Конформаційні властивості 1′-дезоксирибози, модельного цукрового залишку рибонуклеозидів : Квантово-механічне дослідження методом функціонала густини

Abstract

Full conformational analysis of 1′-deoxyribose the model sugar residue of ribonucleosides is performed by means of density functional theory at MP2/6–311++G (d, p) // DFT B3LYP/6– 31G (d, p) level. It is established that only four conformers (three of S- and one of N-type) over the full number of 112 may be incorporated into the periodic structure of a two-strand RNA molecule. The main geometric, energetic, and polar characteristics of all 112 stable conformers are presented, as well as conformational equilibria under normal conditions. By the quantum mechanical electron density topology analysis method (Bader’s Atoms-in-Molecules theory), as many as six types of intramolecular hydrogen bonds are established in all possible conformers of the isolated 1′-deoxyribose molecule. Namely, these are C1′H2 . . . O5′, C2′H . . . O5′, O2′H . . . O3′, O3′H . . . O2′, O3′H . . . O5′, and O5′H . . . O3′.