Dynamics of Energy Transfer and Soft-Landing in Collisions of Protonated Dialanine with Perfluorinated Self-Assembled Monolayer Surfaces

Chemical dynamics simulations are reported which provide atomistic details of collisions of protonated dialanine, ala₂-H⁺, with a perfluorinated octanethiolate self-assembled monolayer (F-SAM) surface. The simulations are performed at collision energies E_i of 5.0, 13.5, 22.5, 30.00, and 70 eV, and incident angles 0° (normal) and 45° (grazing). Excellent agreement with experiment (J. Am. Chem. Soc., 2000, 122, 9703-9714) is found for both the average fraction and distribution of the collision energy transferred to the ala₂-H⁺ internal degrees of freedom. The dominant pathway for this energy transfer is to ala₂-H⁺ vibration, but for E_i = 5.0 eV ∼20% of the energy transfer is to ala₂-H⁺ rotation. Energy transfer to ala₂-H⁺ rotation decreases with increase in E_i and becomes negligible at high E_i. Three types of collisions are observed in the simulations: i.e. those for which ala₂-H⁺ (1) directly scatters off the F-SAM surface; (2) sticks/physisorbs on/in the surface, but desorbs within the 10 ps numerical integration of the simulations; and (3) remains trapped (i.e. soft-landed) on/in the surface when the simulations are terminated. Penetration of the F-SAM by ala₂-H⁺ is important for the latter two types of events. The trapped trajectories are expected to have relatively long residence times on the surface, since a previous molecular dynamics simulation (J. Phys. Chem. B, 2014, 118, 5577-5588) shows that thermally accommodated ala₂-H⁺ ions have an binding energy with the F-SAM surface of at least ∼15 kcal mol^-1.