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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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2-Aminopyrimidinium Decavanadate: Experimental and Theoretical Characterization, Molecular Docking, and Potential Antineoplastic Activity. INORGANICS 2021. [DOI: 10.3390/inorganics9090067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The interest in decavanadate anions has increased in recent decades, since these clusters show interesting applications as varied as sensors, batteries, catalysts, or new drugs in medicine. Due to the capacity of the interaction of decavanadate with a variety of biological molecules because of its high negative charge and oxygen-rich surface, this cluster is being widely studied both in vitro and in vivo as a treatment for several global health problems such as diabetes mellitus, cancer, and Alzheimer’s disease. Here, we report a new decavanadate compound with organic molecules synthesized in an aqueous solution and structurally characterized by elemental analysis, infrared spectroscopy, thermogravimetric analysis, and single-crystal X-ray diffraction. The decavanadate anion was combined with 2-aminopyrimidine to form the compound [2-ampymH]6[V10O28]·5H2O (1). In the crystal lattice, organic molecules are stacked by π–π interactions, with a centroid-to-centroid distance similar to that shown in DNA or RNA molecules. Furthermore, computational DFT calculations of Compound 1 corroborate the hydrogen bond interaction between pyrimidine molecules and decavanadate anions, as well as the π–π stacking interactions between the central pyrimidine molecules. Finally, docking studies with test RNA molecules indicate that they could serve as other potential targets for the anticancer activity of decavanadate anion.
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Green JA, Yaghoubi Jouybari M, Asha H, Santoro F, Improta R. Fragment Diabatization Linear Vibronic Coupling Model for Quantum Dynamics of Multichromophoric Systems: Population of the Charge-Transfer State in the Photoexcited Guanine-Cytosine Pair. J Chem Theory Comput 2021; 17:4660-4674. [PMID: 34270258 DOI: 10.1021/acs.jctc.1c00416] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We introduce a method (FrD-LVC) based on a fragment diabatization (FrD) for the parametrization of a linear vibronic coupling (LVC) model suitable for studying the photophysics of multichromophore systems. In combination with effective quantum dynamics (QD) propagations with multilayer multiconfigurational time-dependent Hartree (ML-MCTDH), the FrD-LVC approach gives access to the study of the competition between intrachromophore decays, like those at conical intersections, and interchromophore processes, like exciton localization/delocalization and the involvement of charge-transfer (CT) states. We used FrD-LVC parametrized with time-dependent density functional theory (TD-DFT) calculations, adopting either CAM-B3LYP or ωB97X-D functionals, to study the ultrafast photoexcited QD of a guanine-cytosine (GC) hydrogen-bonded pair, within a Watson-Crick arrangement, considering up to 12 coupled diabatic electronic states and the effect of all of the 99 vibrational coordinates. The bright excited states localized on C and, especially, on G are predicted to be strongly coupled to the G → C CT state, which is efficiently and quickly populated after an excitation to any of the four lowest energy bright local excited states. Our QD simulations show that more than 80% of the excited population on G and ∼50% of that on C decay to this CT state in less than 50 fs. We investigate the role of vibronic effects in the population of the CT state and show that it depends mainly on its large reorganization energy so that it can occur even when it is significantly less stable than the bright states in the Franck-Condon region. At the same time, we document that the formation of the GC pair almost suppresses the involvement of dark nπ* excited states in the photoactivated dynamics.
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Affiliation(s)
- James A Green
- Istituto di Biostrutture e Bioimmagini (IBB-CNR), Consiglio Nazionale delle Ricerche, via Mezzocannone 16, I-80136 Napoli, Italy
| | - Martha Yaghoubi Jouybari
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), Consiglio Nazionale delle Ricerche, SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Haritha Asha
- Istituto di Biostrutture e Bioimmagini (IBB-CNR), Consiglio Nazionale delle Ricerche, via Mezzocannone 16, I-80136 Napoli, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), Consiglio Nazionale delle Ricerche, SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini (IBB-CNR), Consiglio Nazionale delle Ricerche, via Mezzocannone 16, I-80136 Napoli, Italy
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Francés-Monerris A, Hognon C, Douki T, Monari A. Photoinduced DNA Lesions in Dormant Bacteria: The Peculiar Route Leading to Spore Photoproducts Characterized by Multiscale Molecular Dynamics*. Chemistry 2020; 26:14236-14241. [PMID: 32597544 DOI: 10.1002/chem.202002484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Indexed: 11/07/2022]
Abstract
Some bacterial species enter a dormant state in the form of spores to resist to unfavorable external conditions. Spores are resistant to a wide series of stress agents, including UV radiation, and can last for tens to hundreds of years. Due to the suspension of biological functions, such as DNA repair, they accumulate DNA damage upon exposure to UV radiation. Differently from active organisms, the most common DNA photoproducts in spores are not cyclobutane pyrimidine dimers, but rather the so-called spore photoproducts. This noncanonical photochemistry results from the dry state of DNA and its binding to small, acid-soluble proteins that drastically modify the structure and photoreactivity of the nucleic acid. Herein, multiscale molecular dynamics simulations, including extended classical molecular dynamics and quantum mechanics/molecular mechanics based dynamics, are used to elucidate the coupling of electronic and structural factors that lead to this photochemical outcome. In particular, the well-described impact of the peculiar DNA environment found in spores on the favored formation of the spore photoproduct, given the small free energy barrier found for this path, is rationalized. Meanwhile, the specific organization of spore DNA precludes the photochemical path that leads to cyclobutane pyrimidine dimer formation.
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Affiliation(s)
- Antonio Francés-Monerris
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- Departament de Química Física, Universitat de València, 46100, Burjassot, Spain
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- Université de Lorraine and CNRS, CRAN UMR 7039, 54000, Nancy, France
| | - Thierry Douki
- SyMMES, CEA, CNRS, IRIG, University Grenoble Alpes, 38000, Grenoble, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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Lineros-Rosa M, Francés-Monerris A, Monari A, Miranda MA, Lhiaubet-Vallet V. Experimental and theoretical studies on thymine photodimerization mediated by oxidatively generated DNA lesions and epigenetic intermediates. Phys Chem Chem Phys 2020; 22:25661-25668. [DOI: 10.1039/d0cp04557h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Combined spectroscopic and computational studies reveal that, in spite of their structural similarities, 5-formyluracil and 5-formylcytosine photosensitize cyclobutane thymine dimers through two different types of mechanisms.
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Affiliation(s)
- Mauricio Lineros-Rosa
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | | | - Antonio Monari
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
| | - Miguel Angel Miranda
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
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Londesborough MGS, Dolanský J, Bould J, Braborec J, Kirakci K, Lang K, Císařová I, Kubát P, Roca-Sanjuán D, Francés-Monerris A, Slušná L, Noskovičová E, Lorenc D. Effect of Iodination on the Photophysics of the Laser Borane anti-B18H22: Generation of Efficient Photosensitizers of Oxygen. Inorg Chem 2019; 58:10248-10259. [DOI: 10.1021/acs.inorgchem.9b01358] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Jiří Dolanský
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Jonathan Bould
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Jakub Braborec
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Kaplan Kirakci
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Kamil Lang
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Charles University in Prague, Hlavova 2030/8, 128 43 Prague 2, Czech Republic
| | - Pavel Kubát
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, 182 23 Praha 8, Czech Republic
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, ES-46071, València, Spain
| | | | - Lenka Slušná
- Department of Physical, Theoretical and Computational Chemistry, Mlynská dolina, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Eva Noskovičová
- Department of Physical, Theoretical and Computational Chemistry, Mlynská dolina, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Dušan Lorenc
- International Laser Centre, Ilkovicova 3, 84104, Bratislava, Slovak Republic
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Affiliation(s)
- Teresa L. Mako
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Joan M. Racicot
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Mindy Levine
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
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Francés-Monerris A, Hognon C, Miranda MA, Lhiaubet-Vallet V, Monari A. Triplet photosensitization mechanism of thymine by an oxidized nucleobase: from a dimeric model to DNA environment. Phys Chem Chem Phys 2018; 20:25666-25675. [PMID: 30298156 DOI: 10.1039/c8cp04866e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nucleic acids are constantly exposed to external agents that can induce chemical and photochemical damage. In spite of the great advances achieved in the last years, some molecular mechanisms of DNA damage are not completely understood yet. A recent experimental report (I. Aparici-Espert et al., ACS Chem. Biol. 2018, 13, 542) proved the ability of 5-formyluracil (ForU), a common oxidatively generated product of thymine, to act as an intrinsic sensitizer of nucleic acids, causing single strand breaks and cyclobutane pyrimidine dimers in plasmid DNA. In the present contribution, we use theoretical methodologies to study the triplet photosensitization mechanism of thymine exerted by ForU in a model dimer and in DNA environment. The photochemical pathways in the former system are described combining the CASPT2 and TD-DFT methods, whereas molecular dynamics simulations and QM/MM calculations are employed for the DNA duplex. It is unambiguously shown that the 1n,π* state localised in ForU mediates the population of the triplet manifold, most likely the 3π,π* state centred in ForU, whereas the 3π,π* state localized in thymine can be populated via triplet-triplet energy transfer given the small energy barrier of <0.23 eV determined for this pathway.
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Francés-Monerris A, Gattuso H, Roca-Sanjuán D, Tuñón I, Marazzi M, Dumont E, Monari A. Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA. Chem Sci 2018; 9:7902-7911. [PMID: 30450180 PMCID: PMC6202918 DOI: 10.1039/c8sc03252a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022] Open
Abstract
The intrinsic photostability of nucleic acids is intimately related to evolution of life, while its understanding at the molecular and electronic levels remains a challenge for modern science. Among the different decay pathways proposed in the last two decades, the excited-state hydrogen transfer between guanine-cytosine base pairs has been identified as an efficient non-reactive channel to dissipate the excess of energy provided by light absorption. The present work studies the dynamics of such phenomena taking place in a (dG)·(dC) B-DNA homopolymer in water solution using state-of-the-art molecular modelling and simulation methods. A dynamic effect that boosts the photostability of the inter-strand hydrogen atom transfers, inherent to the Watson-Crick base pairing, is unveiled and ascribed to the energy released during the proton transfer step. Our results also reveal a novel mechanism of DNA decay named four proton transfer (FPT), in which two protons of two adjacent G-C base pairs are transferred to form a biradical zwitterionic intermediate. Decay of the latter intermediate to the ground state triggers the transfer of the protons back to the guanine molecules recovering the Watson-Crick structure of the tetramer. This FPT process is activated by the close interaction of a nearby Na+ counterion with the oxygen atoms of the guanine nucleobases and hence represents a photostable channel operative in natural nucleic acids.
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Affiliation(s)
| | - Hugo Gattuso
- Theoretical Physical Chemistry , Research Unit Molecular Systems (UR MOLSYS) , University of Liège , 4000 Liège , Belgium
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular , Universitat de València , Apartado 22085 , ES-46071 Paterna , Spain
| | - Iñaki Tuñón
- Departamento de Química Física , Universitat de València , 46100 Burjassot , Spain
| | - Marco Marazzi
- Departamento de Química , Centro de Investigación en Síntesis Química (CISQ) , Universidad de La Rioja , 26006 Logroño , Spain
| | - Elise Dumont
- Univ. Lyon , ENS de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F69342 , Lyon , France
| | - Antonio Monari
- Université de Lorraine , CNRS , LPCT , Nancy F-54000 , France . ;
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Welborn VV, Van Voorhis T. Non-radiative deactivation of cytosine derivatives at elevated temperature. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1457806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, MA, USA
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Martinez-Fernandez L, Improta R. Photoactivated proton coupled electron transfer in DNA: insights from quantum mechanical calculations. Faraday Discuss 2018; 207:199-216. [DOI: 10.1039/c7fd00195a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The energetics of the two main proton coupled electron transfer processes that could occur in DNA are determined by means of time dependent-DFT calculations, using the M052X functional and the polarizable continuum model to include solvent effect.
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Affiliation(s)
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche
- Istituto di Biostrutture e Bioimmagini
- 80136 Naples
- Italy
- LIDYL
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Jun J, Han SY. Theoretical exploration of gas-phase conformers of proton-bound non-covalent heterodimers of guanine and cytosine rare tautomers: structures and energies. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2165-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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How Does Thymine DNA Survive Ultrafast Dimerization Damage? Molecules 2016; 22:molecules22010060. [PMID: 28042858 PMCID: PMC6155609 DOI: 10.3390/molecules22010060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/13/2016] [Accepted: 12/24/2016] [Indexed: 11/16/2022] Open
Abstract
The photodimerization reaction between the two adjacent thymine bases within a single strand has been the subject of numerous studies due to its potential to induce DNA mutagenesis and possible tumorigenesis in human skin cells. It is well established that the cycloaddition photoreaction takes place on a picosecond time scale along barrierless or low barrier singlet/triplet pathways. However, the observed dimerization quantum yield in different thymine multimer is considerable lower than might be expected. A reasonable explanation is required to understand why thymine in DNA is able to survive ultrafast dimerization damage. In this work, accurate quantum calculations based on the combined CASPT2//CASSCF/AMBER method were conducted to map the excited state relaxation pathways of the thymine monomer in aqueous solution and of the thymine oligomer in DNA. A monomer-like decay pathway, induced by the twisting of the methyl group, is found to provide a bypass channel to ensure the photostability of thymine in single-stranded oligomers. This fast relaxation path is regulated by the conical intersection between the bright SCT(¹ππ*) state with the intra-base charge transfer character and the ground state to remove the excess excitation energy, thereby achieving the ground-state recovery with high efficiency.
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