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

The theoretical analysis of the energy of the conformers of 2'-deoxyribonuc leosides presents some subtle but significant differences depending on the nature of the base linked to the sugar. In particular, 2'-deoxycytidine beh aves uniquely. Among the structural parameters invoked to explain this phen omenon, one of the most intriguing is the C-H . . .O intramolecular hydroge n bond in which the donor atom is H6 (H8) in the pyrimidine (purine) base a nd the acceptor atom is O5' of the sugar. In the present work, the network of intramolecular weak bonds is thoroughly investigated for every 2'-deoxyn ucleoside in both the North (C3'-endo/anti) and South (C2'-endo/anti) confo rmations. In this respect, we use Bader's atoms in molecules (AIM) theory t o perform a topological study of the electronic density, emphasizing the we ak bonding in the nucleosides. Criteria for hydrogen bonding are comprehens ively reviewed for each hydrogen bond revealed, and the concept of "imprope r'' 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.