# A Review of Large Language Models and Autonomous Agents in Chemistry

arXiv: https://arxiv.org/abs/2407.01603 · HTML: https://mlsanity.com/paper/2407.01603/

## Key facts

- Cited by 99 papers in the map (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 211 of its 577 references that are in the map.
- First posted on arXiv 26 Jun 2024.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 30 of 211)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Proximal Policy Optimization Algorithms](https://mlsanity.com/paper/1707.06347/) (2017)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Training Verifiers to Solve Math Word Problems](https://mlsanity.com/paper/2110.14168/) (2021)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Direct Preference Optimization: Your Language Model is Secretly a Reward Model](https://mlsanity.com/paper/2305.18290/) (2023)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Neural Machine Translation by Jointly Learning to Align and Translate](https://mlsanity.com/paper/1409.0473/) (2014)
- [Reflexion: Language Agents with Verbal Reinforcement Learning](https://mlsanity.com/paper/2303.11366/) (2023)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [SQuAD: 100,000+ Questions for Machine Comprehension of Text](https://mlsanity.com/paper/1606.05250/) (2016)
- [Robust Speech Recognition via Large-Scale Weak Supervision](https://mlsanity.com/paper/2212.04356/) (2022)
- [Generative Agents: Interactive Simulacra of Human Behavior](https://mlsanity.com/paper/2304.03442/) (2023)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [Self-Refine: Iterative Refinement with Self-Feedback](https://mlsanity.com/paper/2303.17651/) (2023)
- [Tree of Thoughts: Deliberate Problem Solving with Large Language Models](https://mlsanity.com/paper/2305.10601/) (2023)
- [Scaling Instruction-Finetuned Language Models](https://mlsanity.com/paper/2210.11416/) (2022)

## Built on by (most cited first, 30 of 99)

- [AlphaEvolve: A coding agent for scientific and algorithmic discovery](https://mlsanity.com/paper/2506.13131/) (2025)
- [From LLM Reasoning to Autonomous AI Agents: A Comprehensive Review](https://mlsanity.com/paper/2504.19678/) (2025)
- [Towards Scientific Intelligence: A Survey of LLM-based Scientific Agents](https://mlsanity.com/paper/2503.24047/) (2025)
- [LLM Agents for Education: Advances and Applications](https://mlsanity.com/paper/2503.11733/) (2025)
- [El Agente: An Autonomous Agent for Quantum Chemistry](https://mlsanity.com/paper/2505.02484/) (2025)
- [SciToolAgent: A Knowledge Graph-Driven Scientific Agent for Multi-Tool Integration](https://mlsanity.com/paper/2507.20280/) (2025)
- [Position: Multimodal Large Language Models Can Significantly Advance Scientific Reasoning](https://mlsanity.com/paper/2502.02871/) (2025)
- [Probing the limitations of multimodal language models for chemistry and materials research](https://mlsanity.com/paper/2411.16955/) (2024)
- [From Language to Action: A Review of Large Language Models as Autonomous Agents and Tool Users](https://mlsanity.com/paper/2508.17281/) (2025)
- [PiFlow: Principle-Aware Scientific Discovery with Multi-Agent Collaboration](https://mlsanity.com/paper/2505.15047/) (2025)
- [MDCrow: Automating Molecular Dynamics Workflows with Large Language Models](https://mlsanity.com/paper/2502.09565/) (2025)
- [MatExpert: Decomposing Materials Discovery by Mimicking Human Experts](https://mlsanity.com/paper/2410.21317/) (2024)
- [RAG-Enhanced Collaborative LLM Agents for Drug Discovery](https://mlsanity.com/paper/2502.17506/) (2025)
- [Assessing the Chemical Intelligence of Large Language Models](https://mlsanity.com/paper/2505.07735/) (2025)
- [Language-Based Bayesian Optimization Research Assistant (BORA)](https://mlsanity.com/paper/2501.16224/) (2025)
- [Large language models as uncertainty-calibrated optimizers for experimental discovery](https://mlsanity.com/paper/2504.06265/) (2025)
- [A Survey of Large Language Models for Text-Guided Molecular Discovery: from Molecule Generation to Optimization](https://mlsanity.com/paper/2505.16094/) (2025)
- [ChemTEB: Chemical Text Embedding Benchmark, an Overview of Embedding Models Performance & Efficiency on a Specific Domain](https://mlsanity.com/paper/2412.00532/) (2024)
- [ChemToolAgent: The Impact of Tools on Language Agents for Chemistry Problem Solving](https://mlsanity.com/paper/2411.07228/) (2024)
- [From Generalist to Specialist: A Survey of Large Language Models for Chemistry](https://mlsanity.com/paper/2412.19994/) (2024)
- [VISION: A Modular AI Assistant for Natural Human-Instrument Interaction at Scientific User Facilities](https://mlsanity.com/paper/2412.18161/) (2024)
- [SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Models](https://mlsanity.com/paper/2503.12602/) (2025)
- [ChemPile: A 250GB Diverse and Curated Dataset for Chemical Foundation Models](https://mlsanity.com/paper/2505.12534/) (2025)
- [Aitomia: Your Intelligent Assistant for AI-Driven Atomistic and Quantum Chemical Simulations](https://mlsanity.com/paper/2505.08195/) (2025)
- [Bohrium + SciMaster: Building the Infrastructure and Ecosystem for Agentic Science at Scale](https://mlsanity.com/paper/2512.20469/) (2025)
- [In Context Learning and Reasoning for Symbolic Regression with Large Language Models](https://mlsanity.com/paper/2410.17448/) (2024)
- [PriM: Principle-Inspired Material Discovery through Multi-Agent Collaboration](https://mlsanity.com/paper/2504.08810/) (2025)
- [Advancing the Scientific Method with Large Language Models: From Hypothesis to Discovery](https://mlsanity.com/paper/2505.16477/) (2025)
- [A Survey of AI for Materials Science: Foundation Models, LLM Agents, Datasets, and Tools](https://mlsanity.com/paper/2506.20743/) (2025)
- [Towards autonomous quantum physics research using LLM agents with access to intelligent tools](https://mlsanity.com/paper/2511.11752/) (2025)

## Abstract (arXiv)

Large language models (LLMs) have emerged as powerful tools in chemistry, significantly impacting molecule design, property prediction, and synthesis optimization. This review highlights LLM capabilities in these domains and their potential to accelerate scientific discovery through automation. We also review LLM-based autonomous agents: LLMs with a broader set of tools to interact with their surrounding environment. These agents perform diverse tasks such as paper scraping, interfacing with automated laboratories, and synthesis planning. As agents are an emerging topic, we extend the scope of our review of agents beyond chemistry and discuss across any scientific domains. This review covers the recent history, current capabilities, and design of LLMs and autonomous agents, addressing specific challenges, opportunities, and future directions in chemistry. Key challenges include data quality and integration, model interpretability, and the need for standard benchmarks, while future directions point towards more sophisticated multi-modal agents and enhanced collaboration between agents and experimental methods. Due to the quick pace of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.