OXtal: An All-Atom Diffusion Model for Organic Crystal Structure Prediction
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arXiv
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| Main Authors: | , , , , , , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866914490466959360 |
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| author | Jin, Emily Nica, Andrei Cristian Galkin, Mikhail Rector-Brooks, Jarrid Lee, Kin Long Kelvin Miret, Santiago Arnold, Frances H. Bronstein, Michael Bose, Avishek Joey Tong, Alexander Liu, Cheng-Hao |
| author_facet | Jin, Emily Nica, Andrei Cristian Galkin, Mikhail Rector-Brooks, Jarrid Lee, Kin Long Kelvin Miret, Santiago Arnold, Frances H. Bronstein, Michael Bose, Avishek Joey Tong, Alexander Liu, Cheng-Hao |
| contents | 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. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2512_06987 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | OXtal: An All-Atom Diffusion Model for Organic Crystal Structure Prediction Jin, Emily Nica, Andrei Cristian Galkin, Mikhail Rector-Brooks, Jarrid Lee, Kin Long Kelvin Miret, Santiago Arnold, Frances H. Bronstein, Michael Bose, Avishek Joey Tong, Alexander Liu, Cheng-Hao Machine Learning Materials Science 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. |
| title | OXtal: An All-Atom Diffusion Model for Organic Crystal Structure Prediction |
| topic | Machine Learning Materials Science |
| url | https://arxiv.org/abs/2512.06987 |