The structures of the ubiquinones Q(A) and Q(B) in the bacterial photosynthetic reaction center of Rhodobacter sphaeroides are calculated by a quantum mechanical/molecular mechanics hybrid technique. The orientations of their methoxy groups are found to differ by less than 30degrees. Calculation of the vibrational spectra reveals that one C=O stretching mode of Q(A) is considerably shifted to lower frequencies in agreement with the experimental data. The orientational differences of the methoxy groups at Q(A) and Q(B) are too small as to provide an explanation for this shift. Instead, it must be due to a very special interaction of the protein with Q(A). Artificial neutralization of the iron cofactor, while keeping all other structural parameters of the reaction center fixed, reveals that this interaction arises from the electrostatic field of the Fe2+ ion, within which Q(A) is oriented in a particular way.