NH ₄ ⁺ + CH ₄ gas phase collisions as a possible analogue to protonated peptide/surface induced dissociation

Results are reported for a direct dynamics simulation of NH ₄ ⁺ + CH ₄ gas phase collisions. We interpret the results with protonated peptide/hydrogenated alkanethiolate self-assembled monolayer (H-SAM) surface collisions in mind. Previous theoretical studies of such systems have made use of nonreactive surfaces, and therefore, our goal is to investigate the types and likelihood of peptide/H-SAM reactions. In that vein, the NH ₄ ⁺ + CH ₄ reaction represents a simple gas phase system which includes many of the important interactions present in protonated peptide/H-SAM surfaces. Thirty-seven open pathways are seen in the 5-35 eV collision energy range. An energy dependence on the likelihood of forming CN bonds is found. This type of bonding could deposit both the peptide and its molecular fragments on the H-SAM surface. For our gas phase collision system, around 50% of the trajectories result in the formation of CN bonds. For all collision energies in which reactive scattering occurs, CN bond formation is an important reaction pathway.