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Zhao L, Geng X, Han G, Guo Y, Liu R, Chen J. Revealing the excited-state dynamics of cytidine and the role of excited-state proton transfer process. Phys Chem Chem Phys 2023; 25:32002-32009. [PMID: 37975722 DOI: 10.1039/d3cp03683a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The high photostability of DNAs and RNAs is inextricably related to the photochemical and photophysical properties of their building blocks, nucleobases and nucleosides, which can dissipate the absorbed UV light energy in a harmless manner. The deactivation mechanism of the nucleosides, especially the decay pathways of cytidine (Cyd), has been a matter of intense debate. In the current study, we employ high-level electronic structure calculations combined with excited state non-adiabatic dynamic simulations to provide a clear picture of the excited state deactivation of Cyd in both gas phase and aqueous solution. In both environments, a barrierless decay path driven by the ring-puckering motion and a relaxation channel with a small energy barrier driven by the elongation motion of CO bond are assigned to <200 fs and sub-picosecond decay time component, respectively. The presence of ribose group has a subtle effect on the dynamic behavior of Cyd in gas phase as the ribose-to-base hydrogen/proton transfer process is energetically inaccessible with a sizable energy barrier of about 1.4 eV. However, this energy barrier is significantly reduced in water, especially when an explicit water molecule is present. Therefore, we argue that the long-lived decay channel found in aqueous solution could be assigned to the Cyd-water intermolecular hydrogen/proton transfer process. The present study postulates a novel scenario toward deep understanding the intrinsic photostability of DNAs and RNAs and provides solid evidence to disclose the long history debate of cytidine excited-state decay mechanism, especially for the assignment of experimentally observed time components.
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Affiliation(s)
- Li Zhao
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Xuehui Geng
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Guoxia Han
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Yahui Guo
- College of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China.
| | - Runze Liu
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, P. R. China
| | - Junsheng Chen
- Nano-Science Center & Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 KøbenhavnØ, Denmark.
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2
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Michaelian K. The Non-Equilibrium Thermodynamics of Natural Selection: From Molecules to the Biosphere. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1059. [PMID: 37510006 PMCID: PMC10378079 DOI: 10.3390/e25071059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023]
Abstract
Evolutionary theory suggests that the origin, persistence, and evolution of biology is driven by the "natural selection" of characteristics improving the differential reproductive success of the organism in the given environment. The theory, however, lacks physical foundation, and, therefore, at best, can only be considered a heuristic narrative, of some utility for assimilating the biological and paleontological data at the level of the organism. On deeper analysis, it becomes apparent that this narrative is plagued with problems and paradoxes. Alternatively, non-equilibrium thermodynamic theory, derived from physical law, provides a physical foundation for describing material interaction with its environment at all scales. Here we describe a "natural thermodynamic selection" of characteristics of structures (or processes), based stochastically on increases in the global rate of dissipation of the prevailing solar spectrum. Different mechanisms of thermodynamic selection are delineated for the different biotic-abiotic levels, from the molecular level at the origin of life, up to the level of the present biosphere with non-linear coupling of biotic and abiotic processes. At the levels of the organism and the biosphere, the non-equilibrium thermodynamic description of evolution resembles, respectively, the Darwinian and Gaia descriptions, although the underlying mechanisms and the objective function of selection are fundamentally very different.
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Affiliation(s)
- Karo Michaelian
- Department of Nuclear Physics and Application of Radiation, Instituto de Física, Universidad Nacional Autónoma de México, Circuito Interior de la Investigación Científica, Ciudad Universitaria, Mexico City C.P. 04510, Mexico
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3
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Wang S, Dauletyarov Y, Horke DA. High-Throughput UV Photoionization and Fragmentation of Neutral Biomolecules as a Structural Fingerprint. Molecules 2023; 28:5058. [PMID: 37446720 DOI: 10.3390/molecules28135058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
We present UV photofragmentation studies of the structural isomers paracetamol, 3-Pyridinepropionic acid (3-PPIA) and (R)-(-)-2-Phenylglycine. In particular, we utilized a new laser-based thermal desorption source in combination with femtosecond multiphoton ionization at 343 nm and 257 nm. The continuous nature of our molecule source, combined with the 50 kHz repetition rate of the laser, allowed us to perform these experiments at high throughput. In particular, we present detailed laser intensity dependence studies at both wavelengths, producing 2D mass spectra with highly differential information about the underlying fragmentation processes. We show that UV photofragmentation produces highly isomer-specific mass spectra, and assign all major fragmentation pathways observed. The intensity-dependence measurements, furthermore, allowed us to evaluate the appearance intensities for each fragmentation channel, which helped to distinguish competing from consecutive fragmentation pathways.
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Affiliation(s)
- Siwen Wang
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Yerbolat Dauletyarov
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Daniel A Horke
- Institute for Molecules and Materials, Radboud University, 6525 AJ Nijmegen, The Netherlands
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4
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Dauletyarov Y, Wang S, Horke DA. Vaporization of Intact Neutral Biomolecules Using Laser-Based Thermal Desorption. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37319337 DOI: 10.1021/jasms.3c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The production of a clean neutral molecular sample is a crucial step in many gas-phase spectroscopy and reaction dynamics experiments investigating neutral species. Unfortunately, conventional methods based on heating cannot be used with most nonvolatile biomolecules due to their thermal instability. In this paper, we demonstrate the application of laser-based thermal desorption (LBTD) to produce neutral molecular plumes of biomolecules such as dipeptides and lipids. Specifically, we report mass spectra of glycylglycine, glycyl-l-alanine, and cholesterol obtained using LBTD vaporization, followed by soft femtosecond multiphoton ionization (fs-MPI) at 400 nm. For all molecules, the signal from the intact precursor ion was observed, highlighting the softness and applicability of the LBTD and fs-MPI approach. In more detail, cholesterol underwent hardly any fragmentation. Both dipeptides fragmented significantly, although mostly through only a single channel, which we attribute to the fs-MPI process.
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Affiliation(s)
- Yerbolat Dauletyarov
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Siwen Wang
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Daniel A Horke
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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5
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Miura Y, Yamamoto YI, Karashima S, Orimo N, Hara A, Fukuoka K, Ishiyama T, Suzuki T. Formation of Long-Lived Dark States during Electronic Relaxation of Pyrimidine Nucleobases Studied Using Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy. J Am Chem Soc 2023; 145:3369-3381. [PMID: 36724068 DOI: 10.1021/jacs.2c09803] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ultrafast electronic relaxation of nucleobases from 1ππ* states to the ground state (S0) is considered essential for the photostability of DNA. However, transient absorption spectroscopy (TAS) has indicated that some nucleobases in aqueous solutions create long-lived 1nπ*/3ππ* dark states from the 1ππ* states with a high quantum yield of 0.4-0.5. We investigated electronic relaxation in pyrimidine nucleobases in both aqueous solutions and the gas phase using extreme ultraviolet (EUV) time-resolved photoelectron spectroscopy. Femtosecond EUV probe pulses cause ionization from all electronic states involved in the relaxation process, providing a clear overview of the electronic dynamics. The 1nπ* quantum yields for aqueous cytidine and uracil (Ura) derivatives were found to be considerably lower (<0.07) than previous estimates reported by TAS. On the other hand, aqueous thymine (Thy) and thymidine exhibited a longer 1ππ* lifetime and a higher quantum yield (0.12-0.22) for the 1nπ* state. A similar trend was found for isolated Thy and Ura in the gas phase: the 1ππ* lifetimes are 39 and 17 fs and the quantum yield for 1nπ* are 1.0 and 0.45 for Thy and Ura, respectively. The result indicates that single methylation to the C5 position hinders the out-of-plane deformation that drives the system to the conical intersection region between 1ππ* and S0, providing a large impact on the photophysics/photochemistry of a pyrimidine nucleobase. The significant reduction of 1nπ* yield in aqueous solution is ascribed to the destabilization of the 1nπ* state induced by hydrogen bonding.
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Affiliation(s)
- Yuta Miura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Yo-Ichi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Shutaro Karashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Natsumi Orimo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Ayano Hara
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Kanae Fukuoka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
| | - Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama930-8555, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto606-8502, Japan
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6
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de Vries MS. Understanding How a New Hachimoji Nucleobase Alters Photodynamics of Genetic Building Blocks. Photochem Photobiol 2022; 99:857-859. [PMID: 36062299 DOI: 10.1111/php.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022]
Abstract
This article is a highlight of the paper by Krul et al. in this issue of Photochemistry and Photobiology. It describes the excited state dynamics of 5-aza-7-deazaguanine (5N7C G), which has recently been proposed as an alternative nucleobase. Upon UV absorption to the lowest energy 1 ππ* state, 5N7C G returns to the electronic ground state an order of magnitude more slowly than guanine with a corresponding greater fluorescence quantum yield. These findings are significant because they suggest that 5N7C G is less UV photostable that its canonical nucleobase equivalent, which would have been a selective disadvantage in prebiotic conditions.
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Affiliation(s)
- Mattanjah S de Vries
- Department of Chemistry and Biochemistry, University of California Santa Barbara, CA, 93106-9510, USA
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7
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Mansour R, Toldo JM, Barbatti M. Role of the Hydrogen Bond on the Internal Conversion of Photoexcited Adenosine. J Phys Chem Lett 2022; 13:6194-6199. [PMID: 35767744 DOI: 10.1021/acs.jpclett.2c01554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Experiments and theory have revealed that hydrogen bonds modify the excited-state lifetimes of nucleosides compared to nucleobases. Nevertheless, how these bonds impact the internal conversion is still unsettled. This work simulates the non-adiabatic dynamics of adenosine conformers in the gas phase with and without hydrogen bonds between the sugar and adenine moieties. The isomer containing the hydrogen bond (syn) exhibits a significantly shorter excited-state lifetime than the isomer without it (anti). However, internal conversion through electron-driven proton transfer between sugar and adenine plays only a minor (although non-negligible) role in the photophysics of adenosine. Either with or without hydrogen bonds, photodeactivation preferentially occurs following the ring-puckering pathways. The role of the hydrogen bond is to avoid the sugar rotation relative to adenine, shortening the distance to the ring-puckering internal conversion.
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Affiliation(s)
- Ritam Mansour
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
| | - Josene M Toldo
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
| | - Mario Barbatti
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
- Institut Universitaire de France, 75231 Paris, France
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8
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Experimental and Computational Analysis of Para-Hydroxy Methylcinnamate following Photoexcitation. Molecules 2021; 26:molecules26247621. [PMID: 34946701 PMCID: PMC8704431 DOI: 10.3390/molecules26247621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023] Open
Abstract
Para-hydroxy methylcinnamate is part of the cinnamate family of molecules. Experimental and computational studies have suggested conflicting non-radiative decay routes after photoexcitation to its S1(ππ*) state. One non-radiative decay route involves intersystem crossing mediated by an optically dark singlet state, whilst the other involves direct intersystem crossing to a triplet state. Furthermore, irrespective of the decay mechanism, the lifetime of the initially populated S1(ππ*) state is yet to be accurately measured. In this study, we use time-resolved ion-yield and photoelectron spectroscopies to precisely determine the S1(ππ*) lifetime for the s-cis conformer of para-hydroxy methylcinnamate, combined with time-dependent density functional theory to determine the major non-radiative decay route. We find the S1(ππ*) state lifetime of s-cis para-hydroxy methylcinnamate to be ∼2.5 picoseconds, and the major non-radiative decay route to follow the [1ππ*→1nπ*→3ππ*→S0] pathway. These results also concur with previous photodynamical studies on structurally similar molecules, such as para-coumaric acid and methylcinnamate.
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9
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Yu XF, Fu TH, Xiao B, Yu HY, Li Q. A theoretical study on the excited-state deactivation paths for the A-5FU dimer. Phys Chem Chem Phys 2021; 23:16089-16106. [PMID: 34291779 DOI: 10.1039/d1cp00030f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The photostability of DNA plays a key role in the normal function of organisms. A-5FU is a base pair derivative of the A-T dimer where the methyl group is replaced by a F atom. Here, accurate static TDDFT calculations and non-adiabatic dynamic simulations are used to systematically investigate the excited-state decay paths of the A-5FU dimer related to the proton transfer and the out-of-plane twisting deformation motion of A and 5FU in the 1ππ* and 1nπ* states. CC2 is used to check the accuracy of the current TDDFT calculations. Our results show that the deformation of the C[double bond, length as m-dash]C or C[double bond, length as m-dash]N double bond in A and 5FU provides an efficient pathway for the depopulation of the lowest excited states, which can compete with the excited-state proton transfer paths in the dimer. This finding indicates that monomer-like decay paths could be important for the photostability of weakly hydrogen-bonded DNA base pairs and provide a new insight into the excited-state decay paths in base pairs and their analogues.
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Affiliation(s)
- Xue-Fang Yu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
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10
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Bocková J, Rebelo A, Ryszka M, Pandey R, Mészáros D, Limão-Vieira P, Papp P, Mason NJ, Townsend D, Nixon KL, Vizcaino V, Poully JC, Eden S. Thermal desorption effects on fragment ion production from multi-photon ionized uridine and selected analogues. RSC Adv 2021; 11:20612-20621. [PMID: 35479354 PMCID: PMC9033967 DOI: 10.1039/d1ra01873f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/09/2021] [Indexed: 12/22/2022] Open
Abstract
Experiments on neutral gas-phase nucleosides are often complicated by thermal lability. Previous mass spectrometry studies of nucleosides have identified enhanced relative production of nucleobase ions (e.g. uracil+ from uridine) as a function of desorption temperature to be the critical indicator of thermal decomposition. On this basis, the present multi-photon ionization (MPI) experiments demonstrate that laser-based thermal desorption is effective for producing uridine, 5-methyluridine, and 2′-deoxyuridine targets without thermal decomposition. Our experiments also revealed one notable thermal dependence: the relative production of the sugar ion C5H9O4+ from intact uridine increased substantially with the desorption laser power and this only occurred at MPI wavelengths below 250 nm (full range studied 222–265 nm). We argue that this effect can only be rationalized plausibly in terms of changing populations of different isomers, tautomers, or conformers in the target as a function of the thermal desorption conditions. Furthermore, the wavelength threshold behavior of this thermally-sensitive MPI channel indicates a critical dependence on neutral excited state dynamics between the absorption of the first and second photons. The experimental results are complemented by density functional theory (DFT) optimizations of the lowest-energy structure of uridine and two further conformers distinguished by different orientations of the hydroxymethyl group on the sugar part of the molecule. The energies of the transitions states between these three conformers are low compared with the energy required for decomposition. This work reveals the first experimental evidence supporting isomer-dependence in the radiation response of a nucleoside.![]()
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Affiliation(s)
- J Bocková
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK
| | - A Rebelo
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK .,Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, FCT - Universidade NOVA de Lisboa P-2829-516 Caparica Portugal
| | - M Ryszka
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK
| | - R Pandey
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK
| | - D Mészáros
- Department of Experimental Physics, Comenius University in Bratislava Mlynská dolina F2 84248 Bratislava Slovakia
| | - P Limão-Vieira
- Atomic and Molecular Collisions Laboratory, CEFITEC, Department of Physics, FCT - Universidade NOVA de Lisboa P-2829-516 Caparica Portugal
| | - P Papp
- Department of Experimental Physics, Comenius University in Bratislava Mlynská dolina F2 84248 Bratislava Slovakia
| | - N J Mason
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK .,School of Physical Sciences, Ingram Building, University of Kent Canterbury CT2 7NH UK
| | - D Townsend
- Institute of Photonics and Quantum Sciences, Heriot-Watt University Edinburgh EH14 4AS UK.,Institute of Chemical Sciences, Heriot-Watt University Edinburgh EH14 4AS UK
| | - K L Nixon
- School of Life, Health, and Chemical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK.,School of Sciences, University of Wolverhampton Wulfruna Street Wolverhampton WV1 1LY UK
| | - V Vizcaino
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, GANIL Bd Becquerel BP 5133 14070 Caen France
| | - J-C Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, GANIL Bd Becquerel BP 5133 14070 Caen France
| | - S Eden
- School of Physical Sciences, The Open University Walton Hall Milton Keynes MK7 6AA UK
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11
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Zhao L, Zhou G, Jia B, Teng G, Zhan K, Zheng H, Luo J, Liu B. New insight into the ultrafast excited state deactivation mechanism of guanosine in the gas phase. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112753] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Li W, Mjekiqi E, Douma W, Wang X, Kavatsyuk O, Hoekstra R, Poully J, Schlathölter T. Hole Migration in Telomere-Based Oligonucleotide Anions and G-Quadruplexes. Chemistry 2019; 25:16114-16119. [PMID: 31614016 PMCID: PMC6972685 DOI: 10.1002/chem.201904105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/11/2019] [Indexed: 01/24/2023]
Abstract
Vacuum ultraviolet photoionization of a gas-phase oligonucleotide anion leads to the formation of a valence hole. This hole migrates towards an energetically favorable site where it can weaken bonds and ultimately lead to bond cleavage. We have studied Vacuum UV photoionization of deprotonated oligonucleotides containing the human telomere sequence dTTAGGG and G-quadruplex structures consisting of four dTGGGGT single strands, stabilized by NH4 + counter ions. The oligonucleotide and G-quadruplex anions were confined in a radiofrequency ion trap, interfaced with a synchrotron beamline and the photofragmentation was studied using time-of-flight mass spectrometry. Oligonucleotide 12-mers containing the 5'-TTAGGG sequence were found to predominantly break in the GGG region, whereas no selective bond cleavage region was observed for the reversed 5'-GGGATT sequence. For G-quadruplex structures, fragmentation was quenched and mostly non-dissociative single and double electron removal was observed.
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Affiliation(s)
- Wen Li
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Edita Mjekiqi
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Wessel Douma
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Xin Wang
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Oksana Kavatsyuk
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
- University College GroningenUniversity of GroningenHoendiepskade 23/249718 BGGroningenThe Netherlands
| | - Ronnie Hoekstra
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Jean‐Christophe Poully
- CIMAP laboratory UMR 6252Université de Caen Normandie/CEA/CNRS/ENSICAENBd Becquerel14070CAEN Cedex 5France
| | - Thomas Schlathölter
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
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13
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Gate G, Szabla R, Haggmark MR, Šponer J, Sobolewski AL, de Vries MS. Photodynamics of alternative DNA base isoguanine. Phys Chem Chem Phys 2019; 21:13474-13485. [DOI: 10.1039/c9cp01622h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pump–probe experiments and quantum-chemical simulations of UV-excited isoguanine elucidate its tautomer dependent photochemical properties.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Rafał Szabla
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
- Institute of Biophysics of the Czech Academy of Sciences
| | - Michael R. Haggmark
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences
- 61265 Brno
- Czech Republic
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14
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Pepino AJ, Segarra-Martí J, Nenov A, Rivalta I, Improta R, Garavelli M. UV-induced long-lived decays in solvated pyrimidine nucleosides resolved at the MS-CASPT2/MM level. Phys Chem Chem Phys 2018; 20:6877-6890. [PMID: 29459916 DOI: 10.1039/c7cp08235e] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most relevant 'dark' electronic excited states in DNA/RNA pyrimidine nucleosides are mapped in water employing hybrid MS-CASPT2/MM optimisations with explicit solvation and including the sugar. Conical intersections (CIs) between initially accessed bright 1ππ* and the lowest energy dark 1nπ* excited states, involving the lone pair localised on the oxygen and/or nitrogen atoms are characterised. They are found in the vicinities of the Franck-Condon (FC) region and are shown to facilitate non-adiabatic population transfer. The excited state population of the 1nOπ* state, localised in the carbonyl moiety on all pyrimidine nucleosides, is predicted to rapidly evolve to its minimum, displaying non-negligible potential energy barriers along its non-radiative decay, and accounting for the ps signal registered in pump-probe experiments as well as for an efficient population of the triplet state. Cytidine displays an additional 1nNπ* state localised in the N3 atom and that leads to its excited state minimum displaying large potential energy barriers in the pathway connecting to the CI with the ground state. Sugar-to-base hydrogen/proton transfer processes are assessed in solution for the first time, displaying a sizable barrier along its decay and thus being competitive with other slow decay channels in the ps and ns timescales. A unified deactivation scheme for the long-lived channels of pyrimidine nucleosides is delivered, where the 1nOπ* state is found to mediate the long-lived decay in the singlet manifold and act as the doorway for triplet population and thus accounting for the recorded phosphorescence and, more generally, for the transient/photoelectron spectral signals registered up to the ns timescale.
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Affiliation(s)
- Ana Julieta Pepino
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy.
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15
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Ingle RA, Roberts GM, Röttger K, Marroux HJ, Sönnichsen FD, Yang M, Szyc Ł, Harabuchi Y, Maeda S, Temps F, Orr-Ewing AJ. Resolving the excited state relaxation dynamics of guanosine monomers and hydrogen-bonded homodimers in chloroform solution. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Williams HL, Erickson BA, Neumark DM. Time-resolved photoelectron spectroscopy of adenosine and adenosine monophosphate photodeactivation dynamics in water microjets. J Chem Phys 2018; 148:194303. [PMID: 30307253 DOI: 10.1063/1.5027258] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The excited state relaxation dynamics of adenosine and adenosine monophosphate were studied at multiple excitation energies using femtosecond time-resolved photoelectron spectroscopy in a liquid water microjet. At pump energies of 4.69-4.97 eV, the lowest ππ* excited state, S1, was accessed and its decay dynamics were probed via ionization at 6.20 eV. By reversing the role of the pump and probe lasers, a higher-lying ππ* state was excited at 6.20 eV and its time-evolving photoelectron spectrum was monitored at probe energies of 4.69-4.97 eV. The S1 ππ* excited state was found to decay with a lifetime ranging from ∼210 to 250 fs in adenosine and ∼220 to 250 fs in adenosine monophosphate. This lifetime drops with increasing pump photon energy. Signal from the higher-lying ππ* excited state decayed on a time scale of ∼320 fs and was measureable only in adenosine monophosphate.
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Affiliation(s)
- Holly L Williams
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Blake A Erickson
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel M Neumark
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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17
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Ghafur O, Crane SW, Ryszka M, Bockova J, Rebelo A, Saalbach L, De Camillis S, Greenwood JB, Eden S, Townsend D. Ultraviolet relaxation dynamics in uracil: Time-resolved photoion yield studies using a laser-based thermal desorption source. J Chem Phys 2018; 149:034301. [DOI: 10.1063/1.5034419] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Omair Ghafur
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Stuart W. Crane
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Michal Ryszka
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Jana Bockova
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Andre Rebelo
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
- CEFITEC, Departamento de Física, FCT–Universidade NOVA de Lisboa, P-2829-516 Caparica, Portugal
| | - Lisa Saalbach
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Simone De Camillis
- School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Jason B. Greenwood
- School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Samuel Eden
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, United Kingdom
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
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18
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Röttger K, Marroux HJB, Böhnke H, Morris DTJ, Voice AT, Temps F, Roberts GM, Orr-Ewing AJ. Probing the excited state relaxation dynamics of pyrimidine nucleosides in chloroform solution. Faraday Discuss 2018; 194:683-708. [PMID: 27711889 DOI: 10.1039/c6fd00068a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ultrafast transient electronic and vibrational absorption spectroscopy (TEAS and TVAS) of 2'-deoxy-cytidine (dC) and 2'-deoxy-thymidine (dT) dissolved in chloroform examines their excited-state dynamics and the recovery of ground electronic state molecules following absorption of ultraviolet light. The chloroform serves as a weakly interacting solvent, allowing comparisons to be drawn with prior experimental studies of the photodynamics of these nucleosides in the gas phase and in polar solvents such as water. The pyrimidine base nucleosides have some propensity to dimerize in aprotic solvents, but the monomer photochemistry can be resolved clearly and is the focus of this study. UV absorption at a wavelength of 260 nm excites a 1ππ* ← S0 transition, but prompt crossing of a significant fraction (50% in dC, 17% in dT) of the 1ππ* population into a nearby 1nπ* state is too fast for the experiments to resolve. The remaining flux on the 1ππ* state leaves the vertical Franck-Condon region and encounters a conical intersection with the ground electronic state of ethylenic twist character. In dC, the 1ππ* state decays to the ground state with a time constant of 1.1 ± 0.1 ps. The lifetime of the 1nπ* state is much longer in the canonical forms of both molecules: recovery of the ground state population from these states occurs with time constants of 18.6 ± 1.1 ps in amino-oxo dC and ∼114 ps in dT, indicating potential energy barriers to the 1nπ*/S0 conical intersections. The small fraction of the imino-oxo tautomer of dC present in solution has a longer-lived 1nπ* state with a lifetime for ground state recovery of 193 ± 55 ps. No evidence is found for photo-induced tautomerization of amino-oxo dC to the imino-oxo form, or for population of low lying triplet states of this nucleoside. In contrast, ∼8% of the UV-excited dT molecules access the long-lived T1 (3ππ*) state through the 1nπ* state. The primary influence of the solvent appears to be the degree to which it destabilizes the states of 1nπ* character, with consequences for the lifetimes of these states as well as the triplet state yields.
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Affiliation(s)
- Katharina Röttger
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Hugo J B Marroux
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Hendrik Böhnke
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - David T J Morris
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Angus T Voice
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Friedrich Temps
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Gareth M Roberts
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Andrew J Orr-Ewing
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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19
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Marchetti B, Karsili TNV, Ashfold MNR, Domcke W. A 'bottom up', ab initio computational approach to understanding fundamental photophysical processes in nitrogen containing heterocycles, DNA bases and base pairs. Phys Chem Chem Phys 2018; 18:20007-27. [PMID: 26980149 DOI: 10.1039/c6cp00165c] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The availability of non-radiative decay mechanisms by which photoexcited molecules can revert to their ground electronic state, without experiencing potentially deleterious chemical transformation, is fundamental to molecular photostability. This Perspective Article combines results of new ab initio electronic structure calculations and prior experimental data in an effort to systematise trends in the non-radiative decay following UV excitation of selected families of heterocyclic molecules. We start with the prototypical uni- and bicyclic molecules phenol and indole, and explore the structural and photophysical consequences of incorporating progressively more nitrogen atoms within the respective ring structures en route to the DNA bases thymine, cytosine, adenine and guanine. For each of the latter, we identify low energy non-radiative decay pathways via conical intersections with the ground state potential energy surface accessed by out-of-plane ring deformations. This is followed by summary descriptions and illustrations of selected rival (electron driven H atom transfer) non-radiative excited state decay processes that demand consideration once the nucleobases are merely components in larger biomolecular systems like nucleosides, and both individual and stacked base-pairs.
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Affiliation(s)
- Barbara Marchetti
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Tolga N V Karsili
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Michael N R Ashfold
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
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20
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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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21
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Ashwood B, Ortiz-Rodríguez LA, Crespo-Hernández CE. Excited-State Dynamics in O 6-Methylguanosine: Impact of O 6-Methylation on the Relaxation Mechanism of Guanine Monomers. J Phys Chem Lett 2017; 8:4380-4385. [PMID: 28850232 DOI: 10.1021/acs.jpclett.7b02090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Absorption of ultraviolet radiation by DNA bases results in ultrafast internal conversion to the ground state, which minimizes photodamage. However, exogenous and endogenous alkylating agents present in the cellular environment can methylate the nucleobases in DNA. In particular, methylation of guanosine at the O6 position in DNA leads to the formation of the O6-methylguanosine adduct, which may alter the photostability of DNA. This contribution demonstrates that O6-methylation of guanosine red shifts its ground-state absorption spectrum and slows down the rate of internal conversion to the ground state by ∼40-fold in aqueous solution. The 40-fold decrease in the rate of excited-state decay increases the probability of photodamage within cellular DNA. It is proposed that the longer decay lifetime corresponds to relaxation of the excited-state population in O6-methylguanosine along a C6-puckered reaction coordinate in the 1ππ*(La) potential energy surface that runs parallel to an ultrafast internal conversion pathway along a C2-puckered coordinate.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Luis A Ortiz-Rodríguez
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Carlos E Crespo-Hernández
- Department of Chemistry and Center for Chemical Dynamics, Case Western Reserve University , Cleveland, Ohio 44106, United States
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22
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Cercola R, Matthews E, Dessent CEH. Photoexcitation of Adenosine 5'-Triphosphate Anions in Vacuo: Probing the Influence of Charge State on the UV Photophysics of Adenine. J Phys Chem B 2017; 121:5553-5561. [PMID: 28521097 DOI: 10.1021/acs.jpcb.7b03435] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the first UV laser photodissociation spectra (4.0-5.8 eV) of gas-phase deprotonated adenosine 5'-triphosphate, diphosphate and monophosphate anions. The photodepletion spectra of these anions display strong absorption bands across the region of 4.6-5.2 eV, consistent with excitation of a primarily adenine-centered π-π* transition. The spectra appear insensitive to the charge of the species (i.e., the spectrum of [ATP-2H]2- closely resembles that of [ATP-H]-), while the spectral profile is affected to a greater extent by the variation of the molecular structure, i.e. the [AMP-H]- and [ADP-H]- photodepletion spectra display similar profiles while the [ATP-H]- spectrum is distinctive. The photodepletion cross-section also decreases for the ATP anions compared to both the AMP and ADP anions, reflecting a high intrinsic photostability of ATP versus both AMP and ADP. A range of photofragments are produced across the 4.0-5.8 eV spectral range for all of the ATP analogues studied. These fragments are primarily associated with fragmentation on the ground-state electronic surface, indicative of a statistical decay process where ultrafast decay is followed by ergodic dissociation. However, while the photofragments observed following photoexcitation of the monoanionic species, [AMP-H]- to [ADP-H]- to [ATP-H]- are entirely consistent with statistical decay, an additional group of photofragments are observed for the dianionic species, [ADP-2H]2- and [ATP-2H]2-, that we associate with electron detachment, and subsequent fragmentation of the resulting electron-detached photofragment. TDDFT calculations are presented to support the interpretation of the experimental data, and confirm that the electronic structure of the adenine moiety is relatively unperturbed by varying the overall charge.
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Affiliation(s)
- Rosaria Cercola
- Department of Chemistry, University of York , Heslington, York, YO10 5DD, U.K
| | - Edward Matthews
- Department of Chemistry, University of York , Heslington, York, YO10 5DD, U.K
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23
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Rovira AR, Fin A, Tor Y. Expanding a fluorescent RNA alphabet: synthesis, photophysics and utility of isothiazole-derived purine nucleoside surrogates. Chem Sci 2017; 8:2983-2993. [PMID: 28451365 PMCID: PMC5380116 DOI: 10.1039/c6sc05354h] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/26/2017] [Indexed: 01/09/2023] Open
Abstract
A series of emissive ribonucleoside purine mimics, all comprised of an isothiazolo[4,3-d]pyrimidine core, was prepared using a divergent pathway involving a key Thorpe-Ziegler cyclization. In addition to an adenosine and a guanosine mimic, analogues of the noncanonical xanthosine, isoguanosine, and 2-aminoadenosine were also synthesized and found to be emissive. Isothiazolo 2-aminoadenosine, an adenosine surrogate, was found to be particularly emissive and effectively deaminated by adenosine deaminase. Competitive studies with adenosine deaminase with each analogue in combination with native adenosine showed preference for the native substrate while still deaminating the isothiazolo analogues.
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Affiliation(s)
- Alexander R Rovira
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093-0358 , USA .
| | - Andrea Fin
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093-0358 , USA .
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093-0358 , USA .
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24
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Wu X, Karsili TNV, Domcke W. Role of Electron-Driven Proton-Transfer Processes in the Ultrafast Deactivation of Photoexcited Anionic 8-oxoGuanine-Adenine and 8-oxoGuanine-Cytosine Base Pairs. Molecules 2017; 22:molecules22010135. [PMID: 28098833 PMCID: PMC6155867 DOI: 10.3390/molecules22010135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/28/2016] [Accepted: 01/10/2017] [Indexed: 11/16/2022] Open
Abstract
It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G- with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S₁/S₀ conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G- nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G--A and 8-oxo-G--C base pairs are likely too short-lived to be efficient electron-transfer repair agents.
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Affiliation(s)
- Xiuxiu Wu
- Department of Chemistry, Technische Universitat Munchen, Lichtenbergstr. 4, Garching D-85747, Germany.
| | - Tolga N V Karsili
- Department of Chemistry, Temple University, 130 Beury Hall, 1901 N. 13th St., Philadelphia, PA 19122, USA.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universitat Munchen, Lichtenbergstr. 4, Garching D-85747, Germany.
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25
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Szabla R, Kruse H, Šponer J, Góra RW. Water–chromophore electron transfer determines the photochemistry of cytosine and cytidine. Phys Chem Chem Phys 2017; 19:17531-17537. [DOI: 10.1039/c7cp02635h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Irradiation of aqueous cytidine may result in a water–chromophore electron transfer process which explains numerous experimental observations, including photodamage.
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Affiliation(s)
- Rafał Szabla
- Institute of Physics
- Polish Academy of Sciences
- PL-02668 Warsaw
- Poland
- Institute of Biophysics
| | - Holger Kruse
- Institute of Biophysics
- Academy of Sciences of the Czech Republic
- 61265, Brno
- Czech Republic
| | - Jiří Šponer
- Institute of Biophysics
- Academy of Sciences of the Czech Republic
- 61265, Brno
- Czech Republic
| | - Robert W. Góra
- Department of Physical and Quantum Chemistry
- Wroclaw University of Science and Technology
- 50-370 Wrocław
- Poland
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26
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Månsson EP, De Camillis S, Castrovilli MC, Galli M, Nisoli M, Calegari F, Greenwood JB. Ultrafast dynamics in the DNA building blocks thymidine and thymine initiated by ionizing radiation. Phys Chem Chem Phys 2017; 19:19815-19821. [DOI: 10.1039/c7cp02803b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ultrafast dynamics and fragmentation of thymidine and thymine after ionization by attosecond extreme ultraviolet radiation studied in the time-domain.
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Affiliation(s)
- E. P. Månsson
- Institute for Photonics and Nanotechnologies CNR-IFN
- 20133 Milano
- Italy
| | - S. De Camillis
- Centre for Plasma Physics
- School of Maths and Physics
- Queen's University Belfast
- UK
| | - M. C. Castrovilli
- Institute for Photonics and Nanotechnologies CNR-IFN
- 20133 Milano
- Italy
- Inst. for the Structure of Matter CNR-ISM
- Monterotondo
| | - M. Galli
- Institute for Photonics and Nanotechnologies CNR-IFN
- 20133 Milano
- Italy
- Department of Physics
- Politecnico di Milano
| | - M. Nisoli
- Institute for Photonics and Nanotechnologies CNR-IFN
- 20133 Milano
- Italy
- Department of Physics
- Politecnico di Milano
| | - F. Calegari
- Institute for Photonics and Nanotechnologies CNR-IFN
- 20133 Milano
- Italy
- Center for Free-Electron Laser Science
- DESY
| | - J. B. Greenwood
- Centre for Plasma Physics
- School of Maths and Physics
- Queen's University Belfast
- UK
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27
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Tuna D, Domcke W. Excited-state deactivation in 8-oxo-deoxyguanosine: comparison between anionic and neutral forms. Phys Chem Chem Phys 2016; 18:947-55. [DOI: 10.1039/c5cp05804j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ab initio explorations of excited-state potential-energy surfaces show that a radiationless deactivation mechanism via intramolecular excited-state proton transfer is available in neutral 8-oxo-deoxyguanosine, whereas it is not available in the anionic form.
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Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim an der Ruhr
- Germany
| | - Wolfgang Domcke
- Department of Chemistry
- Technische Universität München
- 85747 Garching
- Germany
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28
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Buchner F, Heggen B, Ritze HH, Thiel W, Lübcke A. Excited-state dynamics of guanosine in aqueous solution revealed by time-resolved photoelectron spectroscopy: experiment and theory. Phys Chem Chem Phys 2015; 17:31978-87. [DOI: 10.1039/c5cp04394h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved photoelectron spectroscopy is performed on aqueous guanosine solution to study its excited-state relaxation dynamics.
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Affiliation(s)
- Franziska Buchner
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie
- 12489 Berlin
- Germany
| | - Berit Heggen
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr
- Germany
| | - Hans-Hermann Ritze
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie
- 12489 Berlin
- Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim/Ruhr
- Germany
| | - Andrea Lübcke
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie
- 12489 Berlin
- Germany
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