Retrosynthesis plays a crucial role in the fields of organic synthesis and drug development, where the goal is to identify suitable reactants that can yield a target product molecule. Although existing methods have achieved notable success, they typically overlook the 3D conformational details and internal spatial organization of molecules. This oversight makes it challenging to predict reactants that conform to genuine chemical principles, particularly when dealing with complex molecular structures, such as polycyclic and heteroaromatic compounds. In response to this challenge, we introduce a novel transformer-based, template-free approach that incorporates 3D conformer data and spatial information. Our approach includes an Atom-align Fusion module that integrates 3D positional data at the input stage, ensuring correct alignment between atom tokens and their respective 3D coordinates. Additionally, we propose a Distance-weighted Attention mechanism that refines the self-attention process, constricting the model s focus to relevant atom pairs in 3D space. Extensive experiments on the USPTO-50K dataset demonstrate that our model outperforms previous template-free methods, setting a new benchmark for the field. A case study further highlights our method s ability to predict reasonable and accurate reactants.

Recent breakthroughs in Large Language Models (LLMs) have revolutionized natural language understanding and generation, sparking significant interest in applying them to scientific literature analysis. However, existing benchmarks fail to adequately evaluate the proficiency of LLMs in this domain, particularly in scenarios requiring higher-level abilities beyond mere memorization and the handling of multimodal data. In response to this gap, we introduce SciAssess, a benchmark specifically designed for the comprehensive evaluation of LLMs in scientific literature analysis. SciAssess aims to thoroughly assess the efficacy of LLMs by focusing on their capabilities in Memorization (L1), Comprehension (L2), and Analysis \& Reasoning (L3). It encompasses a variety of tasks drawn from diverse scientific fields, including fundamental science, alloy materials, biomedicine, drug discovery, and organic materials. To ensure the reliability of SciAssess, rigorous quality control measures have been implemented, ensuring accuracy, anonymization, and compliance with copyright standards. SciAssess evaluates 11 LLMs, including GPT, Claude, and Gemini, highlighting their strengths and areas for improvement. This evaluation supports the ongoing development of LLM applications in the analysis of scientific literature. SciAssess and its resources are available at \url{https://sci-assess.github.io/}.