Stable conformations and vibrational spectra of 2-methoxy-3-methyl-1,4-benzoquinone were calculated using density functional methods. Two stable conformers have been found which differ in their vibrational spectrum. Although the calculated infrared spectra of the two conformers differ with respect to several modes, a definite assignment of the experimentally available bands to one of the two conformers is difficult. Protein-chromophore interactions have been studied by modeling quinone-H2O, quinone-Li+, and quinone-NH4+ complexes. A complexation with water already considerably affects the relative energies of the two conformers and the torsional barrier for the rotation of the methyl part of the methoxy group. In fully optimized quinone-water complexes, vibrational modes in the C=O and C=C stretching mode region are affected through the complexation. Complexation with a positively charged counter ion dramatically changes the energetics of the system and changes the former minimum energy conformation into a saddle point. Vibrational frequencies are more strongly affected than upon complexation with a water molecule.