Coarse-to-Fine MOF Generation with Periodic U-DiT and Verifier-Guided Linker Editing

Generating novel metal–organic frameworks (MOFs) with application-relevant pore architectures is a vital challenge, requiring both diverse structural exploration and precise geometric control. Small pore apertures are particularly compelling targets given their prevalence in experimental MOFs and critical role in selective molecular separation. To pursue this objective, we introduce CoFi-MOF, a coarse-to-fine framework combining global MOF generation with target-directed linker editing for fine-grained control of small pore apertures, and evaluate its performance in the challenging ultra-microporous regime. At the global scale, a periodic diffusion Transformer generates pore geometry conditioned on the target pore-limiting diameter within a signed-distance-field latent space, which a learned topology-aware Constructor translates into discrete MOF structures. At the local scale, geometric measurements identify promising structures for local refinement by Multi-Edit-Former, which proposes chemically feasible linker modifications to adjust their apertures. Reassembly and verification establish whether these edits improve the realized pore match. Experiments convincingly show that CoFi-MOF generates structurally diverse MOFs with pore distributions concentrated around targets. We further expand PORMAKE’s linker library with carboxylate-based building blocks and introduce MOF-Edit-DB, a large-scale dataset of edited MOFs to train and evaluate target-directed structural editing models. Together, CoFi-MOF enables precise small pore targeting in assembled MOFs and provides a reusable foundation for learning structural refinement.