Conformational structures and vibrational spectra of isolated pyrimidine nucleosides: Fourier transform infrared matrix isolation study of 2-deoxyuridine

Abstract

The conformational structures of 2-deoxyuridine (dU) were investigated using Fourier transform infrared (FTIR) matrix isolation spectroscopy. For the first time the FTIR spectra of dU in Ar matrices were obtained in the range 4000–200 cm−1. The stabilities of conformers were estimated by the methods HF/3-21G (p), HF/6-31G (d,p) and MP2/6-31G (d,p). Ab initio calculations of the infrared spectra were performed by the methods HF/3-21G (p) and HF/6-31G (d,p). The actual occupancy of conformational isomers in matrix samples was determined. It was shown that anti-conformers of dU are dominant. The ribose rings of the main anti-conformers dU _a0, dU _a1 are in the C2′-endo conformation, but the ribose rings of minor anti-conformers dU_a2, dU_a3 have the C3′-endo conformation, stabilized by intramolecular hydrogen bonds O3′H⋯O5′ and O5′H⋯O3′, accordingly. Syn-conformers of dU are stabilized by the intramolecular hydrogen bond O5′H⋯O2 and the dominant conformation of the ribose ring is C2′-endo.