Chemical dynamics simulations of energy transfer in collisions of protonated peptide-ions with a perfluorinated alkylthiol self-assembled monolayer surface

Classical trajectory simulations are performed to study energy transfer in collisions of protonated diglycine, gly-H, and dialanine, ala-H, ions with a fluorinated octanethiol self-assembled monolayer (F-SAM) surface for collision energies E in the range of 5-70 eV and incident angles θ of 0 and 45° with respect to the surface normal. Both explicit-atom (EA) and united-atom (UA) models were used to represent the F-SAM surface. The simulations show the distribution of energy transfer to the peptide-ion's internal degrees of freedom, ΔE, to the surface, ΔE, and in peptide-ion translation, E, are very similar for gly -H, and ala-H. The average percentage energy transferred to ΔE and E increases and decreases, respectively, with an increase in E, while the average percentage energy transfer to ΔE is nearly independent of E. Changing θ from 0 to 45° decreases and increases the percentage of energy transfer to ΔE and E, respectively, but has little change in the transfer to ΔE. Average percentage energy transfer to the surface is found to approximately depend on E according to exp(-b/E). Comparisons with previous simulations show that peptide-H collisions with the EA F-SAM model transfer approximately a factor of 2 more energy to ΔE than do collisions with the hydrogenated SAM, that is, H-SAM. Replacing the mass of the F atoms by that of a H atom in the simulations, without changing the potential, shows that the different ΔE energy transfer efficiencies for the F-SAM and H-SAM surfaces is a mass effect. The simulations for ala-H colliding with the EA F-SAM surface give P(ΔE) distributions in good agreement with previous experiments and an average transfer to ΔE of 15% as compared with the experimental value of 21%. The UA F-SAM model gives energy transfer efficiencies in qualitative agreement with those of the EA model, but there are important quantitative differences. © 2008 American Chemical Society.