Results are reported for a direct dynamics Simulation of NH4+ + CH4 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 noreactive surfaces, and therefore, our goal is to investigate the types and likelihood of peptide/H-SAM reactions. In that vein, the NH4+ + CH4 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. Ail energy dependence oil 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.