El Agente Estructural: An Artificially Intelligent Molecular Editor
This provides a tool for chemists and molecular modellers to interactively edit 3D molecular structures with high precision, though it appears incremental as it builds on existing vision-language models and domain tools.
The authors tackled the problem of precise 3D molecular geometry manipulation in chemistry by developing El Agente Estructural, a multimodal AI agent that enables chemically meaningful control over atomic replacements, connectivity, and stereochemistry without rebuilding core frameworks, as demonstrated through case studies like site-selective functionalization and ligand binding.
We present El Agente Estructural, a multimodal, natural-language-driven geometry-generation and manipulation agent for autonomous chemistry and molecular modelling. Unlike molecular generation or editing via generative models, Estructural mimics how human experts directly manipulate molecular systems in three dimensions by integrating a comprehensive set of domain-informed tools and vision-language models. This design enables precise control over atomic or functional group replacements, atomic connectivity, and stereochemistry without the need to rebuild extensive core molecular frameworks. Through a series of representative case studies, we demonstrate that Estructural enables chemically meaningful geometry manipulation across a wide range of real-world scenarios. These include site-selective functionalization, ligand binding, ligand exchange, stereochemically controlled structure construction, isomer interconversion, fragment-level structural analysis, image-guided generation of structures from schematic reaction mechanisms, and mechanism-driven geometry generation and modification. These examples illustrate how multimodal reasoning, when combined with specialized geometry-aware tools, supports interactive and context-aware molecular modelling beyond structure generation. Looking forward, the integration of Estructural into El Agente Quntur, an autonomous multi-agent quantum chemistry platform, enhances its capabilities by adding sophisticated tools for the generation and editing of three-dimensional structures.