Correlating Kinetics and Thermodynamics of Conformational Changes in Ammonium Complexes of a Flexible Naphthocage

08 November 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Although conformational changes are fundamental processes in many natural and synthetic supramolecular systems, understanding of the relationship between conformational kinetics and thermodynamics of host-guest binding is very limited because low-energy structural changes are usually fast and difficult to monitor. Described in this work is a kinetic study of the conformational conversion of the inclusion complexes consists of a flexible naphthocage host and quaternary ammonium guests featuring a relatively slow “guest dissociation-host conformational change-guest re-association” con-formational exchange mechanism. For guests of comparable structural features, the overall rate of the conformational change is found to be inversely correlated to the thermodynamic stability of the host-guest complexes, which in turn is related to both the overall structure and local steric properties of the guests. Results from this work that bridge the kinet-ics and thermodynamics of molecular recognition to conformational changes are valuable for an in-depth understanding of the kinetic contributions in guest binding and selectivity.


conformational changes
molecular cage
host-guest chemistry

Supplementary materials

Supporting information
Experimental procedures and data


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