Using density functional theory (DFT) techniques, we have investigated possible conformers of the radical anions of plastoquinone (psQ), ubiquinone (ubQ), and menaquinone (mnQ), which are formed in the reaction centers of photosynthetic bacteria, blue-green bacteria, and green plants. Replacing the hydrocarbon tail connected to the quinone ring by an ethyl group, we have computed the rotational potential energy surfaces for psQ(-) and ubQ(-). Our results show that in the absence of environmental effects both systems have global minima for near-perpendicular orientations of the gamma-carbon relative to the quinone ring. For psQ(-), however, a low-lying local minimum is also observed for an in-plane arrangement with C gamma pointing away from the O4 oxygen. These differences in head-to-tail rotational energy surfaces may explain the experimentally observed differences in beta-proton hyperfine couplings of psQ(-) vs ubQ(-) and mnQ(-), and their corresponding model compounds. By replacing the C6 methyl group in ubQ and mnQ by hydrogen, or the C6 hydrogen in psQ by methyl, we show that the crucial factor determining the rotational arrangements of the quinones in biological systems (planar psQ in green plants; perpendicular ubQ and mnQ in bacteria) is the presence or absence of this methyl group. The computed barrier height to rotation in ubQ(-), ca. 6 kcal/mol, and the beta-proton hyperfine coupling constants for the planar vs perpendicular arrengements are in excellent accord with experimental data. Finally, we show that the methoxy group at the C2 position in ubiquinone displays a conformational preference as a result of the electron addition process, which may effect the hydrogen bonding pattern and hence promote the electron-transfer processes.