MolCrystalFlow: Molecular Crystal Structure Prediction via Flow Matching
Authors: Cheng Zeng, Harry W. Sullivan, Thomas Egg, Maya M. Martirossyan, Philipp Höllmer, Jirui Jin, Richard G. Hennig, Adrian Roitberg, Stefano Martiniani, Ellad B. Tadmor, Mingjie Liu
Organizations: Department of Chemistry, University of Florida, Gainesville, FL 32611, USA · Quantum Theory Project, University of Florida, Gainesville, FL 32611, USA · Department of Chemical Engineering and Material Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA · Center for Soft Matter Research, Department of Physics, New York University, New York 10003, USA · Simons Center for Computational Physical Chemistry, Department of Chemistry, New York University, New York 10003, USA · Department of Materials Science & Engineering, University of Florida, Gainesville, FL 32611, USA · Courant Institute of Mathematical Sciences, New York University, New York 10003, USA · Center for Neural Science, New York University, New York 10003, USA · Department of Aerospace Engineering and Mechanics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
Molecular crystal structure prediction represents a grand challenge in computational chemistry due to large sizes of constituent molecules and complex intra- and intermolecular interactions. While generative modeling has revolutionized structure discovery for molecules, inorganic solids, and metal-organic frameworks, extending such approaches to fully periodic molecular crystals is still elusive. Here, we present MolCrystalFlow, a flow-based generative model for molecular crystal structure prediction. The framework disentangles intramolecular complexity from intermolecular packing by embedding molecules as rigid bodies and jointly learning the lattice matrix, molecular orientations, and centroid positions. Centroids and orientations are represented on their native Riemannian manifolds, allowing geodesic flow construction and graph neural network operations that respects geometric symmetries. We benchmark our model against a state-of-the-art generative model (MOFFlow) for large-size periodic crystals and a rule-based structure generation method (Genarris) on two open-source molecular crystal datasets. MolCrystalFlow outperforms MOFFlow while achieving competitive performance against Genarris. We also demonstrate an integration of MolCrystalFlow model with universal machine learning potential to accelerate molecular crystal structure prediction, paving the way for data-driven generative discovery of molecular crystals.
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Figure 1: Overview of the MolCrystalFlow framework. a, Schematic illustration of a polymorph energy landscape in molecular crystals. The topology, barrier heights, and relative basin depths are not quantitative and are shown for conceptual purposes only. b, Representation of a molecular crystal structure. A molecular crystal is decomposed to a lattice matrix spanning by three vectors l1 , l2 and l3 , and a constituent molecular conformer building block which can be characterized by a rigid-body centroid and rotational orientation given by three eigenvectors derived from a principal component analysis over the atomic positions of the building block. Hence a coarse-grained crystal includes all the modalities to be generated. c, MolCrystalFlow works by encoding each building block in the crystal (for example two molecules in the schematic) with an equivariant graph neural network (EGNN) that produces an invariant embedding. The invariant embedding is augmented with auxiliary features to form the input for the joint flow-matching generative process that simultaneously produce the lattice matrix using a linear interpolant for each lattice matrix entry, centroid fractional coordinates on a torus geodesic, and rotational orientation on an SO(3) geodesic. Together, the three learned modalities will reconstruct the full atomic structure of the molecular crystal. d. An example generation trajectory with four time steps, showing the co-evolution of centroid positions, molecular orientations and lattice.
Figure 2: Neural network architecture of MolCrystalFlow. a, Molecular building block (BB) embedding network with EGNN. An atomic node embedding is constructed by the atom interacting with neighbors in the local chemical environment through multiple graph convolution layers. The final building block embedding is a weighted atomic embedding where each weight is learned and comes from the node embedding interacting with invariant atomic distance to the centroid. b, MolCrystalNet parameterizes the joint flow matching for lattice matrix L , centroid fractional coordinates ( F ), and rotational orientation ( R ). Given interpolants at time t , a concatenation of BB embedding, auxiliary features and time embedding, followed by a multilayer perceptron (MLP), gives rise to the initial node embedding for each molecular building block. In the update block, the initial embedding interacts with a χ embedding for each building block. Message passing relies on the relative positions and orientations between building blocks, and current lattice matrix at time t . The final output is the velocity field for centroid fractional coordinates ( ut(Ft) ), the denoised rotational orientation ( R1 ) and lattice matrix ( L1 ). Interactions of lattice with fractional coordinates (F,L) and orientations (R,L) are also included in the message passing. c, For rotation-dedicated message passing ( mR ), we use the axis-angle representation of relative rotational orientation between two building blocks. We embed the rotational angle ω and azimuthal angle ρ using Fourier-series like trigonometric functions while using an MLP to create the embedding for the inclination angle κ . d, Concatenation-summation operation to strengthen the signal of each building block’s χ . e, χ -grouped optimal transport to reduce cross-links between paths of different building blocks and facilitate inference.
Figure 3: Performance of MolCrystalFlow against MOFFlow and Genarris-3 baselines. a, Comparison of MolCrystalFlow with MOFFlow and Genarris-3 over 10-sample matching rates evaluated for directly generated structures without any optimization under different levels of site tolerances. b, Comparison of MolCrystalFlow with Genarris-3 and MOFFlow over 10-sample matching rates evaluated for generated structures after a rigid-press optimization (‘R-P’) under different levels of site tolerances. For MolCrystalFlow, we also show results over samples going through a rigid-body optimization using the UMA-OMC model (‘UMA-Opt’). Regarding the box plots, the median is shown as a solid line. The edges of the box correspond to the first and third quartiles, and the whiskers extend to values within 1.5 × interquartile ranges. c–e, Lattice volume deviation of generated structures for MolCrystalFlow (c), MOFFlow (d), and Genarris-3 with rigid-press optimization (e). A kernel density estimation is used to show data distributions for 10 samples. Relative mean absolute deviation (RMAD) is reported as mean and standard deviation across 10 samples. d, Grid search for the optimal velocity annealing scalings for centroid ( suF ) and rotation ( suR ) using 10 samples and stol=0.8. For figure a and b, five independent runs for 10 samples are generated the statistics and the results for each run are overlaid on the box plots.
Figure 4: Molecular crystal structure prediction by integrating MolCrystalFlow generator, u-MLIP and DFT stability ranking. a, Four-step pipeline to integrate MolCrystalFlow for structure generation, u-MLIP for structural optimization and obtaining coarse energy landscape, and DFT for final stability ranking. b, Molecular graphs and conformer structures of three open targets from the 3 rd CCDC CSP competition. c–e, Energy ranking results evaluated with u-MLIP, PBE-D3 and PBE-MBD for three generated and relaxed polymorphs whose PBE-MBD energies are the lowest, combined with the experimental structure evaluated at the same level of theory. Figure c, d and e correspond to target VIII, X and XI, respectively. f, Packing similarity analysis of the PBE-MBD lowest-energy polymorph relative to the experimental structure was performed using the COMPACK algorithm as implemented in the CSD Python API.
Crystal structure governs material properties, making crystal structure prediction (CSP) a fundamental problem in materials science. Generative models are a promising approach for solving this problem, but the prevalence of polymorphism, coupled with large unit cells and complex packing geometry, makes the molecular CSP task challenging for existing models. To address this, we introduce Coarse-Grained Open Materials Generation (CG-OMatG), an equivariant Riemannian flow-based generative model. CG-OMatG predicts molecular crystal structures via a coarse-grained, hierarchical representation. CG-OMatG treats molecules as rigid bodies---performing both inter- and intra-molecular message passing to construct a geometric representation for molecular packings---and learns to reconstruct molecule centroid positions, orientations, and lattice parameters, conditioned on chemical species and conformer geometry. We train the model on subsets of the Open Molecular Crystals (OMC25) and Cambridge Structural Database (CSD) datasets. Further, we fine-tune the model via policy gradient reinforcement learning to steer the model towards generating low-energy candidate structures. We validate the generated structures on the CSP blind test benchmark, assessing agreement with experimentally determined crystals using COMPACK packing-similarity analysis. CG-OMatG exhibits strong performance for generative molecular crystal structure prediction, paving the way for accelerated polymorph screening and organic solid-state materials discovery.
Thomas Egg, Harry Winston Sullivan, Maya M. Martirossyan +8
Center for Soft Matter Research, Department of Physics, New York University, New York 10003, USA · Simons Center for Computational Physical Chemistry, Department of Chemistry, New York University, New York 10003, USA · Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA +7
Crystal structure prediction is a long-standing challenge in materials science, with most data-driven methods developed for inorganic systems. This leaves an important gap for organic crystals, which are central to pharmaceuticals, polymers, and functional materials, but present unique challenges, such as larger unit cells and strict chemical connectivity. We introduce a flow-matching model for predicting organic crystal structures directly from molecular graphs. The architecture integrates molecular connectivity with periodic boundary conditions while preserving the symmetries of crystalline systems. A bond-aware loss guides the model toward realistic local chemistry by enforcing distributions of bond lengths and connectivity. To support reliable and efficient training, we built a curated dataset of organic crystals, along with a preprocessing pipeline that precomputes bonds and edges, substantially reducing computational overhead during both training and inference. Experiments show that our method achieves a Match Rate more than 10 times higher than existing baselines while requiring fewer sampling steps for inference. These results establish generative modeling as a practical and scalable framework for organic crystal structure prediction.
Mohammadmahdi Vahediahmar, Matthew A. McDonald, Feng Liu
Department of Computer Science, Drexel University · Department of Chemical and Biological Engineering, Drexel University
Crystal modeling spans a family of conditional and unconditional generation tasks, including crystal structure prediction (CSP) and de novo generation (DNG). While recent deep generative models have shown promising performance, they remain largely task-specific, lacking a unified framework that shares crystal representations across tasks. To address this limitation, we propose Multimodal Crystal Flow (MCFlow), a unified multimodal flow model that realizes multiple crystal generation tasks as distinct inference trajectories via independent time variables for atom types and crystal structures. To enable multimodal flow in a standard transformer model, we introduce a composition- and symmetry-aware atom ordering with hierarchical permutation augmentation, injecting compositional and crystallographic priors without explicit structural templates. Experiments on the MP-20 and MPTS-52 benchmarks show that a single MCFlow model is competitive with task-specific baselines across CSP, DNG, and structure-conditioned atom type generation.
Kiyoung Seong, Sungsoo Ahn, Sehui Han +1
Graduate School of AI, KAIST, Seoul, South Korea · Materials Intelligence Lab, LG AI Research, Seoul, South Korea