Classical chemical dynamics simulation results are presented for the thermal desorption kinetics and energetics of protonated dialanine ions (ala-H) physisorbed on/in a perfluorinated self-assembled monolayer (F-SAM) surface. Previously developed analytic potentials were used for the F-SAM and the ala-H/F-SAM intermolecular interaction, and the AMBER valence force field was used for ala-H. The activation energy, E = 13.2 kcal/mol, determined from the simulations is consistent with previous simulations of the ala-H/F-SAM binding energy. The A-factor, 7.8 × 10 s, is about an order of magnitude lower than those representative of small molecule desorption from metal and semiconductor surfaces. This finding is consistent with the decreased entropies of ala-H and the F-SAM upon desorption. Using the Arrhenius parameters for ala-H desorption from the F-SAM, the lifetime of ala-H adsorbed on the F-SAM at 300 K is 5 × 10 s. Larger peptide ions are expected to have longer adsorption lifetimes.
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