Guest-induced amorphization and cage-selective guest dynamics in solid organic clathrates

Solid-state host-guest reactions, in which a crystalline solid transforms upon direct uptake of a gaseous guest, represent a class of phase transformation whose molecular-scale mechanisms remain poorly understood. Here, we exploit xenon-loaded hydroquinone clathrates as a model system to reveal the molecular mechanisms governing both the formation pathway and the cage-filling behavior of solid host-guest materials, by combining structural analysis, spectroscopy, kinetic modeling, and molecular simulations. The phase transition is initiated by guest-induced amorphization (GIA) at the hydroquinone surface, producing transient quasi-liquid layers (∼11 Å thick) that facilitate nucleation and growth of the clathrate framework. The resulting amorphous interface facilitates local nucleation while limiting further guest penetration, followed by diffusion-controlled growth through the developing clathrate layer. We further show that two structurally distinct cage environments, designated C_β1 and C_β2 based on hydrogen-bond directionality, govern cage-selective guest occupancy and release. The exceptional thermal stability and high gas storage capacity (2.77 mmol g^-1) of the clathrate arise from strong host-guest van der Waals interactions that stabilize energetically favorable cage geometries. These findings establish GIA as a general initiating mechanism in solid-state host-guest reactions and demonstrate that cage-selective guest dynamics govern both the formation pathway and guest release behavior. The resulting mechanistic framework provides molecular-level design principles transferable to porous crystalline materials, including metal-organic frameworks, porous organic cages, and hydrogen-bonded organic frameworks.