The MP2/6-311++G(2df,2pd) level of theory was used to calculate intermolecular potential curves between CF 4, as a model for the C and F atoms of a fluorinated alkane surface, and CH 4, NH 3, NH 4 +, H 2CO, and H 2O 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 CF 4 is treated as a united atom (UA), were developed by isotropically averaging the CF 4 orientation for each of the EA potential energy curves. The intermolecular potential energy curves calculated for CF 4 are compared with curves calculated previously for CH 4 interacting with the same molecules, to consider the relative efficiency of energy transfer for protonated peptide ion collisions with hydrogenated and fluorinated alkane surfaces.