Structures and Vibrational Frequencies of the Quinones in Rb. sphaeroides Derived by a Combined Density Functional/Molecular Mechanics Approach

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 30°. 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 Fe 2+ ion, within which Q A is oriented in a particular way.