INDO studies have been carried out for the elucidation of the difference in the nonbonded polarizable environment of Q(I) (Q(A)) and Q(II) (Q(B)) in thylakoid discs in chloroplast (in bacteria). The free energy of reduction of Q(II) by Q(I)(-) (-0.13 eV in vivo) has been explained by considering a more polar environment for Q(I). Three environmental features have been accommodated. Each plastoquinone is hydrogen bonded to the imidazole ring of a histidine molecule that serves as the most proximate environment. The RC protein surrounding the plastoquinone has been viewed as a dielectric continuum. As the most logical way of accounting for the difference in the protein environment of Q(I) and Q(II), two additional peptide fragments have been symmetrically placed on the two sides of the plastoquinone ring plane of Q(I). Our calculation indicates that the protein environment is closer to Q(I) than to Q(II). The proximity indicates that Q(I) must be tightly bound as its escape would be prohibited by steric effect, and Q(II) would be held much less tightly within a larger cage. If no new bond is formed while Q(II) acquires an electron, the product Q(II)(-) would be bound to the protein cage more strongly than Q(II) by an amount of the order of 1 eV.