Intramolecular hydrogen bonding in ribonucleosides: an AIM topological study of the electronic density

Abstract

Just as for 2′-deoxyribonucleosides, the theoretical analysis of the energy of the conformers of ribonucleosides presents some subtle but significant differences depending on the nature of the base linked to the sugar. In particular, just like 2′-deoxycytidine, cytidine behaves uniquely. One intriguing parameter 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 ribonucleoside in both the North (C3′-endo/anti) and South (C2′-endo/anti) conformations. This article is the logical successor to a previous one which deals with 2′-deoxyribonucleosides (, A. Hocquet, Phys. Chem. Chem. Phys., 2001, 3, 3192–3199). In this prospect, we use Bader's atoms in molecules (AIM) theory to perform a topological study of the electronic density, emphasizing with intramolecular weak bonding. Hydrogen bonding criteria are comprehensively reviewed for each highlighted hydrogen bond, and the concept of “improper” hydrogen bonding is addressed. The AIM analysis thus allows us to gain insight into the intrinsic reasons for strange conformational behaviour of 2′-deoxycytidine and cytidine.