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+, H2CO, and H2O as models for different types of atoms and functional groups comprising protonated peptide ions. This level of theory was tested by comparisons with the MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVTZ theories. Explicit-atom (EA) analytic potential energy functions were then derived by fitting these potential energy curves with two-body potentials between the atoms of the two interacting molecules. An intermolecular potential for the interaction of a protonated peptide ion with a fluorinated alkane surface may be constructed from these two-body potentials. Intermolecular potentials, for which CF4 is treated as a united atom (UA), were developed by isotropically averaging the CF4 orientation for each of the EA potential energy curves. The intermolecular potential energy curves calculated for CF4 are compared with curves calculated previously for CH4 interacting with the same molecules, to consider the relative efficiency of energy transfer for protonated peptide ion collisions with hydrogenated and fluorinated alkane surfaces.