通过分而治之策略,高效生成大分子过渡态结构。
FragmentFlow: Scalable Transition State Generation for Large Molecules
- 以反应核心为对象训练生成模型,避免分子增大带来的分布偏移。
- 在含33个重原子的分子上,90%过渡态识别准确,优化步数减少30%。
- 适合需要高通量反应性分析的研究者使用。
过渡态(TS)是理解与定量预测化学反应活性及反应机理的核心。传统方法计算成本高,近年生成模型虽能对小分子生成有意义的过渡态,但因分子尺寸增大引发的分布偏移,难以推广至实际相关反应底物。此外,大分子过渡态数据缺乏,无法从头训练生成模型。为此,我们提出FragmentFlow:一种分而治之的方法,训练生成模型预测定义反应机理的反应核心原子的过渡态几何结构,再通过重新连接取代基片段重建完整过渡态。通过在反应核心上操作,其大小和组成在不同分子背景下相对稳定,从而缓解生成建模中的分布偏移。在包含最多33个重原子反应物的新标注数据集上评估,FragmentFlow正确识别了90%的过渡态,且所需鞍点优化步骤比经典初始化方案减少30%。结果表明该方法可实现高通量反应性研究中的可扩展过渡态生成。
原文摘要 · Abstract (English)
Transition states (TSs) are central to understanding and quantitatively predicting chemical reactivity and reaction mechanisms. Although traditional TS generation methods are computationally expensive, recent generative modeling approaches have enabled chemically meaningful TS prediction for relatively small molecules. However, these methods fail to generalize to practically relevant reaction substrates because of distribution shifts induced by increasing molecular sizes. Furthermore, TS geometries for larger molecules are not available at scale, making it infeasible to train generative models from scratch on such molecules. To address these challenges, we introduce FragmentFlow: a divide-and-conquer approach that trains a generative model to predict TS geometries for the reactive core atoms, which define the reaction mechanism. The full TS structure is then reconstructed by re-attaching substituent fragments to the predicted core. By operating on reactive cores, whose size and composition remain relatively invariant across molecular contexts, FragmentFlow mitigates distribution shifts in generative modeling. Evaluated on a new curated dataset of reactions involving reactants with up to 33 heavy atoms, FragmentFlow correctly identifies 90% of TSs while requiring 30% fewer saddle-point optimization steps than classical initialization schemes. These results point toward scalable TS generation for high-throughput reactivity studies.
Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。