From Dynamic Frustration to Steric Trapping: The Microscopic Mechanism of a Monotropic Phase Transition

The atomic-level mechanisms governing solvent-driven single-crystal-to-single-crystal (SCSC) topotactic transitions are notoriously difficult to capture, as transient, symmetry-broken intermediates (Z′ > 1) rarely survive structural collapse. Here, we map the complete molecular trajectory of a cooperative solid-state transition within a heavily hydrated di-iron-µ-O-2'-cytidine monophosphate complex, [Fe2(µ-O)(TPA)2(2′-CMP)](ClO4)2·xH2O. By tuning crystallization kinetics, we isolated two distinct solvatomorphic pathways: a thermodynamically stable Z′ = 1 phase and an elusive, kinetically trapped Z′ = 2 interphase. In the reversible Z′ = 1 pathway, the host lattice maintains volumetric invariance across 120–298 K while undergoing a continuous, entropically driven internal hydrogen-bond toggle. Conversely, the metastable Z′ = 2 solvatomorph physically bridges the transition pathway by co-crystallizing incompatible 'open' and 'closed' conformations of two chemical latches. These two chemical latches are the two kind of hydrogen bonds-the cytosine C6-H6 to sugar C5′-hydroxyl oxygen (C6-H6···O5′) and sugar C3′-hydroxyl to phosphate P=O oxygen (O3′-H3′···O=P) contacts within a single asymmetric unit. Fine-sliced variable-temperature X-ray diffraction (150–310 K) reveals that prior to collapse, one of the molecules in the asymmetric unit, acts as a dynamic shock absorber. This molecule reversibly breaking and reforming of its C6···O5′ latch (3.22-3.65 Å) drives a ~ 31° glycosidic swing and bimodal occupancy shifting, while the competing O3′···O=P contact contracts (3.11 to 2.90 Å) to buffer thermal strain. Crossing a 280 K kinetic threshold triggers an abrupt, monotropic 50% volumetric collapse (Z′ = 2 → Z′ = 1), subjecting the merged nucleotide site to severe structural shock before permanently clamping both frustrated latches into a sterically jammed, statically disordered state (C6···O5′at 3.26 Å; O3′···O=P at 2.76 Å). Strikingly, the sheer mechanical force driven by this frustrated latch clamping violently expels few crystallized water near the freezing point of bulk water (273-280 K)- while the collapsed matrix retains permanent microporosity to dynamically resorb and order guest water upon cooling.