Teaching a transformer to think like a chemist: predicting nanocluster stability

Abstract Atomically precise metal nanoclusters bridge the molecular and bulk regimes, but designing bimetallic motifs with targeted stability and reactivity remains challenging. Here, we combine density functional theory (DFT) and physics-grounded predictive artificial intelligence to map the configurational landscape of 13-atom icosahedral nanoclusters X 12 TM, with hosts X = (Ti, Zr, Hf) and Fe, and a single transition-metal dopant spanning the 3 d –5 d series. Spin-polarized DFT calculations on 240 bimetallic nanoclusters reveal systematic trends in binding and formation energies, distortion penalties, effective coordination number, d -band center, and HOMO-LUMO gap that govern the competition between core-shell ( i n ) and surface-segregated ( o u t ) arrangements. We then pretrain a transformer architecture on a curated set of 2968 unary clusters from the Quantum Cluster Database and fine-tune it on bimetallic data to predict formation energies and i n / o u t preference, achieving mean absolute errors of about 0.6–0.7 eV and calibrated uncertainty intervals. The resulting model rapidly adapts to an unseen Fe-host domain with only a handful of labeled examples. At the same time, attention patterns and Shapley attributions highlight size mismatch, d -electron count, and coordination environment as key descriptors. All data, code, and workflows follow FAIR/TRUE principles, enabling reproducible, interpretable screening of unexplored nanocluster chemistries for catalysis and energy conversion.