Molecular dynamics simulations of native ubiquinone-10 binding in the photosynthetic reaction center of Rhodobacter sphaeroides are presented that support the theory that the neutral and radical anionic quinones Q(B) and Q(B) (.-) bind in different locations. The differences in binding are attributed to differing protonation states of the nearby amino acids GLUL212?, and ASP L213. Q(B) binding at the ''dark-adapted" Q(B) Site observed by Stowell et al. is most consistent with protonation of GLUL212. Q(B) (.-) binding at the experimentally observed "light-adapted'' Q(B)(.-) Site is consistent only with protonation of both GLU L212, and ASP L313. The experimentally established pH dependence of electron-transfer rate, combined with our MD results, implies that protonation of ASP L213 must occur before electron transfer. Additionally, the molecular dynamics results suggest that movement of the semiquinone anion Q(B) (.-) between sites (for different amino acid protonation states) is spontaneous near room temperature and cannot by itself account for the higher of two experimentally observed activation energies for electron transfer from Q(A) to Q(B).