用扩散模型直接预测有机晶体三维结构,精度和效率远超以往方法。
OXtal: An All-Atom Diffusion Model for Organic Crystal Structure Prediction
- 基于扩散模型学习分子构象与晶格排布的联合分布
- 在60万实验验证数据上实现<0.5Å RMSD和80%以上晶格相似率
- 无需对称性约束,适合复杂分子与柔性体系的晶体预测
从二维化学结构图准确预测可实验实现的三维有机分子晶体结构,是计算化学中的长期难题。晶体堆积直接影响有机固体的物理化学性质,在药物研发与有机半导体等领域具有重要意义。本文提出OXtal,一个1亿参数的全原子扩散模型,直接学习分子内构象与周期性排列的联合分布。为提升可扩展性,模型放弃显式的对称性归纳偏置,转而采用数据增强策略。同时提出一种受结晶启发的无晶格训练方案S^4(Stoichiometric Stochastic Shell Sampling),有效捕捉长程相互作用,避免显式晶格参数化,从而支持更灵活的全原子级架构设计。基于包含60万实验验证结构的大规模数据集(涵盖刚性/柔性分子、共晶与溶剂合物),OXtal相较以往第一性原理机器学习方法实现数量级提升,且成本远低于传统量子化学方法。具体而言,其构象均方根误差低于0.5 Å,晶格相似率超过80%,展现出对分子结晶热力学与动力学规律的建模能力。
原文摘要 · Abstract (English)
Accurately predicting experimentally realizable 3D molecular crystal structures from their 2D chemical graphs is a long-standing open challenge in computational chemistry called crystal structure prediction (CSP). Efficiently solving this problem has implications ranging from pharmaceuticals to organic semiconductors, as crystal packing directly governs the physical and chemical properties of organic solids. In this paper, we introduce OXtal, a large-scale 100M parameter all-atom diffusion model that directly learns the conditional joint distribution over intramolecular conformations and periodic packing. To efficiently scale OXtal, we abandon explicit equivariant architectures imposing inductive bias arising from crystal symmetries in favor of data augmentation strategies. We further propose a novel crystallization-inspired lattice-free training scheme, Stoichiometric Stochastic Shell Sampling ($S^4$), that efficiently captures long-range interactions while sidestepping explicit lattice parametrization -- thus enabling more scalable architectural choices at all-atom resolution. By leveraging a large dataset of 600K experimentally validated crystal structures (including rigid and flexible molecules, co-crystals, and solvates), OXtal achieves orders-of-magnitude improvements over prior ab initio machine learning CSP methods, while remaining orders of magnitude cheaper than traditional quantum-chemical approaches. Specifically, OXtal recovers experimental structures with conformer $\text{RMSD}_1<0.5$ Å and attains over 80\% packing similarity rate, demonstrating its ability to model both thermodynamic and kinetic regularities of molecular crystallization.
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