Bacteriorhodopsin, a chromoprotein having retinal as chromophore is linked to protein opsin through a protonated Schiff base, and undergoes a cyclic photoreaction on light absorption involving a number of intermediate species. The conformational preferences of the protonated and deprotonated Schiff bases of all-trans and 13-cis retinal withn-pentylamine as model for lysine have been investigated using molecular orbital PCILO (Perturbative Configuration Interaction of Localised Orbitals) method. The theoretical calculations reveal that there is an intrinsic differential flexibility between the protonated and deprotonated Schiff bases irrespective of the retinal isomers. The deprotonation of the Schiff base enhances the flexibility of the chromophore in the molecule. Based upon this information and that there are no major changes in the conformation of the protein opsin, two models for the photoreaction cycle involving intermediates of different structures have been proposed. Of these, experimental evidences seem to favour model 1 in which deprotonation and notrans-cis isomerisation accompanies the primary photochemical event. In other words, the intermediate species of the photoreaction cycle of bacteriorhodopsin have all-trans retinal as the chromophore with varying degree of non-covalent interaction with the protein opsin.