The effect of the methyl substitutions at different carbon atoms of the polyene chain of the retinal Schiff base has been studied on the structure, charge distribution, and proton affinity (PA) in a Schiff base model with the same number of conjugated double bonds (six conjugated double bonds including the Schiff base group). The methyl groups were added to the nitrogen atom and/or different carbon atoms along the main chain, and the results were compared to those of the retinal Schiff base. To study the effect of the polarization functions on hydrogen atoms, all of the structures were studied using 6-31G* and 6-31G** basis sets at the Becke3LYP (B3LYP) level of theory. For each optimized model, the PA was then calculated on the basis of the difference of the total energy of the protonated and unprotonated species. The influence of the zero-point energy corrections on the PA values was also examined at the same level of theory. The results show that, for all species, the application of the larger basis set (6-31G**) does not significantly influence the structures and the derived charges. Utilization of the larger basis set, however, results in PAs which are, by about 2.0 kcal/mol, systematically higher than the corresponding values obtained from the B3LYP/6-31G* level of theory. The consideration of the thermal energy corrections in the PA calculation, on the other hand, systematically shifts the PA, by about 9.0 kcal/mol, to higher values. The effects of the applied basis set and zero-point energy corrections, therefore, can be neglected in the calculation of the relative PA values. The methyl substitutions have substantial effects on the calculated PA of the studied Schiff base structures. On the basis of the calculated PA values of our models, the presence of at least two methyl groups on the terminal carbon atom of the conjugated chain is of great importance in order to obtain a PA value close to the retinal Schiff base. These groups should be considered in the theoretical studies of the pK(a) change in this system. The effect of the methyl groups on the overall shape of the chromophore was also found to be significant. These structural features combined with the stabilizing effects of the methyl groups on the positive charge of the main chain potentially influence the isomerization barriers in the retinal Schiff base. Therefore, the location and amount of the twist in the backbone of the chromophore, and consequently the pK(a) of the Schiff base group, can be manipulated by the protein environment via steric interactions between the methyl groups and the binding pocket of retinal proteins such as bacteriorhodopsin.