ORACLE: A Persistent Chemical State for Reproducible Molecular Workflows

Abstract ORACLE introduces a persistent chemical state for reproducible molecular workflows. Atomic synthons and the effective atomic number combine continuous geometric and electronic evidence into element-preserving local identities that can be compared, clustered, and transferred. The state links molecular topology, interactions, symmetry, fragmentation, and primitive coordinates with quantum-mechanical observables such as atomic charges, bond orders, and spin populations. These observables refine the same chemical representation across structure generation, parameter transfer, and optimization, including through overlapping fragments for large molecules. ORACLE also represents reactive contacts in transition states and connects them to downstream coordinate construction. The framework is evaluated across equilibrium and non-equilibrium chemical states, including changes in electronic structure, environment, and topology. It is designed to support sophisticated quantum-mechanical studies of chemically relevant molecules of roughly 100–200 atoms in medicinal chemistry, photovoltaics, catalysis, and related molecular materials.