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Tichý O, Burda JV. Estimation of electron absorption spectra and lifetime of the two lowest singlet excited states of pyrimidine nucleobases and their derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Green JA, Jouybari MY, Aranda D, Improta R, Santoro F. Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases. Molecules 2021; 26:1743. [PMID: 33804640 PMCID: PMC8003674 DOI: 10.3390/molecules26061743] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 11/16/2022] Open
Abstract
We have recently proposed a protocol for Quantum Dynamics (QD) calculations, which is based on a parameterisation of Linear Vibronic Coupling (LVC) Hamiltonians with Time Dependent (TD) Density Functional Theory (TD-DFT), and exploits the latest developments in multiconfigurational TD-Hartree methods for an effective wave packet propagation. In this contribution we explore the potentialities of this approach to compute nonadiabatic vibronic spectra and ultrafast dynamics, by applying it to the five nucleobases present in DNA and RNA. For all of them we computed the absorption spectra and the dynamics of ultrafast internal conversion (100 fs timescale), fully coupling the first 2-3 bright states and all the close by dark states, for a total of 6-9 states, and including all the normal coordinates. We adopted two different functionals, CAM-B3LYP and PBE0, and tested the effect of the basis set. Computed spectra are in good agreement with the available experimental data, remarkably improving over pure electronic computations, but also with respect to vibronic spectra obtained neglecting inter-state couplings. Our QD simulations indicate an effective population transfer from the lowest energy bright excited states to the close-lying dark excited states for uracil, thymine and adenine. Dynamics from higher-energy states show an ultrafast depopulation toward the more stable ones. The proposed protocol is sufficiently general and automatic to promise to become useful for widespread applications.
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Affiliation(s)
- James A. Green
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Martha Yaghoubi Jouybari
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Daniel Aranda
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
| | - Roberto Improta
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy;
| | - Fabrizio Santoro
- CNR—Consiglio Nazionale Delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area Della Ricerca, Via G. Moruzzi 1, I-56124 Pisa, Italy; (M.Y.J.); (D.A.)
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Prötzel D, Heß M, Schwager M, Glaw F, Scherz MD. Neon-green fluorescence in the desert gecko Pachydactylus rangei caused by iridophores. Sci Rep 2021; 11:297. [PMID: 33432052 PMCID: PMC7801506 DOI: 10.1038/s41598-020-79706-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
Biofluorescence is widespread in the natural world, but only recently discovered in terrestrial vertebrates. Here, we report on the discovery of iridophore-based, neon-green flourescence in the gecko Pachydactylus rangei, localised to the skin around the eyes and along the flanks. The maximum emission of the fluorescence is at a wavelength of 516 nm in the green spectrum (excitation maximum 465 nm, blue) with another, smaller peak at 430 nm. The fluorescent regions of the skin show large numbers of iridophores, which are lacking in the non-fluorescent parts. Two types of iridophores are recognized, fluorescent iridophores and basal, non-fluorescent iridophores, the latter of which might function as a mirror, amplifying the omnidirectional fluorescence. The strong intensity of the fluorescence (quantum yield of 12.5%) indicates this to be a highly effective mechanism, unique among tetrapods. Although the fluorescence is associated with iridophores, the spectra of emission and excitation as well as the small Stokes shifts argue against guanine crystals as its source, but rather a rigid pair of fluorophores. Further studies are necessary to identify their morphology and chemical structures. We hypothesise that this nocturnal gecko uses the neon-green fluorescence, excited by moonlight, for intraspecific signalling in its open desert habitat.
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Affiliation(s)
- David Prötzel
- grid.452282.b0000 0001 1013 3702Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247 Munich, Germany
| | - Martin Heß
- grid.5252.00000 0004 1936 973XDepartment Biologie II, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Planegg-Martinsried, Germany
| | - Martina Schwager
- grid.434949.70000 0001 1408 3925Department of Applied Sciences and Mechatronics, Munich University of Applied Sciences, Lothstr. 34, 80335 Munich, Germany
| | - Frank Glaw
- grid.452282.b0000 0001 1013 3702Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247 Munich, Germany
| | - Mark D. Scherz
- grid.452282.b0000 0001 1013 3702Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstr. 21, 81247 Munich, Germany
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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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Polewski K, Zinger D, Trunk J, Sutherland JC. Ultraviolet absorption and luminescence of matrix-isolated adenine. Radiat Phys Chem Oxf Engl 1993 2011. [DOI: 10.1016/j.radphyschem.2011.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Parac M, Doerr M, Marian CM, Thiel W. QM/MM calculation of solvent effects on absorption spectra of guanine. J Comput Chem 2010; 31:90-106. [DOI: 10.1002/jcc.21233] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mons M, Dimicoli I, Piuzzi F. Isolated Guanine: Tautomerism, Spectroscopy And Excited State Dynamics. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8184-2_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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Shukla MK, Leszczynski J. Electronic Spectra, Excited State Structures and Interactions of Nucleic Acid Bases and Base Assemblies: A Review. J Biomol Struct Dyn 2007; 25:93-118. [PMID: 17676942 DOI: 10.1080/07391102.2007.10507159] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A comprehensive review of recent theoretical and experimental advances in the singlet electronic transitions, excited state structures and dynamics of nucleic acid bases (NABs) and base assemblies are presented. It is well known that NABs absorb ultraviolet radiation, but the absorbed energy is efficiently dissipated in the form of ultrafast internal conversion processes believed to occur in the subpicosecond time scale and, therefore, enabling NABs highly photostable. It is not known how much evolutionary role was played in evolving these molecules and the ultimate selection by nature as genetic materials, but it is well accepted that survival-of-fittest prevails. Recently, significant efforts have been continuously paid to understand the mechanism of electronic excitation deactivation, but universally acceptable mechanism is still elusive. However, recent investigations reveal that electronic excited state geometries of DNA bases are usually nonplanar and this structural nonplanarity may facilitate nonradiative deactivation. Investigation of excited state structures is challenging and, therefore, it is not surprising that despite the impressive theoretical and computational advances, this research area is still hampered by the methodological and computational limitations. Further, stacking has significant influence on the emission properties of molecules. The 2-aminopurine, a fluorescent adenine derivative frequently used in studying DNA dynamics, shows significant attenuations in fluorescence quantum yield when incorporated in the DNA. Theoretical and computational bottlenecks limit a thorough theoretical understanding of effect of stacking interactions on the excited state dynamics of NABs. Despite these limitations the investigations of excited state properties are progressing in the right direction and our better understanding of excited state structure and dynamics of NABs and nucleic acids may help to design preventive strategy for radiation induced illness and photostable materials.
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Affiliation(s)
- M K Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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The role of out-of-plane deformations in subpicosecond internal conversion of photoexcited purine bases: Absence of the ultrafast decay channel in propanodeoxyguanosine. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.04.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
The complete active space with second-order perturbation theory/complete active space self-consistent-field method was used to explore the nonradiative decay mechanism for excited 9H-guanine. On the 1pipi* (1L(a)) surface we determined a conical intersection (CI), labeled (S0pipi*)(CI), between the 1pipi* (1L(a)) excited state and the ground state, and a minimum, labeled (pipi*)min. For the 1pipi* (1L(a)) state, its probable deactivation path is to undergo a spontaneous relaxation to (pipi*)min first and then decay to the ground state through (S0pipi*)(CI), during which a small activation energy is required. On the 1n(N)pi* surface a CI between the 1n(N)pi* and 1pipi* (1L(a)) states was located, which suggests that the 1n(N)pi* excited state could transform to the 1pipi* (1L(a)) excited state first and then follow the deactivation path of the 1pipi* (1L(a)) state. This CI was also possibly involved in the nonradiative decay path of the second lowest 1pipi* (1L(b)) state. On the 1n(O)pi* surface a minimum was determined. The deactivation of the 1n(O)pi* state to the ground state was estimated to be energetically unfavorable. On the 1pisigma* surface, the dissociation of the N-H bond of the six-membered ring is difficult to occur due to a significant barrier.
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Affiliation(s)
- Hui Chen
- Department of Chemistry, Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, Nanjing University, Nanjing 210093, People's Republic of China
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Shukla MK, Leszczynski J. Excited State Proton Transfer in Guanine in the Gas Phase and in Water Solution: A Theoretical Study. J Phys Chem A 2005; 109:7775-80. [PMID: 16834154 DOI: 10.1021/jp052340i] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Theoretical investigations were performed to study the phenomena of ground and electronic excited state proton transfer in the isolated and monohydrated forms of guanine. Ground and transition state geometries were optimized at both the B3LYP/6-311++G(d,p) and HF/6-311G(d,p) levels. The geometries of tautomers including those of transition states corresponding to the proton transfer from the keto to the enol form of guanine were also optimized in the lowest singlet pipi* excited state using the configuration interaction singles (CIS) method and the 6-311G(d,p) basis set. The time-dependent density function theory method augmented with the B3LYP functional (TD-B3LYP) and the 6-311++G(d,p) basis set was used to compute vertical transition energies using the B3LYP/6-311++G(d,p) geometries. The TD-B3LYP/6-311++G(d,p) calculations were also performed using the CIS/6-311G(d,p) geometries to predict the adiabatic transition energies of different tautomers and the excited state proton transfer barrier heights of guanine tautomerization. The effect of the bulk aqueous environment was considered using the polarizable continuum model (PCM). The harmonic vibrational frequency calculations were performed to ascertain the nature of potential energy surfaces. The excited state geometries including that of transition states were found to be largely nonplanar. The nonplanar fragment was mostly localized in the six-membered ring. Geometries of the hydrated transition states in the ground and lowest singlet pipi* excited states were found to be zwitterionic in which the water molecule is in the form of hydronium cation (H3O(+)) and guanine is in the anionic form, except for the N9H form in the excited state where water molecule is in the hydroxyl anionic form (OH(-)) and the guanine is in the cationic form. It was found that proton transfer is characterized by a high barrier height both in the gas phase and in the bulk water solution. The explicit inclusion of a water molecule in the proton transfer reaction path reduces the barrier height drastically. The excited state barrier height was generally found to be increased as compared to that in the ground state. On the basis of the current theoretical calculation it appears that the singlet electronic excitation of guanine may not facilitate the excited state proton transfer corresponding to the tautomerization of the keto to the enol form.
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Affiliation(s)
- M K Shukla
- Computational Centre for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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Crespo-Hernández CE, Cohen B, Hare PM, Kohler B. Ultrafast Excited-State Dynamics in Nucleic Acids. Chem Rev 2004; 104:1977-2019. [PMID: 15080719 DOI: 10.1021/cr0206770] [Citation(s) in RCA: 962] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mons M, Dimicoli I, Piuzzi F, Tardivel B, Elhanine M. Tautomerism of the DNA Base Guanine and Its Methylated Derivatives as Studied by Gas-Phase Infrared and Ultraviolet Spectroscopy. J Phys Chem A 2002. [DOI: 10.1021/jp0139742] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michel Mons
- Laboratoire Francis Perrin (FRE CNRS−CEA 2298), Service des Photons, Atomes et Molécules, Centre d’Etudes de Saclay, Bât. 522, 91191 Gif-sur-Yvette Cedex, France
| | - Iliana Dimicoli
- Laboratoire Francis Perrin (FRE CNRS−CEA 2298), Service des Photons, Atomes et Molécules, Centre d’Etudes de Saclay, Bât. 522, 91191 Gif-sur-Yvette Cedex, France
| | - François Piuzzi
- Laboratoire Francis Perrin (FRE CNRS−CEA 2298), Service des Photons, Atomes et Molécules, Centre d’Etudes de Saclay, Bât. 522, 91191 Gif-sur-Yvette Cedex, France
| | - Benjamin Tardivel
- Laboratoire Francis Perrin (FRE CNRS−CEA 2298), Service des Photons, Atomes et Molécules, Centre d’Etudes de Saclay, Bât. 522, 91191 Gif-sur-Yvette Cedex, France
| | - Mohamed Elhanine
- Laboratoire Francis Perrin (FRE CNRS−CEA 2298), Service des Photons, Atomes et Molécules, Centre d’Etudes de Saclay, Bât. 522, 91191 Gif-sur-Yvette Cedex, France
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Affiliation(s)
- Eyal Nir
- Department of Chemistry The Hebrew University of Jerusalem Jerusalem 91904, Israel
| | - Louis Grace
- Department of Chemistry The Hebrew University of Jerusalem Jerusalem 91904, Israel
| | - Beth Brauer
- Department of Chemistry The Hebrew University of Jerusalem Jerusalem 91904, Israel
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