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Petropoulos V, Uboldi L, Maiuri M, Cerullo G, Martinez-Fernandez L, Balanikas E, Markovitsi D. Effect of the DNA Polarity on the Relaxation of Its Electronic Excited States. J Phys Chem Lett 2023; 14:10219-10224. [PMID: 37931204 DOI: 10.1021/acs.jpclett.3c02580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
The DNA polarity, i.e., the order in which nucleobases are connected together via the phosphodiester backbone, is crucial for several biological processes. But, so far, there has not been experimental evidence regarding its effect on the relaxation of DNA electronic excited states. Here we examine this aspect for two dinucleotides containing adenine and guanine: 5'-dApdG-3' and 5'-dGpdA-3' in water. We used two different femtosecond transient absorption setups: one providing high temporal resolution and broad spectral coverage (330-650 nm) between 30 fs and 50 ps, and the other recording decays at selected wavelengths until 1.2 ns. The transient absorption spectra corresponding to the minima in the potential energy surface of the first excited state were computed by quantum chemistry methods. Our results show that the excited charge transfer state in 5'-dGpdA-3' is formed with a ∼75% higher quantum yield and exhibits slower decay (170 ± 10 ps vs 112 ± 12 ps) compared to 5'-dApdG-3'.
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Affiliation(s)
- Vasilis Petropoulos
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Lorenzo Uboldi
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - 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, Cantoblanco, 28049 Madrid, Spain
| | - Evangelos Balanikas
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva-4, Switzerland
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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2
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Weng G, Pang A, Vlček V. Spatial Decay and Limits of Quantum Solute-Solvent Interactions. J Phys Chem Lett 2023; 14:2473-2480. [PMID: 36867592 DOI: 10.1021/acs.jpclett.3c00208] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular excitations in the liquid-phase environment are renormalized by the surrounding solvent molecules. Herein, we employ the GW approximation to investigate the solvation effects on the ionization energy of phenol in various solvent environments. The electronic effects differ by up to 0.4 eV among the five investigated solvents. This difference depends on both the macroscopic solvent polarizability and the spatial decay of the solvation effects. The latter is probed by separating the electronic subspace and the GW correlation self-energy into fragments. The fragment correlation energy decays with increasing intermolecular distance and vanishes at ∼9 Å, and this pattern is independent of the type of solvent environment. The 9 Å cutoff defines an effective interacting volume within which the ionization energy shift per solvent molecule is proportional to the macroscopic solvent polarizability. Finally, we propose a simple model for computing the ionization energies of molecules in an arbitrary solvent environment.
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Affiliation(s)
- Guorong Weng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Amanda Pang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Vojtěch Vlček
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
- Materials Department, University of California, Santa Barbara, California 93106-5050, United States
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3
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Ray J, Ramesh SG. Excited-state proton transfer in the 2-aminopyridine dimer: A surface hopping study. Phys Chem Chem Phys 2022; 24:7274-7292. [DOI: 10.1039/d1cp05517h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a theoretical investigation of the excited-state intermolecular proton transfer process in the 2-aminopyridine dimer. Prior experimental and theoretical studies on this doubly hydrogen bonded system have attributed an...
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4
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Balanikas E, Martinez-Fernandez L, Baldacchino G, Markovitsi D. Electron Holes in G-Quadruplexes: The Role of Adenine Ending Groups. Int J Mol Sci 2021; 22:ijms222413436. [PMID: 34948235 PMCID: PMC8704496 DOI: 10.3390/ijms222413436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
The study deals with four-stranded DNA structures (G-Quadruplexes), known to undergo ionization upon direct absorption of low-energy UV photons. Combining quantum chemistry calculations and time-resolved absorption spectroscopy with 266 nm excitation, it focuses on the electron holes generated in tetramolecular systems with adenine groups at the ends. Our computations show that the electron hole is placed in a single guanine site, whose location depends on the position of the adenines at the 3' or 5' ends. This position also affects significantly the electronic absorption spectrum of (G+)● radical cations. Their decay is highly anisotropic, composed of a fast process (<2 µs), followed by a slower one occurring in ~20 µs. On the one hand, they undergo deprotonation to (G-H2)● radicals and, on the other, they give rise to a reaction product absorbing in the 300-500 nm spectral domain.
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Affiliation(s)
- Evangelos Balanikas
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
| | - Lara Martinez-Fernandez
- Departamento de Química, Modúlo 13, Facultad de Ciencias and IADCHEM (Institute for Advanced Research in Chemistry), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- Correspondence: (L.M.-F.); or (D.M.)
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
- Correspondence: (L.M.-F.); or (D.M.)
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5
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Balanikas E, Martinez-Fernandez L, Improta R, Podbevšek P, Baldacchino G, Markovitsi D. The Structural Duality of Nucleobases in Guanine Quadruplexes Controls Their Low-Energy Photoionization. J Phys Chem Lett 2021; 12:8309-8313. [PMID: 34428044 DOI: 10.1021/acs.jpclett.1c01846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Guanine quadruplexes are four-stranded DNA/RNA structures composed of a guanine core (vertically stacked guanine tetrads) and peripheral groups (dangling ends and/or loops). Such a dual structural arrangement of the nucleobases favors their photoionization at energies significantly lower than the guanine ionization potential. This effect is important with respect to the oxidative DNA damage and for applications in the field of optoelectronics. Photoionization quantum yields, determined at 266 nm by nanosecond transient absorption spectroscopy, strongly depend on both the type and position of the peripheral nucleobases. The highest value (1.5 × 10-2) is found for the tetramolecular structure (AG4A)4 in which adenines are intermittently stacked on the adjacent guanine tetrads, as determined by nuclear magnetic resonance spectroscopy. Quantum chemistry calculations show that peripheral nucleobases interfere in a key step preceding electron ejection: charge separation, initiated by the population of charge transfer states during the relaxation of electronic excited states.
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Affiliation(s)
| | - 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
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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6
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Wang Y, Wan K, Pan F, Zhu X, Jiang Y, Wang H, Chen Y, Shi X, Liu M. Bamboo-like π-Nanotubes with Tunable Helicity and Circularly Polarized Luminescence. Angew Chem Int Ed Engl 2021; 60:16615-16621. [PMID: 33960094 DOI: 10.1002/anie.202104843] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 01/02/2023]
Abstract
We report the fabrication of an exotic bamboo-like π-nanotube via the hierarchical self-assembly of a dipeptide-substituted naphthalenediimide gelator with tunable helicity and circularly polarized luminescence (CPL). It was found that in the presence of trifluoroacetic acid (TFA) the gelator molecules self-assembled into a bamboo-like π-nanotube, which is composed of truncated nanocones and CPL active. When defining the diameter ratio of the lower to upper edge of each nanocone as a parameter to express the helicity of different nanotubes, it was found that both the helicity and CPL of these nanotubes can be adjusted by the amount of TFA. Moreover, the helicity of the nanotube can be conveyed to the achiral quantum dots (QDs) and produce a hybrid nanotube/QDs CPL active materials with adjustable dissymmetry factor. This work finds a new type self-assembled bamboo-like π-nanotube and unveils their helicity and CPL control.
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Affiliation(s)
- Yuan Wang
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kaiwei Wan
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Fei Pan
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China.,Institute of Solid Mechanics, Beihang University, Beijing, 100191, China
| | - Xuefeng Zhu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yuqian Jiang
- Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Hui Wang
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Yuli Chen
- Institute of Solid Mechanics, Beihang University, Beijing, 100191, China
| | - Xinghua Shi
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, P. R. China
| | - Minghua Liu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Wang Y, Wan K, Pan F, Zhu X, Jiang Y, Wang H, Chen Y, Shi X, Liu M. Bamboo‐like π‐Nanotubes with Tunable Helicity and Circularly Polarized Luminescence. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104843] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yuan Wang
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Kaiwei Wan
- University of Chinese Academy of Sciences Beijing 100049 China
- Laboratory of Theoretical and Computational Nanoscience CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
| | - Fei Pan
- Laboratory of Theoretical and Computational Nanoscience CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
- Institute of Solid Mechanics Beihang University Beijing 100191 China
| | - Xuefeng Zhu
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Yuqian Jiang
- Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
| | - Hui Wang
- Laboratory of Theoretical and Computational Nanoscience CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
| | - Yuli Chen
- Institute of Solid Mechanics Beihang University Beijing 100191 China
| | - Xinghua Shi
- University of Chinese Academy of Sciences Beijing 100049 China
- Laboratory of Theoretical and Computational Nanoscience CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology (NCNST) Beijing 100190 P. R. China
| | - Minghua Liu
- Beijing National Laboratory for Molecular Science CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 China
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8
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Abstract
The intrinsic fluorescence of nucleic acids is extremely weak compared to that of the fluorescent labels used to probe their structural and functional behavior. Thus, for technical reasons, the investigation of the intrinsic DNA fluorescence was limited for a long time. But with the improvement in spectroscopic techniques, the situation started to change around the turn of the century. During the past two decades, various factors modulating the static and dynamic properties of the DNA fluorescence have been determined; it was shown that, under certain conditions, quantum yields may be up 100 times higher than what was known so far. The ensemble of these studies opened up new paths for the development of label-free DNA fluorescence for biochemical applications. In parallel, these studies have shed new light on the primary processes leading to photoreactions that damage DNA when it absorbs UV radiation.We have been studying a variety of DNA systems, ranging from the monomeric nucleobases to double-stranded and four-stranded structures using fluorescence spectroscopy. The specificity of our work resides in the quantitative association of the steady-state fluorescence spectra with time-resolved data recorded from the femtosecond to the nanosecond timescales, made possible by the development of specific methodologies.Among others, our fluorescence studies provide information on the energy and the polarization of electronic transitions. These are valuable indicators for the evolution of electronic excitations in complex systems, where the electronic coupling between chromophores plays a key role. Highlighting collective effects that originate from electronic interactions in DNA multimers is the objective of the present Account.In contrast to the monomeric chromophores, whose fluorescence decays within a few picoseconds, that of DNA multimers persists on the nanosecond timescale. Even if long-lived states represent only a small fraction of electronic excitations, they may be crucial to the DNA photoreactivity because the probability to reach reactive conformations increases over time, owing to the incessant structural dynamics of nucleic acids.Our femtosecond studies have revealed that an ultrafast excitation energy transfer takes place among the nucleobases within duplexes and G-quadruplexes. Such an ultrafast process is possible when collective states are populated directly upon photon absorption. At much longer times, we discovered an unexpected long-lived high-energy emission stemming from what was coined "HELM excitons". These collective states, whose emission increases with the duplex size, could be responsible for the delayed fluorescence of ππ* states observed for genomic DNA.Most studies dealing with excited-state relaxation in DNA were carried out with excitation in the absorption band peaking at around 260 nm. We went beyond this and also performed the first time-resolved study with excitation in the UVA spectral range, where a very weak absorption tail is present. The resulting fluorescence decays are much slower and the fluorescence quantum yields are much higher than for UVC excitation. We showed that the base pairing of DNA strands enhances the UVA fluorescence and, in parallel, increases the photoreactivity because it modifies the nature of the involved collective excited states.
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Affiliation(s)
- Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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9
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Piccinni V, Reiter S, Keefer D, de Vivie-Riedle R. Multiscale Conformational Sampling Reveals Excited-State Locality in DNA Self-Repair Mechanism. J Phys Chem A 2020; 124:9133-9140. [PMID: 33089694 DOI: 10.1021/acs.jpca.0c07207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet (UV) irradiation is known to be responsible for DNA damage. However, experimental studies in DNA oligonucleotides have shown that UV light can also induce sequence-specific self-repair. Following charge transfer from a guanine adenine sequence adjacent to a cyclobutane pyrimidine dimer (CPD), the covalent bond between the two thymines could be cleaved, recovering the intact base sequence. Mechanistic details promoting the self-repair remained unclear, however. In our theoretical study, we investigated whether optical excitation could directly lead to a charge-transfer state, thereby initiating the repair, or whether the initial excited state remains localized on a single nucleobase. We performed conformational sampling of 200 geometries of the damaged DNA double strand solvated in water and used a hybrid quantum and molecular mechanics approach to compute excited states at the complete active space perturbation level of theory. Analysis of the conformational data set clearly revealed that the excited-state properties are uniformly distributed across the fluctuations of the nucleotide in its natural environment. From the electronic wavefunction, we learned that the electronic transitions remained predominantly local on either adenine or guanine, and no direct charge transfer occurred in the experimentally accessed energy range. The investigated base sequence is not only specific to the CPD repair mechanism but ubiquitously occurs in nucleic acids. Our results therefore give a very general insight into the charge locality of UV-excited DNA, a property that is regarded to have determining relevance in the structural consequences following absorption of UV photons.
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Affiliation(s)
- Viviana Piccinni
- Department Chemie, Ludwig-Maximilians-Universität München, München D-81377, Germany
| | - Sebastian Reiter
- Department Chemie, Ludwig-Maximilians-Universität München, München D-81377, Germany
| | - Daniel Keefer
- Department Chemie, Ludwig-Maximilians-Universität München, München D-81377, Germany
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10
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Dao DQ, Phan TTT, Nguyen TLA, Trinh PTH, Tran TTV, Lee JS, Shin HJ, Choi BK. Insight into Antioxidant and Photoprotective Properties of Natural Compounds from Marine Fungus. J Chem Inf Model 2020; 60:1329-1351. [DOI: 10.1021/acs.jcim.9b00964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Duy Quang Dao
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam
| | - Thi Thu Trang Phan
- Faculty of Pharmacy, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam
| | - Thi Le Anh Nguyen
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam
| | - Phan Thi Hoai Trinh
- Nha Trang Institute of Technology Research and Application, Vietnam Academy of Science and Technology (VAST), 02 Hung Vuong, Nha Trang 650000, Vietnam
| | - Thi Thanh Van Tran
- Nha Trang Institute of Technology Research and Application, Vietnam Academy of Science and Technology (VAST), 02 Hung Vuong, Nha Trang 650000, Vietnam
| | - Jong Seok Lee
- Korea Institute of Ocean Science and Technology, 385, Haeyang-ro, Yeongdo-gu, Busan Metropolitan City 49111, Korea
| | - Hee Jae Shin
- Korea Institute of Ocean Science and Technology, 385, Haeyang-ro, Yeongdo-gu, Busan Metropolitan City 49111, Korea
| | - Byeoung-Kyu Choi
- Korea Institute of Ocean Science and Technology, 385, Haeyang-ro, Yeongdo-gu, Busan Metropolitan City 49111, Korea
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11
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Jaiswal VK, Segarra-Martí J, Marazzi M, Zvereva E, Assfeld X, Monari A, Garavelli M, Rivalta I. First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases. Phys Chem Chem Phys 2020; 22:15496-15508. [DOI: 10.1039/d0cp01823f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
TD-DFT characterization of the high-energy singlet excited state manifold of the canonical DNA/RNA nucleobasesin vacuumis assessed against RASPT2 reference computations for reliable simulations of linear and non-linear electronic spectra.
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Affiliation(s)
- Vishal K. Jaiswal
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Viale del Risorgimento 4
- I-40136 Bologna
- Italy
| | - Javier Segarra-Martí
- Univ Lyon, Ens de Lyon, CNRS
- Université Lyon 1
- Laboratoire de Chimie UMR 5182
- Lyon
- France
| | - Marco Marazzi
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
- CNRS, Laboratoire de Physique et Chimie Théoriques
| | - Elena Zvereva
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
- CNRS, Laboratoire de Physique et Chimie Théoriques
| | - Xavier Assfeld
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
- CNRS, Laboratoire de Physique et Chimie Théoriques
| | - Antonio Monari
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
- CNRS, Laboratoire de Physique et Chimie Théoriques
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Viale del Risorgimento 4
- I-40136 Bologna
- Italy
| | - Ivan Rivalta
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Viale del Risorgimento 4
- I-40136 Bologna
- Italy
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12
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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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13
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Gupta A, Mishra BK, Sathyamurthy N. Influence of stacking on the ground and excited states of 2-aminopyridine. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Francés-Monerris A, Gattuso H, Roca-Sanjuán D, Tuñón I, Marazzi M, Dumont E, Monari A. Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA. Chem Sci 2018; 9:7902-7911. [PMID: 30450180 PMCID: PMC6202918 DOI: 10.1039/c8sc03252a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022] Open
Abstract
The intrinsic photostability of nucleic acids is intimately related to evolution of life, while its understanding at the molecular and electronic levels remains a challenge for modern science. Among the different decay pathways proposed in the last two decades, the excited-state hydrogen transfer between guanine-cytosine base pairs has been identified as an efficient non-reactive channel to dissipate the excess of energy provided by light absorption. The present work studies the dynamics of such phenomena taking place in a (dG)·(dC) B-DNA homopolymer in water solution using state-of-the-art molecular modelling and simulation methods. A dynamic effect that boosts the photostability of the inter-strand hydrogen atom transfers, inherent to the Watson-Crick base pairing, is unveiled and ascribed to the energy released during the proton transfer step. Our results also reveal a novel mechanism of DNA decay named four proton transfer (FPT), in which two protons of two adjacent G-C base pairs are transferred to form a biradical zwitterionic intermediate. Decay of the latter intermediate to the ground state triggers the transfer of the protons back to the guanine molecules recovering the Watson-Crick structure of the tetramer. This FPT process is activated by the close interaction of a nearby Na+ counterion with the oxygen atoms of the guanine nucleobases and hence represents a photostable channel operative in natural nucleic acids.
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Affiliation(s)
| | - Hugo Gattuso
- Theoretical Physical Chemistry , Research Unit Molecular Systems (UR MOLSYS) , University of Liège , 4000 Liège , Belgium
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular , Universitat de València , Apartado 22085 , ES-46071 Paterna , Spain
| | - Iñaki Tuñón
- Departamento de Química Física , Universitat de València , 46100 Burjassot , Spain
| | - Marco Marazzi
- Departamento de Química , Centro de Investigación en Síntesis Química (CISQ) , Universidad de La Rioja , 26006 Logroño , Spain
| | - Elise Dumont
- Univ. Lyon , ENS de Lyon , CNRS UMR 5182 , Université Claude Bernard Lyon 1 , Laboratoire de Chimie , F69342 , Lyon , France
| | - Antonio Monari
- Université de Lorraine , CNRS , LPCT , Nancy F-54000 , France . ;
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15
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Abstract
The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.
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Affiliation(s)
- Samuel Boldissar
- Department of Chemistry and Biochemistry University of California Santa Barbara
- USA
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16
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Padula D, Jurinovich S, Di Bari L, Mennucci B. Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum. Chemistry 2016; 22:17011-17019. [PMID: 27699878 DOI: 10.1002/chem.201602777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Indexed: 12/18/2022]
Abstract
We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.
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Affiliation(s)
- Daniele Padula
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
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17
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 338] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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18
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Pan L, Zhang J, Bian W. Theoretical study on the photodegradation reaction of deca-BDE in THF in the presence of furan. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1760-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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Villani G. Effect of Methylation on the Properties of the H-Bridges in DNA. A Systematic Theoretical Study on the Couples of Base Pairs. J Phys Chem B 2015; 119:7931-43. [DOI: 10.1021/acs.jpcb.5b02901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti
OrganoMetallici, UOS Pisa Area della Ricerca del CNR, Via G. Moruzzi,
1, I-56124 Pisa, Italy
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20
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Altavilla SF, Segarra-Martí J, Nenov A, Conti I, Rivalta I, Garavelli M. Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate. Front Chem 2015; 3:29. [PMID: 25941671 PMCID: PMC4403598 DOI: 10.3389/fchem.2015.00029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/30/2015] [Indexed: 01/17/2023] Open
Abstract
The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ(*) La and Lb states, whereas the energy of the oxygen lone-pair nπ(*) state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ(*) state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region.
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Affiliation(s)
| | | | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Irene Conti
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Ivan Rivalta
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
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21
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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22
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Villani G. Coupling between hydrogen atoms transfer and stacking interaction in adenine-thymine/guanine-cytosine complexes: a theoretical study. J Phys Chem B 2014; 118:5439-52. [PMID: 24813562 DOI: 10.1021/jp502792r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four different complexes of two base pairs, an adenine-thymine and a guanine-cytosine one, have been studied in order to understand the modifications induced by the staking interaction between the two base pairs on the hydrogen atoms transfers between the bases in either base pair. The inclusion of these two kinds of interactions allows us to clarify if some properties, as the mechanism of hydrogen transfer, is exclusively a local effect of a base pair or can be modified by a more long-range interaction between the base pairs. The results on these four complexes are compared with those of the monomeric systems, the A-T and G-C base pair, and with those of the A-T and G-C dimers. The specificity of each complex and of each hydrogen bond has been analyzed.
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM-UOS Pisa Area della Ricerca del CNR, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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23
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Improta R. Quantum mechanical calculations unveil the structure and properties of the absorbing and emitting excited electronic states of guanine quadruplex. Chemistry 2014; 20:8106-15. [PMID: 24828154 DOI: 10.1002/chem.201400065] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Indexed: 12/20/2022]
Abstract
Herein, a full quantum mechanical study, in solution, of several models of guanine-quadruplex helices, both parallel and antiparallel, containing up to eight guanine residues, in their electronic excited state is reported. By exploiting TD-DFT calculations and including solvent effects by the polarizable continuum model, we provide the first atomistic description of the processes triggered by the absorption of UV light, reproducing and assigning the experimental optical and electronic circular dichroism spectra. The absorbing excited states are delocalized over multiple bases, whereas emission involves a stacked guanine dimer or a monomer. Several states, with a varying degree of localization and charge-transfer character, rule the photoexcited dynamics, which are deeply affected by the quadruplex topology. The lowest excited-state minimum for parallel quadruplex is an asymmetric excimer involving two stacked guanines, with a small charge transfer character, whereas for the anti-parallel structure, with the same topology of the thrombin binding aptamer, it is a fully symmetric excimer, characterized by a strong decrease of the stacking distance. A monomer-like decay path is the most relevant nonradiative decay pathway. Insights on the effect of the ions (K(+) or Na(+)) on the excited state decay are also provided.
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Affiliation(s)
- Roberto Improta
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, I-80134, Napoli (Italy).
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24
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Electronic Excitation Processes in Single-Strand and Double-Strand DNA: A Computational Approach. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:1-37. [DOI: 10.1007/128_2013_517] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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25
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Chen J, Zhang Y, Kohler B. Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:39-87. [DOI: 10.1007/128_2014_570] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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26
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Stuhldreier MC, Temps F. Ultrafast photo-initiated molecular quantum dynamics in the DNA dinucleotide d(ApG) revealed by broadband transient absorption spectroscopy. Faraday Discuss 2013; 163:173-88; discussion 243-75. [PMID: 24020202 DOI: 10.1039/c3fd00003f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ultrafast photo-initiated quantum dynamics of the adenine-guanine dinucleotide d(ApG) in aqueous solution (pH 7) has been studied by femtosecond time-resolved spectroscopy after excitation at lambda = 260 nm. The results reveal a hierarchy of processes on time scales from tau < 100 fs to tau > 100 ps. Characteristic spectro-temporal signatures are observed indicating the transformation of the molecules in the electronic relaxation from the photo-excited state to a long-lived exciplex. In particular, broadband UV/VIS excited-state absorption (ESA) measurements detected a distinctive absorption by the excited dinucleotide around lambda = 335 nm, approximately 0.5 eV to the blue compared to the maximum of the broad and unstructured ESA spectrum after excitation of an equimolar mixture of the mononucleotides dAMP and dGMP. A similar feature has been identified as signature of the excimer in the dynamics of the adenine dinucleotide d(ApA). The lifetime of the d(ApG) exciplex was found to be tau = 124 +/- 4 ps both from the ESA decay time and from the ground-state recovery time, far longer than the sub-picosecond lifetimes of excited dAMP or dGMP. Fluorescence-time profiles measured by the up-conversion technique indicate that the exciplex state is reached around approximately 6 ps after excitation. Very weak residual fluorescence at longer times red-shifted to the emission from the photo-excited state shows that the exciplex is almost optically dark, but still has enough oscillator strength to give rise to the dual fluorescence of the dinucleotide in the static fluorescence spectrum.
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Affiliation(s)
- Mayra C Stuhldreier
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
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27
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Pan L, Bian W, Zhang J. The Effect of Explicit Solvent on Photodegradation of Decabromodiphenyl Ether in Toluene: Insights from Theoretical Study. J Phys Chem A 2013; 117:5291-8. [DOI: 10.1021/jp403958g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lu Pan
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wensheng Bian
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiaxu Zhang
- Beijing National Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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28
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29
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Vayá I, Brazard J, Gustavsson T, Markovitsi D. Electronically excited states of DNA oligonucleotides with disordered base sequences studied by fluorescence spectroscopy. Photochem Photobiol Sci 2013; 11:1767-73. [PMID: 23034563 DOI: 10.1039/c2pp25180a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA double-stranded oligomers are studied by steady-state and time-resolved fluorescence spectroscopy from the femtosecond to the nanosecond time-scale, following excitation at 267 nm. It is shown that emission arises from three types of excited states. (i) Bright ππ* states emitting around 330 nm and decaying on the sub-picosecond time-scale with an average lifetime of ca. 0.4 ps and a quantum yield lower than 4 × 10(-6). (ii) Excimers/exciplexes emitting around 430 nm and decaying on the sub-nanosecond time-scale. (iii) Excited states emitting mainly at short wavelengths (λ < 330 nm) and decaying on the nanosecond time-scale, possibly correlated to GC pairs. The properties of the examined duplexes, exhibiting significant disorder with respect to the nearest neighbour base sequence, are radically different than those of the much longer and disordered calf thymus DNA. Such behaviour suggests that long range and/or sequence effects play a key role in the fate of excitation energy.
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Affiliation(s)
- Ignacio Vayá
- CNRS, IRAMIS, SPAM, Laboratoire Francis Perrin, URA 2453, F-91191 Gif-sur-Yvette, France
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30
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Voityuk AA. Effects of dynamic disorder on exciton delocalization and photoinduced charge separation in DNA. Photochem Photobiol Sci 2013; 12:1303-9. [DOI: 10.1039/c2pp25389e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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31
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Dai Y, Guo M, Peng J, Shen W, Li M, He R, Zhu C, Lin SH. Noncovalent interaction and its influence on excited-state behavior: A theoretical study on the mixed coaggregates of dicyanonaphthalene and pyrazoline. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2012.11.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Ikabata Y, Nakai H. Extension of local response dispersion method to excited-state calculation based on time-dependent density functional theory. J Chem Phys 2012; 137:124106. [DOI: 10.1063/1.4754508] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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33
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Padula D, Di Bari L, Santoro F, Gerlach H, Rizzo A. Analysis of the Electronic Circular Dichroism Spectrum of (−)-[9](2,5)Pyridinophane. Chirality 2012; 24:994-1004. [DOI: 10.1002/chir.22087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 05/30/2012] [Indexed: 12/28/2022]
Affiliation(s)
- Daniele Padula
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; Pisa Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; Pisa Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche - CNR; Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca; Pisa Italy
| | - Hans Gerlach
- Department of Chemistry; University of Bayreuth; Bayreuth Germany
| | - Antonio Rizzo
- Consiglio Nazionale delle Ricerche - CNR; Istituto per i Processi Chimico-Fisici (IPCF-CNR); Pisa Italy
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34
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Su C, Middleton CT, Kohler B. Base-Stacking Disorder and Excited-State Dynamics in Single-Stranded Adenine Homo-oligonucleotides. J Phys Chem B 2012; 116:10266-74. [DOI: 10.1021/jp305350t] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Charlene Su
- Department
of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus,
Ohio 43210, United States
| | - Chris T. Middleton
- Department
of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus,
Ohio 43210, United States
| | - Bern Kohler
- Department of Chemistry and
Biochemistry, Montana State University,
Bozeman, Montana 59717-3400, United States
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35
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Zelený T, Ruckenbauer M, Aquino AJ, Müller T, Lankaš F, Dršata T, Hase WL, Nachtigallova D, Lischka H. Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine. J Am Chem Soc 2012; 134:13662-9. [DOI: 10.1021/ja3028845] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tomáš Zelený
- Regional Centre of
Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University Olomouc,
17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Matthias Ruckenbauer
- Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17,
A-1090 Vienna, Austria
| | - Adelia J.A. Aquino
- Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17,
A-1090 Vienna, Austria
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United
States
- Institute of Soil
Research, University of Natural Resources and Life Sciences,
Peter-Jordan-Straße 82, A-1190 Vienna, Austria
| | - Thomas Müller
- Institute of Advanced Simulation, Jülich Supercomuter Centre, Forschungszentrum
Jülich, D-52425 Jülich, Germany
| | - Filip Lankaš
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Tomáš Dršata
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United
States
| | - Dana Nachtigallova
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Hans Lischka
- Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17,
A-1090 Vienna, Austria
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United
States
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36
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Plasser F, Aquino AJA, Hase WL, Lischka H. UV Absorption Spectrum of Alternating DNA Duplexes. Analysis of Excitonic and Charge Transfer Interactions. J Phys Chem A 2012; 116:11151-60. [DOI: 10.1021/jp304725r] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Felix Plasser
- Institute of Theoretical
Chemistry, University of Vienna, Währingerstrasse
17, A-1090,
Vienna, Austria
| | - Adelia J. A. Aquino
- Institute
of Soil Research, University of Natural Resources and Life Sciences,
Peter-Jordan-Strasse 82, A-1190, Vienna, Austria
- Department of Chemistry
and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - William L. Hase
- Department of Chemistry
and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Hans Lischka
- Institute of Theoretical
Chemistry, University of Vienna, Währingerstrasse
17, A-1090,
Vienna, Austria
- Department of Chemistry
and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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37
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Lu Y, Lan Z, Thiel W. Monomeric adenine decay dynamics influenced by the DNA environment. J Comput Chem 2012; 33:1225-35. [DOI: 10.1002/jcc.22952] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 01/09/2012] [Accepted: 01/16/2012] [Indexed: 01/25/2023]
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38
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Cerón-Carrasco JP, Requena A, Jacquemin D. Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1188-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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39
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Plasser F, Barbatti M, Aquino AJA, Lischka H. Electronically excited states and photodynamics: a continuing challenge. Theor Chem Acc 2012. [DOI: 10.1007/s00214-011-1073-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Ivanova B, Spiteller M. Conformation, optical properties, and absolute configuration of 2′,3′-isopropylideneadenosines: Theoretical vs. experimental study. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.08.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Ravelli D, Dondi D, Fagnoni M, Albini A, Bagno A. Predicting the UV spectrum of polyoxometalates by TD-DFT. J Comput Chem 2011; 32:2983-7. [DOI: 10.1002/jcc.21879] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 05/16/2011] [Accepted: 06/13/2011] [Indexed: 12/29/2022]
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