Ab initio comprehensive conformational analysis of 2′-Deoxyuridine, the biologically significant DNA minor nucleoside, and reconstruction of its low-temperature matrix infrared spectrum

A comprehensive conformational analysis of isolated 2'-deoxyuridine (dU), a minor DNA nucleoside, has been performed by means of ab initio calculations at the MP2/6-311++G (d,p)//DFT B3LYP/6-31G (d,p) level of theory. At 298.15 and 420 K, all 94 allowed conformers of dU are within 8.96 and 7.91 kcal/mol Gibbs energy ranges, respectively. Syn orientation for the base and South (S) conformers for the sugar dominate at 298.15 K: syn/anti = 62.3%:37.7% and S/N = 77.2%:22.8%. At 420 K in the majority of conformers, the base is anti oriented and the population of North (N) sugars increases: syn/anti = 39.3%:60.7% and S/N = 63.0%:37.0%. Values of all conformational parameters and correlations between them, as well, as their correlations with valence bonds, and also correlations between valence bonds and angles were estimated. In General, 14 types of intramolecular H-bonds were detected (1-3 H-bonds per conformer, the total number 175), namely, Cl'H center dot center dot center dot O2 (16 H-bonds), C2'H1 center dot center dot center dot O5' (9), C2'H2 center dot center dot center dot O2 (21), C3'H center dot center dot center dot O2 (21), C5'H1 center dot center dot center dot O2 (14), C5'H2 center dot center dot center dot O2 (11), C6H center dot center dot center dot O4'(37) C6H center dot center dot center dot O5' (22), C3'H center dot center dot center dot HC6 (4), 05'H center dot center dot center dot HC6 (2), 03'H center dot center dot center dot O5' (5), O5'H center dot center dot center dot O4'(1), O5'H center dot center dot center dot O3'(4), and O5'H center dot center dot center dot O2 (8). Geometric, vibrational, structural-topological, and energetic features of the OH center dot center dot center dot O intramolecular H-bonds in dU conformers were determined. The close similarity between energetic and geometric characteristics of dU` and thymidine DNA-like conformers in anti and relevant syn conformations and their transition states of the anti -> syn interconversion implies that mismatch DNA glycosylase discriminates between the two nucleosides, mainly because of the difference in the shapes of their bases. Convolution of calculated IR spectra of all the dU conformers within the limits 3400-3700 cm(-1) appears to be consistent with its low-temperature matrix IR spectrum (Ivanov et al. Spectrochim. Acta, Part A 2003, 59 1959), wavenumber discrepancy not exceeding 1%. It was concluded that, for a reliable reproduction of the experimental spectrum, the whole set of conformers should be taken into consideration. The suggested method makes reconstruction of the isolated nucleoside IR spectrum at a physiological interval of temperature reasonably possible.