Affiliation(s)
- Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Brennan Ashwood
- Center
for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Carlos E. Crespo-Hernández
- Center
for Chemical Dynamics and Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
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22
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Wiebeler C, Borin V, Sanchez de Araújo AV, Schapiro I, Borin AC. Excitation Energies of Canonical Nucleobases Computed by Multiconfigurational Perturbation Theories. Photochem Photobiol 2017; 93:888-902. [DOI: 10.1111/php.12765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/16/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Christian Wiebeler
- Fritz Haber Center for Molecular Dynamics; Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem Israel
| | - Veniamin Borin
- Fritz Haber Center for Molecular Dynamics; Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem Israel
| | - Adalberto Vasconcelos Sanchez de Araújo
- Department of Fundamental Chemistry; Institute of Chemistry; NAP-PhotoTech the USP Consortium for Photochemical Technology; University of São Paulo; São Paulo SP Brazil
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics; Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem Israel
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry; Institute of Chemistry; NAP-PhotoTech the USP Consortium for Photochemical Technology; University of São Paulo; São Paulo SP Brazil
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23
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Peccati F, Mai S, González L. Insights into the deactivation of 5-bromouracil after ultraviolet excitation. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:20160202. [PMID: 28320905 PMCID: PMC5360901 DOI: 10.1098/rsta.2016.0202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/03/2016] [Indexed: 06/06/2023]
Abstract
5-Bromouracil is a nucleobase analogue that can replace thymine in DNA strands and acts as a strong radiosensitizer, with potential applications in molecular biology and cancer therapy. Here, the deactivation of 5-bromouracil after ultraviolet irradiation is investigated in the singlet and triplet manifold by accurate quantum chemistry calculations and non-adiabatic dynamics simulations. It is found that, after irradiation to the bright ππ* state, three main relaxation pathways are, in principle, possible: relaxation back to the ground state, intersystem crossing (ISC) and C-Br photodissociation. Based on accurate MS-CASPT2 optimizations, we propose that ground-state relaxation should be the predominant deactivation pathway in the gas phase. We then employ different electronic structure methods to assess their suitability to carry out excited-state dynamics simulations. MRCIS (multi-reference configuration interaction including single excitations) was used in surface hopping simulations to compute the ultrafast ISC dynamics, which mostly involves the 1nOπ* and 3ππ* states.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.
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Affiliation(s)
- Francesca Peccati
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
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24
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Keefer D, Thallmair S, Matsika S, de Vivie-Riedle R. Controlling Photorelaxation in Uracil with Shaped Laser Pulses: A Theoretical Assessment. J Am Chem Soc 2017; 139:5061-5066. [DOI: 10.1021/jacs.6b12033] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Keefer
- Department
Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Sebastian Thallmair
- Department
Chemie, Ludwig-Maximilians-Universität München, D-81377 München, Germany
| | - Spiridoula Matsika
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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25
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Segarra-Martí J, Francés-Monerris A, Roca-Sanjuán D, Merchán M. Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2. Molecules 2016; 21:molecules21121666. [PMID: 27918489 PMCID: PMC6274573 DOI: 10.3390/molecules21121666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/16/2022] Open
Abstract
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.
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Affiliation(s)
- Javier Segarra-Martí
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
- Present Address: Laboratoire de Chimie UMR 5182, École Normale Supérieure de Lyon, CNRS, Université de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France.
| | - Antonio Francés-Monerris
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Manuela Merchán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
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26
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Ruckenbauer M, Mai S, Marquetand P, González L. Photoelectron spectra of 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil. J Chem Phys 2016; 144:074303. [PMID: 26896982 DOI: 10.1063/1.4941948] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Ground- and excited-state UV photoelectron spectra of thiouracils (2-thiouracil, 4-thiouracil, and 2,4-dithiouracil) have been simulated using multireference configuration interaction calculations and Dyson norms as a measure for the photoionization intensity. Except for a constant shift, the calculated spectrum of 2-thiouracil agrees very well with experiment, while no experimental spectra are available for the two other compounds. For all three molecules, the photoelectron spectra show distinct bands due to ionization of the sulphur and oxygen lone pairs and the pyrimidine π system. The excited-state photoelectron spectra of 2-thiouracil show bands at much lower energies than in the ground state spectrum, allowing to monitor the excited-state population in time-resolved UV photoelectron spectroscopy experiments. However, the results also reveal that single-photon ionization probe schemes alone will not allow monitoring all photodynamic processes existing in 2-thiouracil. Especially, due to overlapping bands of singlet and triplet states the clear observation of intersystem crossing will be hampered.
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Affiliation(s)
- Matthias Ruckenbauer
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Sebastian Mai
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
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27
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Ruckenbauer M, Mai S, Marquetand P, González L. Revealing Deactivation Pathways Hidden in Time-Resolved Photoelectron Spectra. Sci Rep 2016; 6:35522. [PMID: 27762396 PMCID: PMC5071879 DOI: 10.1038/srep35522] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/27/2016] [Indexed: 11/09/2022] Open
Abstract
Time-resolved photoelectron spectroscopy is commonly employed with the intention to monitor electronic excited-state dynamics occurring in a neutral molecule. With the help of theory, we show that when excited-state processes occur on similar time scales the different relaxation pathways are completely obscured in the total photoionization signal recorded in the experiment. Using non-adiabatic molecular dynamics and Dyson norms, we calculate the photoionization signal of cytosine and disentangle the transient contributions originating from the different deactivation pathways of its tautomers. In the simulations, the total signal from the relevant keto and enol tautomers can be decomposed into contributions either from the neutral electronic state populations or from the distinct mechanistic pathways across the multiple potential surfaces. The lifetimes corresponding to these contributions cannot be extracted from the experiment, thereby illustrating that new experimental setups are necessary to unravel the intricate non-adiabatic pathways occurring in polyatomic molecules after irradiation by light.
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Affiliation(s)
- Matthias Ruckenbauer
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - 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
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28
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Martínez-Fernández L, Pepino AJ, Segarra-Martí J, Banyasz A, Garavelli M, Improta R. Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models. J Chem Theory Comput 2016; 12:4430-9. [DOI: 10.1021/acs.jctc.6b00518] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- L. Martínez-Fernández
- Istituto di Biostrutture
e Bioimmagini, CNR, Via Mezzocannone
16, I-80134 Napoli, Italy
| | - A. J. Pepino
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, Bologna, Italy
| | - J. Segarra-Martí
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, Bologna, Italy
- École
Normale Supérieure de Lyon, CNRS, UMR 5182, Université de Lyon, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France
| | - A. Banyasz
- LIDYL,
CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - M. Garavelli
- Dipartimento
di Chimica “G. Ciamician”, Università di Bologna, Bologna, Italy
- École
Normale Supérieure de Lyon, CNRS, UMR 5182, Université de Lyon, 46 Allée d’Italie, F-69364 Lyon Cedex 07, France
| | - R. Improta
- Istituto di Biostrutture
e Bioimmagini, CNR, Via Mezzocannone
16, I-80134 Napoli, Italy
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29
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Gattuso H, Besancenot V, Grandemange S, Marazzi M, Monari A. From non-covalent binding to irreversible DNA lesions: nile blue and nile red as photosensitizing agents. Sci Rep 2016; 6:28480. [PMID: 27329409 PMCID: PMC4916457 DOI: 10.1038/srep28480] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/03/2016] [Indexed: 12/15/2022] Open
Abstract
We report a molecular modeling study, coupled with spectroscopy experiments, on the behavior of two well known organic dyes, nile blue and nile red, when interacting with B-DNA. In particular, we evidence the presence of two competitive binding modes, for both drugs. However their subsequent photophysical behavior is different and only nile blue is able to induce DNA photosensitization via an electron transfer mechanism. Most notably, even in the case of nile blue, its sensitization capabilities strongly depend on the environment resulting in a single active binding mode: the minor groove. Fluorescence spectroscopy confirms the presence of competitive interaction modes for both sensitizers, while the sensitization via electron transfer, is possible only in the case of nile blue.
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Affiliation(s)
- Hugo Gattuso
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
| | - Vanessa Besancenot
- Université de Lorraine – Nancy Santé, Biologie, Signal - CRAN, Vandoeuvre-lès-Nancy, France
- CNRS, Santé, Biologie, Signal, CRAN, Vandoeuvre-lès-Nancy, France
| | - Stéphanie Grandemange
- Université de Lorraine – Nancy Santé, Biologie, Signal - CRAN, Vandoeuvre-lès-Nancy, France
- CNRS, Santé, Biologie, Signal, CRAN, Vandoeuvre-lès-Nancy, France
| | - Marco Marazzi
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Université de Lorraine – Nancy, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation SRSMC, Vandoeuvre-lès-Nancy, France
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30
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Richter M, Fingerhut BP. Simulation of Multi-Dimensional Signals in the Optical Domain: Quantum-Classical Feedback in Nonlinear Exciton Propagation. J Chem Theory Comput 2016; 12:3284-94. [PMID: 27248511 DOI: 10.1021/acs.jctc.6b00371] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an algorithm for the simulation of nonlinear 2D spectra of molecular systems in the UV-vis spectral region from atomistic molecular dynamics trajectories subject to nonadiabatic relaxation. We combine the nonlinear exciton propagation (NEP) protocol, that relies on a quasiparticle approach with the surface hopping methodology to account for quantum-classical feedback during the dynamics. Phenomena, such as dynamic Stokes shift due to nuclear relaxation, spectral diffusion, and population transfer among electronic states, are thus naturally included and benchmarked on a model of two electronic states coupled to a harmonic coordinate and a classical heatbath. The capabilities of the algorithm are further demonstrated for the bichromophore diphenylmethane that is described in a fully microscopic fashion including all 69 classical nuclear degrees of freedom. We demonstrate that simulated 2D signals are especially sensitive to the applied theoretical approximations (i.e., choice of active space in the CASSCF method) where population dynamics appears comparable.
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Affiliation(s)
- Martin Richter
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie , D-12489 Berlin, Germany
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31
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Mai S, Marquetand P, González L. Intersystem Crossing Pathways in the Noncanonical Nucleobase 2-Thiouracil: A Time-Dependent Picture. J Phys Chem Lett 2016; 7:1978-83. [PMID: 27167106 PMCID: PMC4893732 DOI: 10.1021/acs.jpclett.6b00616] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The deactivation mechanism after ultraviolet irradiation of 2-thiouracil has been investigated using nonadiabatic dynamics simulations at the MS-CASPT2 level of theory. It is found that after excitation the S2 quickly relaxes to S1, and from there intersystem crossing takes place to both T2 and T1 with a time constant of 400 fs and a triplet yield above 80%, in very good agreement with recent femtosecond experiments in solution. Both indirect S1 → T2 → T1 and direct S1 → T1 pathways contribute to intersystem crossing, with the former being predominant. The results contribute to the understanding of how some noncanonical nucleobases respond to harmful ultraviolet light, which could be relevant for prospective photochemotherapeutic applications.
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32
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Spata VA, Lee W, Matsika S. Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides. J Phys Chem Lett 2016; 7:976-984. [PMID: 26911276 DOI: 10.1021/acs.jpclett.5b02756] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A lot has been learned about the physical and chemical transformations that originate from the absorption of light by DNA, and computational chemistry has played a critical role in revealing the mechanisms of how these transformations occur. Nucleic acids consist of chromophores interacting via π stacking and hydrogen bonding. The fate of these systems after they absorb light is determined by the interplay and competition between pathways involving one chromophore or interacting chromophores. This Perspective highlights the role of π stacking in photophysical and photochemical processes in oligonucleotides and reveals the importance of excimers and exciplexes. Special types of excimers/exciplexes, characterized as bonded excimers/exciplexes, are also found to be important.
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Affiliation(s)
- Vincent A Spata
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Wook Lee
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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33
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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: 341] [Impact Index Per Article: 42.6] [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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34
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Assmann M, Weinacht T, Matsika S. Surface hopping investigation of the relaxation dynamics in radical cations. J Chem Phys 2016; 144:034301. [DOI: 10.1063/1.4939842] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Mariana Assmann
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Thomas Weinacht
- Department of Physics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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35
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Brister MM, Crespo-Hernández CE. Direct Observation of Triplet-State Population Dynamics in the RNA Uracil Derivative 1-Cyclohexyluracil. J Phys Chem Lett 2015; 6:4404-9. [PMID: 26538051 DOI: 10.1021/acs.jpclett.5b01901] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Investigation of the excited-state dynamics in nucleic acid monomers is an area of active research due to the crucial role these early events play in DNA and RNA photodamage. The dynamics and rate at which the triplet state is populated are key mechanistic pathways yet to be fully elucidated. Direct spectroscopic evidence is presented in this contribution for intersystem crossing dynamics in a uracil derivative, 1-cyclohexyluracil. It is shown that intersystem crossing to the triplet manifold occurs in one picosecond or less in acetonitrile solution-at least an order of magnitude faster than previously estimated experimentally. Broadband transient absorption measurements also reveal the primary electronic relaxation pathways of the uracil chromophore, including the absorption spectra of the (1)ππ*, (1)nπ*, and (3)ππ* states and the rates of vibrational cooling in the ground and (3)ππ* states. The experimental results are supported by density functional calculations.
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Affiliation(s)
- Matthew M Brister
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Carlos E Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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36
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Carbonniere P, Pouchan C, Improta R. Intramolecular vibrational redistribution in the non-radiative excited state decay of uracil in the gas phase: an ab initio molecular dynamics study. Phys Chem Chem Phys 2015; 17:11615-26. [PMID: 25866850 DOI: 10.1039/c4cp05265j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a study of intramolecular vibrational distribution (IVR) occurring in the electronic ground state of uracil (S0) in the gas phase, following photoexcitation in the lowest energy bright excited state (Sπ) and decay through the ethylene-like Sπ/S0 Conical Intersection (CI-0π). To this aim we have performed 20 independent ab initio molecular dynamics simulations starting from CI-0π (ten of them with 1 eV kinetic energy randomly distributed over the different molecular degrees of freedom) and 10 starting from the ground state minimum (Franck-Condon, FC, point), with the excess kinetic energy equal to the energy gap between CI-0π and the FC point. The simulations, exploiting PBE0/6-31G(d) calculations, were performed over an overall period of 10 ps. A thorough statistical analysis of the variation of the geometrical parameters of uracil during the simulation time and of the distribution of the kinetic energy among the different vibrational degrees of freedom provides a consistent picture of the IVR process. In the first 0-200 fs the structural dynamics involve mainly the recovery of the average planarity. In the 200-600 fs time range, a substantial activation of CO and NH degrees of freedom is observed. After 500-600 fs most of the geometrical parameters reach average values similar to those found after 10 ps, though the system cannot be considered to be in equilibrium yet.
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Affiliation(s)
- Philippe Carbonniere
- Université de Pau et des Pays de l'Adour UMR5254, IPREM, Equipe Chimie-Physique Hélioparc, 2 av. Président Angot 64053, Pau Cedex 09, France.
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37
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Altavilla SF, Segarra-Martí J, Nenov A, Conti I, Rivalta I, Garavelli M. Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate. Front Chem 2015; 3:29. [PMID: 25941671 PMCID: PMC4403598 DOI: 10.3389/fchem.2015.00029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/30/2015] [Indexed: 01/17/2023] Open
Abstract
The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ(*) La and Lb states, whereas the energy of the oxygen lone-pair nπ(*) state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ(*) state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region.
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Affiliation(s)
| | | | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Irene Conti
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Ivan Rivalta
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
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38
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Crespo-Hernández CE, Martínez-Fernández L, Rauer C, Reichardt C, Mai S, Pollum M, Marquetand P, González L, Corral I. Electronic and structural elements that regulate the excited-state dynamics in purine nucleobase derivatives. J Am Chem Soc 2015; 137:4368-81. [PMID: 25763596 PMCID: PMC4410903 DOI: 10.1021/ja512536c] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 12/20/2022]
Abstract
The excited-state dynamics of the purine free base and 9-methylpurine are investigated using experimental and theoretical methods. Femtosecond broadband transient absorption experiments reveal that excitation of these purine derivatives in aqueous solution at 266 nm results primarily in ultrafast conversion of the S2(ππ*) state to the vibrationally excited (1)nπ* state. Following vibrational and conformational relaxation, the (1)nπ* state acts as a doorway state in the efficient population of the triplet manifold with an intersystem crossing lifetime of hundreds of picoseconds. Experiments show an almost 2-fold increase in the intersystem crossing rate on going from polar aprotic to nonpolar solvents, suggesting that a solvent-dependent energy barrier must be surmounted to access the singlet-to-triplet crossing region. Ab initio static and surface-hopping dynamics simulations lend strong support to the proposed relaxation mechanism. Collectively, the experimental and computational results demonstrate that the accessibility of the nπ* states and the topology of the potential energy surfaces in the vicinity of conical intersections are key elements in controlling the excited-state dynamics of the purine derivatives. From a structural perspective, it is shown that the purine chromophore is not responsible for the ultrafast internal conversion in the adenine and guanine monomers. Instead, C6 functionalization plays an important role in regulating the rates of radiative and nonradiative relaxation. C6 functionalization inhibits access to the (1)nπ* state while simultaneously facilitating access to the (1)ππ*(La)/S0 conical intersection, such that population of the (1)nπ* state cannot compete with the relaxation pathways to the ground state involving ring puckering at the C2 position.
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Affiliation(s)
- Carlos E. Crespo-Hernández
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Lara Martínez-Fernández
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
| | - Clemens Rauer
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Christian Reichardt
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Marvin Pollum
- Department
of Chemistry and Center for Chemical Dynamics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United
States
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, University of
Vienna, Währinger
Str. 17, 1090 Vienna, Austria
| | - Inés Corral
- Departamento
de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Módulo 13, Cantoblanco, 28049 Madrid, Spain
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39
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Changenet-Barret P, Gustavsson T, Improta R, Markovitsi D. Ultrafast Excited-State Deactivation of 8-Hydroxy-2'-deoxyguanosine Studied by Femtosecond Fluorescence Spectroscopy and Quantum-Chemical Calculations. J Phys Chem A 2015; 119:6131-9. [PMID: 25752921 DOI: 10.1021/acs.jpca.5b00688] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The fluorescence properties of the 8-hydroxy-2'-deoxyguanosine (8-oxo-dG) in aqueous solution at pH 6.5 are studied by steady-state spectroscopy and femtosecond fluorescence up-conversion and compared with those of 2'-deoxyguanine (dG) and 2'-deoxyguanine monophosphate (dGMP). The steady-state fluorescence spectrum of 8-oxo-dG is composed of a broad band that peaks at 356 nm and extends over the entire visible spectral region, and its fluorescence quantum yield is twice that of dG/dGMP. After excitation at 267 nm, the initial fluorescence anisotropy at all wavelengths is lower than 0.1, giving evidence of an ultrafast internal conversion (<100 fs) between the two lowest excited ππ* states (Lb and La). The fluorescence decays of 8-oxo-dG are biexponential with an average lifetime of 0.7 ± 0.1 ps, which is about two times longer than that of dGMP. In contrast with dGMP, only a moderate dynamical shift (∼1400 vs 10,000 cm(-1)) of the fluorescence spectra of 8-oxo-dG is observed on the time scale of a few picoseconds without modification of the spectral shape. PCM/TD-DFT calculations, employing either the PBE0 or the M052X functionals, provide absorption spectra in good agreement with the experimental one and show that the deactivation path is similar to that proposed for dGMP, with a fast motion toward an energy plateau, where the purine ring keeps an almost planar geometry, followed by decay to S0, via out-of-the plane motion of amino substituent.
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Affiliation(s)
- Pascale Changenet-Barret
- †CNRS, IRAMIS, LIDyL, Laboratoire Francis Perrin, URA 2453, CEA Saclay, 91191 Gif sur Yvette, France
| | - Thomas Gustavsson
- †CNRS, IRAMIS, LIDyL, Laboratoire Francis Perrin, URA 2453, CEA Saclay, 91191 Gif sur Yvette, France
| | - Roberto Improta
- ‡Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80136 Naples, Italy
| | - Dimitra Markovitsi
- †CNRS, IRAMIS, LIDyL, Laboratoire Francis Perrin, URA 2453, CEA Saclay, 91191 Gif sur Yvette, France
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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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