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Martínez-Fernández L, Green JA, Esposito L, Jouybari MY, Zhang Y, Santoro F, Kohler B, Improta R. The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study. Chem Sci 2024; 15:9676-9693. [PMID: 38939156 PMCID: PMC11206432 DOI: 10.1039/d4sc00910j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/04/2024] [Indexed: 06/29/2024] Open
Abstract
Study of alternating DNA GC sequences by different time-resolved spectroscopies has provided fundamental information on the interaction between UV light and DNA, a process of great biological importance. Multiple decay paths have been identified, but their interplay is still poorly understood. Here, we characterize the photophysics of GC-DNA by integrating different computational approaches, to study molecular models including up to 6 bases described at a full quantum mechanical level. Quantum dynamical simulations, exploiting a nonadiabatic linear vibronic coupling (LVC) model, coupled with molecular dynamics sampling of the initial structures of a (GC)5 DNA duplex, provide new insights into the photophysics in the sub-picosecond time-regime. They indicate a substantial population transfer, within 50 fs, from the spectroscopic states towards G → C charge transfer states involving two stacked bases (CTintra), thus explaining the ultrafast disappearance of fluorescence. This picture is consistent with that provided by quantum mechanical geometry optimizations, using time dependent-density functional theory and a polarizable continuum model, which we use to parametrize the LVC model and to map the main excited state deactivation pathways. For the first time, the infrared and excited state absorption signatures of the various states along these pathways are comprehensively mapped. The computational models suggest that the main deactivation pathways, which, according to experiment, lead to ground state recovery on the 10-50 ps time scale, involve CTintra followed by interstrand proton transfer from the neutral G to C-. Our calculations indicate that CTintra is populated to a larger extent and more rapidly in GC than in CG steps and suggest the likely involvement of monomer-like and interstrand charge transfer decay routes for isolated and less stacked CG steps. These findings underscore the importance of the DNA sequence and thermal fluctuations for the dynamics. They will also aid the interpretation of experimental results on other sequences.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física Blas Cabrera, CSIC 28006 Madrid Spain
| | - James Alexander Green
- Institut für Physikalische Theoretische Chemie, Goethe-Universität Frankfurt am Main Frankfurt am Main Germany
| | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
| | - Martha Yaghoubi Jouybari
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie Ottawa Ontario K1N 6N5 Canada
- National Research Council of Canada 100 Sussex Drive Ottawa Ontario K1A 0R6 Canada
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
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2
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Zhou J, Wang X, Jia M, He X, Pan H, Chen J. Ultrafast spectroscopy study of DNA photophysics after proflavine intercalation. J Chem Phys 2024; 160:124305. [PMID: 38526107 DOI: 10.1063/5.0194608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/06/2024] [Indexed: 03/26/2024] Open
Abstract
Proflavine (PF), an acridine DNA intercalating agent, has been widespread applied as an anti-microbial and topical antiseptic agent due to its ability to suppress DNA replication. On the other hand, various studies show that PF intercalation to DNA can increase photogenotoxicity and has potential chances to induce carcinomas of skin appendages. However, the effects of PF intercalation on the photophysical and photochemical properties of DNA have not been sufficiently explored. In this study, the excited state dynamics of the PF intercalated d(GC)9 • d(GC)9 and d(AT)9 • d(AT)9 DNA duplex are investigated in an aqueous buffer solution. Under 267 nm excitation, we observed ultrafast charge transfer (CT) between PF and d(GC)9 • d(GC)9 duplex, generating a CT state with an order of magnitude longer lifetime compared to that of the intrinsic excited state reported for the d(GC)9 • d(GC)9 duplex. In contrast, no excited state interaction was detected between PF and d(AT)9 • d(AT)9. Nevertheless, a localized triplet state with a lifetime over 5 µs was identified in the PF-d(AT)9 • d(AT)9 duplex.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Menghui Jia
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Xiaoxiao He
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Haifeng Pan
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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3
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Martinez-Fernandez L, Improta R. The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study. Photochem Photobiol 2024; 100:314-322. [PMID: 37409732 DOI: 10.1111/php.13832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time-dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady-state infrared and absorption spectra of a protonated cytidine (CH+ ), and predict that an easily accessible non-radiative deactivation route exists for the spectroscopic state, explaining its sub-ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out-of-plane motion of the hydrogen substituents of the CC double bond, the so-called ethylenic conical intersection typical of cytidine and other pyrimidine bases. This deactivation route is operative for the two bases forming an hemiprotonated cytidine base pair, [CH·C]+ , the building blocks of I-motif secondary structures, whereas interbase processes play a minor role. N3 protonation disfavors instead the nπ* transitions, associated with the long-living components of cytidine photoactivated dynamics.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Sciences (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Madrid, Spain
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Naples, Italy
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4
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Wang X, Martínez-Fernández L, Zhang Y, Wu P, Kohler B, Improta R, Chen J. Ultrafast Formation of a Delocalized Triplet-Excited State in an Epigenetically Modified DNA Duplex under Direct UV Excitation. J Am Chem Soc 2024; 146:1839-1848. [PMID: 38194423 DOI: 10.1021/jacs.3c04567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Epigenetic modifications impart important functionality to nucleic acids during gene expression but may increase the risk of photoinduced gene mutations. Thus, it is crucial to understand how these modifications affect the photostability of duplex DNA. In this work, the ultrafast formation (<20 ps) of a delocalized triplet charge transfer (CT) state spreading over two stacked neighboring nucleobases after direct UV excitation is demonstrated in a DNA duplex, d(G5fC)9•d(G5fC)9, made of alternating guanine (G) and 5-formylcytosine (5fC) nucleobases. The triplet yield is estimated to be 8 ± 3%, and the lifetime of the triplet CT state is 256 ± 22 ns, indicating that epigenetic modifications dramatically alter the excited state dynamics of duplex DNA and may enhance triplet state-induced photochemistry.
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Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemical Science (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, Madrid 28049, Spain
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Peicong Wu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini CNR, Via De Amicis 95, Napoli I-80145, Italy
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, Shanxi, China
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5
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Mathew R, Verma P, Barak A, Adithya Lakshmanna Y. Excited-State Dynamics in 4-[4'(Dimethylamino)styryl]pyridine, a Photobase: Role of Photoinitiated Proton-Coupled Electron Transfer. J Phys Chem A 2023; 127:7419-7428. [PMID: 37647516 DOI: 10.1021/acs.jpca.3c02502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The photoinitiated proton-coupled electron transfer (PCET) process in photoacid-based adducts is predominantly governed by the evolution of the electron-proton transfer state. However, such a process is underexplored in the case of photobases as the excited states evolve through multiple competitive channels. Here, we elucidate the excited-state dynamics of a photobase, 4-[4'-(dimethylamino)styryl]pyridine (DMASP), in the presence of hexafluoroisopropanol (HFIP) that enables PCET. Transient absorption measurements show the evolution of a protonated species in the excited state with a time constant of ∼2.5 ps. Fluorescence upconversion measurements reveal the signatures of an emissive intramolecular charge transfer state and a protonated state. The role of such states is further confirmed by time-resolved measurements in the presence of trifluoroacetic acid and computational analysis. Furthermore, the proton-abstraction dynamics of DMASP is analyzed in bulk methanol and butanol solvents. The extent of proton abstraction by DMASP is found to be higher in the presence of HFIP when compared with the normal alcohols over a time period of a few picoseconds.
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Affiliation(s)
- Reshma Mathew
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram 695551, India
| | - Preetika Verma
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram 695551, India
| | - Arvind Barak
- Department of Inorganic and Physical Chemistry, Indian Institute of Science Bangalore, Bangalore 560012, India
| | - Yapamanu Adithya Lakshmanna
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram 695551, India
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6
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Häcker S, Schrödter M, Kuhlmann A, Wagenknecht HA. Probing of DNA Photochemistry with C-Nucleosides of Xanthones and Triphenylene as Photosensitizers To Study the Formation of Cyclobutane Pyrimidine Dimers. JACS AU 2023; 3:1843-1850. [PMID: 37502149 PMCID: PMC10369418 DOI: 10.1021/jacsau.3c00167] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 07/29/2023]
Abstract
The direct and sequence-dependent investigation of photochemical processes in DNA on the way to cyclobutane pyrimidine dimers (CPDs) as DNA damage requires the probing by photochemically different photosensitizers. The C-nucleosides of xanthone, thioxanthone, 3-methoxyxanthone, and triphenylene as photosensitizers were synthesized by Heck couplings and incorporated into ternary photoactive DNA architectures. This structural approach allows the site-selective excitation of the DNA by UV light. Together with a single defined site for T-T dimerization, not only the direct CPD formation but also the distance-dependent CPD formation in DNA as well as the possibility for energy transport processes could be investigated. Direct CPD formation was observed with xanthone, 3-methoxyxanthone, and triphenylene as sensitizers but not with thioxanthone. Only xanthone was able to induce CPDs remotely by a triplet energy transfer over up to six intervening A-T base pairs. Taken together, more precise information on the sequence dependence of the DNA triplet photochemistry was obtained.
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7
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Szemik-Hojniak A, Deperasińska I, Erez Y, Gawłowska M, Jerzykiewicz L. Ultrafast excited state dynamics of pyridine N-oxide derivative in solution; femtosecond fluorescence up-conversion and theoretical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121896. [PMID: 36183536 DOI: 10.1016/j.saa.2022.121896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/29/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
In this study we have investigated 2-ethylamino-4-nitro-6-methyl pyridine N-oxide (2E6M) molecule that belongs to important group of Proton Coupled Electron Transfer (PCET) compounds where both the charge transfer (CT) and proton transfer processes in excited states may proceed. In this case, this is possible due to the donors and acceptors of electrons and protons in this system, as well as due to the presence of intramolecular {N-H… O [2,566(3) Å}, hydrogen bond.Using stationary and time-resolved spectroscopy, as well as quantum chemical calculations on the DFT and TD DFT B3LYP/6-31G (d,p) level of theory, a partial CT nature of the S0 → S1 transition in both tautomeric forms (N and T) has been revealed. Additionally, the excited state intramolecular proton transfer (ESIPT) process shown to be more favorable in apolar and weakly polar solvents than in strongly polar acetonitrile (EN(S1) > ET(S1). The displacement of charge from the amine group and the ring to the nitro group has been observed on the changing shapes of the HOMO and LUMO orbitals involved in this transition what further quantitatively allowed to realize the increase in the dipole moment of both forms in the electronic excited state. The calculations show that in two solvents with radically different polarity (heptane, acetonitrile), dipole moments of both forms are very similar [in acetonitrile uN(S1) and uT(S1) are 11.0 D and 11.5 D, respectively]. Hence, in polar media both forms can be stabilized in a comparable manner. This made it difficult for us to assign a single fluorescent band in acetonitrile to one of the tautomeric forms. However, it seems that due to application of time-resolved spectroscopy, this problem has been clarified. The TCSPC decay curve in acetonitrile with an ultrafast lifetime assigned to the (N) form, along with the femtosecond up-conversion signals that demonstrated only an ultrafast decay without any rise-time of a new excited (T) species, allowed us to conclude that in 2E6M in strongly polar solvent the ESIPT does not occur.The unique fluorescence band origins from the (N) form. In protic solvents, the significant kinetic isotopic effects have provided us with conclusive evidence for the presence of the solvent-assisted ESIPT process. Furthermore, it was noticed that the fluorescence lifetime in D2O (100-120 fs) estimated from the up-conversion signals is about 40 times shorter relative to methanol. This may suggest that the sine qua non for the ESIPT process in 2E6M in protic solvents is the formation of a complex with a solvent molecule in the hydrogen bridge between the proton donor and proton acceptor, respectively.
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Affiliation(s)
- Anna Szemik-Hojniak
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14 st, 50-383 Wrocław, Poland; The Angelus Silesius State University of Applied Sciences, Institute of Health, Zamkowa 4 str 58-300 Wałbrzych, Poland.
| | - Irena Deperasińska
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46,02-668 Warsaw, Poland
| | - Yuval Erez
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 69978, Israel
| | - Monika Gawłowska
- The Angelus Silesius State University of Applied Sciences, Institute of Health, Zamkowa 4 str 58-300 Wałbrzych, Poland
| | - L Jerzykiewicz
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14 st, 50-383 Wrocław, Poland
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8
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Asha H, Green JA, Esposito L, Martinez-Fernandez L, Santoro F, Improta R. Effect of the Thermal Fluctuations of the Photophysics of GC and CG DNA Steps: A Computational Dynamical Study. J Phys Chem B 2022; 126:10608-10621. [PMID: 36508709 DOI: 10.1021/acs.jpcb.2c05688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we refine and assess two computational procedures aimed to include the effect of thermal fluctuations on the electronic spectra and the ultrafast excited state dynamics of multichromophore systems, focusing on DNA duplexes. Our approach is based on a fragment diabatization procedure that, from a given Quantum Mechanical (QM) reference method, can provide the parameters (energy and coupling) of the reference diabatic states on the basis of the isolated fragments, either for a purely electronic excitonic Hamiltonian (FrDEx) or a linear vibronic coupling Hamiltonian (FrD-LVC). After having defined the most cost-effective procedure for DNA duplexes on two smaller fragments, FrDEx is used to simulate the absorption and Electronic Circular Dichroism (ECD) spectra of (GC)5 sequences, including the coupling with the Charge Transfer (CT) states, on a number of structures extracted from classical Molecular Dynamics (MD) simulations. The computed spectra are close to the reference TD-DFT calculations and fully consistent with the experimental ones. We then couple MD simulations and FrD-LVC to simulate the interplay between local excitations and CT transitions, both intrastrand and interstrand, in GC and CG steps when included in a oligoGC or in oligoAT DNA sequence. We predict that for both sequences a substantial part of the photoexcited population on G and C decays, within 50-100 fs, to the corresponding intrastrand CT states. This transfer is more effective for GC steps that, on average, are more closely stacked than CG ones.
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Affiliation(s)
- Haritha Asha
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438Frankfurt am Main, Germany
| | - Luciana Esposito
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autònoma de Madrid, Campus de Excelencia UAM-CSIC, 28049Madrid, Spain
| | - 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-56124Pisa, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800Kongens Lyngby, Denmark
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9
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Blockade of persistent colored isomer formation in photochromic 3H-naphthopyrans by excited-state intramolecular proton transfer. Sci Rep 2022; 12:19159. [DOI: 10.1038/s41598-022-23759-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractIn photochemistry the excited-state intramolecular proton transfer process (ESIPT) is often observed as a highly efficient singlet excited state depletion pathway, which in the presence of a strong intramolecular hydrogen bond may proceed on a subpicosecond time scale. The present work describes the suppression of unwanted transoid-trans isomer formation in photochromic 3H-naphthopyran derivatives by the introduction of a 5-hydroxy substituent. According to time-resolved spectroscopy experiments and excited-state ab initio calculations, transoid-cis → transoid-trans photoisomerization is reduced by a competitive ESIPT channel in nonpolar solvent (cyclohexane). Upon specific solute–solvent interactions (methanol, acetonitrile) the intramolecular hydrogen bond in the transoid-cis form is perturbed, favoring the internal conversion S1 → S0 process as photostabilizing channel.
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10
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Green JA, Gómez S, Worth G, Santoro F, Improta R. Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine-Cytosine in Chloroform. Chemistry 2022; 28:e202201731. [PMID: 35950519 PMCID: PMC9828530 DOI: 10.1002/chem.202201731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Indexed: 01/12/2023]
Abstract
We study the ultrafast photoactivated dynamics of the hydrogen bonded dimer Guanine-Cytosine in chloroform solution, focusing on the population of the Guanine→Cytosine charge transfer state (GC-CT), an important elementary process for the photophysics and photochemistry of nucleic acids. We integrate a quantum dynamics propagation scheme, based on a linear vibronic model parameterized through time dependent density functional theory calculations, with four different solvation models, either implicit or explicit. On average, after 50 fs, 30∼40 % of the bright excited state population has been transferred to GC-CT. This process is thus fast and effective, especially when transferring from the Guanine bright excited states, in line with the available experimental studies. Independent of the adopted solvation model, the population of GC-CT is however disfavoured in solution with respect to the gas phase. We show that dynamical solvation effects are responsible for this puzzling result and assess the different chemical-physical effects modulating the population of CT states on the ultrafast time-scale. We also propose some simple analyses to predict how solvent can affect the population transfer between bright and CT states, showing that the effect of the solute/solvent electrostatic interactions on the energy of the CT state can provide a rather reliable indication of its possible population.
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Affiliation(s)
- James A. Green
- Istituto di Biostrutture e Bioimmagini-CNRVia De Amicis 95I-80145Napoli
| | - Sandra Gómez
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUnited Kingdom
- Departamento de Química FísicaUniversity of SalamancaSalamanca37008Spain
| | - Graham Worth
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUnited Kingdom
| | - Fabrizio Santoro
- Istituto di Chimica die Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNRVia Moruzzi 1I-56124Pisa
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNRVia De Amicis 95I-80145Napoli
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11
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Takakado A, Iwata K. Sequence-dependent thymine dimerization and lifetimes of the photoexcited state of oligonucleotides. Chem Commun (Camb) 2022; 58:10198-10201. [PMID: 36000476 DOI: 10.1039/d2cc03902h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-sequence-dependent thymine-thymine (TT) dimerization was investigated from the perspective of the UV-induced charge transfer state. Steady-state and transient absorption measurements suggest that the relatively small oxidation potential and long-lived charge transfer state at the neighboring nucleobases of the TT site may reduce DNA lesion accumulation.
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Affiliation(s)
- Akira Takakado
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
| | - Koichi Iwata
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
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12
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Martínez Fernández L, Santoro F, Improta R. Nucleic Acids as a Playground for the Computational Study of the Photophysics and Photochemistry of Multichromophore Assemblies. Acc Chem Res 2022; 55:2077-2087. [PMID: 35833758 DOI: 10.1021/acs.accounts.2c00256] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
ConspectusThe interaction between light and multichromophoric assemblies (MCAs) is the primary event of many fundamental processes, from photosynthesis to organic photovoltaics, and it triggers dynamical processes that share remarkable similarities at the molecular scale: light absorption, energy and charge transfer, internal conversions, emission, and so on. Those events often involve many chromophores and different excited electronic states that are coupled on an ultrafast time scale. This Account aims to discuss some of the chemical physical effects ruling these processes, a fundamental step toward their control, based on our experience on nucleic acids.In the last 15 years, we have, indeed, studied the photophysics and photochemistry of DNA and its components. By combining different quantum mechanical methods, we investigated the molecular processes responsible for the damage of the genetic code or, on the contrary, those preventing it by dissipating the excess energy deposited in the system by UV absorption. Independently of its fundamental biological role, DNA, with its fluctuating closely stacked bases stabilized by weak nonbonding interactions, can be considered a prototypical MCA. Therefore, it allows one to tackle within a single system many of the conceptual and methodological challenges involved in the study of photoinduced processes in MCA.In this Account, by using the outcome of our studies on oligonucleotides as a guideline, we thus highlight the most critical modellistic issues to be faced when studying, either experimentally or computationally, the interaction between UV light and DNA and, at the same time, bring out their general relevance for the study of MCAs.We first discuss the rich photoactivated dynamics of nucleobases (the chromophores), highlighting the main effects modulating the interplay between their excited states and how the latter can affect the photoactivated dynamics of the polynucleotides, either providing effective monomer-like nonradiative decay routes or triggering reactive processes (e.g., triplet generation).We then tackle the reaction paths involving multiple bases, showing that in the DNA duplex the most important ones involve two stacked bases, forming a neutral excimer or a charge transfer (CT) state, which exhibit different spectral signatures and photochemical reactivity. In particular, we analyze the factors affecting the dynamic equilibrium between the excimer and CT, such as the fluctuations of the backbone or the rearrangement of the solvent.Next, we highlight the importance of the effects not directly connected to the chromophores, such as the flexibility of the backbone or the solvent effect. The former, affecting the stacking geometry of the bases, can determine the preference between different deactivation paths. The latter is particularly influential for CT states, making very important an accurate treatment of dynamical solvation effects, involving both the solvent bulk and specific solute-solvent interactions.In the last section, we describe the main methodological challenges related to the study of polynucleotide excited states and stress the benefits derived by the integration of complementary approaches, both computational and experimental. Only exploiting different point of views, in our opinion, it is possible to shed light on the complex phenomena triggered by light absorption in DNA, as in every MCA.
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Affiliation(s)
- Lara Martínez Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
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13
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Vayá I, Gustavsson T, Markovitsi D. High-Energy Long-Lived Emitting Mixed Excitons in Homopolymeric Adenine-Thymine DNA Duplexes. Molecules 2022; 27:molecules27113558. [PMID: 35684495 PMCID: PMC9181881 DOI: 10.3390/molecules27113558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
The publication deals with polymeric pA●pT and oligomeric A20●T20 DNA duplexes whose fluorescence is studied by time-correlated single photon counting. It is shown that their emission on the nanosecond timescale is largely dominated by high-energy components peaking at a wavelength shorter than 305 nm. Because of their anisotropy (0.02) and their sensitivity to base stacking, modulated by the duplex size and the ionic strength of the solution, these components are attributed to mixed ππ*/charge transfer excitons. As high-energy long-lived excited states may be responsible for photochemical reactions, their identification via theoretical studies is an important challenge.
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Affiliation(s)
- Ignacio Vayá
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, 46022 Valencia, Spain;
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
| | - Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France;
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
- Correspondence:
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14
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Bauer B, Sharma R, Chergui M, Oppermann M. Exciton decay mechanism in DNA single strands: back-electron transfer and ultrafast base motions. Chem Sci 2022; 13:5230-5242. [PMID: 35655577 PMCID: PMC9093102 DOI: 10.1039/d1sc06450a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/09/2022] [Indexed: 12/03/2022] Open
Abstract
The photochemistry of DNA systems is characterized by the ultraviolet (UV) absorption of π-stacked nucleobases, resulting in exciton states delocalized over several bases. As their relaxation sensitively depends on local stacking conformations, disentangling the ensuing electronic and structural dynamics has remained an experimental challenge, despite their fundamental role in protecting the genome from potentially harmful UV radiation. Here we use transient absorption and transient absorption anisotropy spectroscopy with broadband femtosecond deep-UV pulses (250–360 nm) to resolve the exciton dynamics of UV-excited adenosine single strands under physiological conditions. Due to the exceptional deep-UV bandwidth and polarization sensitivity of our experimental approach, we simultaneously resolve the population dynamics, charge-transfer (CT) character and conformational changes encoded in the UV transition dipoles of the π-stacked nucleotides. Whilst UV excitation forms fully charge-separated CT excitons in less than 0.3 ps, we find that most decay back to the ground state via a back-electron transfer. Based on the anisotropy measurements, we propose that this mechanism is accompanied by a structural relaxation of the photoexcited base-stack, involving an inter-base rotation of the nucleotides. Our results finally complete the exciton relaxation mechanism for adenosine single strands and offer a direct view into the coupling of electronic and structural dynamics in aggregated photochemical systems. Despite its key role in DNA photochemistry, the decay mechanism of excitons in stacked bases has remained difficult to resolve. Ultrafast polarization spectroscopy now reveals a back-electron transfer and ultrafast base motions in adenosine strands.![]()
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Affiliation(s)
- Benjamin Bauer
- Laboratory of Ultrafast Spectroscopy (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB CH-1015 Lausanne Switzerland
| | - Rahul Sharma
- Laboratory for Computation and Visualization in Mathematics and Mechanics, École Polytechnique Fédérale de Lausanne, MATH-FSB CH-1015 Lausanne Switzerland
| | - Majed Chergui
- Laboratory of Ultrafast Spectroscopy (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB CH-1015 Lausanne Switzerland
| | - Malte Oppermann
- Laboratory of Ultrafast Spectroscopy (LSU), Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB CH-1015 Lausanne Switzerland
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15
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Huang SR, Tureček F. Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization. J Phys Chem A 2022; 126:2480-2497. [PMID: 35439003 DOI: 10.1021/acs.jpca.2c00894] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation radicals of DNA nucleosides, 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms. The noncanonical isomers were calculated to have very low adiabatic ion-electron recombination energies (REad) for the lowest-energy isomers 2'-deoxy-(N-3H)adenos-1'-yl (4.74 eV), 2'-deoxy-(N-7H)guanos-1'-yl (4.66 eV), 2'-deoxy-(N-3H)cytid-1'-yl (5.12 eV), and 2'-deoxy-5-methylene-(O-2H)uridine (5.24 eV). These were substantially lower than the REad value calculated for the canonical 2'-deoxyadenosine, 2'-deoxy guanosine, 2'-deoxy cytidine, and 2'-deoxy thymidine cation radicals, which were 7.82, 7.46, 8.14, and 8.20 eV, respectively, for the lowest-energy ion conformers of each type. Charge and spin distributions in noncovalent cation-radical dA⊂dT and dG⊂dC nucleoside pairs and dAT, dCT, dTC, and dGC dinucleotides were analyzed to elucidate the electronic structure of the cation radicals. Born-Oppenheimer molecular dynamics trajectory calculations of the dinucleotides and nucleoside pairs indicated rapid exothermic proton transfer from noncanonical T+· to A in both dAT+· and dA⊂dT+·, leading to charge and radical separation. Noncanonical T+· in dCT+· and dTC+· initiated rapid proton transfer to cytosine, whereas the canonical dCT+· dinucleotide ion retained the cation radical structure without isomerization. No spontaneous proton transfer was found in dGC+· and dG⊂dC+· containing canonical neutral and noncanonical ionized deoxycytidine.
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Affiliation(s)
- Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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16
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Ciaco S, Gavvala K, Greiner V, Mazzoleni V, Didier P, Ruff M, Martinez-Fernandez L, Improta R, Mely Y. Thienoguanosine brightness in DNA duplexes is governed by the localization of its ππ* excitation in the lowest energy absorption band. Methods Appl Fluoresc 2022; 10. [PMID: 35472854 DOI: 10.1088/2050-6120/ac6ab6] [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: 03/08/2022] [Accepted: 04/26/2022] [Indexed: 11/11/2022]
Abstract
Thienoguanosine (thG) is an isomorphic fluorescent guanosine (G) surrogate, which almost perfectly mimics the natural G in DNA duplexes and may therefore be used to sensitively investigate for example protein-induced local conformational changes. To fully exploit the information given by the probe, we carefully re-investigated the thG spectroscopic properties in 12-bp duplexes, when the Set and Ring Associated (SRA) domain of UHRF1 flips its 5' flanking methylcytosine (mC). The SRA-induced flipping of mC was found to strongly increase the fluorescence intensity of thG, but this increase was much larger when thG was flanked in 3' by a C residue as compared to an A residue. Surprisingly, the quantum yield and fluorescence lifetime values of thG were nearly constant, regardless of the presence of SRA and the nature of the 3' flanking residue, suggesting that the differences in fluorescence intensities might be related to changes in absorption properties. We evidenced that thG lowest energy absorption band in the duplexes can be deconvoluted into two bands peaking at ~350 nm and ~310 nm, respectively red-shifted and blue-shifted, compared to the spectrum of thG monomer. Using quantum mechanical calculations, we attributed the former to a nearly pure * excitation localized on thG and the latter to excited states with charge transfer character. The amplitude of thG red-shifted band strongly increased when its 3' flanking C residue was replaced by an A residue in the free duplex, or when its 5' flanking mC residue was flipped by SRA. As only the species associated with the red-shifted band were found to be emissive, the highly unusual finding of this work is that the brightness of thG in free duplexes as well as its changes on SRA-induced mC flipping almost entirely depend on the relative population and/or absorption coefficient of the red-shifted absorbing species.
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Affiliation(s)
- Stefano Ciaco
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Krishna Gavvala
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Vanille Greiner
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Viola Mazzoleni
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Pascal Didier
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Marc Ruff
- IGBMC, University of Strasbourg, 1 Rue Laurent Fries, 67400 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
| | - Lara Martinez-Fernandez
- Departamento de Química, Universidad Autónoma de Madrid, Facultad de Ciencias and Institute for Advanced Research in Chemistry, Madrid, Madrid, 28049, SPAIN
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini Consiglio Nazionale delle Ricerche, Consiglio Nazionale delle Ricerche, Napoli, Campania, 80134, ITALY
| | - Yves Mely
- UMR 7021, University of Strasbourg, 74 route du Rhin, CS 60024, 67401 ILLKIRCH Cedex, Strasbourg, Grand Est, 67070, FRANCE
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17
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Cruz-Ortiz AF, Jara-Toro RA, Aranguren JP, Scuderi D, Pino GA. Inter- and Intramolecular Proton Transfer in an Isolated (Cytosine-Guanine)H + Pair: Direct Evidence from IRMPD Spectroscopy. J Phys Chem A 2022; 126:1403-1411. [PMID: 35175052 DOI: 10.1021/acs.jpca.1c10651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The collision-induced dissociation of the protonated cytosine-guanine pair was studied using tandem mass spectrometry (MS3) coupled to infrared multiple photon dissociation spectroscopy with the free electron laser at Orsay (CLIO) to determine the structure of the CH+ and GH+ ionic fragments. The results were rationalized with the help of electronic structure calculations at the density functional theory level with the B3LYP/6-311++G(3df,2p) method. Several tautomers of each fragment were identified for the first time, some of which were previously predicted by other authors. In addition, two unexpected and minor tautomers were also found: cytosine keto-imino [CKI(1,2,3,4)H+] and guanine keto-amino [GKA(1,3,7)H+]. These results highlight the importance of the DNA base tautomerization assisted by inter- and intramolecular proton or hydrogen transfer within the protonated pairs.
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Affiliation(s)
- Andrés F Cruz-Ortiz
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET─UNC, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Rafael A Jara-Toro
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET─UNC, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Juan P Aranguren
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET─UNC, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Debora Scuderi
- Institut de Chimie Physique, CNRS-Université Paris Saclay, UMR8000, F-91405 Orsay, France
| | - Gustavo A Pino
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET─UNC, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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18
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Acid–base
reaction of a
super‐photoacid
with a cooperative amide
hydrogen‐bonded
chain. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Wagenknecht H. Remote Photodamaging of DNA by Photoinduced Energy Transport. Chembiochem 2022; 23:e202100265. [PMID: 34569126 PMCID: PMC9292490 DOI: 10.1002/cbic.202100265] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/14/2021] [Indexed: 12/11/2022]
Abstract
Local DNA photodamaging by light is well-studied and leads to a number of structurally identified direct damage, in particular cyclobutane pyrimidine dimers, and indirect oxidatively generated damage, such as 8-oxo-7,8-hydroxyguanine. Similar damages have now been found at remote sites, at least more than 105 Å (30 base pairs) away from the site of photoexcitation. In contrast to the established mechanisms of local DNA photodamaging, the processes of remote photodamage are only partially understood. Known pathways include those to remote oxidatively generated DNA photodamages, which were elucidated by studying electron hole transport through the DNA about 20 years ago. Recent studies with DNA photosensitizers and mechanistic proposals on photoinduced DNA-mediated energy transport are summarized in this minireview. These new mechanisms to a new type of remote DNA photodamaging provide an important extension to our general understanding to light-induced DNA damage and their mutations.
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Affiliation(s)
- Hans‐Achim Wagenknecht
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
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20
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Chan RCT, Ma C, Wong AKW, Chan CTL, Chow JCL, Kwok WM. Dual Time-Scale Proton Transfer and High-Energy, Long-Lived Excitons Unveiled by Broadband Ultrafast Time-Resolved Fluorescence in Adenine-Uracil RNA Duplexes. J Phys Chem Lett 2022; 13:302-311. [PMID: 34978832 DOI: 10.1021/acs.jpclett.1c03553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In contrast to the immense amount of research on electronically excited DNA, surprisingly little has been done about the excited states of RNA. Herein, we demonstrate an ultrafast broadband time-resolved fluorescence and fluorescence anisotropy study to probe directly the intrinsic fluorescence and overall dynamics of the fluorescence from a homopolymeric adenine·uracil RNA duplex adopting the A-form structure. The results unveiled complex deactivation through distinctive multichannels mediated by states of varied energy, a character of charge transfer, and a lifetime from sub-picosecond to nanoseconds. In particular, we observed an unprecedented kinetic isotopic effect and participation of unusual proton transfer from states in two discrete energies and time domains. We also identified a high-energy nanosecond emission that we attributed to its fluorescence anisotropy to long-lived weakly emissive excitons not reported in DNA. These distinguishing features originate from the stacking, pairing, and local hydration environment specific to the A-form conformation of the adenine·uracil double helix.
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Affiliation(s)
- Ruth Chau-Ting Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, 518071, Shenzhen, Guangdong, P. R. China
| | - Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, 518071, Shenzhen, Guangdong, P. R. China
| | - Allen Ka-Wa Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Chris Tsz-Leung Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Joshua Chiu-Lok Chow
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 999077, P. R. China
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21
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Burdick RK, Schatz GC, Goodson T. Enhancing Entangled Two-Photon Absorption for Picosecond Quantum Spectroscopy. J Am Chem Soc 2021; 143:16930-16934. [PMID: 34613733 DOI: 10.1021/jacs.1c09728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Entangled two-photon absorption (ETPA) is known to create photoinduced transitions with extremely low light intensity, reducing the risk of phototoxicity compared to classical two-photon absorption. Previous works have predicted the ETPA cross-section, σe, to vary inversely with the product of entanglement time (Te) and entanglement area (Ae), i.e., σe ∼ 1/AeTe. The decreasing σe with increasing Te has limited ETPA to fs-scale Te, while ETPA applications for ps-scale spectroscopy have been unexplored. However, we show that spectral-spatial coupling, which reduces Ae as the SPDC bandwidth (σf) decreases, plays a significant role in determining σe when Te > ∼100 fs. We experimentally measured σe for zinc tetraphenylporphyrin at several σf values. For type-I ETPA, σe increases as σf decreases down to 0.1 ps-1. For type-II SPDC, σe is constant for a wide range of σf. With a theoretical analysis of the data, the maximum type-I σe would occur at σf = 0.1 ps-1 (Te = 10 ps). At this maximum, σe is 1 order of magnitude larger than fs-scale σe and 3 orders of magnitude larger than previous predictions of ps-scale σe. By utilizing this spectral-spatial coupling, narrowband type-I ETPA provides a new opportunity to increase the efficiency of measuring nonlinear optical signals and to control photochemical reactions requiring ps temporal precision.
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Affiliation(s)
- Ryan K Burdick
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - George C Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Theodore Goodson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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22
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Mashmoushi N, Juhász DR, Coughlan NJA, Schneider BB, Le Blanc JCY, Guna M, Ziegler BE, Campbell JL, Hopkins WS. UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban. J Phys Chem A 2021; 125:8187-8195. [PMID: 34432451 DOI: 10.1021/acs.jpca.1c05564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two ion populations of protonated Rivaroxaban, [C19H18ClN3O5S + H]+, are separated under pure N2 conditions using differential mobility spectrometry prior to characterization in a hybrid triple quadrupole linear ion trap mass spectrometer. These populations are attributed to bare protonated Rivaroxaban and to a proton-bound Rivaroxaban-ammonia complex, which dissociates prior to mass-selecting the parent ion. Ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) studies indicate that both protonated Rivaroxaban ion populations are comprised of the computed global minimum prototropic isomer. Two ion populations are also observed when the collision environment is modified with 1.5% (v/v) acetonitrile. In this case, the protonated Rivaroxaban ion populations are produced by the dissociation of the ammonium complex and by the dissociation of a proton-bound Rivaroxaban-acetonitrile complex prior to mass selection. Again, both populations exhibit a similar CID behavior; however, UVPD spectra indicate that the two ion populations are associated with different prototropic isomers. The experimentally acquired spectra are compared with computed spectra and are assigned to two prototropic isomers that exhibit proton sharing between distal oxygen centers.
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Affiliation(s)
- Nour Mashmoushi
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Daniel R Juhász
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Neville J A Coughlan
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | | | | | - Mircea Guna
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Blake E Ziegler
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada.,Bedrock Scientific, Milton, Ontario L6T 6J9, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada.,Centre for Eye and Vision Research, New Territories 999077, Hong Kong
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23
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Yang TQ, Hu XD, Shan BQ, Peng B, Zhou JF, Zhang K. Caged structural water molecules emit tunable brighter colors by topological excitation. NANOSCALE 2021; 13:15058-15066. [PMID: 34533160 DOI: 10.1039/d1nr02389f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Intrinsically, free water molecules are a colourless liquid. If it is colourful, why and how does it emit the bright colours? We provided direct evidence that when water was trapped into the sub-nanospace of zeolites, the structural water molecules (SWs) exhibited strong tunable photoluminescence (PL) emissions from blue to red colours with unprecedented ultra-long lifetimes up to the second scale at liquid nitrogen temperature. Further controlled experiments and combined characterizations by time-resolved steady-state and ultra-fast femtosecond (fs) transient optical spectroscopy showed that the singly adsorbed hydrated hydroxide complex {OH-·H2O} as SWs in the confined nanocavity is the true emitter centre, whose PL efficiency strongly depends on the type and stability of the SWs, which is dominated by H-bond interactions, such as the solvent effect, pH value and operating temperature. The emission of SWs exhibits the characteristic of topological excitations (TAs) due to the many-body quantum electron correlations in confined nanocavities, which differs from the local excitation of organic chromophores. Our model not only elucidates the origin of the PL of metal nanoclusters (NCs), but also provides a completely new insight to understand the nature of heterogeneous catalysis and interface bonding (or state) at the molecule level, beyond the metal-centred d band theory.
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Affiliation(s)
- Tai-Qun Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
- Jiangsu Provincial Research Center of Light Industrial Optoelectronic Engineering and Technology, School of Science, Jiangnan University, Wuxi 214122, China
| | - Xiao-Dan Hu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Bing-Qian Shan
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Bo Peng
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Jia-Feng Zhou
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Kun Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
- Laboratoire de chimie, Ecole Normale Supérieure de Lyon, Institut de Chimie de Lyon, Université de Lyon, 46 Allée d'italie, 69364 Lyon cedex 07, France
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, P. R. China
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24
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Baptista FA, Krizsan D, Stitch M, Sazanovich IV, Clark IP, Towrie M, Long C, Martinez-Fernandez L, Improta R, Kane-Maguire NAP, Kelly JM, Quinn SJ. Adenine Radical Cation Formation by a Ligand-Centered Excited State of an Intercalated Chromium Polypyridyl Complex Leads to Enhanced DNA Photo-oxidation. J Am Chem Soc 2021; 143:14766-14779. [PMID: 34464120 PMCID: PMC8447253 DOI: 10.1021/jacs.1c06658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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Assessment of the
DNA photo-oxidation and synthetic photocatalytic
activity of chromium polypyridyl complexes is dominated by consideration
of their long-lived metal-centered excited states. Here we report
the participation of the excited states of [Cr(TMP)2dppz]3+ (1) (TMP = 3,4,7,8-tetramethyl-1,10-phenanthroline;
dppz = dipyrido[3,2-a:2′,3′-c]phenazine) in DNA photoreactions. The interactions of
enantiomers of 1 with natural DNA or with oligodeoxynucleotides
with varying AT content (0–100%) have been studied by steady
state UV/visible absorption and luminescence spectroscopic methods,
and the emission of 1 is found to be quenched in all
systems. The time-resolved infrared (TRIR) and visible absorption
spectra (TA) of 1 following excitation in the region
between 350 to 400 nm reveal the presence of relatively long-lived
dppz-centered states which eventually yield the emissive metal-centered
state. The dppz-localized states are fully quenched when bound by
GC base pairs and partially so in the presence of an AT base-pair
system to generate purine radical cations. The sensitized formation
of the adenine radical cation species (A•+T) is identified by assigning the TRIR spectra with help of
DFT calculations. In natural DNA and oligodeoxynucleotides containing
a mixture of AT and GC of base pairs, the observed time-resolved spectra
are consistent with eventual photo-oxidation occurring predominantly
at guanine through hole migration between base pairs. The combined
targeting of purines leads to enhanced photo-oxidation of guanine.
These results show that DNA photo-oxidation by the intercalated 1, which locates the dppz in contact with the target purines,
is dominated by the LC centered excited state. This work has implications
for future phototherapeutics and photocatalysis.
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Affiliation(s)
| | - Dorottya Krizsan
- School of Chemistry, University College Dublin, Dublin 4, Ireland
| | - Mark Stitch
- School of Chemistry, University College Dublin, Dublin 4, Ireland
| | - Igor V Sazanovich
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, U.K
| | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, U.K
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11 0QX, U.K
| | - Conor Long
- The School of Chemical Sciences, Dublin City University, Dublin 9, Ireland
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry(IADCHEM) Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini, 80136 Naples, Italy
| | - Noel A P Kane-Maguire
- Department of Chemistry, Furman University, 3300 Poinsett Highway, Greenville, South Carolina 29613-1120, United States
| | - John M Kelly
- School of Chemistry, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Susan J Quinn
- School of Chemistry, University College Dublin, Dublin 4, Ireland
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25
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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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26
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Wang X, Martínez-Fernández L, Zhang Y, Zhang K, Improta R, Kohler B, Xu J, Chen J. Solvent-Dependent Stabilization of a Charge Transfer State is the Key to Ultrafast Triplet State Formation in an Epigenetic DNA Nucleoside. Chemistry 2021; 27:10932-10940. [PMID: 33860588 DOI: 10.1002/chem.202100787] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 11/10/2022]
Abstract
2'-Deoxy-5-formylcytidine (5fdCyd), a naturally occurring nucleoside found in mammalian DNA and mitochondrial RNA, exhibits important epigenetic functionality in biological processes. Because it efficiently generates triplet excited states, it is an endogenous photosensitizer capable of damaging DNA, but the intersystem crossing (ISC) mechanism responsible for ultrafast triplet state generation is poorly understood. In this study, time-resolved mid-IR spectroscopy and quantum mechanical calculations reveal the distinct ultrafast ISC mechanisms of 5fdCyd in water versus acetonitrile. Our experiment indicates that in water, ISC to triplet states occurs within 1 ps after 285 nm excitation. PCM-TD-DFT computations suggest that this ultrafast ISC is mediated by a singlet state with significant cytosine-to-formyl charge-transfer (CT) character. In contrast, ISC in acetonitrile proceeds via a dark 1 nπ* state with a lifetime of ∼3 ps. CT-induced ISC is not favored in acetonitrile because reaching the minimum of the gateway CT state is hampered by intramolecular hydrogen bonding, which enforces planarity between the aldehyde group and the aromatic group. Our study provides a comprehensive picture of the non-radiative decay of 5fdCyd in solution and new insights into the factors governing ISC in biomolecules. We propose that the intramolecular CT state observed here is a key to the excited-state dynamics of epigenetic nucleosides with modified exocyclic functional groups, paving the way to study their effects in DNA strands.
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Affiliation(s)
- Xueli Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, P. R. China
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid Campus de Excelencia UAM-CSIC Cantoblanco, 28049, Madrid, Spain
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, USA
| | - Kun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, P. R. China
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio, 43210, USA
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, P. R. China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, P. R. China
| | - Jinquan Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai, 200241, P. R. China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi, 030006, P. R. China
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27
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Shan BQ, Zhou JF, Ding M, Hu XD, Zhang K. Surface electronic states mediate concerted electron and proton transfer at metal nanoscale interfaces for catalytic hydride reduction of -NO 2 to -NH 2. Phys Chem Chem Phys 2021; 23:12950-12957. [PMID: 34086019 DOI: 10.1039/d1cp01792f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Concerted electron and proton transfer is a key step for the reversible conversion of molecular hydrogen in both heterogeneous nanocatalysis and metalloenzyme catalysis. However, its activation mechanism involving electron and proton transfer kinetics remains elusive. With the most widely used catalytic hydride reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) as a model reaction, we evaluate the catalytic activity of noble metal nanoparticles (NPs) trapped in porous silica in aqueous NaBH4 solution. By virtue of a novel combination of catalyst design, reaction kinetics, isotope labeling, and multiple spectroscopic techniques, the real catalytic site for the conversion of -NO2 to -NH2 is identified to be the water-hydroxyl transition metal complex, which could further react with NaBH4 to form a new triangular configuration metal complex of H3B-water-hydroxyl with dynamic features. It yields an ensemble of surface electronic states (SESs) though space overlapping of p orbitals of one B and several O atoms (including the O atoms of 4-NP), which could act as an alternative channel for concerted electron and proton transfer. This work highlights the critical role of the conceptual SESs model in heterogeneous catalysis to tune the chemical reactivity and also sheds light on the intricate working of the [FeFe]-hydrogenases.
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Affiliation(s)
- Bing-Qian Shan
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China.
| | - Jia-Feng Zhou
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China.
| | - Meng Ding
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China.
| | - Xiao-Dan Hu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China.
| | - Kun Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Laboratory of Interface and Water Science, College of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China. and Laboratoire de chimie, Ecole Normale Supérieure de Lyon, Institut de Chimie de Lyon, Université de Lyon, 46 Allée d'italie, Lyon cedex 07 69364, France and Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, P. R. China
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28
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Kohl FR, Zhang Y, Charnay AP, Martínez-Fernández L, Kohler B. Ultrafast excited state dynamics of silver ion-mediated cytosine-cytosine base pairs in metallo-DNA. J Chem Phys 2021; 153:105104. [PMID: 32933288 DOI: 10.1063/5.0020463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To better understand the nexus between structure and photophysics in metallo-DNA assemblies, the parallel-stranded duplex formed by the all-cytosine oligonucleotide, dC20, and silver nitrate was studied by circular dichroism (CD), femtosecond transient absorption spectroscopy, and time-dependent-density functional theory calculations. Silver(I) ions mediate Cytosine-Cytosine (CC) base pairs by coordinating to the N3 atoms of two cytosines. Although these silver(I) mediated CC base pairs resemble the proton-mediated CC base pairs found in i-motif DNA at first glance, a comparison of experimental and calculated CD spectra reveals that silver ion-mediated i-motif structures do not form. Instead, the parallel-stranded duplex formed between dC20 and silver ions is proposed to contain consecutive silver-mediated base pairs with high propeller twist-like ones seen in a recent crystal structure of an emissive, DNA-templated silver cluster. Femtosecond transient absorption measurements with broadband probing from the near UV to the near IR reveal an unusually long-lived (>10 ns) excited state in the dC20 silver ion complex that is not seen in dC20 in single-stranded or i-motif forms. This state is also absent in a concentrated solution of cytosine-silver ion complexes that are thought to assemble into planar ribbons or sheets that lack stacked silver(I) mediated CC base pairs. The large propeller twist angle present in metal-mediated base pairs may promote the formation of long-lived charged separated or triplet states in this metallo-DNA.
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Affiliation(s)
- Forrest R Kohl
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Aaron P Charnay
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
| | - Lara Martínez-Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Bern Kohler
- Department of Chemistry and Biochemistry, 100 W. 18th Ave., Columbus, Ohio 43210, USA
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29
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Beiranvand N, Freindorf M, Kraka E. Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study. Molecules 2021; 26:2268. [PMID: 33919989 PMCID: PMC8071019 DOI: 10.3390/molecules26082268] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.
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Affiliation(s)
| | | | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA; (N.B.); (M.F.)
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30
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Chan RCT, Chan CTL, Ma C, Gu KY, Xie HX, Wong AKW, Xiong QW, Wang ML, Kwok WM. Long living excited state of protonated adenosine unveiled by ultrafast fluorescence spectroscopy and density functional theoretical study. Phys Chem Chem Phys 2021; 23:6472-6480. [PMID: 33729247 DOI: 10.1039/d0cp06439d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenosine (Ado) possesses ultrafast nonradiative dynamics accounting for its remarkably high photostability. The deactivation dynamics of Ado after protonation in an aqueous solution remains an elusive issue. Herein we report an investigation of the excited state dynamics of protonated Ado (AdoH+) performed using ultrafast time-resolved fluorescence spectroscopy combined with density functional theoretical calculation. The result obtained from comparison of conformers with protonation at different sites revealed that the syn-conformer with protonation occurring at the N3 position (syn-N3) is the predominant form of AdoH+ in the ground state, similar to that of Ado. In contrast, the fluorescence of AdoH+ with maximum intensity at 385 nm, significantly red-shifted from that of Ado, displaying decay dynamics composed of an ultrafast component with the lifetime of ∼0.5 ps and a slower one of ∼2.9 ns. The former is because of the decay of the syn-N3 conformer, similar to that reported for AdoH+ under the gas phase condition. The latter is due to the syn-N1 conformer formed via ultrafast proton transfer of the syn-N3. The excited state of syn-N1 has a peculiar nonplanar conformation over the purine molecule, which is responsible for the substantial Stokes shift showed in the fluorescence spectrum and correlates with a large energy barrier for nonradiative decay likely involving a reversed proton transfer. This study demonstrates the importance of protonation and solvent environment in altering dramatically the excited states of Ado, providing insight for better understanding nonradiative dynamics of both the monomeric bases and the oligomeric or polymeric DNAs.
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Affiliation(s)
- Ruth Chau-Ting Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China.
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31
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Photoinduced double proton transfer in the glyoxal-methanol complex along T1 reaction path – a quantum chemical topological study. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Kuhlmann A, Bihr L, Wagenknecht H. How Far Does Energy Migrate in DNA and Cause Damage? Evidence for Long-Range Photodamage to DNA. Angew Chem Int Ed Engl 2020; 59:17378-17382. [PMID: 32869949 PMCID: PMC7540310 DOI: 10.1002/anie.202009216] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Indexed: 12/23/2022]
Abstract
A new DNA architecture addresses the question, how far energy migrates in DNA and forms cyclobutane pyrimidine dimers (CPDs) as photodamages causing skin cancer. The 3-methoxyxanthone nucleoside allows site-selective photoenergy injection into DNA. The designated CPD site lacks the phosphodiester bond and can be placed in defined distances. The CPD formation links two oligonucleotides together and allows probing by gel electrophoresis. We obtained a sigmoidal distance dependence with R0 of 25±3 Å. Below R0 , short-range energy migration occurs with high CPD yields and shallow distance dependence, characteristic for a coherent process. 5-methyl-C as epigenetic modification on the 3'-side facilitates CPD formation. Above R0 , long-range incoherent energy migration occurs over 30 A-T pairs (105.4 Å). The evidence of long-range CPD formation is fundamental for our understanding of DNA photodamaging. Open access funding enabled and organized by Projekt DEAL.
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Affiliation(s)
- Arthur Kuhlmann
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Larissa Bihr
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Hans‐Achim Wagenknecht
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
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33
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Kuhlmann A, Bihr L, Wagenknecht H. Wie weit wandert Energie in der DNA und verursacht Schäden? Nachweis des langreichweitigen Photoschadens in DNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Arthur Kuhlmann
- Institut für Organische Chemie Karlsruher Institut für Technologie (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Larissa Bihr
- Institut für Organische Chemie Karlsruher Institut für Technologie (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Hans‐Achim Wagenknecht
- Institut für Organische Chemie Karlsruher Institut für Technologie (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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34
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Karas LJ, Wu CH, Ottosson H, Wu JI. Electron-driven proton transfer relieves excited-state antiaromaticity in photoexcited DNA base pairs. Chem Sci 2020; 11:10071-10077. [PMID: 34094268 PMCID: PMC8162126 DOI: 10.1039/d0sc02294b] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Watson–Crick A·T and G·C base pairs are not only electronically complementary, but also photochemically complementary. Upon UV irradiation, DNA base pairs undergo efficient excited-state deactivation through electron driven proton transfer (EDPT), also known as proton-coupled electron transfer (PCET), at a rate too fast for other reactions to take place. Why this process occurs so efficiently is typically reasoned based on the oxidation and reduction potentials of the bases in their electronic ground states. Here, we show that the occurrence of EDPT can be traced to a reversal in the aromatic/antiaromatic character of the base upon photoexcitation. The Watson–Crick A·T and G·C base pairs are aromatic in the ground state, but the purines become highly antiaromatic and reactive in the first 1ππ* state, and transferring an electron and a proton to the pyrimidine relieves this excited-state antiaromaticity. Even though proton transfer proceeds along the coordinate of breaking a N–H σ-bond, the chromophore is the π-system of the base, and EDPT is driven by the strive to alleviate antiaromaticity in the π-system of the photoexcited base. The presence and absence of alternative excited-state EDPT routes in base pairs also can be explained by sudden changes in their aromatic and antiaromatic character upon photoexcitation. The Watson–Crick A·T and G·C base pairs are not only electronically complementary, but also photochemically complementary.![]()
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Affiliation(s)
- Lucas J Karas
- Department of Chemistry, University of Houston Houston TX 77004 USA
| | - Chia-Hua Wu
- Department of Chemistry, University of Houston Houston TX 77004 USA
| | - Henrik Ottosson
- Department of Chemistry, Ångström Laboratory, Uppsala University 751 20 Uppsala Sweden
| | - Judy I Wu
- Department of Chemistry, University of Houston Houston TX 77004 USA
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35
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Wang E, Shan X, Chen L, Pfeifer T, Chen X, Ren X, Dorn A. Ultrafast Proton Transfer Dynamics on the Repulsive Potential of the Ethanol Dication: Roaming-Mediated Isomerization versus Coulomb Explosion. J Phys Chem A 2020; 124:2785-2791. [PMID: 32159968 PMCID: PMC7307916 DOI: 10.1021/acs.jpca.0c02074] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
If
a molecular dication is produced on a repulsive potential energy
surface (PES), it normally dissociates. Before that, however, ultrafast
nuclear dynamics can change the PES and significantly influence the
fragmentation pathway. Here, we investigate the electron-impact-induced
double ionization and subsequent fragmentation processes of the ethanol
molecule using multiparticle coincident momentum spectroscopy and
ab initio dynamical simulations. For the electronic ground state of
the ethanol dication, we observe several fragmentation channels that
cannot be reached by direct Coulomb explosion (CE) but require preceding
isomerization. Our simulations show that ultrafast hydrogen or proton
transfer (PT) can stabilize the repulsive PES of the dication before
the direct CE and form intermediate H2 or H2O. These neutrals stay in the vicinity of the precursor, and roaming
mechanisms lead to isomerization and finally PT resulting in emission
of H3+ or H3O+. The present
findings can help to understand the complex fragmentation dynamics
of molecular cations.
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Affiliation(s)
- Enliang Wang
- Max Planck Institut für Kernphysik, Saupfercheckweg, 1, 69117 Heidelberg, Germany
| | - Xu Shan
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lei Chen
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Thomas Pfeifer
- Max Planck Institut für Kernphysik, Saupfercheckweg, 1, 69117 Heidelberg, Germany
| | - Xiangjun Chen
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xueguang Ren
- Max Planck Institut für Kernphysik, Saupfercheckweg, 1, 69117 Heidelberg, Germany.,School of Science, Xi'an Jiaotong University, Xianning West Road 28, Xi'an 710049, China
| | - Alexander Dorn
- Max Planck Institut für Kernphysik, Saupfercheckweg, 1, 69117 Heidelberg, Germany
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36
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Green JA, Improta R. Vibrations of the guanine-cytosine pair in chloroform: an anharmonic computational study. Phys Chem Chem Phys 2020; 22:5509-5522. [PMID: 32104818 DOI: 10.1039/c9cp06373k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We compute at the anharmonic level the vibrational spectra of the Watson-Crick dimer formed by guanosine (G) and cytidine (C) in chloroform, together with those of G, C and the most populated GG dimer. The spectra for deuterated and partially deuterated GC are also computed. We use DFT calculations, with B3LYP and CAM-B3LYP as reference functionals. Solvent effects from chloroform are included via the Polarizable Continuum Model (PCM), and by performing tests on models including up two chloroform molecules. Both B3LYP and CAM-B3LYP calculations reproduce the shape of the experimental spectra well in the fingerprint region (1500-1700 cm-1) and in the N-H stretching region (2800-3600 cm-1), with B3LYP providing better quantitative agreement with experiments. According to our calculations, the N-H amido streching mode of G falls at ∼2900 cm-1, while the N-H amino of G and C falls at ∼3100 cm-1 when hydrogen-bonded, or ∼3500 cm-1 when free. Overtone and combination bands strongly contribute to the absorption band at ∼3300 cm-1. Inclusion of bulk solvent effects significantly increases the accuracy of the computed spectra, while solute-solvent interactions have a smaller, though still noticeable, effect. Some key aspects of the anharmonic treatment of strongly vibrationally coupled supermolecular systems and the related methodological issues are also discussed.
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Affiliation(s)
- James A Green
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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37
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Norell J, Odelius M, Vacher M. Ultrafast dynamics of photo-excited 2-thiopyridone: Theoretical insights into triplet state population and proton transfer pathways. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:024101. [PMID: 32206689 PMCID: PMC7078009 DOI: 10.1063/1.5143228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Ultrafast non-adiabatic dynamics of the small heteroaromatic compound 2-thiopyridone has been studied with surface hopping simulations based on multi-configurational quantum chemistry. Initial excitation of the bright S 2 ( π , π * ) state is found to promptly relax to S 1 ( n , π * ) through in-plane motion. The subsequent dynamics are oppositely driven by out-of-plane motion, which results in both complex population transfers among all the available states and intersystem crossing predominantly through the "El-Sayed forbidden" S 1 ( n , π * ) to T 2 ( n , π * ) channel, through significant mixing of electronic excitation characters. Despite this complexity, the femto- to picosecond triplet population, expected from several spectroscopic measurements, is well described as a simple exponential decay of the singlet state manifold. No proton transfer is found in the reported trajectories, but two mechanisms for its possible mediation in previously reported experiments are proposed based on the observed structural dynamics: (i) ultrafast intra-molecular transfer driven by the initially coherent in-plane motion and (ii) inter-molecular solvent-mediated transfer driven by the out-of-plane modes that dominate the later motion.
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Affiliation(s)
- Jesper Norell
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael Odelius
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
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38
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Wang K, Yang L, Wang S, Guo L, Ma J, Tang J, Bo W, Wu Z, Zeng B, Gong Y. Transient proton transfer of base pair hydrogen bonds induced by intense terahertz radiation. Phys Chem Chem Phys 2020; 22:9316-9321. [DOI: 10.1039/d0cp01247e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Intense terahertz radiation was applied to trigger transient proton transfer in DNA base pairs through quantum simulation.
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Affiliation(s)
- Kaicheng Wang
- School of Electronic Science and Engineering
- University of Electronic Science and Technology of China
- Chengdu
- China
| | - Lixia Yang
- School of Life Science and Technology
- University of Electronic Science and Technology of China
- Chengdu
- China
| | - Shaomeng Wang
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore
| | - Lianghao Guo
- School of Electronic Science and Engineering
- University of Electronic Science and Technology of China
- Chengdu
- China
| | - Jialu Ma
- School of Electronic Science and Engineering
- University of Electronic Science and Technology of China
- Chengdu
- China
| | - Jingchao Tang
- School of Electronic Science and Engineering
- University of Electronic Science and Technology of China
- Chengdu
- China
| | - Wenfei Bo
- School of Electronic Science and Engineering
- University of Electronic Science and Technology of China
- Chengdu
- China
| | - Zhe Wu
- School of Physics
- University of Electronic Science and Technology of China
- Chengdu
- China
| | - Baoqing Zeng
- School of Electronic Science and Engineering
- University of Electronic Science and Technology of China
- Chengdu
- China
| | - Yubin Gong
- School of Electronic Science and Engineering
- University of Electronic Science and Technology of China
- Chengdu
- China
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39
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Kumar G, Paul K, Luxami V. Deciphering the excited state intramolecular charge-coupled double proton transfer in an asymmetric quinoline–benzimidazole system. NEW J CHEM 2020. [DOI: 10.1039/d0nj01651a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Asymmetrical H-bonding responsible for charge coupled-excited state intramolecular double proton transfer.
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Affiliation(s)
- Gulshan Kumar
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology
- Patiala-147001
- India
| | - Kamaldeep Paul
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology
- Patiala-147001
- India
| | - Vijay Luxami
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology
- Patiala-147001
- India
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40
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Martínez-Fernández L, Esposito L, Improta R. Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives. Photochem Photobiol Sci 2020; 19:436-444. [DOI: 10.1039/d0pp00065e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química
- Facultad de Ciencias
- Modulo 13 Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC Cantoblanco
- 28049 Madrid
| | | | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini
- CNR
- I-80134 Napoli
- Italy
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41
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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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42
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Ma C, Chan RCT, Chan CTL, Wong AKW, Kwok WM. Real-time Monitoring Excitation Dynamics of Human Telomeric Guanine Quadruplexes: Effect of Folding Topology, Metal Cation, and Confinement by Nanocavity Water Pool. J Phys Chem Lett 2019; 10:7577-7585. [PMID: 31769690 DOI: 10.1021/acs.jpclett.9b02932] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Guanine(G)-rich human telomeric (HT) DNA repeats, crucial to maintenance of genome stability, readily form G-quadruplexes (GQs) with various folding topologies. Research on excitation dynamics of HT-GQs is, however, scarce. Herein, we report a femtosecond time-resolved fluorescence coupled with transient absorption investigation on HT-GQ with the basket-type structure in Na+ solution. The result unveils an unusual multichannel nonradiative mechanism dominated by states with varying character of charge transfer lasting ten and hundreds of picoseconds, accounting altogether for an overwhelming ∼85% of the overall deactivation involving proton transfer. Our comparative study shows that encapsulating the GQ in nanocavity water pool or changing it into hydrid-type topologies with the presence of K+ ions alter differently energies and lifetimes of these states, yet without affecting the nature of the electronic excitation involved. The finding of this work underscores a leading role of structural rigidity in regulating the interplay with the microenvironment of photoexcited monomolecularly folded HT-GQs.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen , Guangdong P. R. China
| | - Ruth C-T Chan
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen , Guangdong P. R. China
| | - Chris T-L Chan
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen , Guangdong P. R. China
| | - Allen K-W Wong
- Department of Applied Biology and Chemical Technology , The Hong Kong Polytechnic University , Hung Hom, Kowloon , Hong Kong , P. R. China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology , The Hong Kong Polytechnic University , Hung Hom, Kowloon , Hong Kong , P. R. China
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43
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Soler-Polo D, Mendieta-Moreno JI, Trabada DG, Mendieta J, Ortega J. Proton Transfer in Guanine-Cytosine Base Pairs in B-DNA. J Chem Theory Comput 2019; 15:6984-6991. [DOI: 10.1021/acs.jctc.9b00757] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Diego Soler-Polo
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Jesús I. Mendieta-Moreno
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Daniel G. Trabada
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Jesús Mendieta
- Departamento de Biotecnología, Universidad Francisco de Vitoria, E-28223 Pozuelo de Alarcón, Madrid, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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44
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Theoretical prediction of proton and electron affinities, gas phase basicities, and ionization energies of sulfinamides. Struct Chem 2019. [DOI: 10.1007/s11224-019-01401-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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45
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Segatta F, Cupellini L, Garavelli M, Mennucci B. Quantum Chemical Modeling of the Photoinduced Activity of Multichromophoric Biosystems. Chem Rev 2019; 119:9361-9380. [PMID: 31276384 PMCID: PMC6716121 DOI: 10.1021/acs.chemrev.9b00135] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Indexed: 01/21/2023]
Abstract
Multichromophoric biosystems represent a broad family with very diverse members, ranging from light-harvesting pigment-protein complexes to nucleic acids. The former are designed to capture, harvest, efficiently transport, and transform energy from sunlight for photosynthesis, while the latter should dissipate the absorbed radiation as quickly as possible to prevent photodamages and corruption of the carried genetic information. Because of the unique electronic and structural characteristics, the modeling of their photoinduced activity is a real challenge. Numerous approaches have been devised building on the theoretical development achieved for single chromophores and on model Hamiltonians that capture the essential features of the system. Still, a question remains: is a general strategy for the accurate modeling of multichromophoric systems possible? By using a quantum chemical point of view, here we review the advancements developed so far highlighting differences and similarities with the single chromophore treatment. Finally, we outline the important limitations and challenges that still need to be tackled to reach a complete and accurate picture of their photoinduced properties and dynamics.
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Affiliation(s)
- Francesco Segatta
- Dipartimento
di Chimica Industriale “Toso Montanari” University of Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Lorenzo Cupellini
- Dipartimento
di Chimica e Chimica Industriale, University
of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari” University of Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University
of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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46
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Martínez Fernández L, Cerezo J, Asha H, Santoro F, Coriani S, Improta R. The Absorption Spectrum of Guanine Based Radicals: a Comparative Computational Analysis. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lara Martínez Fernández
- Departamento de Química, Facultad de Ciencias, Mòdulo13Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco 28049 Madrid Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Mòdulo13Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco 28049 Madrid Spain
| | - Haritha Asha
- Istituto di Biostrutture e Bioimmagini-CNR Via Mezzocannone 6 I-80134 Napoli
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR)Area della Ricerca del CNR Via Moruzzi 1 I-56124 Pisa
| | - Sonia Coriani
- DTU ChemistryTechnical University of Denmark, Kemitorvet Building 207 DK-2800 Kongens Lyngby Denmark
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR Via Mezzocannone 6 I-80134 Napoli
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47
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Snyder JA, Charnay AP, Kohl FR, Zhang Y, Kohler B. DNA-like Photophysics in Self-Assembled Silver(I)–Nucleobase Nanofibers. J Phys Chem B 2019; 123:5985-5994. [PMID: 31283245 DOI: 10.1021/acs.jpcb.9b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Joshua A. Snyder
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Aaron P. Charnay
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Forrest R. Kohl
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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48
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Zhang Y, de La Harpe K, Hariharan M, Kohler B. Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent. Faraday Discuss 2019; 207:267-282. [PMID: 29383346 DOI: 10.1039/c7fd00205j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.
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Affiliation(s)
- Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA.
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49
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Banyasz A, Ketola T, Martínez-Fernández L, Improta R, Markovitsi D. Adenine radicals generated in alternating AT duplexes by direct absorption of low-energy UV radiation. Faraday Discuss 2019; 207:181-197. [PMID: 29372211 DOI: 10.1039/c7fd00179g] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
There is increasing evidence that the direct absorption of photons with energies that are lower than the ionization potential of nucleobases may result in oxidative damage to DNA. The present work, which combines nanosecond transient absorption spectroscopy and quantum mechanical calculations, studies this process in alternating adenine-thymine duplexes (AT)n. We show that the one-photon ionization quantum yield of (AT)10 at 266 nm (4.66 eV) is (1.5 ± 0.3) × 10-3. According to our PCM/TD-DFT calculations carried out on model duplexes composed of two base pairs, (AT)1 and (TA)1, simultaneous base pairing and stacking does not induce important changes in the absorption spectra of the adenine radical cation and deprotonated radical. The adenine radicals, thus identified in the time-resolved spectra, disappear with a lifetime of 2.5 ms, giving rise to a reaction product that absorbs at 350 nm. In parallel, the fingerprint of reaction intermediates other than radicals, formed directly from singlet excited states and assigned to AT/TA dimers, is detected at shorter wavelengths. PCM/TD-DFT calculations are carried out to map the pathways leading to such species and to characterize their absorption spectra; we find that, in addition to the path leading to the well-known TA* photoproduct, an AT photo-dimerization path may be operative in duplexes.
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Affiliation(s)
- Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.
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50
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Borràs VJ, Francés‐Monerris A, Roca‐Sanjuán D. Hydroxyl Radical Addition to Thymine and Cytosine and Photochemistry of the Adducts at the C6 Position. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Vicent J. Borràs
- Institut de Ciència MolecularUniversitat de València P.O. Box 22085 46071 Valencia Spain
- Departamento de QuímicaUniversidad Autónoma de Madrid 28049 Madrid Spain
| | - Antonio Francés‐Monerris
- Laboratoire de Physique et Chimie Théoriques (LPCT)Université de Lorraine, CNRS 54000 Nancy France
| | - Daniel Roca‐Sanjuán
- Institut de Ciència MolecularUniversitat de València P.O. Box 22085 46071 Valencia Spain
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