Competition between H-bonded and stacked dimers of pyrimidine: IR and theoretical ab-initio study

A combined matrix isolation Fourier transform infrared experimental and ab-initio theoretical approach has been used to examine the vibrational spectra of pyrimidine dimers. It was found that the presence of pyrimidine dimers resulted in experimentally observed frequencies shifted relative to those of the pyrimidine monomer. Four stable pyrimidine dimer conformers were found via ab-initio calculations. Two of these conformers namely a stacked geometry and a H-bonded geometry in which pyrimidine monomer dipole moments orient antiparallel, had the lowest but very similar energies. Ab-initio harmonic frequencies of these two dimers and their shifts relative to the monomer's values were determined. The effect of Basis Set Superposition error on these calculated frequency shifts was also investigated. The comparison of the ab-initio predicted and experimentally observed frequency shifts and an accompanying potential energy distribution analysis suggest that the lowest-energy H-bonded configuration is responsible for the experimentally observed phenomena.