Abstract
<jats:p>Cyclodextrin inclusion is often described primarily in terms of hydrophobic displacement of cavity-bound water, a framework that explains volume-dependent affinity but does not account for why closely related guests exhibit distinct stabilization within the same host cavity. Hydrogen bonding is increasingly recognized as an additional recognition element in macrocyclic hosts, but whether this principle operates within an unmodified, native cyclodextrin cavity—and whether it can be switched reversibly—has not been established. Here, we show that guest protonation supports switchable encapsulation behavior, using albendazole and fenbendazole as structurally matched benzimidazole drugs that allow hydrogen-bond donor–acceptor character to be tuned independently of the hydrophobic scaffold. Solubility measurements across native α-, β-, and γ-cyclodextrin show that protonation enhances association in all three hosts, while NMR spectroscopy, variable-temperature thermodynamic analysis, and semiempirical molecular dynamics simulations focused on β-cyclodextrin reveal that this enhancement reflects two mechanistically distinct outcomes. Although both protonated guests form 1:1 complexes with comparable hydrophobic cavity occupancy, albendazole achieves deeper cavity insertion that positions its protonated benzimidazole to engage a broader network of hydrogen bonds at the host rim, yielding a larger enthalpic gain offset by greater entropic compensation. Comparison with simplified benzimidazole fragments lacking the hydrophobic anchor shows that hydrogen bonding alone cannot sustain stable association in water, establishing that hydrophobic anchoring is a prerequisite for productive protonation-dependent recognition. These results identify protonation as a general, structurally contingent switch for redistributing enthalpic and entropic contributions to host–guest stabilization in native cyclodextrin systems.</jats:p>