Structured Chemistry Reasoning with Large Language Models
On the map: LLM reasoning → Clinical and biomedical applications
Abstract (arXiv)
Large Language Models (LLMs) excel in diverse areas, yet struggle with complex scientific reasoning, especially in the field of chemistry. Different from the simple chemistry tasks (e.g., molecule classification) addressed in previous studies, complex chemistry problems require not only vast knowledge and precise calculation, but also compositional reasoning about rich dynamic interactions of different concepts (e.g., temperature changes). Our study shows that even advanced LLMs, like GPT-4, can fail easily in different ways. Interestingly, the errors often stem not from a lack of domain knowledge within the LLMs, but rather from the absence of an effective reasoning structure that guides the LLMs to elicit the right knowledge, incorporate the knowledge in step-by-step reasoning, and iteratively refine results for further improved quality. On this basis, we introduce StructChem, a simple yet effective prompting strategy that offers the desired guidance and substantially boosts the LLMs' chemical reasoning capability. Testing across four chemistry areas -- quantum chemistry, mechanics, physical chemistry, and kinetics -- StructChem substantially enhances GPT-4's performance, with up to 30% peak improvement. Our analysis also underscores the unique difficulties of precise grounded reasoning in science with LLMs, highlighting a need for more research in this area. Code is available at urlhttps://github.com/ozyyshr/StructChem.
Key facts. Cited by 27 papers in the map (data through 7 Oct 2026). Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning. Builds on 11 of its 45 references that are in the map. First posted on arXiv 16 Nov 2023.
Builds on
11 of 45 references.
References · 11
- 2023Llama 2: Open Foundation and Fine-Tuned Chat Modelscited by 12,865
- 2023Judging LLM-as-a-Judge with MT-Bench and Chatbot Arenacited by 8,393
- 2023Self-Refine: Iterative Refinement with Self-Feedbackcited by 3,317
- 2023Large Language Models Cannot Self-Correct Reasoning Yetcited by 965
- 2023ChemCrow: Augmenting large-language models with chemistry toolscited by 609
- 2022Large Language Models are Better Reasoners with Self-Verificationcited by 304
- 2023SciBench: Evaluating College-Level Scientific Problem-Solving Abilities of Large Language Modelscited by 246
- 2023TheoremQA: A Theorem-driven Question Answering datasetcited by 189
- 2022Translation between Molecules and Natural Languagecited by 173
- 2023Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Modelscited by 131
- 2023GPT-4 Doesn't Know It's Wrong: An Analysis of Iterative Prompting for Reasoning Problemscited by 88
Built on by
Citing papers per year: 2023: 2; 2024: 11; 2025: 9; 2026: 5.
27 papers.
Sort:
By area:
- 2024A Review of Large Language Models and Autonomous Agents in Chemistrycited by 96
- 2024RepoGraph: Enhancing AI Software Engineering with Repository-level Code Graphcited by 88
- 2023Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought Reasoning to Language Agentscited by 72
- 2024LLM Reasoners: New Evaluation, Library, and Analysis of Step-by-Step Reasoning with Large Language Modelscited by 70
- 2024MedCalc-Bench: Evaluating Large Language Models for Medical Calculationscited by 64
- 2023Language Models, Agent Models, and World Models: The LAW for Machine Reasoning and Planningcited by 59
- 2025ScienceBoard: Evaluating Multimodal Autonomous Agents in Realistic Scientific Workflowscited by 47
- 2025Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operationscited by 46
- 2025ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoningcited by 41
- 2024Capabilities of Large Language Models in Control Engineering: A Benchmark Study on GPT-4, Claude 3 Opus, and Gemini 1.0 Ultracited by 36
- 2024LLaMP: Large Language Model Made Powerful for High-fidelity Materials Knowledge Retrieval and Distillationcited by 32
- 2024Improving Physics Reasoning in Large Language Models Using Mixture of Refinement Agentscited by 22
15 more
- 2025DyFlow: Dynamic Workflow Framework for Agentic Reasoningcited by 22
- 2024ControlAgent: Automating Control System Design via Novel Integration of LLM Agents and Domain Expertisecited by 20
- 2026Large Language Model Reasoning Failurescited by 20
- 2024Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Surveycited by 16
- 2024Benchmarking the Capabilities of Large Language Models in Transportation System Engineering: Accuracy, Consistency, and Reasoning Behaviorscited by 13
- 2025FGBench: A Dataset and Benchmark for Molecular Property Reasoning at Functional Group-Level in Large Language Modelscited by 8
- 2025CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Predictioncited by 5
- 2024Bridging Text and Molecule: A Survey on Multimodal Frameworks for Moleculecited by 4
- 2025Normative Conflicts and Shallow AI Alignmentcited by 4
- 2025Atom-anchored LLMs speak Chemistry: A Retrosynthesis Demonstrationcited by 4
- 2026Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesiscited by 4
- 2026Implicit Turn-Wise Policy Optimization for Proactive User-LLM Interactioncited by 3
- 2025PepThink-R1: LLM for Interpretable Cyclic Peptide Optimization with CoT SFT and Reinforcement Learningcited by 1
- 2026Full-Stack Domain Enhancement for Combustion LLMs: Construction and Optimizationcited by 0
- 2026The Periodic Table of LLM Reasoning: A Structured Survey of Reasoning Paradigms, Methods, and Failure Modescited by 0
- 2026The Periodic Table of LLM Reasoning: A Structured Survey of Reasoning Paradigms, Methods, and Failure Modes9 Jun 2026
- 2026Implicit Turn-Wise Policy Optimization for Proactive User-LLM Interaction21 Mar 2026
- 2026Full-Stack Domain Enhancement for Combustion LLMs: Construction and Optimization27 Feb 2026
- 2026Large Language Model Reasoning Failures5 Feb 2026
- 2026Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesis25 Jan 2026
- 2025Atom-anchored LLMs speak Chemistry: A Retrosynthesis Demonstration18 Oct 2025
- 2025DyFlow: Dynamic Workflow Framework for Agentic Reasoning30 Sep 2025
- 2025PepThink-R1: LLM for Interpretable Cyclic Peptide Optimization with CoT SFT and Reinforcement Learning20 Aug 2025
- 2025CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction5 Aug 2025
- 2025FGBench: A Dataset and Benchmark for Molecular Property Reasoning at Functional Group-Level in Large Language Models1 Aug 2025
- 2025Normative Conflicts and Shallow AI Alignment5 Jun 2025
- 2025Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations27 May 2025
15 more
- 2025ScienceBoard: Evaluating Multimodal Autonomous Agents in Realistic Scientific Workflows26 May 2025
- 2025ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning11 Jan 2025
- 2024Improving Physics Reasoning in Large Language Models Using Mixture of Refinement Agents1 Dec 2024
- 2024ControlAgent: Automating Control System Design via Novel Integration of LLM Agents and Domain Expertise17 Oct 2024
- 2024RepoGraph: Enhancing AI Software Engineering with Repository-level Code Graph3 Oct 2024
- 2024Benchmarking the Capabilities of Large Language Models in Transportation System Engineering: Accuracy, Consistency, and Reasoning Behaviors15 Aug 2024
- 2024A Review of Large Language Models and Autonomous Agents in Chemistry26 Jun 2024
- 2024MedCalc-Bench: Evaluating Large Language Models for Medical Calculations17 Jun 2024
- 2024LLM Reasoners: New Evaluation, Library, and Analysis of Step-by-Step Reasoning with Large Language Models8 Apr 2024
- 2024Capabilities of Large Language Models in Control Engineering: A Benchmark Study on GPT-4, Claude 3 Opus, and Gemini 1.0 Ultra4 Apr 2024
- 2024Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule7 Mar 2024
- 2024Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey3 Mar 2024
- 2024LLaMP: Large Language Model Made Powerful for High-fidelity Materials Knowledge Retrieval and Distillation30 Jan 2024
- 2023Language Models, Agent Models, and World Models: The LAW for Machine Reasoning and Planning8 Dec 2023
- 2023Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought Reasoning to Language Agents20 Nov 2023
- 2023Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought Reasoning to Language Agentscited by 72
- 2025Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operationscited by 46
- 2025ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoningcited by 41
- 2024Improving Physics Reasoning in Large Language Models Using Mixture of Refinement Agentscited by 22
- 2025DyFlow: Dynamic Workflow Framework for Agentic Reasoningcited by 22
- 2026Large Language Model Reasoning Failurescited by 20
- 2024Benchmarking the Capabilities of Large Language Models in Transportation System Engineering: Accuracy, Consistency, and Reasoning Behaviorscited by 13
- 2025FGBench: A Dataset and Benchmark for Molecular Property Reasoning at Functional Group-Level in Large Language Modelscited by 8
- 2025CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Predictioncited by 5
- 2025PepThink-R1: LLM for Interpretable Cyclic Peptide Optimization with CoT SFT and Reinforcement Learningcited by 1
- 2026The Periodic Table of LLM Reasoning: A Structured Survey of Reasoning Paradigms, Methods, and Failure Modescited by 0
- 2026The Periodic Table of LLM Reasoning: A Structured Survey of Reasoning Paradigms, Methods, and Failure Modes9 Jun 2026
- 2026Large Language Model Reasoning Failures5 Feb 2026
- 2025DyFlow: Dynamic Workflow Framework for Agentic Reasoning30 Sep 2025
- 2025PepThink-R1: LLM for Interpretable Cyclic Peptide Optimization with CoT SFT and Reinforcement Learning20 Aug 2025
- 2025CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction5 Aug 2025
- 2025FGBench: A Dataset and Benchmark for Molecular Property Reasoning at Functional Group-Level in Large Language Models1 Aug 2025
- 2025Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations27 May 2025
- 2025ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning11 Jan 2025
- 2024Improving Physics Reasoning in Large Language Models Using Mixture of Refinement Agents1 Dec 2024
- 2024Benchmarking the Capabilities of Large Language Models in Transportation System Engineering: Accuracy, Consistency, and Reasoning Behaviors15 Aug 2024
- 2023Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought Reasoning to Language Agents20 Nov 2023
- 2024A Review of Large Language Models and Autonomous Agents in Chemistrycited by 96
- 2025ScienceBoard: Evaluating Multimodal Autonomous Agents in Realistic Scientific Workflowscited by 47
- 2024ControlAgent: Automating Control System Design via Novel Integration of LLM Agents and Domain Expertisecited by 20
- 2026Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesiscited by 4
- 2026Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesis25 Jan 2026
- 2025ScienceBoard: Evaluating Multimodal Autonomous Agents in Realistic Scientific Workflows26 May 2025
- 2024ControlAgent: Automating Control System Design via Novel Integration of LLM Agents and Domain Expertise17 Oct 2024
- 2024A Review of Large Language Models and Autonomous Agents in Chemistry26 Jun 2024
- 2025Normative Conflicts and Shallow AI Alignmentcited by 4
- 2025Normative Conflicts and Shallow AI Alignment5 Jun 2025
- 2024RepoGraph: Enhancing AI Software Engineering with Repository-level Code Graphcited by 88
- 2024MedCalc-Bench: Evaluating Large Language Models for Medical Calculationscited by 64
- 2024Capabilities of Large Language Models in Control Engineering: A Benchmark Study on GPT-4, Claude 3 Opus, and Gemini 1.0 Ultracited by 36
- 2024LLaMP: Large Language Model Made Powerful for High-fidelity Materials Knowledge Retrieval and Distillationcited by 32
- 2024Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Surveycited by 16
- 2024Bridging Text and Molecule: A Survey on Multimodal Frameworks for Moleculecited by 4
- 2025Atom-anchored LLMs speak Chemistry: A Retrosynthesis Demonstrationcited by 4
- 2026Implicit Turn-Wise Policy Optimization for Proactive User-LLM Interactioncited by 3
- 2026Full-Stack Domain Enhancement for Combustion LLMs: Construction and Optimizationcited by 0
- 2026Implicit Turn-Wise Policy Optimization for Proactive User-LLM Interaction21 Mar 2026
- 2026Full-Stack Domain Enhancement for Combustion LLMs: Construction and Optimization27 Feb 2026
- 2025Atom-anchored LLMs speak Chemistry: A Retrosynthesis Demonstration18 Oct 2025
- 2024RepoGraph: Enhancing AI Software Engineering with Repository-level Code Graph3 Oct 2024
- 2024MedCalc-Bench: Evaluating Large Language Models for Medical Calculations17 Jun 2024
- 2024Capabilities of Large Language Models in Control Engineering: A Benchmark Study on GPT-4, Claude 3 Opus, and Gemini 1.0 Ultra4 Apr 2024
- 2024Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule7 Mar 2024
- 2024Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey3 Mar 2024
- 2024LLaMP: Large Language Model Made Powerful for High-fidelity Materials Knowledge Retrieval and Distillation30 Jan 2024
Similar, not cited
Close in wording, no citation either way
- 2025SUPERChem: A Multimodal Reasoning Benchmark in Chemistry
- 2025Training a Scientific Reasoning Model for Chemistry
- 2026ChemDIRT: A Diversified Instruction, Representation, and Task Benchmark for Robust Chemistry-LLM Evaluation
- 2025ChemAU: Harness the Reasoning of LLMs in Chemical Research with Adaptive Uncertainty Estimation
- 2025QCBench: Evaluating Large Language Models on Domain-Specific Quantitative Chemistry
- 2025ChemVTS-Bench: Evaluating Visual-Textual-Symbolic Reasoning of Multimodal Large Language Models in Chemistry
- 2025Evaluating Large Language Models on Multimodal Chemistry Olympiad Exams
- 2025ChemDFM-R: A Chemical Reasoning LLM Enhanced with Atomized Chemical Knowledge