ChemGraph as an agentic framework for computational chemistry workflows

Thang D. Pham, Aditya Tanikanti, Murat Keçeli

Abstract: Atomistic simulations are essential in chemistry and materials science but remain challenging to run due to the expert knowledge required for the setup, execution, and validation stages of these calculations. We present ChemGraph, an agentic framework powered by artificial intelligence and state-of-the-art simulation tools to streamline and automate computational chemistry and materials science workflows. ChemGraph leverages graph neural network-based foundation models for accurate yet computationally efficient calculations and large language models (LLMs) for natural language understanding, task planning, and scientific reasoning to provide an intuitive and interactive interface. We evaluate ChemGraph across 13 benchmark tasks and demonstrate that smaller LLMs (GPT-4o-mini, Claude-3.5-haiku, Qwen-2.5-14B) perform well on simple workflows, while more complex tasks benefit from using larger models. Importantly, we show that decomposing complex tasks into smaller subtasks through a multi-agent framework enables GPT-4o to reach perfect accuracy and smaller LLMs to match or exceed single-agent GPT-4o’s performance in these benchmarks. Atomistic simulations are vital for computational chemistry and materials science, but their adoption remains challenging due to the need for expert knowledge and manual effort for the setup, execution, and validation stages. Here, the authors present ChemGraph, an agentic framework powered by artificial intelligence and state-of-the-art simulation tools to streamline and automate computational chemistry and materials science workflows.

External IDs:doi:10.1038/s42004-025-01776-9