# El Agente Estructural: An Artificially Intelligent Molecular Editor

arXiv: https://arxiv.org/abs/2602.04849 · HTML: https://mlsanity.com/paper/2602.04849/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 90 references that are in the map.
- First posted on arXiv 4 Feb 2026.

## Builds on (most cited first, 17 of 17)

- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Cognitive Architectures for Language Agents](https://mlsanity.com/paper/2309.02427/) (2023)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [Deep Reinforcement Learning for De-Novo Drug Design](https://mlsanity.com/paper/1711.10907/) (2017)
- [SELFIES and the future of molecular string representations](https://mlsanity.com/paper/2204.00056/) (2022)
- [ChemVLM: Exploring the Power of Multimodal Large Language Models in Chemistry Area](https://mlsanity.com/paper/2408.07246/) (2024)
- [ORGANA: A Robotic Assistant for Automated Chemistry Experimentation and Characterization](https://mlsanity.com/paper/2401.06949/) (2024)
- [Training a Scientific Reasoning Model for Chemistry](https://mlsanity.com/paper/2506.17238/) (2025)
- [El Agente: An Autonomous Agent for Quantum Chemistry](https://mlsanity.com/paper/2505.02484/) (2025)
- [DREAMS: Density Functional Theory Based Research Engine for Agentic Materials Simulation](https://mlsanity.com/paper/2507.14267/) (2025)
- [ChemGraph: An Agentic Framework for Computational Chemistry Workflows](https://mlsanity.com/paper/2506.06363/) (2025)
- [Aitomia: Your Intelligent Assistant for AI-Driven Atomistic and Quantum Chemical Simulations](https://mlsanity.com/paper/2505.08195/) (2025)
- [AtomWorld: A Benchmark for Evaluating Spatial Reasoning in Large Language Models on Crystalline Materials](https://mlsanity.com/paper/2510.04704/) (2025)
- [Sampling molecular conformations and dynamics in a multi-user virtual reality framework](https://mlsanity.com/paper/1801.02884/) (2018)
- [SynCraft: Guiding Large Language Models to Predict Edit Sequences for Molecular Synthesizability Optimization](https://mlsanity.com/paper/2512.20333/) (2025)

## Built on by (most cited first, 5 of 5)

- [El Agente Gr'afico: A Semantic Execution Runtime for Scientific Agents](https://mlsanity.com/paper/2602.17902/) (2026)
- [El Agente Forjador: Task-Driven Agent Generation for Quantum Simulation](https://mlsanity.com/paper/2604.14609/) (2026)
- [La Agente 'Optima: Towards Agentic Self-Driving Laboratories](https://mlsanity.com/paper/2609.04564/) (2026)
- [Science Done on a Machine by a Machine: AI Agents in Computational Chemistry](https://mlsanity.com/paper/2608.18508/) (2026)
- [El Agente Potente: High-Throughput Agentic Atomistic Simulations](https://mlsanity.com/paper/2609.14840/) (2026)

## Abstract (arXiv)

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.