Intramolecular hydrogen bonds: common motifs, probabilities of formation and implications for supramolecular organization.

A systematic survey of the Cambridge Structural Database (CSD) has identified all intramolecular hydrogen-bonded ring motifs comprising less than 20 atoms with N and O donors and acceptors. The probabilities of formation P(m) of the 50 most common motifs, which chiefly comprise five- and six-membered rings, have been derived by considering the number of intramolecular motifs which could possibly form. The most probable motifs (P(m) > 85%) are planar conjugated six-membered rings with a propensity for resonance-assisted hydrogen bonding and these form the shortest contacts, whilst saturated six-membered rings typically have P(m) < 10%. The influence of intramolecular-motif formation on intermolecular hydrogen-bond formation has been assessed for a planar conjugated model substructure, showing that a donor-H is considerably less likely to form an intermolecular bond if it forms an intramolecular one. On the other hand, the involvement of a carbonyl acceptor in an intramolecular bond does not significantly affect its ability to act as an intermolecular acceptor and thus carbonyl acceptors display a substantially higher inclination for bifurcation if one hydrogen bond is intramolecular.

Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge Structural Database.

The hydrogen-bond networks and crystal packing of 81 unique secondary di- and polyamides in the Cambridge Structural Database are investigated. Graph-set analysis, as implemented in the RPluto program, is used to classify network motifs. These have been rationalized in terms of the relative dispositions of the amide groups. Peptide and retropeptides exhibit significant conformational flexibility, which permits alternative hydrogen-bonding patterns. In peptides, dihedral angles of -psi approximately varphi approximately 105 degrees allow an antiparallel ladder arrangement, containing rings of either the same or alternating sizes. For retropeptides, and diamides with an odd number of CH(2) spacers, this conformation leads to a parallel ladder with rings of equal size. If varphi approaches -60 degrees and psi 180 degrees, ladders adopt a helical twist, and if the conformation is distorted further, a three-dimensional network is usually adopted. Diamides with aromatic or an even number of CH(2) spacers generally form either antiparallel ladders or sheets, although some exhibit both polymorphs. Symmetry relationships within and between hydrogen-bonded chains, ladders and sheets in the crystal packing have also been analysed. Polyamides form considerably more complex networks, although many of the structural motifs present in the diamides occur as components of these networks.