Density functional theory (DFT) calculations have been performed on a number of Schiff base structures related to the retinal Schiff base in bacteriorhodopsin (BR). The proton affinity (PA) of the Schiff base group was calculated in species with different lengths of the conjugated double-bond system and at different cis/trans isomerization states. The results show that the length of the conjugated electronic structure has a positive effect on the PA of the system which can be related to the more delocalized electronic structures in the longer chains. Although there is no significant difference of PA between different cis/trans isomers at single or double bonds in the main chain of the polyene structure, very pronounced PA changes are predicted during the rotation of these bonds. The calculations show that the rotation of the single bond adjacent to the Schiff base group significantly decreases the PA of the Schiff base. The results of closed-shell DFT calculations indicate that the rotation of the second double bond in the chain has a completely contrary effect on the PA and predict an effective increase of PA value during this rotation. The open-shell DFT calculations, on the other hand, although indicating a different pattern of PA changes, do not show any significant decrease in the PA of the Schiff base during the rotation of the double bond, either. The predicted changes of the calculated PA values are explained on the basis of bond order characteristics and charge distributions along the polyene structure in each case.