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Metal–organic frameworks (MOFs) are crystalline materials that self-assemble from inorganic nodes and organic linkers, and isoreticular chemistry allows for modular and synthetic reagents of various sizes. In this study, a MOF’s components—metal nodes and organic linkers—are constructed in a coarse-grained model from isotropic beads, retaining the basic symmetries of the molecular components. Lennard-Jones and Weeks– Chandler–Andersen pair potentials are used to model attractive and repulsive particle interactions, respectively. We analyze the crystallinity of the self-assembled products and explore the role of modulators—molecules that compete with the organic linkers in binding to the metal nodes, and which we construct analogously—during the selfassembly process of defect-engineered MOFs. Coarse-grained simulation allows for the uncoupling of experimentally interdependent variables to broadly map and determine essential MOF self-assembly conditions, among which are properties of the modulator: binding strength, size (steric hindrance), and concentration. Of these, the simulated modulator’s binding strength has the most pronounced effect on the resulting MOF’s crystal size.