Aug 2026· Journal of Physical Chemistry Letters· Vol 17 35, pp.
10115-10121
· 0 citations· 47 references
Medicine
Abstract
We evaluated a fully machine-learning-assisted workflow for NMR crystallography by combining the Universal Model for Atoms (UMA) interatomic potential for crystal structure optimization with the ShiftML3 prediction of solid-state NMR shieldings. Benchmarking against conventional periodic density functional theory (DFT) calculations for 1H, 13C, and 15N chemical shifts demonstrates that ML-based geometry optimization consistently improves the accuracy of 13C and 15N predictions relative to standard PBE optimization, highlighting the dominant role of structural refinement. ShiftML3 achieves DFT-level accuracy for shielding prediction and, when combined with UMA-optimized geometries, matches or surpasses periodic DFT for 13C and 15N while reducing the computational cost by orders of magnitude. We further show that hybrid PBE0 single-molecule corrections remain effective for both DFT- and ShiftML3-derived shieldings, extending their applicability to modern machine-learning models. These results establish a new computational paradigm for NMR crystallography by replacing both computational bottlenecks of the conventional DFT workflow with modern machine-learning models.
Nuclear magnetic resonance (NMR) crystallography is a robust method for structure determination, but its reliance on density functional theory (DFT) calculations for geometry refinement limits its speed and accessibility. Recent machine-learning predictors such as ShiftML3 can evaluate magnetic shieldings in seconds, b...
Shubha S. Gunaga, Rob Schurko, Sean T. Holmes et al.· Chemical Science· 2 citations
Fast and accurate chemical shielding estimators are essential for shielding-driven Nuclear Magnetic Resonance (NMR) crystallography. Machine-learning models for shielding predictions have matured significantly and today are primarily limited by the electronic structure reference data they are trained on. Here, we intro...
Matthias Kellner, Ruben Rodriguez-Madrid, Jacob B. Holmes et al.· 0 citations
A machine-learning-assisted framework to improve quantum-chemical prediction of 19F NMR chemical shifts by using machine learning to diagnose and correct subset-dependent limitations in the shielding-shift relationship within a practical quantum-chemical workflow is developed.
Dong-Dong Chen, Yuan-Xiang Ye, Yi-Jie Zhu et al.· Journal of Chemical Informat...· 0 citations
Accurate assessment of ligand coordinate–density consistency across different resolutions remains challenging in macromolecular crystallography. We introduce the atomic Box Correlation Coefficient (aBCC), an atom-level metric for evaluating the consistency between ligand atomic coordinates and electron density in a res...
I. Miyaguchi, H. Hata, Takaaki Kuribayashi et al.· bioRxiv· 0 citations
Recent developments of universal machine learning interatomic potentials (UMLIPs) offer a fast route for screening molecular crystals based on geometry relaxation and energy ranking, but their reliability across chemically diverse energetic materials remains elusive. In particular, it is unclear whether or not these UM...
Musiha Mahfuza Mukta, Osman Goni Ridwan, R. Perriot et al.· 0 citations
Structural elucidation remains a central challenge in modern chemistry, particularly in the determination of relative stereochemistry when experimental spectroscopic data are insufficient. Among computational approaches, the DP4+ method has become a widely adopted tool for NMR-based stereochemical assignment by combini...
Ezequiel R. Luciano, Martín G. Armas Argentino, M. B. Comba et al.· Journal of Chemical Informat...· 0 citations
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