Matrix isolation IR spectroscopy and high-level ab initio calculations were applied to investigate the structure and vibrational spectra of quinone-pyrimidine heterodimers formed in low-temperature Ar matrices. A specially developed experimental technique was used to separate bands of quinone-pyrimidine dimer from bands of quinone and pyrimidine monomers and homodimers in the IR spectra. As a result, nine bands assigned to the quinone-pyrimidine heterodimer were identified. Ab initio calculations at the MP2/6-31+G*, MP2/6-31++G** and SCF/6-31++G** levels of theory have been carried out to determine the relative energies and vibrational spectra of three stable configurations of the quinone-pyrimidine dimer found theoretically. These configurations are two planar complexes with two weak C-H ... O and C-H ... N hydrogen bonds and one stacked complex stabilized by dispersion forces. The effect of basis set superposition error (BSSE) on the relative stabilities and the vibrational spectra of the dimers was also investigated. The non-BSSE-corrected calculations at the MP2/6-31+G* and MP2/6-31++G** levels of theory predict the stacked dimer to be the most stable conformer, but accounting for BSSE resulted in a reverse stability ordering of the stacked and the planar dimers. The comparison of the observed frequency shifts with the theoretically predicted shifts has shown that the planar configuration is responsible for the experimentally observed bands. This is in agreement with the stability ordering derived from the BSSE-corrected relative energies. To account for the matrix effects on the stability of the planar and stacked dimers, additional calculations were carried out using the Onsager's reaction field model and the MP2/6-31++G** level of theory. These calculations confirm that the planar H-bonded dimer is the most stable configuration.