| Classical trajectory simulations are performed to study energy transfer in collisions of protonated diglicine, (gly)2H+, and dialanine, (ala)2H+, ions with the surfaces, such as diamond {lcub}111{rcub} and perfluorinated alkane self-assembled monolayer (F-SAM), for a collision energy Ei in the range of 5-110 eV and incident angles of 0° and 45° with respect to the surface normal. Energy transfer efficiency and distribution is studied.; In the peptide ion collision with diamond {lcub}111{rcub} surface, the distribution of energy transfer to vibrational/rotational degrees of freedom, Delta Eint, and to the surface, DeltaEsurf, and of energy remaining in peptide ion translation, Ef, are very similar for (gly)2H+ and (ala)2H +. The AMBER and AM1 models for the (gly)2H+ intramolecular potential give statistically identical energy transfer distributions. The energy transfer efficiencies to DeltaEint, Delta Esurf, and Ef are similar for (gly)nH+, n=1-5. The energy transfer distributions for (gly)2H+ + diamond {lcub}111{rcub} collisions depend on the collision angle and do not scale in accord with the normal component of the collision energy Ein for collisions with thetai of 0 and 45 degrees.; This research initiates the development of F-SAM surface. The MP2/6-311++G(2df,2pd) level of theory was used to calculate intermolecular potential curves between CF4, as a model for the C and F atoms of a fluorinated alkane surface, and CH4, NH3, NH4+, H 2CO, and H2O as models for different types of atoms and functional groups comprising protonated peptide ions. Explicit atom (EA) and united atom (UA) which CF4 is treated as a united atom were developed for F-SAM surfaces. An intermolecular potential for the interaction of a protonated peptide ion with a fluorinated alkane surface may be constructed by fitting these potential energy curves with two-body potentials curves.; In peptide ion collision with F-SAM surface, simulation results showed the energy transfer efficiencies to DeltaEint is independent with low initial energies. Energy transfer to peptide ion's internal modes is ∼17% for EA model and ∼22% for UA model which is close to experimental results. F-SAM transfer more energy to peptide ion's internal modes than H-SAM.; An intermolecular analytical potential for soft landing, where peptide ions are "trapped" by the F-SAM surface and can be released by bombing/thermal desorption, are developed following above procedure but different fitting focus. MP2/aug-cc-pVTZ level of theory is applied to calculate intermolecular potential curves between model molecules of F-SAM and peptide ion for accurate description of attraction well in the potential energy curves. |
