Relative Position and Relative Rotation in Supramolecular Systems through the Analysis of the Principal Axes of Inertia: Ferrocene/Cucurbit[7]uril and Ferrocenyl Azide/β-Cyclodextrin Case Studies

Abstract

Parameters comprising the relative position and relative rotation of molecules can be evaluated when the principal axes of inertia of the entities in a supramolecular association are employed as reference. Such information applies to the characterization and identification of experimental and theoretical nonbonded systems. The parameters are relevant to geometric comparison (for theory and experiment) and, for instance, to monitoring structures by theoretical simulations. This work introduces a software developed to obtain such parameters through the discussion of some intriguing host-guest systems, the ferrocene/cucurbit[7]uril and ferrocenyl azide/β-cyclodextrin. The ideas within this contribution naturally apply to the study of other nonbonded associations beyond host-guest chemistry. A modified version of the software discussed herein serves to obtain user-defined spatial arrangements for two nonbonded entities. Therefore, with a given geometry, for instance, from X-ray data, the parameters can be derived, and with the parameters, from a theoretical perspective, a spatial arrangement can be obtained.