Quinones are ubiquitous in biochemistry, where they typically function as electron carriers in processes such as photosynthesis and respiration. Quinones bound in protein complexes are often studied using Fourier-transform infrared (FTIR) difference spectroscopy (DS). With FTIR DS it is possible to probe even small changes in hydrogen bonding between the quinones and nearby protein residues. However, the interpretation of FTIR DS is complicated by multiple overlapping contributions to the spectra. Here we employ density functional theory (DFT) based vibrational frequency calculations on benzoquinone (BQ) and naphthoquinone (NQ) model systems to help untangle the intrinsic and environmental factors that could shift the quinone’s vibrational mode frequencies and intensities. Specifically, we systematically study the effect that hydrogen bonds and quinone substituents have on the ��=�� mode vibrational frequencies of the neutral and one-electron reduced BQs and NQs.