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. Co3(HHTP)2 and Cu3(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 Co3(HHTP)2 versus intact metal nodes in hydrated Cu3(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 Co3(HHTP)2. Our accurate ωB97M-v quantum mechanical calculations further confirm the higher tendency of the open Co2+ sites for coordination to water molecules compared to Cu2+. 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.

Contents S1. Developing ab initio force fields Co 31 +0.761 Co 327 +0.672 Co 651 +0.713 Co 32 +0.733 Co 378 +0.725 Co 699 +0.786 Co 63 +0.761 Co 379 +0.769 Co 712 +0.681 Co 75 +0.729 Co 390 +0.670 Co 739 +0.692 Co 126 +0.735 Co 441 +0.683 Co 789 +0.661 Co 127 +0.715 Co 443 +0.727 Co 790 +0.743 Co 138 +0.793 Co 474 +0.675 Co 825 +0.811 Co 189 +0.776 Co 537 +0.701 Co 840 +0.715 Co 191 +0.690 Co 538 +0.710 Co 888 +0.704 Co 222 +0.728 Co 573 +0.717 Co 889 +0.725 Co 283 +0.735 Co 588 +0.773 Co 903 +0.678 Co 284 +0.703 Co 636 +0.778 Co 951 +0.737 Co 315 +0.724 Co 637 +0.733 Co 964 +0.704 Co 991 +0.741 Sites (b) Co 64 +0.997 Co 316 +1.027 Co 574 +0.974 Co 826 +1.000 Co 190 +1.091 Co 442 +0.971 Co 700 +0.867 Co 952

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