Nucleoside conformers in low-temperature argon matrices: Fourier transform IR spectroscopy of isolated thymidine and deuterothymidine molecules and quantum-mechanical calculations

Abstract

The conformational equilibrium of thymidine and deuterothymidine molecules in low-temperature Ar matrices has been studied using low-temperature matrix-isolation Fourier IR spectroscopy and quantum-chemical calculations by the DFT/B3LYP and MP2 methods. It has been found that two anti-conformers ta2_0 and ta3_0 with different structures of the sugar ring, C2 '-endo and C3 '-endo, predominate in low-temperature matrices. In isolated state, each of these conformers has a few low-barrier satellites that can fully pass into more stable structures when a molecule enters the matrix. The main syn conformer ts2_0 is stabilized by an intramolecular hydrogen bond between the O5 ' H group of the sugar and the C2O group of the base (O5 ' HO2), while C2 '-endo is the predominant conformation of the deoxyribose ring. The considerably lower population of ts2_0 compared to the anti-conformers ta2_0, ta3_0 can be explained by the smaller population of satellite conformations. It has been shown that the absorption band of nu N3D stretching vibration is split by the Fermi resonance.