Bridging the Plausibility-Validity Gap by Fine-Tuning a Reasoning-Enhanced LLM for Chemical Synthesis and Discovery

Abstract: LLMs often generate scientifically plausible but factually invalid information, a challenge we term the "plausibility-validity gap," particularly in specialized domains like chemistry. This paper presents a systematic methodology to bridge this gap by developing a specialized scientific assistant. We utilized the Magistral Small model, noted for its integrated reasoning capabilities, and fine-tuned it using Low-Rank Adaptation (LoRA). A key component of our approach was the creation of a "dual-domain dataset," a comprehensive corpus curated from various sources encompassing both molecular properties and chemical reactions, which was standardized to ensure quality. Our evaluation demonstrates that the fine-tuned model achieves significant improvements over the baseline model in format adherence, chemical validity of generated molecules, and the feasibility of proposed synthesis routes. The results indicate a hierarchical learning pattern, where syntactic correctness is learned more readily than chemical possibility and synthesis feasibility. While a comparative analysis with human experts revealed competitive performance in areas like chemical creativity and reasoning, it also highlighted key limitations, including persistent errors in stereochemistry, a static knowledge cutoff, and occasional reference hallucination. This work establishes a viable framework for adapting generalist LLMs into reliable, specialized tools for chemical research, while also delineating critical areas for future improvement.