Influence of the sugar configuration on the structure of DNA by conformational analysis of the deoxyribose-phosphate unit

The conformational analysis by the Extended Hückel Theory of the deoxyribose‐phosphate unit in the principal configurations of the sugar is discussed. The work is divided into three parts in order to determine the role of the different elements constituting such a unit. (1) The simultaneous study, for the four principal configurations of the sugar, of the possible ranges of the rotational parameters ψ and ϕ′ with P3 and P5 without their oxygen atoms. (2) The study of the influence of the oxygen atoms, situated on P3 and P5, on the rotations ψ and ϕ′ for the C3′endo and C2′endo sugar configurations. (3) The study of the influence of a nucleobase on the rotation ψ, and whether the oxygen atoms of the phosphate groups should be taken into account or not. The results show the equivalences C3′endo ≃ C2′exo and C2′endo ≃ C3′exo; that the allowed angular ranges of our rotational parameters depend, in some degree on the chosen sugar configuration; and that the rotations ψ and ϕ′ appear as “quasi” independent. In addition, an energetic classification which, according to the Extended Hückel Theory, seems to show that the C2′endo sugar configuration is the most favored for our unit was established; it was shown that the introduction of the oxygen atoms has no influence on the rotation ψ, but on the contrary leads to a restriction of the possible range for the ϕ′ parameter; and it was determined that the influence of the adenine base fixed in its position of minimal energy (i.e., anti‐conformation) on the rotation ψ, as a function of the presence or absence of the oxygen atoms, is relatively limited.