Mass spectrometry (fragmentation ratios) of DNA base molecules following 80keV proton impact with separation of direct ionization and electron capture processes

Tabet, Jean Claude; Eden, S.; Feil, S.; Abdoul‐Carime, H.; Farizon, B.; Farizon, M.; Ouaskit, S.; Märk, T.D.

doi:10.1016/j.ijms.2010.03.002

Cited by 43 publications

(53 citation statements)

References 42 publications

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“…In the following years, mechanistic studies involving selectively isotope-labeled A were conducted [5][6][7][8] and subsequently the fragmentation patterns of A + , HA + , and A 2+ using various ionization techniques were reported. [9][10][11][12][13][14] The protonated and doubly charged species showed similar reactivity patterns to the singly charged one. Jochims et al determined appearance energies of certain decomposition products of A by photo-ionization mass spectrometry and assigned fragment structures entirely without theoretical support.…”

Section: Introductionmentioning

confidence: 79%

Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics

Bauer

Grimme

2014

J. Phys. Chem. A

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The gas phase fragmentation pathways of the nucleobase adenine upon 70 eV electron ionization are investigated by means of a combined stochastic and first-principles based molecular dynamics approach. We employ no preconceived fragmentation channels in our calculations, which simulate standard electron ionization mass spectrometry (EI-MS) conditions. The reactions observed compare well to a wealth of experimental and theoretical data available for this important nucleic acid building block. All significant peaks in the experimental mass spectrum of adenine are reproduced. Additionally, the fragment ion connectivities obtained from our simulations at least partially concur with results from previous experimental studies on selectively isotope labeled adenines. Moreover, we are able to assign noncyclic structures that are entropically favored and have not been proposed in nondynamic quantum chemical studies before to the decomposition products, which result automatically from our molecular dynamics procedure. From simulations under various conditions it is evident that most of the fragmentation reactions even at low internal excess energy (<10 eV) occur very fast within a few picoseconds.

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Section: Introductionmentioning

confidence: 79%

Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics

Bauer

Grimme

2014

J. Phys. Chem. A

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“…The molecular oven was operated at a lower temperature (400 K measured by a platinum resistance probe) than previous experimental studies which reported no evidence for thermal decomposition of neutral adenine. 19,23 The negative ions produced in the collision region were extracted by a 250 V/cm pulsed electrostatic field towards the entrance of the TOF where they were analysed and detected in single-pulse counting mode. In the present electron transfer experiments, the total energy available for anion excitation (the collision energy in the centre-of-mass frame minus the ionisation energy of potassium) varied from ∼6 up to ∼68 eV.…”

Section: Methodsmentioning

confidence: 99%

Communication: Site-selective bond excision of adenine upon electron transfer

Cunha

Mendes

Silva

et al. 2018

The Journal of Chemical Physics

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This work demonstrates that selective excision of hydrogen atoms at a particular site of the DNA base adenine can be achieved in collisions with electronegative atoms by controlling the impact energy. The result is based on analysing the time-of-flight mass spectra yields of potassium collisions with a series of labeled adenine derivatives. The production of dehydrogenated parent anions is consistent with neutral H loss either from selective breaking of C-H or N-H bonds.

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“…The ratio of a particular ionization process to the total ionization is called the branching ratio for that process, for which there have been several experimental investigations recently [8,[69][70][71]. It is possible to distinguish between various ionization mechanisms using TDDFT.…”

Section: Ionizationmentioning

confidence: 99%

“…The track-structure simulations require knowledge of the interaction cross section (or ionization and excitation cross sections) for the medium, which can be explicitly calculated, approximated from the dielectric function, or taken from experimental data [31,32,63,[66][67][68]. An important consideration for secondary damage, however, is that the interaction cross section is a↵ected by various ionization mechanisms [8,[69][70][71][72][73][74][75]. Therefore, correctly modeling the overall damage by radiation requires a proper treatment of ionization.…”

Section: Introductionmentioning

confidence: 99%

Time-dependent density-functional-theory investigation of the collisions of protons and α particles with uracil and adenine

et al. 2017

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Time-dependent density functional theory was employed to study the e↵ects of proton and ↵-particle radiation on uracil and adenine. This method has the advantage of treating nuclear motion and electronic motion simultaneously, allowing for the study of electronic excitation, charge transfer, ionization, and nuclear motion. Particle energies were surveyed in the range of 15-500 keV for protons and 100-2000 keV for ↵-particles in conjunction with impact points both on and o↵ carbon bonds in order to investigate the electron and nuclear dynamics of irradiated molecules and the form and quantity of transferred energy. The stopping power, energy transferred, and ionization were found and the relationship between incident particle energy and electron density of to the target molecule was characterized for proton and ↵-particle radiation incident on adenine and uracil.

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Mass spectrometry (fragmentation ratios) of DNA base molecules following 80keV proton impact with separation of direct ionization and electron capture processes

Cited by 43 publications

References 42 publications

Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics

Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics

Communication: Site-selective bond excision of adenine upon electron transfer

Time-dependent density-functional-theory investigation of the collisions of protons and α particles with uracil and adenine

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