# ChemToolAgent: The Impact of Tools on Language Agents for Chemistry Problem Solving

arXiv: https://arxiv.org/abs/2411.07228 · HTML: https://mlsanity.com/paper/2411.07228/

## Key facts

- Cited by 11 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 26 of its 49 references that are in the map.
- First posted on arXiv 11 Nov 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, 26 of 26)

- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [GPQA: A Graduate-Level Google-Proof Q&A Benchmark](https://mlsanity.com/paper/2311.12022/) (2023)
- [A Survey on Large Language Model based Autonomous Agents](https://mlsanity.com/paper/2308.11432/) (2023)
- [Qwen2 Technical Report](https://mlsanity.com/paper/2407.10671/) (2024)
- [MMMU: A Massive Multi-discipline Multimodal Understanding and Reasoning Benchmark for Expert AGI](https://mlsanity.com/paper/2311.16502/) (2023)
- [MMLU-Pro: A More Robust and Challenging Multi-Task Language Understanding Benchmark](https://mlsanity.com/paper/2406.01574/) (2024)
- [Teaching Large Language Models to Self-Debug](https://mlsanity.com/paper/2304.05128/) (2023)
- [Large Language Models Can Be Easily Distracted by Irrelevant Context](https://mlsanity.com/paper/2302.00093/) (2023)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Adaptive Chameleon or Stubborn Sloth: Revealing the Behavior of Large Language Models in Knowledge Conflicts](https://mlsanity.com/paper/2305.13300/) (2023)
- [ReConcile: Round-Table Conference Improves Reasoning via Consensus among Diverse LLMs](https://mlsanity.com/paper/2309.13007/) (2023)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [Tool Learning with Large Language Models: A Survey](https://mlsanity.com/paper/2405.17935/) (2024)
- [Are We Done with MMLU?](https://mlsanity.com/paper/2406.04127/) (2024)
- [What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks](https://mlsanity.com/paper/2305.18365/) (2023)
- [EASYTOOL: Enhancing LLM-based Agents with Concise Tool Instruction](https://mlsanity.com/paper/2401.06201/) (2024)
- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (2024)
- [A Review of Large Language Models and Autonomous Agents in Chemistry](https://mlsanity.com/paper/2407.01603/) (2024)
- [CRISPR-GPT for Agentic Automation of Gene-editing Experiments](https://mlsanity.com/paper/2404.18021/) (2024)
- [BioPlanner: Automatic Evaluation of LLMs on Protocol Planning in Biology](https://mlsanity.com/paper/2310.10632/) (2023)
- [MAGDi: Structured Distillation of Multi-Agent Interaction Graphs Improves Reasoning in Smaller Language Models](https://mlsanity.com/paper/2402.01620/) (2024)
- [CACTUS: Chemistry Agent Connecting Tool-Usage to Science](https://mlsanity.com/paper/2405.00972/) (2024)
- [Chemist-X: Large Language Model-empowered Agent for Reaction Condition Recommendation in Chemical Synthesis](https://mlsanity.com/paper/2311.10776/) (2023)
- [Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation](https://mlsanity.com/paper/1905.13741/) (2019)

## Built on by (most cited first, 11 of 11)

- [Advances and Challenges in Foundation Agents: From Brain-Inspired Intelligence to Evolutionary, Collaborative, and Safe Systems](https://mlsanity.com/paper/2504.01990/) (2025)
- [From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery](https://mlsanity.com/paper/2508.14111/) (2025)
- [A Survey of Agentic Reasoning for Large Language Models: Towards Recursively Self-Improving and Collective Agents](https://mlsanity.com/paper/2601.12538/) (2026)
- [PiFlow: Principle-Aware Scientific Discovery with Multi-Agent Collaboration](https://mlsanity.com/paper/2505.15047/) (2025)
- [AutoLabs: Cognitive Multi-Agent Systems with Self-Correction for Autonomous Chemical Experimentation](https://mlsanity.com/paper/2509.25651/) (2025)
- [Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics](https://mlsanity.com/paper/2510.09901/) (2025)
- [LARC: Towards Human-level Constrained Retrosynthesis Planning through an Agentic Framework](https://mlsanity.com/paper/2508.11860/) (2025)
- [MADD: Multi-Agent Drug Discovery Orchestra](https://mlsanity.com/paper/2511.08217/) (2025)
- [BrainAgent: A Large Language Model-Driven Multi-Agent Framework for Autonomous Brain Signal Understanding](https://mlsanity.com/paper/2606.25400/) (2026)
- [Bolek: A Multimodal Language Model for Molecular Reasoning](https://mlsanity.com/paper/2605.02745/) (2026)
- [Eta Given Delta: Defining LLM Tool Efficiency With Marginal Tool Utility](https://mlsanity.com/paper/2607.14108/) (2026)

## Abstract (arXiv)

To enhance large language models (LLMs) for chemistry problem solving, several LLM-based agents augmented with tools have been proposed, such as ChemCrow and Coscientist. However, their evaluations are narrow in scope, leaving a large gap in understanding the benefits of tools across diverse chemistry tasks. To bridge this gap, we develop ChemToolAgent, an enhanced chemistry agent over ChemCrow, and conduct a comprehensive evaluation of its performance on both specialized chemistry tasks and general chemistry questions. Surprisingly, ChemToolAgent does not consistently outperform its base LLMs without tools. Our error analysis with a chemistry expert suggests that: For specialized chemistry tasks, such as synthesis prediction, we should augment agents with specialized tools; however, for general chemistry questions like those in exams, agents' ability to reason correctly with chemistry knowledge matters more, and tool augmentation does not always help.