During the past few years nitrate chemical ionization has been used to detect highly oxidized products from OH-and O-3-initiated alkene autoxidation. These have been speculated to play a significant role in atmospheric aerosol formation. As less oxidized autoxidation products have not been detected using nitrate chemical ionization, and the absolute concentrations of the highly oxidized species are as yet unknown, other reagent ions, such as acetate, are needed both to verify the detection efficiency of nitrate chemical ionization and to measure the less oxidized compounds. Here we compare the formation free energies of the acetate and nitrate clusters of several atmospherically relevant RO2 intermediates and products derived from cyclohexene ozonolysis, calculated at the omega B97xD/aug-cc-pVTZ level of theory. We found that, for the molecules with one hydrogen bonding peroxy acid group, the binding with nitrate is on average 7.5 kcal/mol weaker than with acetate and the binding is on average 10.5 kcal/mol weaker for molecules with two hydrogen bonding peroxy acid groups. We also calculated the deprotonation energies of the RO2 intermediates and the closed-shell products and found that acetate is able to deprotonate almost all of these molecules, while deprotonation with nitrate is (as expected for the conjugate base of a strong acid) not favorable.