Abstract: Molecular dynamics (MD) simulations were performed to provide atomic scale insight in the initial interaction between hydroxyl radicals (OH) and peptide systems in solution. These OH radicals are representative reactive oxygen species produced by cold atmospheric plasmas. The use of plasma for biomedical applications is gaining increasing interest, but the fundamental mechanisms behind the plasma modifications still remain largely elusive. This study helps to gain more insight in the underlying mechanisms of plasma medicine but is also more generally applicable to peptide oxidation, of interest for other applications. Combining both reactive and nonreactive MD simulations, we are able to elucidate the reactivity of the amino acids inside the peptide systems and their effect on their structure up to 1 μs. Additionally, experiments were performed, treating the simulated peptides with a plasma jet. The computational results presented here correlate well with the obtained experimental data and highlight the importance of the chemical environment for the reactivity of the individual amino acids, so that specific amino acids are attacked in higher numbers than expected. Furthermore, the long time scale simulations suggest that a single oxidation has an effect on the 3D conformation due to an increase in hydrophilicity and intra- and intermolecular interactions.

Abstract: Electron energy loss spectroscopy was used to investigate the bonding of plasma deposited carbon films. The experimental conditions include the use of a specific collection angle for which the shape of the spectra is free of the orientation dependency usually encountered in graphite due to its anisotropic structure. The first quantification process of the energy loss near-edge structure was performed by a standard fit of the collected spectrum, corrected for background and multiple scattering, with three Gaussian functions followed by a comparison with the graphite spectrum obtained under equivalent experimental conditions. In a second approach a fitting model directly incorporating the background subtraction and multiple scattering removal was applied. The final numerical results are interpreted in view of the deposition conditions of the films and the actual fitting procedure with the related choice of parameters.