Intramolecular hydrogen bonding in 2′-deoxyribonucleosides: an AIM topological study of the electronic density

Abstract

The theoretical analysis of the energy of the conformers of 2′-deoxyribonucleosides presents some subtle but significant differences depending on the nature of the base linked to the sugar. In particular, 2′-deoxycytidine behaves uniquely. Among the structural parameters invoked to explain this phenomenon, one of the most intriguing is the C–H···O intramolecular hydrogen bond in which the donor atom is H6 (H8) in the pyrimidine (purine) base and the acceptor atom is O5′ of the sugar. In the present work, the network of intramolecular weak bonds is thoroughly investigated for every 2′-deoxynucleoside in both the North (C3′-endo/anti) and South (C2′-endo/anti) conformations. In this respect, we use Bader's atoms in molecules (AIM) theory to perform a topological study of the electronic density, emphasizing the weak bonding in the nucleosides. Criteria for hydrogen bonding are comprehensively reviewed for each hydrogen bond revealed, and the concept of “improper” hydrogen bonding is addressed. The AIM analysis thus allows us to gain insight into the intrinsic reasons for the strange conformational behaviour of 2′-deoxycytidine.