Investigation of structure and vibrational properties of cyclobutane pirimidine dimer

We performed a theoretical analysis of the structure and vibrational properties of cyclobutane pyrimidine dimer, which is the main product in a photochemical reaction involving two molecules of 1-methylthymine. Thymine is a pyrimidine base that has the highest yield of the dimerization photoproducts. Methylation in position one was chosen because in this position thymine is linked to sugar in DNA. The calculations were performed at the B3LYP/cc-pVTZ level with a Gaussian program package. All molecular geometries were optimized without symmetry constraints in vacuum and D2O. Vibrational frequencies were calculated in the harmonic approximation. It was shown that there are two stable isomers, CPD(cis-syn) and CPD(trans-syn). CPD(trans-syn) is more stable both in vacuum and in D2O. By dissolving these molecules in D2O, both structures become more stable, although the stabilization of the less stable isomer is more pronounced due to its larger dipole moment. Thus, the difference in stability of the two isomers in D2O is almost two times lower than in vacuum. Because of the similarity of the two isomers’ structures, the difference in their vibrational spectra is not pronounced. Within the harmonic approximation, there is only a slight difference in the C=O and C-H stretching region. The difference in the N-H stretching region is more pronounced; in the CPD(cis-syn) molecule the two bonds vibrate separately, whereas in the CPD(trans-syn) the two modes couple, and this coupling results in symmetric and asymmetric N-H stretching. The observation shows that a slight difference in geometry can be reflected in the shape of the infrared spectra. A more detailed analysis of the vibrational properties would involve computation of anharmonic coupling terms, which would enable a more precise determination of the peak positions