Results of 4.2 K hole burning, chemical reduction (sodium dithionite, in dark and with illumination), and oxidation (ferricyanide) experiments are reported for the isolated PS II reaction center containing five chlorophyll (Chl) molecules (RC-5). Q(y) states at 679.6 and 668.3 nm are identified as being highly localized on pheophytin a of the D-1 branch (Pheo(1)) and pheophytin a of the D-2 branch (Pheo(2)), respectively. The Pheo(1)-Q(x) and Pheo(2)-Q(x) transitions were found to lie on the low and high energy sides of the single Pheo-Q(x) absorption band, at 544.4 and 541.2 nm, respectively. The Q(y) band of the 684 nm absorbing Chl, which is more apparent in absorption in RC-5 than in RC-6 samples, is assigned to the peripheral Chl on the D1 side. The results are consistent with that peripheral Chl being Chl, (Stewart, D. H.; Cua, A.; Chisholm, D. A.; Diner, B. A.; Bocian, D. F.; Brudvig, G. W. Biochemistry 1998, 37, 10040). The results indicate that P680, the primary electron donor, is the main acceptor for energy transfer from the Pheo(1)-Q(y) state and that excitation energy transfer from the Pheo(1)-Q(y) state and P680* to the 684 nm Chl is inefficient. It is concluded that the procedure used to prepare RC-5 has only a small effect on the energies of the Q(y) states associated with the core cofactors of the 6-Chl RC as well as the 684 nm Chl. Implications of the results for the multimer model (Durrant, J. R.; Klug, D. R; Kwa, S. L. S.; van Grondelle, R.; Porter, G.; Dekker, J. P. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 4798) are considered. In that model the Q(y)-states of the core are significantly delocalized over several cofactors. The results presented provide no support for this model.