Features of the conformational structures of 2′-deoxyuridine, matrix isolated in Ar and Kr

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The conformational equilibrium of molecules of the nucleoside 2′-deoxyuridine (dU) in Ar and Kr low-temperature matrices is investigated with the aid of low-temperature matrix-isolation FTIR spectroscopy and quantum calculations by the DFT and MP2 methods. It is found that in the low-temperature matrices the dominant forms are two anti-conformers of dU with different structures of the sugar ring: C2′-endo and C3′-endo. The main syn-confomer is stabilized by intramolecular hydrogen bond O5′H—O2, while C2′-endo is the dominant conformation of its deoxyribose ring in Ar and Kr low-temperature matrices. The possibility that minor syn-conformers without the intramolecular hydrogen bond O5′H—O2 are present in the matrix samples is also demonstrated. An influence of the matrix on the orientation of the hydroxyl group O3′H of the sugar ring of the main syn-conformer is found.