We have applied density functional methods for the determination of structures, vibrational spectra, electron affinities, and isotropic hyperfine coupling constants of the radical anions of 2,3-dimethoxy-1,4-benzoquinone and 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone. Our calculations predict three stable conformers with respect to the orientation of the two methoxy groups for both molecules. Different orientations of the methoxy groups are shown to affect force constants and vibrational spectra less dramatically than in the corresponding neutral quinone. The different mode decompositions predicted in symmetrical and nonsymmetrical conformers, respectively, suggest that site specific labeling of one carbonyl group might allow one to distinguish among these conformers. The presented calculations allow us to provide a mode assignment for the C=C and C=O modes which, in most cases, agrees well with previous assignments based solely on experimental data. Electron affinities are shown to vary by up to 40 kJ/mol for different orientations of the methoxy groups. Our calculations demonstrate that the two additional substituents at positions 5 and 6 have to be considered if the molecule is supposed to serve as a model compound for quinones participating in bacterial photosynthesis.