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.
The resulting MLIP/ShiftML3 workflow reduces computational costs by at least three orders of magnitude, making high-accuracy NMR crystallography accessible without HPC infrastructure, and opening the door to fast molecular dynamics simulations at the hybrid DFT level.
Shubha S. Gunaga, Rob Schurko, Sean T. Holmes et al.· Chemical Science· 3 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...
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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.
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The aBCC provides a common framework for assessing and communicating the local coordinate reliability between structural biologists and researchers in structure-based drug discovery and provide a foundation for further development and refinement of machine learning-based coordinate validation.
I. Miyaguchi, H. Hata, Takaaki Kuribayashi et al.· bioRxiv· 0 citations
This work tested the hypothesis that classical force-field pre-relaxation can provide a more suitable starting geometry for subsequent UMLIP relaxation on a large database of high energy molecular crystals, and revealed distinct trade-offs among the evaluated models.
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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...
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