用机器学习从少数分子出发自动构建化学反应网络,揭示生命起源关键路径。
ReactionAtlas: Ab origine exploration of chemical reaction networks with machine learning

- 基于生成模型和力场筛选,无需人工规则从种子分子出发探索反应路径。
- 发现约4.7万条反应,覆盖约1.2万种化合物,精度达PBE0水平的85%。
- 适用于研究前生命化学、糖类形成等复杂反应体系,适合计算化学与合成生物学研究者。
构建化学反应网络——连接势阱与过渡态(TS)及其基本反应的图谱——是理解催化、燃烧乃至生命起源的自然语言。传统方法依赖密度泛函理论(DFT),需输入反应物与产物,效率极低,难以处理成千上万的过渡态。本文提出ReactionAtlas,可从少量种子分子出发,无需人工规则,实现反应网络的从头构建。其机器学习生成模型提出候选反应,由经DFT训练的机器学习力场(MLFF)筛选有效过渡态,新产物作为新种子进入搜索。以8种前生命种子分子(CH₂O、H₂O、OH⁻、H₃O⁺、CO₂、H₂CO₃、HCO₃⁻、H)为起点,该框架发现了约47,000条反应,涉及约12,000种化合物。MLFF预测的过渡态在85%的情况下与PBE0参考结果的均方根偏差小于0.5 Å,且可轻松提升至PBE0精度。该方法首次以空前规模与精度映射了碳数不超过C₄H₈O₄的小糖类化学体系,包含电荷与立体信息。它揭示了包括甲醛循环在内的经典反应路径的新细节,并展示了形式素化学的替代路径可能性,对生命起源研究具有重要意义。
原文摘要 · Abstract (English)
Mapping a chemical reaction network, the graph of minima and transition states (TS) and the elementary reactions connecting them, is the natural language of chemistry, from catalysis to combustion to the origin of life. Constructing such a reaction network for a given chemistry has been impractical: it requires finding and characterizing tens of thousands of TS, a task for which traditional methods such as density functional theory (DFT) are typically prohibitively slow and require reactant and product as input. We introduce ReactionAtlas, which builds a reaction network $\textit{ab origine}$ from a handful of seed molecules and without hand-crafted rules. Specifically, our machine-learned generative model proposes reactions from kinetically sampled candidate compounds and a DFT-trained machine learned force field (MLFF) filters them to valid TS, the resulting products of which enter the search as new seeds. Starting from eight pre-biotic seeds (CH$_2$O, H$_2$O, OH$^-$, H$_3$O$^+$, CO$_2$, H$_2$CO$_3$, HCO$_3^-$, H), ReactionAtlas discovers $\sim$47,000 reactions among $\sim$12,000 compounds. The MLFF TSs match the PBE0 references within 0.5 Å RMSD in 85% of the cases and can be easily brought to the PBE0 level. Thus, ReactionAtlas maps small carbohydrate chemistry up to C$_4$H$_8$O$_4$ at unprecedented scale and accuracy, including charge and stereo information. It enables novel insights into many well-studied reaction paths, including the formose cycle, which we highlight for its centrality to the chemical origins of life. Notably, our framework also allows establishing alternative reaction pathways for formose chemistry.
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