用统一机器学习势模型实现快速精准分子晶体结构预测
FastCSP: Accelerated Molecular Crystal Structure Prediction with Universal Model for Atoms
- 仅用一个预训练通用原子势模型,全流程无需微调或密度泛函计算
- 在74种实验多晶型中准确复现全部已知结构,误差小于9 kJ/mol
- 特别适合柔性分子多晶型筛选,显著降低药物研发计算门槛
分子晶体结构预测(CSP)对制药和有机电子领域至关重要,但因需在大搜索空间中达到亚千焦每摩尔精度而计算成本高。尽管包含色散项的密度泛函理论(DFT)具备足够精度,其计算开销却难以支撑大量构象评估。本文提出FastCSP——一个完全基于单一预训练通用机器学习势(UMA)的开源端到端CSP流程,无需系统特化微调或任何DFT计算。FastCSP整合了构象生成、通过Genarris 3的随机结构生成、几何优化、自由能评估及构象能修正,全部由UMA驱动。在28个半刚性和10个柔性分子(共74个实验多晶型)上验证,FastCSP可靠复现所有已知结构,排序误差小于9 kJ/mol。UMA在化学多样性化合物上高度复现含色散项DFT结果。对于具有构象多晶性的柔性分子(如ROY),构象修正尤为关键。该模型的精度、可迁移性与低计算成本,使经典力场与DFT重排序在早期筛选中不再必要。整个FastCSP流程开源发布,大幅降低访问门槛,使制药级与高通量多晶型筛选可在实际计算资源下完成。
原文摘要 · Abstract (English)
Molecular crystal structure prediction (CSP) is essential for applications in pharmaceuticals and organic electronics. However, CSP remains challenging and computationally intensive due to the need to explore a large search space with sub-kJ/mol accuracy to distinguish between competing polymorphs. While dispersion-inclusive density functional theory (DFT) offers the necessary precision, its computational cost is impractical for a large number of putative structures. Here, we present FastCSP, an open-source, end-to-end CSP workflow driven entirely by a single pretrained universal machine learning interatomic potential (MLIP), the Universal Model for Atoms (UMA), without any system-specific fine-tuning or DFT calculations. FastCSP integrates conformer generation, random structure generation via Genarris 3, geometry optimization, free energy evaluation, and conformer energy corrections, all powered by UMA. Benchmarked on 28 semi-rigid and 10 flexible molecules spanning 74 experimental polymorphs, FastCSP reliably recovers all known structures, ranking them within 9 kJ/mol of the global minimum. UMA reproduces dispersion-inclusive DFT results with high fidelity across chemically diverse compounds. Conformer corrections are particularly beneficial for flexible compounds with conformational polymorphism, such as ROY. UMA's accuracy, transferability, and computational cost thus eliminate the need for classical force fields in early-stage screening and DFT-based re-ranking in CSP workflows. The open-source release of the entire FastCSP workflow lowers the barrier to accessing CSP, enabling both pharmaceutical-grade and high-throughput polymorph screening within practical computational reach.
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