El Agente Estructural: An Artificially Intelligent Molecular Editor

TL;DR

El Agente Estructural is a multimodal, natural-language-driven molecular editor that enables precise, interactive manipulation of molecular structures for chemistry and modeling tasks.

Contribution

It introduces a novel AI agent that mimics expert manipulation of molecules using domain-informed tools and vision-language models, surpassing traditional generative approaches.

Findings

Enables site-selective functionalization and stereochemistry control.

Supports diverse real-world molecular manipulation scenarios.

Integrates with quantum chemistry platforms for advanced editing.

Abstract

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.