The flexible and ever-changing layered structure of electrically conductive 2D metal–organic frameworks (MOFs) poses a formidable challenge for establishing any structure–application relationship. Here, we employ a combined quantum mechanics and classical molecular dynamics approach allowing large-scale/long-time simulations of the dynamics of both dry and hydrated systems to investigate the intrinsic flexibility and dynamical motions of layered 2D MOFs and its effect on their physical and chemical properties. Co_(3)(HHTP)_(2) and Cu_(3)(HHTP)_(2), HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene, MOFs as two representatives of the layered family of MOFs are studied in great detail with a focus on their experimentally observed differential framework stabilities in aqueous solutions. Our comprehensive molecular dynamics simulations reproduce structural properties of both MOFs as well as selective hydrolysis of the secondary building units with open metal sites in the hydrated Co_(3)(HHTP)_(2) versus intact metal nodes in hydrated Cu_(3)(HHTP)_(2) in agreement with available experimental reports. Our extensively detailed simulations reveal that the reason behind this behavior is the presence of intrinsic deformation sites in dry Co_(3)(HHTP)_(2). Our accurate ωB97M-v quantum mechanical calculations further confirm the higher tendency of the open Co~(2+) sites for coordination to water molecules compared to Cu~(2+). Our multi-faceted strategy paves the way toward simulation of realistic MOF-based materials and their interface with confined water molecules, which is especially relevant to designing more robust water stable materials with desired properties and applications.
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