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arXiv · 2505.07735

Assessing the Chemical Intelligence of Large Language Models

Nicholas T. Runcie·Charlotte M. Deane·Fergus Imrie
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Abstract

Large Language Models are versatile, general-purpose tools with a wide range of applications. Recently, the advent of "reasoning models" has led to substantial improvements in their abilities in advanced problem-solving domains such as mathematics and software engineering. In this work, we assessed the ability of reasoning models to perform chemistry tasks directly, without any assistance from external tools. We created a novel benchmark, called ChemIQ, consisting of 816 questions assessing core concepts in organic chemistry, focused on molecular comprehension and chemical reasoning. Unlike previous benchmarks, which primarily use multiple choice formats, our approach requires models to construct short-answer responses, more closely reflecting real-world applications. The reasoning models, OpenAI's o3-mini, Google's Gemini Pro 2.5, and DeepSeek R1, answered 50%-57% of questions correctly in the highest reasoning modes, with higher reasoning levels significantly increasing performance on all tasks. These models substantially outperformed the non-reasoning models which achieved only 3%-7% accuracy. We found that Large Language Models can now convert SMILES strings to IUPAC names, a task earlier models were unable to perform. Additionally, we show that the latest reasoning models can elucidate structures from 1D and 2D 1H and 13C NMR data, with Gemini Pro 2.5 correctly generating SMILES strings for around 90% of molecules containing up to 10 heavy atoms, and in one case solving a structure comprising 25 heavy atoms. For each task, we found evidence that the reasoning process mirrors that of a human chemist. Our results demonstrate that the latest reasoning models can, in some cases, perform advanced chemical reasoning.

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Nicholas T. Runcie, Charlotte M. Deane, Fergus Imrie. 2025-07-10. Assessing the Chemical Intelligence of Large Language Models. https://arxiv.org/abs/2505.07735

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