Fragmentation patterns of core-ionized thymine and 5-bromouracil (original) (raw)
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Molecular fragmentation of pyrimidine derivatives following site-selective carbon core ionization
Journal of Electron Spectroscopy and Related Phenomena, 2011
Ionization-site-dependent fragmentation of three cyclic biomolecules -uracil, 5-bromouracil and thymine -has been studied using electron-energy-resolved photoelectronphotoion-photoion coincidence spectroscopy. Previous studies concerning ionization site dependent fragmentation have mainly been carried out with linear molecules. The results reported here show that all studied molecules have dicationic fragmentation channels whose intensity depends on the initial core-ionization site, although these channels cover only a relatively small fraction of the total fragment yield. The present study shows on one hand, that it is often the surrounding bond(s) of the ionized atom that will break following the initial core ionization, and on the other hand, that some specific fragmentation channels can display strong site-dependency where there is no direct correlation between the ionization site and the bond breakage locations.
Fragmentation of thymidine induced by ultraviolet photoionization and thermal degradation
Fragmentation of gas phase thymidine at different temperatures was studied with vacuum ultraviolet radiation and time-of-flight spectroscopy. Partial ion yield measurements were carried out in order to study the appearance energies of thymidine and its main fragments. The appearance energies of thymi-dine and its deoxyribose-and thymine-based fragments were determined to be 8.39, 8.77 and 8.81 eV, independently of temperature. The thermal decomposition of the sample was observed to start around 138–139 • C and it was explained by the breakage of the glycosidic bond, accompanied by hydrogen transfer from the deoxyribose ring to the thymine base.
Journal of Physics B: Atomic, Molecular and Optical Physics, 2011
A simple statistical model describing the dissociation of molecular dications into correlated fragment pairs has been developed. This model is based on a combinatory approach in which all possible fragments are enumerated and is refined by taking into account the initial structure of the parent molecule, considering the number of chemical bonds to be broken to give rise to the fragments. We show how this model can be used as a tool to help interpreting experimental results of coincidence experiments. It shows that dissociation of doubly ionized molecules upon 100 keV proton irradiation is dominated by statistical processes but it also enables an easy identification of the dissociation products originating from non-statistical processes requiring further investigation, possibly conveying information on the radiation-molecule interaction itself. Confidential: not for distribution.
Cross sections for ionization and ionic fragmentation of pyrimidine molecules by electron collisions
The European Physical Journal D, 2012
The electron impact mass spectroscopy and the total ion collection measurements were used to investigate the ionization and ionic fragmentation of the pyrimidine, C4H4N2, molecules in the gas phase. The cation mass spectra were measured in the 10−85 amu range and the observed mass peaks assigned to corresponding ionic fragments. The most abundant cation in the mass spectra is the parent cation, C4H4N + 2 , at 80 amu. The appearance energies of the ionic fragments were determined and the possible fragmentation processes are discussed. The electron impact absolute total and partial ionization cross sections in pyrimidine were obtained over the energy range from the respective ionization thresholds up to 150 eV.
Electron transfer-induced fragmentation of thymine and uracil in atom–molecule collisions
Physical Chemistry Chemical Physics, 2011
Ion-pair formation has been studied in hyperthermal (30-100 eV) neutral potassium collisions with gas phase thymine (C 5 H 6 N 2 O 2) and uracil (C 4 H 4 N 2 O 2). Negative ions formed by electron transfer from the alkali atom to the target molecule were analysed by time-of-flight (TOF) mass spectrometry. The most abundant product anions are assigned to CNO À and (U-H) À /(T-H) À and the associated electron transfer mechanisms are discussed. Special emphasis is given to the enhancement of ring breaking pathways in the present experiments, notably CNO À formation, compared with free electron attachment measurements.
Fragmentation patterns of core ionized uracil
International Journal of Mass Spectrometry, 2011
Photofragmentation of the uracil molecule following carbon 1s core ionization and the subsequent Auger deacy has been investigated. The applied technique, photoelectron–photoion–photoion coincidence (PEPIPICO) spectroscopy allows simultaneous detection of momentum-correlated photoions together with the photoelectron and makes possible a detailed investigation of different fragmentation processes. In order to help the fragment identification, also uracil where one of the carbon atoms
The Journal of Physical Chemistry A, 2014
We report experimental and theoretical studies on ring cleavage enhancement in collisions of potassium atoms with uracil/thymine to further increase the understanding of the complex mechanisms yielding such fragmentation pathways. In these electron transfer processes time-of-flight (TOF) negative ion mass spectra were obtained in the collision energy range 13.5−23.0 eV. We note that CNO − is the major ring breaking anion formed and its threshold formation is discussed within the collision energy range studied. Such a decomposition process is supported by the first theoretical calculations to clarify how DNA/RNA pyrimidine base fragmentation is enhanced in electron transfer processes yielding ion-pair formation.
Journal of The American Society for Mass Spectrometry, 2014
Alkylation and oxidation constitute major routes of DNA damage induced by endogenous and exogenous genotoxic agents. Understanding the biological consequences of DNA lesions often necessitates the availability of oligodeoxyribonucleotide (ODN) substrates harboring these lesions, and sensitive and robust methods for validating the identities of these ODNs. Tandem mass spectrometry is well suited for meeting these latter analytical needs. In the present study, we evaluated how the incorporation of an ethyl group to different positions (i.e., O 2 , N3 and O 4) of thymine and the oxidation of its 5-methyl carbon impact collisionally activated dissociation (CAD) pathways of electrospray-produced deprotonated ions of ODNs harboring these thymine modifications. Unlike an unmodified thymine, which often manifests poor cleavage of the C3′-O3′ bond, the incorporation of an alkyl group to the O 2 position and, to a much lesser extent, the O 4 position, but not the N3 position of thymine, led to facile cleavage of the C3′-O3′ bond on the 3′ side of the modified thymine. Similar efficient chain cleavage was observed when thymine was oxidized to 5-formyluracil or 5-carboxyluracil, but not 5-hydroxymethyluracil. Additionally, with the support of computational modeling, we revealed that proton affinity and acidity of the modified nucleobases govern the fragmentation of ODNs containing the alkylated and oxidized thymidine derivatives, respectively. These results provided important insights into the effects of thymine modifications on ODN fragmentation.