Recently, large language models (LLMs) have shown significant progress, approaching human perception levels. In this work, we demonstrate that despite these advances, LLMs still struggle to reason using molecular structural information. This gap is critical because many molecular properties, including functional groups, depend heavily on such structural details. To address this limitation, we propose an approach that sketches molecular structures for reasoning. Specifically, we introduce Molecular Structural Reasoning (MSR) framework to enhance the understanding of LLMs by explicitly incorporating the key structural features. We present two frameworks for scenarios where the target molecule is known or unknown. We verify that our MSR improves molecular understanding through extensive experiments.

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures, commonly encoded in the SMILES representation. However, current LLMs struggle to interpret SMILES, even failing to carry out basic tasks such as counting molecular rings. To address this limitation, we introduce CLEANMOL, a novel framework that formulates SMILES parsing into a suite of clean and deterministic tasks explicitly designed to promote graph-level molecular comprehension. These tasks span from subgraph matching to global graph matching, providing structured supervision aligned with molecular structural properties. We construct a molecular pretraining dataset with adaptive difficulty scoring and pre-train open-source LLMs on these tasks. Our results show that CLEANMOL not only enhances structural comprehension but also achieves the best or competes with the baseline on the Mol-Instructions benchmark.

Large language models (LLMs) have large potential for molecular optimization, as they can gather external chemistry tools and enable collaborative interactions to iteratively refine molecular candidates. However, this potential remains underexplored, particularly in the context of structured reasoning, interpretability, and comprehensive tool-grounded molecular optimization. To address this gap, we introduce MT-Mol, a multi-agent framework for molecular optimization that leverages tool-guided reasoning and role-specialized LLM agents. Our system incorporates comprehensive RDKit tools, categorized into five distinct domains: structural descriptors, electronic and topological features, fragment-based functional groups, molecular representations, and miscellaneous chemical properties. Each category is managed by an expert analyst agent, responsible for extracting task-relevant tools and enabling interpretable, chemically grounded feedback. MT-Mol produces molecules with tool-aligned and stepwise reasoning through the interaction between the analyst agents, a molecule-generating scientist, a reasoning-output verifier, and a reviewer agent. As a result, we show that our framework shows the state-of-the-art performance of the PMO-1K benchmark on 15 out of 23 tasks and outperforms LLM baselines on ChemCoTBench benchmark.

Large language models (LLMs) have shown impressive performance by generating reasoning paths before final answers, but learning such a reasoning path requires costly human supervision. To address this issue, recent studies have explored self-training methods that improve reasoning capabilities using pseudo-labels generated by the LLMs themselves. Among these, confidence-based self-training fine-tunes LLMs to prefer reasoning paths with high-confidence answers, where confidence is estimated via majority voting. However, such methods exclusively focus on the quality of the final answer and may ignore the quality of the reasoning paths, as even an incorrect reasoning path leads to a correct answer by chance. Instead, we advocate the use of reasoning-level confidence to identify high-quality reasoning paths for self-training, supported by our empirical observations. We then propose a new self-training method, **CORE-PO**, that fine-tunes LLMs to prefer high-**CO**nfidence **RE**asoning paths through **P**olicy **O**ptimization. Our experiments show that CORE-PO improves the accuracy of outputs on four in-distribution and two out-of-distribution benchmarks, compared to existing self-training methods.