Geometry, reorganization energy, and vibrational and electronic spectra of pigment molecules in bacterial photosynthetic reaction centers (Rhodobacter sphaeroides) are determined using quantum chemical methods. B3LYP calculations on a slightly truncated form of bacteriochlorophyll a give vibrational modes at 23, 40, 64, and 128 cm(-1), which we conclude correspond to those seen in resonance Raman (RR) spectra of reaction centers with labeled cofactor atoms, and, as oscillations, in optical transient spectra. On heavy atom substitution at the axial imidazole connection to the protein, a mode with considerable contribution of bending deformations of the whole imidazole is transformed to predominantly rocking modes of the whole macrocycle at 10 cm-1. Other modes, with significant character of out-of-plane, torsion, and in-plane motion of the acetyl side group of ring 1, are less changed. We show that there is a connection between the mentioned modes, particularly the torsion mode of the acetyl group of ring 1, and electron transfer and intensity in RR spectra. Coupling energies. calculated at a transition state between P*BA and P+BA-, are found to agree reasonably well with experimental data. The lower activity of the B-side compared to the A-side is caused partly by less electronic overlap between P-A and B-B than between P-B and B-A and partly by higher energy of the P+BB-state than of the P+BA- state. Finally, we compare to results for other species and for mutants. Measured rates correlate well with the energies of the P*B-A (and PBA*) states relative to the energy of the intermediary P+BA- state.