3DOpt: Benchmark for Automated Design of 3D Molecular Structures across the Periodic Table.

The automated design of three-dimensional (3D) molecular structures is a rapidly advancing field with major applications in drug discovery, catalysis, and materials science. Despite this progress, there remains a lack of standardized benchmarks for objectively evaluating and comparing generative methods for 3D molecular design beyond the domain of organic drug-like compounds. Here, we present 3DOpt, the first benchmark designed to assess the ability of generative methods to identify optimal 3D structures across the full chemical spectrum, including organometallic and transition-metal complexes. Each benchmark task is defined by a target 3D structure, a rigorously curated starting population of pre-evaluated candidate molecules, and a scoring function that quantifies similarity to the target in terms of both geometry and composition. We demonstrate the utility of 3DOpt by applying baseline generative methods and provide reference performance metrics for widely used molecular design strategies. Overall, 3DOpt establishes a general-purpose framework for the systematic evaluation of 3D molecular generative design methods across diverse chemical spaces.