Photosystem II (PSII) conducts the light-driven oxidation of water and reduction of plastoquinone. Difference Fourier transform infrared (FT-IR) spectroscopy can be used to obtain information about structural changes which occur in protein and cofactors when charge separation occurs. The focus of this work was the assignment of vibrational lines to two different species in PSII: the tyrosyl radical, Z ., and the plastosemiquinone anion radical, Q(A)(-) Difference FT-m experiments were conducted with cyanobacterial PSII samples, in which the tyrosine ring was uniformly C-13-labeled, in which tyrosine was C-13-labeled at carbon 4, and in which plastoquinone was methyl-deuterated. At 80 K, difference FT-LR spectra reflect the oxidation of chlorophyll/carotenoid and the one-electron reduction of Q(A); no significant D or Z contribution to the spectrum is observed under these conditions. At 264 K, difference FT-IR spectra reflect the oxidation of redox-active tyrosines Z and D; no significant Q(A)(-) contribution is observed under these conditions. At 80 K, isotope-induced shifts were observed in spectral features at 1482 and 1469 cm(-1) upon deuteration of plastoquinone. At 264 K, isotope-induced shifts were observed in a 1478 cm(-1) line upon C-13- labeling of tyrosine, but little change was observed upon plastoquinone deuteration. These data support the assignment of a positive 1478 cm(-1) line to a tyrosyl radical vibrational mode and positive 1482 and 1469 cm(-1) lines to plastosemiquinone anion vibrational modes. Hybrid Hartree-Fock/density functional calculations of p-cresyl radical's vibrational frequencies and isotopic frequency shifts support this assignment.