When we explore the topological properties of Coordination Polymers / Metal Organic Frameworks
(CP/MOFs) the key notion is the concept of underlying net. While the whole structure topology is reflected
by an atomic net including all atoms as nodes and all interatomic bonds as edges, the nodes and edges of the
underlying net correspond to structural groups and connections between them. In fact, any structure
representation that separates building blocks (for instance, molecules in molecular packings or ligands in
coordination compounds) implicitly applies the underlying net concept. The resulting simpler representation
allows one to find structural resemblances between chemically quite different compounds.
In ToposPro where a number of structure representations can be built in an automated mode; each representation can be transformed to an underlying net by simplification procedures (see Module 4). Any structure representation in ToposPro corresponds to a particular way to choose structural units; this way depends on the task under consideration. For any class of chemical compounds some standard representation can be proposed that conforms to a conventional crystallochemical description (see Table below). The standard representation of valence-bonded CP/MOFs considers metal atoms and organic ligands as structure units, ignoring guest ions and molecules. Then the procedure of contracting multiatomic groups to their centroids is applied to all ligands to obtain a primary simplified net. This net can be directly transformed to the underlying net by the procedure of secondary simplification that consists in successive removing 0-coordinated nodes (intraframework molecular moieties), 1-coordinated nodes (terminal/dangling ligands) and transforming 2-coordinated nodes (bridge µ2 ligands or metal atoms connected to only two bridge ligands) into edges. If the bridge µn ligands are connected with more than two metal atoms (n>2) they form additional nodes of the underlying net.
|Structure type||Structure units = simplified net nodes||Type of bond within the structure units||Type of bond between the structure units = simplified net edges|
|valence-bonded CP/MOFs||metal atoms, ligands||valence||valence|
|H-bonded CP/MOFs||complex groups||valence||H-bond|
|organic crystals, supramolecular complexes||organic molecules||valence||intermolecular: H-bonds, specific (e.g. Halogen Bond), van der Waals|