Visualization and characterization of non-covalent networks in molecular crystals: automated assignment of graph-set descriptors for asymmetric molecules

Abstract

A method of visualizing intermolecular networks (for example, hydrogen-bonded networks) in the crystalline state has been developed, based on the concept of link atoms, i.e. those atoms deemed to be in contact with each unique molecule or ion in the crystal chemical unit (CCU). Extension of a structure using each of these primary links can be achieved, enabling the generation and investigation of extended networks. Algorithms have been developed for the automatic assignment of graph-set notation for patterns up to second level, i.e. those involving one or two crystallographically independent non-covalent bonds, in the absence of internal crystallographic symmetry in the unique molecules of the CCU. The self, ring, chain and discrete motifs may be displayed by highlighting the atoms and bonds comprising the pattern. These methodologies have been implemented in the Cambridge Structural Database program PLUTO.