In the accompanying paper (Scholes, G. D.; Jordanides, X. J.; Fleming, G. R. J. Phys. Chem. 2001, 105, 1640), a generalization of Forster theory is developed to calculate electronic energy transfer (EET) in molecular aggregates. Here we apply the theory to wild-type and mutant photosynthetic reaction centers (RCs) from Rb. sphaeroides, as well as to the wild-type RC from Rps. viridis. Experimental information from the X-ray crystallographic structure, resonance Raman excitation profiles, and hole-burning measurements are integrated with calculated electronic couplings to model the EET dynamics within the RC complex. Optical absorption and circular dichroism spectra are calculated at various temperatures between 10 K and room temperature, and compare well with the experimentally observed spectra. The calculated rise time of the population of the lower exciton state of P, P-, as a result of energy transfer from the accessory bacteriochlorophyll, B, to the special pair, P, in Rb. sphaeroides (Rps. viridis) wild-type at 298 K is 193 fs (239 fs), and is in satisfactory agreement with experimental results. Our calculations, which employ a weak-coupling mechanism suggest that the upper exciton state of P, P+ plays a central role in trapping excitation from B. Our ability to predict the experimental rates is partly attributed to a proper calculation of the spectral overlap J(partial derivative alpha)(epsilon) using the vibronic progressions. The main advance we have made, however, is to calculate the electronic couplings V-partial derivative alpha in terms of the molecular composition of donor and/or acceptor aggregates, rather than treating the accepters P+ and P- as point dipoles associated with each spectroscopic band. Thus, we believe our electronic couplings capture the essence of the many-body interactions within the RC. Calculations for EET in two mutants, (M)L214H (the beta mutant) and (M)H202L (the heterodimer), are in reasonable agreement with experimental results. In the case of the heterodimer the agreement depends on a decrease in the electronic couplings between D-M and the rest of the pigments.