How Many Conformers Determine the Thymidine Low-Temperature Matrix Infrared Spectrum? DFT and MP2 Quantum Chemical Study.

A comprehensive conformational analysis of isolated 2‘--deoxy-thymidine (T), canonical DNA nucleoside, has been performed by means of ab initiocalculations at the MP2/6-311G(d,p)//DFT B3LYP/6-31G(d,p) level of theory. At 298.15 K, all 92 conformers of isolated dT are within a 7.49 kcal/mol Gibbs energy range. Syn orientation for the base and South (S) conformers for the sugar dominate at this temperature:  syn/anti 61.6%:38.4% and S/N 74.5%:25.5%. However, at 420 K, the majority of conformers contain anti base and the population of North (N) sugars increases:  syn/anti 38.0%:62.0% and S/N 59.5%:40.5%. The whole conformational parameters (P, , , , , , max) were analyzed as well as the energies of the OH···O intramolecular H-bonds on the basis of (OH) stretching vibrations. Convolution of calculated IR spectra of all of the T conformers appears consistent with its low-temperature matrix spectrum (Ivanov et al. LowTemp.Phys.2003, 29, 809). The maximal discrepancy in frequencies between calculated and experimental spectra is less than 1%. A conclusion was made that for reliable reconstruction of the isolated nucleoside IR spectrum the quasi whole set of conformers should be taken into consideration. In essence, this result opens up a possibility to reconstruct IR spectra of isolated nucleosides at physiological temperatures with rather satisfactory probability. [ABSTRACT FROM AUTHOR]