mlsanityData to 7 Oct 2026

A Review of Large Language Models and Autonomous Agents in Chemistry

arXiv 2407.01603 ↗First posted 26 Jun 2024cs.LG cs.AI cs.CLcited by 96

On the map: LLM agents and tool use → Medical and scientific domain agents

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.

Key facts. Cited by 96 papers in the map (data through 7 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.

Builds on

211 of 577 references.

Closest ancestors · 6

Same direction, newest first

  1. 2024CACTUS: Chemistry Agent Connecting Tool-Usage to Science2 May
  2. 2024CRISPR-GPT for Agentic Automation of Gene-editing Experiments27 Apr
  3. 2024ChemMiner: A Large Language Model Agent System for Chemical Literature Data Mining20 Feb
  4. 2024ProtAgents: Protein discovery via large language model multi-agent collaborations combining physics and machine learning27 Jan
  5. 2023Agent-based Learning of Materials Datasets from Scientific Literature18 Dec
  6. 2023Chemist-X: Large Language Model-empowered Agent for Reaction Condition Recommendation in Chemical Synthesis16 Nov

Other references · 205

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50 most cited of 205 All 205 (JSON)

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2024: 12; 2025: 53; 2026: 31.

96 papers.

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  2. 2025From LLM Reasoning to Autonomous AI Agents: A Comprehensive Reviewcited by 146
  3. 2025Towards Scientific Intelligence: A Survey of LLM-based Scientific Agentscited by 96
  4. 2025LLM Agents for Education: Advances and Applicationscited by 59
  5. 2025El Agente: An Autonomous Agent for Quantum Chemistrycited by 43
  6. 2025SciToolAgent: A Knowledge Graph-Driven Scientific Agent for Multi-Tool Integrationcited by 40
  7. 2025Position: Multimodal Large Language Models Can Significantly Advance Scientific Reasoningcited by 33
  8. 2025From Language to Action: A Review of Large Language Models as Autonomous Agents and Tool Userscited by 32
  9. 2024Probing the limitations of multimodal language models for chemistry and materials researchcited by 31
  10. 2025PiFlow: Principle-Aware Scientific Discovery with Multi-Agent Collaborationcited by 25
  11. 2025MDCrow: Automating Molecular Dynamics Workflows with Large Language Modelscited by 22
  12. 2024MatExpert: Decomposing Materials Discovery by Mimicking Human Expertscited by 18
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  3. 2025Language-Based Bayesian Optimization Research Assistant (BORA)cited by 13
  4. 2025A Survey of Large Language Models for Text-Guided Molecular Discovery: from Molecule Generation to Optimizationcited by 12
  5. 2024ChemToolAgent: The Impact of Tools on Language Agents for Chemistry Problem Solvingcited by 11
  6. 2024ChemTEB: Chemical Text Embedding Benchmark, an Overview of Embedding Models Performance & Efficiency on a Specific Domaincited by 11
  7. 2024From Generalist to Specialist: A Survey of Large Language Models for Chemistrycited by 11
  8. 2024VISION: A Modular AI Assistant for Natural Human-Instrument Interaction at Scientific User Facilitiescited by 10
  9. 2025Large language models as uncertainty-calibrated optimizers for experimental discoverycited by 10
  10. 2025SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Modelscited by 9
  11. 2025Aitomia: Your Intelligent Assistant for AI-Driven Atomistic and Quantum Chemical Simulationscited by 8
  12. 2025Bohrium + SciMaster: Building the Infrastructure and Ecosystem for Agentic Science at Scalecited by 8
  13. 2024In Context Learning and Reasoning for Symbolic Regression with Large Language Modelscited by 7
  14. 2025ChemPile: A 250GB Diverse and Curated Dataset for Chemical Foundation Modelscited by 7
  15. 2025Advancing the Scientific Method with Large Language Models: From Hypothesis to Discoverycited by 7
  16. 2025A Survey of AI for Materials Science: Foundation Models, LLM Agents, Datasets, and Toolscited by 7
  17. 2025Towards autonomous quantum physics research using LLM agents with access to intelligent toolscited by 7
  18. 2024AstroMLab 2: AstroLLaMA-2-70B Model and Benchmarking Specialised LLMs for Astronomycited by 6
  19. 2025PriM: Principle-Inspired Material Discovery through Multi-Agent Collaborationcited by 6
  20. 2025CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Predictioncited by 5
  21. 2025Molecular Machine Learning in Chemical Process Designcited by 5
  22. 2024Tokenization for Molecular Foundation Modelscited by 4
  23. 2024MAMMAL -- Molecular Aligned Multi-Modal Architecture and Languagecited by 4
  24. 2025Enforcement Agents: Enhancing Accountability and Resilience in Multi-Agent AI Frameworkscited by 4
  25. 2025An LLM-enabled Multi-Agent Autonomous Mechatronics Design Frameworkcited by 4
  26. 2025LM Agents May Fail to Act on Their Own Risk Knowledgecited by 4
  27. 2025VASP Agent: An Agentic Framework for Autonomous First-principles Calculationscited by 4
  28. 2026OpenSage: Self-programming Agent Generation Enginecited by 4
  29. 2024SwiftDossier: Tailored Automatic Dossier for Drug Discovery with LLMs and Agentscited by 3
  30. 2025A Status Quo Investigation of Large Language Models towards Cost-Effective CFD Automation with OpenFOAMGPT: ChatGPT vs. Qwen vs. Deepseekcited by 3
  31. 2025ChemOrch: Empowering LLMs with Chemical Intelligence via Synthetic Instructionscited by 3
  32. 2025RxnCaption: Reformulating Reaction Diagram Parsing as Visual Prompt Guided Captioningcited by 3
  33. 2026Evaluating the Progression of Large Language Model Capabilities for Small-Molecule Drug Designcited by 3
  34. 2025Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?cited by 2
  35. 2025Perspective on Utilizing Foundation Models for Laboratory Automation in Materials Researchcited by 2
  36. 2025A Survey of Large Language Models in Discipline-specific Research: Challenges, Methods and Opportunitiescited by 2
  37. 2025SasAgent: Multi-Agent AI System for Small-Angle Scattering Data Analysiscited by 2
  38. 2025MiST: Understanding the Role of Mid-Stage Scientific Training in Developing Chemical Reasoning Modelscited by 2

50 most cited of 96 All 96 (JSON)

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  5. 2026Molecular LLM Agents: From Architectural Design to Scientific Autonomy
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