Abstract The role of the separation of the protogenic groups and side chain chemistry on proton dissociation and the energetics of proton transfer is compared on single side chain fragments of 3M multi acid side chain (MASC) ionomers. Three ionomers were considered each containing a bis(sulfonyl imide) group and a sulfonic acid group with structural and chemical differences mediating protogenic group separation: two structural isomers with protogenic group separation determined by the location of the sulfonic acid group on an aromatic ring (side chains: O(CF2)4SO2(NH)SO2C6H4SO3H) with the sulfonic acid group located in either the meta or the ortho position) and a perfluorinated ionomer (PFIA) with protogenic groups separated by CF2 groups (side chain: O(CF2)4SO2(NH)SO2(CF2)3SO3H). Optimized (B3LYP/6-311G**) geometries on isolated fragments revealed that differences in side chain chemistry and proximity of the protogenic groups resulted in charge delocalization effects that facilitated proton dissociation at low hydration levels. Specifically, direct hydrogen bonding between the acid groups in the ortho bis acid and electron withdrawing CF2 groups in PFIA allowed for first proton dissociation at a lower hydration than the meta bis acid which lacked these effects. However, the tightly held intramolecular hydrogen bond in the ortho bis acid promoted interactions between water molecules and precluded dissociation of the second proton which required more water molecules to occur than the other MASC ionomers with more widely spread distribution of charge and hydrogen bonding. This was also realized through potential energy surface scans of proton transfer for second proton dissociation where the energetic penalty associated with proton transfer was found to be considerably higher in the ortho bis acid than the other MASC ionomers. The calculations reveal that the electron withdrawing CF2 units between protogenic groups in the PFIA not only promote proton dissociation but also do not sterically fix the protogenic group separation, as with the aromatic-based MASC ionomers, allowing for the development of a hydrogen bond network that readily adjusts for the transfer of charge at low hydration levels.