The exciton Hamiltonian of the chlorophyll (Chl) and pheophytin (Pheo) pigments in the reaction center (RC) of photosystem II is computed based on recent crystal structures by using the Poisson-Boltzmann/quantum-chemical method. Computed site energies largely confirm a previous model inferred from fits of optical spectra, in which Chl has the lowest site energy, while that of Pheo is higher than that of Pheo. The latter assignment has been challenged recently under reference to mutagenesis experiments. We argue that these data are not in contradiction to our results. We conclude that Chl is the primary electron donor in both isolated RCs and intact core complexes at least at cryogenic temperatures. The main source of asymmetry in site energies is the charge distribution in the protein. Because many small contributions from various structural elements have to be taken into account, it can be assumed that this asymmetry was established in evolution by global optimization of the RC protein.
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