On the basis of semiempirical calculations, the present study proposes a comprehensive interpretation of the crystallographic, vibrational, and electrochemical data on methoxy-substituted quinones, and in particular for ubiquinones, in terms of the orientation of the methoxy groups relative to the quinone ring plane. "Hindered" and "free" methoxy groups are considered depending on the presence or absence on the quinone ring of a bulky group in ortho position of the considered methoxy group, respectively. The free methoxy groups have their O-CH3 bond in the quinone ring plane while the hindered methoxy groups cannot adopt this conformation and have their methyl group tilted out of the quinone ring plane. The electron donation of the methoxy is dependent on the orientation of the O-CH3 bond and is maximum for a free methoxy group. This effect is revealed by the analysis of both electrochemical and IR data. An assignment of the nu(C=O) modes of the quinones bearing such groups is proposed. From electrochemical data in literature, a new coefficient sigma(para), used in the Hammett equation, is determined for a hindered methoxy group (sigma(para) = -0.07 compared to -0.27 for a free methoxy group). In the specific and biologically important case of the bulky group being another methoxy group, such as in ubiquinones (2,3-dimethoxy-substituted 1,4-benzoquinones), two types of conformation have to be considered. In the first type (conformer A), one methoxy adopts the conformation of a free methoxy group and the second that of a hindered methoxy group. In the second type (conformer B), both methoxy groups adopt the conformation of a hindered methoxy group; Both conformers appear equiprobable within the precision of our semiempirical calculations and a low rotational barrier, compared to k(B)T at room temperature, is found between them. Only conformers A are encountered in crystals. Using specific C-13 labeling, IR data show that conformers A are mostly encountered at room temperature in solution while a mixture of both conformers is present at low temperature. On the other hand, electrochemical data on these quinones are best interpreted as the reduction of conformers B. This is explained by the higher electron affinity of conformers B compared to conformers A and-by the low rotational barrier between the two conformers. Taking into account IR data of ubiquinone in the bacterial photosynthetic reaction center of Rhodobacter sphaeroides, the 70 mV difference found in the redox potential of ubiquinone in the two quinone binding sites can be explained by a difference of orientation of the methoxy groups imposed by the protein. By selecting a different orientation of the methoxy groups in the two sites, the protein would thus tune the redox potential of the quinone present in each site.