Electron impact ionisation cross sections of fluoro-substituted nucleosides

Abstract

We report calculated electron-impact ionisation cross sections (EICSs) for 2-deoxycytidine (Cyt), 2-deoxy-5-fluorocytidine (fCyt) and 2 ,2-difluorocytidine (gemcitabine, Gem) from threshold to 10 keV. We compare the Deutsch-Märk (DM) and the binary-encounter-Bethe (BEB) methods used to obtain these cross sections. The methods yield excellent agreement with each other, within 3−4% at the cross section maxima. In particular, the DM cross sections for Cyt, fCyt and Gem yield maxima of 29.88Å 2 at 79 eV, 28.96Å 2 at 82.2 eV and 29.51Å 2 at 83.4 eV, respectively, whereas the BEB cross sections yield maxima of 28.89Å 2 at 87.6 eV, 27.97Å 2 at 91.6 eV and 29.02Å 2 at 93.4 eV, respectively. In addition, we compute EICSs for small sequences built from the considered nucleosides, i.e. for the sequences Cyt-Cyt, fCyt-Cyt, Cyt-fCyt, Gem-Cyt and Cyt-Gem. We find that the resulting EICSs differ only slightly between different sequences of the same constituents. Moreover, they can be approximated with an accuracy within 6% by simply adding the EICSs of individual molecular subsystems. Finally, we find that alterations in the ionisation energy due to the presence of an aqueous solvent can be substantial and may hence also considerably affect the resulting EICSs especially at low energies close to the ionisation threshold.

Special issue: Dynamics of systems on the nanoscale (2018). Editorial

“…These software packages have been designed to become powerful and universal instruments of computational research in the field of MBN Science, which should play a role of a "virtual microscope" and a "camera" capable to explore, simulate, record and visualize both structure and dynamics of the MBN-world with an atomistic level of accuracy, in order to both reproduce its known features and predict the new ones. In this Topical Issue, many contributions [12][13][14][15][16][17][18][19][20][21][22][24][25][26][27][28][29][30][31][32][33][34][35] provide case studies conducted with these packages and demonstrate their application to a broad variety of topical areas in MBN science as listed at the beginning of this Editorial. To be noted that these universal and powerful software packages are fully applicable to a broad variety of the topical areas of the MBN Science listed above in the introductory part of the Editorial.…”

“…Gemcitabine is a therapetic based on cytidine, which is doubly fluorinated at the sugar moiety [31]. Huber et al [32] have calculated the electron impact ionization cross sections of cytidine, singly and doubly fluorinated cytidine (i.e. Gemcitabine) and different variations of respective dimer sequences using the Deutsch-Märk and the binaryencounter-Bethe methods.…”

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

“…Areas of Applications: As described above, the ab initio scattering methods have been utilized mainly to calculate the cross sections of elastic and inelastic scattering from single atoms and few-atom molecular targets. The semiempirical models based on the Deutsch−Mark and BED/BEB formalism have been widely used to evaluate electron-impact ionization cross sections for various atomic and molecular targets, including simpler molecules (e.g., H 2 , CH 4 , or CO 2 ) and more complex systems, such as DNA building blocks 218,219 and organometallic compounds, 220 thus overcoming the limitations of ab initio scattering theory methods for calculating molecular ionization cross sections. The Rudd model has been used, in particular, to calculate ionization cross sections of simple diatomic and few-atom molecular targets 207 and DNA nucleobases.…”

Dependence of Electronic Properties of DNA Single Strands on Size and Environment

“…18 On the other hand, electron impact ionization processes constitute dominant processes for electron molecule scattering phenomena. In this respect, the (vertical) ionization energies are an important parameter for the description of these processes, especially concerning the eventual differences between the gas phase and the condensed state; for example, see ref 19.…”