Revealing Pathway Complexity in Host–Guest Binding: Allosteric Regulation and Temporal Chiral Inversion During Complexation of Naphtho[2,2]urils

Abstract Studies on pathway complexity in supramolecular polymerization have uncovered intriguing kinetic behaviors, though these are not directly transferable to host–guest systems. Here, we report unprecedented chiral inversion kinetics in a host–guest complexation process, arising from the coupling of sequential binding and conformational interconversion. Naphtho[n,n]urils (NGU[n,n]), constructed by alternating glycoluril and naphthyl units, were synthesized via a one‐pot three‐component condensation, yielding hybrid architectures with well‐defined cavities. In NGU[2,2], the two naphthyl units adopt either S P or R P planar chiral conformations, giving rise to interconvertible racemic and meso conformers. NGU[2,2] binds chiral amino acid derivatives stepwise through hydrogen bonding and cation–dipole interactions, forming 1:1 and 1:2 complexes. Complexation shifts the equilibrium between racemic and meso conformers, inducing a circular dichroism (CD) response. Notably, the transition from the 1:1 to the 1:2 complex triggers an inversion of conformational preference in NGU[2,2], representing a unique case of chiral allosteric regulation. Furthermore, temporal inversion of the CD signal was observed upon mixing NGU[2,2] with the guest, displaying a transient overshoot and sign reversal. This kinetic behavior originates from the interplay between binding dynamics and conformational interconversion, with the meso conformer playing a central role.