1
|
Chevalier F, Schlathölter T, Poully JC. Radiation-Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems. Chembiochem 2023; 24:e202300543. [PMID: 37712497 DOI: 10.1002/cbic.202300543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
In biological tissues, ionizing radiation interacts with a variety of molecules and the consequences include cell killing and the modification of mechanical properties. Applications of biological radiation action are for instance radiotherapy, sterilization, or the tailoring of biomaterial properties. During the first femtoseconds to milliseconds after the initial radiation action, biomolecular systems typically respond by transfer of charge, atoms, or energy. In the condensed phase, it is usually very difficult to distinguish direct effects from indirect effects. A straightforward solution for this problem is the use of gas-phase techniques, for instance from the field of mass spectrometry. In this review, we survey mainly experimental but also theoretical work, focusing on radiation-induced intra- and inter-molecular transfer of charge, atoms, and energy within biomolecular systems in the gas phase. Building blocks of DNA, proteins, and saccharides, but also antibiotics are considered. The emergence of general processes as well as their timescales and mechanisms are highlighted.
Collapse
Affiliation(s)
- François Chevalier
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Groningen (The, Netherlands
- University College Groningen, University of Groningen, Groningen (The, Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/CNRS/ENSICAEN/Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| |
Collapse
|
2
|
Milešević D, Popat D, Gellersen P, Liu Z, Stimson J, Robertson P, Green A, Vallance C. Design and characterization of an optical-fiber-coupled laser-induced desorption source for gas-phase dynamics experiments. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:114105. [PMID: 37987631 DOI: 10.1063/5.0170080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
Preparation of neutral non-volatile molecules intact in the gas phase for mass spectrometry or chemical dynamics experiments remains a challenge for many classes of molecules. Here, we report the design and characterization of a fiber-coupled laser-based thermal desorption source capable of preparing intact neutral molecules at high molecular densities in the gas phase for use in velocity-map imaging experiments. Within this source, the sample is deposited onto a thin tantalum foil. Irradiation of the foil from the reverse side by a focused laser beam leads to highly localized heating of the sample, resulting in desorption of a plume of molecules into the gas phase. The fiber-coupled design simplifies the alignment of the desorption laser beam, and the ability to rotate the foil relative to the fixed laser beam allows the sample to be continually refreshed under vacuum. We use 118 nm photoionization of three test molecules-uracil, adenine, and phenylalanine-to characterize the source and to demonstrate various aspects of its performance. These include the dependence of the velocity-map imaging performance on the size of the interaction region and the dependence of the laser-induced desorption source emission on desorption laser power and heating time. Signal levels recorded in these measurements are comparable to those we typically obtain in similar experiments using a pulsed supersonic molecular beam, and we, therefore, believe that the source has considerable potential for use in a wide range of chemical dynamics and other experiments.
Collapse
Affiliation(s)
- Dennis Milešević
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
| | - Divya Popat
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
| | - Paul Gellersen
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
| | - Zhihao Liu
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
| | - Joseph Stimson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
| | - Patrick Robertson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
| | - Andrew Green
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
| | - Claire Vallance
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd., Oxford OX1 3TA, United Kingdom
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Wang S, Dauletyarov Y, Krüger P, Horke DA. High-throughput UV-photofragmentation studies of thymine and guanine. Phys Chem Chem Phys 2023; 25:12322-12330. [PMID: 37083208 PMCID: PMC10155487 DOI: 10.1039/d3cp00328k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
High-throughput photofragmentation studies of thymine and guanine were performed at 257 and 343 nm and for a wide range of ionisation laser intensities. Combining a continuous laser-based thermal desorption source with femtosecond multiphoton ionisation using a 50 kHz repetition rate laser allowed us to produce detailed 2D maps of fragmentation as a function of incident laser intensity. The fragmentation was distinctly soft, the parent ions being at least an order of magnitude more abundant than fragment ions. For thymine there was a single dominant fragmentation channel, which involves consecutive HNCO and CO losses. In contrast, for guanine there were several competing ones, the most probable channel corresponding to CH2N2 loss through opening of the pyrimidine ring. The dependence of parent ion abundance on the ionisation laser intensity showed that at 257 nm the ionisation of thymine is a 1 + 1 resonance enhanced process through its open-shell singlet state.
Collapse
Affiliation(s)
- Siwen Wang
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Yerbolat Dauletyarov
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Peter Krüger
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Daniel A Horke
- Institute for Molecules and Materials, Radboud University, Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| |
Collapse
|
6
|
Liu M, O'Reilly D, Schwob L, Wang X, Zamudio-Bayer V, Lau JT, Bari S, Schlathölter T, Poully JC. Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides. Chemistry 2023; 29:e202203481. [PMID: 36478608 DOI: 10.1002/chem.202203481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Understanding how charge and energy, as well as protons and hydrogen atoms, are transferred in molecular systems as a result of an electronic excitation is fundamental for understanding the interaction between ionizing radiation and biological matter on the molecular level. To localize the excitation at the atomic scale, it was chosen to target phosphorus atoms in the backbone of gas-phase oligonucleotide anions and cations, by means of resonant photoabsorption at the L- and K-edges. The ionic photoproducts of the excitation process were studied by a combination of mass spectrometry and X-ray spectroscopy. The combination of absorption site selectivity and photoproduct sensitivity allowed the identification of X-ray spectral signatures of specific processes. Moreover, charge and/or energy as well as H transfer from the backbone to nucleobases has been directly observed. Although the probability of one versus two H transfer following valence ionization depends on the nucleobase, ionization of sugar or phosphate groups at the carbon K-edge or the phosphorus L-edge mainly leads to single H transfer to protonated adenine. Moreover, our results indicate a surprising proton-transfer process to specifically form protonated guanine after excitation or ionization of P 2p electrons.
Collapse
Affiliation(s)
- Min Liu
- CIMAP UMR 6252, CEA/, CNRS/, ENSICAEN/, Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | - David O'Reilly
- CIMAP UMR 6252, CEA/, CNRS/, ENSICAEN/, Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| | | | - Xin Wang
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | | | - J Tobias Lau
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.,Abteilung für Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Germany
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.,University College Groningen, University of Groningen, Groningen, The Netherlands
| | - Jean-Christophe Poully
- CIMAP UMR 6252, CEA/, CNRS/, ENSICAEN/, Université de Caen Normandie, Bd Becquerel, 14070, Caen, France
| |
Collapse
|
7
|
de Faria JC, Paupitz R, van Duin ACT, Bernal MA. Evaluation of the Reax Force-Field for Studying the Collision of an Energetic Proton with the DNA. J Chem Theory Comput 2022; 18:6463-6471. [DOI: 10.1021/acs.jctc.2c00756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jhaison C. de Faria
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Campinas 13083-859, SP, Brazil
| | - Ricardo Paupitz
- Instituto de Geociências e Ciências Exatas de Rio Claro, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro 13506-900, SP, Brazil
| | - Adri C. T. van Duin
- Department of Mechanical Engineering, Chemical Engineering, Engineering Science and Mechanics, Chemistry, Materials Science and Engineering, Penn State University, University Park, State College, Pennsylvania 16802, United States
| | - Mario A. Bernal
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Campinas 13083-859, SP, Brazil
| |
Collapse
|
8
|
Stochastic dynamic quantitative and 3D structural matrix assisted laser desorption/ionization mass spectrometric analyses of mixture of nucleosides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
9
|
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.![]()
Collapse
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
| |
Collapse
|
10
|
Schwob L, Lalande M, Chesnel JY, Domaracka A, Huber BA, Maclot S, Poully JC, Rangama J, Rousseau P, Vizcaino V, Adoui L, Méry A. A tandem mass spectrometer for crossed-beam irradiation of mass-selected molecular systems by keV atomic ions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:043104. [PMID: 29716322 DOI: 10.1063/1.5023182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In the present paper, we describe a new home-built crossed-beam apparatus devoted to ion-induced ionization and fragmentation of isolated biologically relevant molecular systems. The biomolecular ions are produced by an electrospray ionization source, mass-over-charge selected, accumulated in a 3D ion trap, and then guided to the extraction region of an orthogonal time-of-flight mass spectrometer. Here, the target molecular ions interact with a keV atomic ion beam produced by an electron cyclotron resonance ion source. Cationic products from the collision are detected on a position sensitive detector and analyzed by time-of-flight mass spectrometry. A detailed description of the operation of the setup is given, and early results from irradiation of a protonated pentapeptide (leucine-enkephalin) by a 7 keV He+ ion beam are presented as a proof-of-principle.
Collapse
Affiliation(s)
- Lucas Schwob
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Mathieu Lalande
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Jean-Yves Chesnel
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Alicja Domaracka
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Bernd A Huber
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Sylvain Maclot
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | | | - Jimmy Rangama
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Patrick Rousseau
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Violaine Vizcaino
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Lamri Adoui
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| | - Alain Méry
- Normandie Univ., ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Sadr-Arani L, Mignon P, Chermette H, Abdoul-Carime H, Farizon B, Farizon M. Fragmentation mechanisms of cytosine, adenine and guanine ionized bases. Phys Chem Chem Phys 2016; 17:11813-26. [PMID: 25869111 DOI: 10.1039/c5cp00104h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The different fragmentation channels of cytosine, adenine and guanine have been studied through DFT calculations. The electronic structure of bases, their cations, and the fragments obtained by breaking bonds provides a good understanding of the fragmentation process that can complete the experimental approach. The calculations allow assigning various fragments to the given peaks. The comparison between the energy required for the formation of fragments and the peak intensity in the mass spectrum is used. For cytosine and guanine the elimination of the HNCO molecule is a major route of dissociation, while for adenine multiple loss of HCN or HNC can be followed up to small fragments. For cytosine, this corresponds to the initial bond cleavage of N3-C4/N1-C2, which represents the main dissociation route. For guanine the release of HNCO is obtained through the N1-C2/C5-C6 bond cleavage (reverse order also possible) leading to the largest peak of the spectrum. The corresponding energies of 3.5 and 3.9 eV are typically in the range available in the experiments. The loss of NH3 or HCN is also possible but requires more energy. For adenine, fragmentation consists of multiple loss of the HCN molecule and the main route corresponding to HC8N9 loss is followed by the release of HC2N1.
Collapse
Affiliation(s)
- Leila Sadr-Arani
- Université de Lyon, Université Claude Bernard Lyon1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de la Doua, 69100 Villeurbanne, France.
| | | | | | | | | | | |
Collapse
|
13
|
Camillis SD, Miles J, Alexander G, Ghafur O, Williams ID, Townsend D, Greenwood JB. Ultrafast non-radiative decay of gas-phase nucleosides. Phys Chem Chem Phys 2015; 17:23643-50. [DOI: 10.1039/c5cp03806e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
De-excitation of DNA nucleosides on picosecond timescales was measured and found to be twice as fast as the equivalent nucleobases.
Collapse
Affiliation(s)
- Simone De Camillis
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Jordan Miles
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Grace Alexander
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Omair Ghafur
- Institute of Photonics and Quantum Sciences
- Heriot-Watt University
- Edinburgh EH14 4AS
- UK
| | - Ian D. Williams
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| | - Dave Townsend
- Institute of Photonics and Quantum Sciences
- Heriot-Watt University
- Edinburgh EH14 4AS
- UK
- Institute of Chemical Sciences
| | - Jason B. Greenwood
- Centre for Plasma Physics
- School of Mathematics and Physics
- Queen's University Belfast
- Belfast BT7 1NN
- UK
| |
Collapse
|