Identifying Supramolecular Constructs XPac

Like most general methods for assessing structural similarity, XPac dispenses with traditional descriptions of unit cells and space groups by considering the environments of molecules [55, 56]. A reference molecule (referred to as the kernel molecule) is defined, and a coordination shell is generated on the basis of some distance criterion. A molecule is considered to form part of the coordination shell if it forms at least one contact to the kernel molecule in which the interatomic distance is less than the sum of the van der Waals radii plus some defined tolerance. The tolerance is usually set to a value of 1.5 A, which is liberal in the context of conventional views of what constitutes a significant intermolecular interaction. The kernel molecule and all associated shell molecules form 

For the latter case, the process is applied again to aU possible combinations of pairs containing a common molecule. Thus, the comparison is applied over three molecules rather than two. After this step, any similar molecular triples are combined to form the seed of an SC. Any comparable molecular triples that share a common molecule must form part of the same seed. In some cases, there may be more than one distinct seed. Finally, the unique seeds are expanded by the symmetry operators of the stmcture to yield the SC(s). At this point, information concerning the dimensionality and the base vectors of the SC can be extracted. 

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Figure 1.17 The four primary supramolecular constructs (A-D) in the CBZ family, identified by the XPac program. Reproduced from [57] by permission of The Royal Society of Chemistry...

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