Unexpected A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions between the classical A·T DNA base pairs: A QM/QTAIM comprehensive study

摘要

In this study, using QM/QTAIM calculations in the continuum with Ε= 1 under normal conditions, we have revealed for the first time the nondissociative A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions. It was established that they proceed via the essentially nonplanar transition states (&Scy;1symmetry) through the intermediates, which are wobbled conformers (&Scy;1symmetry) theoretically predicted in our previous work (Brovarets’et al., Frontiers in Chemistry, 2018, 6:8, 10.3389/fchem.2018.00008) of the classical &Acy;·&Tcy;DNA base pairs—Watson–Crick &Acy;·&Tcy;(WC), reverse Watson–Crick &Acy;·&Tcy;(rWC), Hoogsteen &Acy;·&Tcy;(&Ncy;) and reverse Hoogsteen &Acy;·&Tcy;(r&Ncy;). At this, the A·T(H)↔A·T(rWC) and A·T(WC)↔A·T(rH) conformational transformations are controlled by the transition states (TSs) stabilized by the participation of the intermolecular (T)N3H···N6(A) H-bond (∼3.70 kcal·mol−1) between the imino group N3H of T and pyramidilized amino group N6H2of A. Gibbs free energies of activation for these processes consist 12.22 and 11.11 kcal·mol−1, accordingly, under normal conditions. TSs, which control the A·T(WC)↔A·T(rWC) and A·T(H)↔A·T(rH) conformational transitions are stabilized by the participation of the intermolecular (T)N3H···N6(A) H-bond (5.82 kcal·mol−1) and bifurcating intermolecular (T)N3H···N6(A) (5.00) and (T)N3H···N7(A) (0.61 kcal·mol−1) H-bonds, accordingly. Notably, in these two TSs amino group N6H2of A is significantly pyramidilized;Gibbs free energies of activation for these reactions are 19.07 and 19.71 kcal·mol−1, accordingly.<br/>

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