MOFjson: An Explicit Topological Representation of Metal-Organic Frameworks for Language Models

Computation-ready metal-organic framework (MOF) databases are essential for high-throughput screening, yet many reported crystal structures remain chemically unreasonable or disordered, compromising simulation fidelity. Existing validation approaches can identify non-computation-ready structures, but they often rely on heuristic rules, license requirement, or offer limited interpretability. Here, we show that large language models (LLMs) can serve as interpretable validators of MOF structures when crystallographic information is transformed into chemically meaningful text. By benchmarking nine descriptors, we find that successful LLM-based validation depends not on the amount of structural information alone, but on whether local coordination, framework connectivity, and chemical context are organized into a linguistically learnable representation. Fine-tuned LLMs using specialized descriptors (mof2text) achieve performance comparable to graph-based models in identifying unreasonable MOFs. Importantly, these models extend beyond black-box classification by generating diagnostic rationales for likely error sources, including abnormal bonding, connectivity, and charge states, as well as error-category predictions for annotated datasets. This work establishes chemically informed textualization as the key step that transforms LLMs from generic text models into practical and explainable tools for curating MOF databases.

Inverse design of metal-organic frameworks (MOFs) requires searching a combinatorially vast space where property labels are expensive and most machine-learning models reveal little about why a structure succeeds. We introduce LLM4MOF, a closed-loop framework in which language-model agents reason about chemistry, build candidate MOFs, and test them in simulation, refining hypotheses over ten autonomous iterations. One agent proposes interpretable design hypotheses over metal nodes, linkers, pore geometry, and functional chemistry, and a second translates them into constraints that select candidate MOFs, each made of a metal node, organic linker, and matching topology. Each hypothesis is tested through four diagnostic beams that apply different subsets of its constraints, so comparing them shows whether geometry, chemistry, or metal choice drives performance. Even when blind to the global property landscape of databases, LLM4MOF concentrates its search on top-performing structures across six adsorption, separation, and electronic-structure tasks within 400 property evaluations. The same loop also generates new MOFs de novo and validates them in live simulation, where it adapts the geometry to each requested condition, outperforming random search and a genetic algorithm at roughly $1 per campaign. LLM4MOF shows that language-model agents can run interpretable, simulation-grounded inverse design without training a model per objective.

Large language models are increasingly used as reasoning components in AI-driven materials Co-Scientists, yet the reliability of the resulting verification pipeline remains unclear. Metal-organic frameworks (MOFs) provide a particularly challenging setting because structures may appear under different identifiers, synthesis outcomes depend strongly on experimental conditions, evidence is distributed across heterogeneous sources, and some hypotheses require computation rather than literature alone. We introduce a diagnostic benchmark with four task families covering structural grounding, synthesis-condition verification, evidence-sufficiency verification, and MLIP-based computational verification. T-MOF-1-3 are evaluated under closed-book, retrieval-enabled, and oracle-evidence settings to localize failures in knowledge access, evidence acquisition, and reasoning, while T-MOF-4 separately evaluates computational verification. Guided by these diagnosed failure modes, we develop MOF-Verify, a failure-aware agentic harness that targets structural, literature, evidence-sufficiency, and computational bottlenecks before producing a final verdict. Across multiple backbone LLMs, MOF-Verify substantially improves hypothesis-verification performance over direct inference and retrieval-based baselines. Benchmark datasets are released at https://github.com/IMMS-Ewha/MOF-Verify-Benchmark.