Broken-symmetry density functional calculations have been performed on the [Fe-a3(4+),Cu-B(2+)] state of the dinuclear center (DNC) for the P-R -> F part of the catalytic cycle of ba(3) cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H2O molecules in the DNC affects the pK(a) values of the residue side chains of Tyr237 and His376(+), which are crucial for proton transfer/pumping in ba(3) CcO from Tt. The calculated lowest energy structure of the DNC in the [Fe-a3(4+),Cu-B(2+)] state (state F) is of the form Fe-a3(4+)=O2-center dot center dot center dot Cu-B(2+), in which the H2O ligand that resulted from protonation of the OH- ligand in the P-R state is dissociated from the Cu-B(2+) site. The calculated Fe-a3(4+)=O2- distance in F (1.68 angstrom) is 0.03 angstrom longer than that in PR (1.65 angstrom), which can explain the different Fe-a3(4+)=O2- stretching modes in P (804 cm(-1)) and F (785 cm(-1)) identified by resonance Raman experiments. In this F state, the Cu-B(2+)center dot center dot center dot O2- (ferryl-oxygen) distance is only around 2.4 angstrom. Hence, the subsequent O-H state [Fe-a3(3+)-OH--Cu-B(2+)] with a mu-hydroxo bridge can be easily formed, as shown by our calculations.