Reaction Graph: Toward Modeling Chemical Reactions with 3D Molecular Structures
Keywords: Chemical Reaction Modeling, Reaction Graph, 3D Molecular Structure, AI for Chemistry
TL;DR: In this paper, we introduce Reaction Graph (RG), a unified graph representation that encapsulates the 3D molecular structures within chemical reactions.
Abstract: Accurately modeling chemical reactions using Artificial Intelligence (AI) can accelerate discovery and development, especially in fields like drug design and material science. Although AI has made remarkable advancements in single molecule recognition, such as predicting molecular properties, the study of interactions between molecules, particularly chemical reactions, has been relatively overlooked. In this paper, we introduce Reaction Graph (RG), a unified graph representation that encapsulates the 3D molecular structures within chemical reactions. RG integrates the molecular graphs of reactants and products into a cohesive framework, effectively capturing the interatomic relationships pertinent to the reaction process. Additionally, it incorporates the 3D structure information of molecules in a simple yet effective manner. We conduct experiments on a range of tasks, including chemical reaction classification, condition prediction, and yield prediction. RG achieves the highest accuracy across six datasets, demonstrating the effectiveness of the proposed method. The code will be publicly available.
Supplementary Material: zip
Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)
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Submission Number: 4277
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