Aug 2026· Journal of Chemical Theory and Computation· Vol 22 16, pp.
8541-8555
· 0 citations· 55 references
Medicine
TL;DR
DeGAT enables efficient and accurate prediction of partial atomic charges in MOFs while maintaining charge neutrality and physical consistency, providing a scalable parametrization scheme for high-throughput screening and molecular simulations of porous materials.
Abstract
The high computational cost of deriving REPEAT charges via periodic density functional theory (DFT) limits the large-scale screening of metal-organic frameworks (MOFs). To address this, we developed DeGAT, a dual-expert graph attention network for the rapid prediction of partial atomic charges. By incorporating an uncertainty-driven active learning strategy on the ARC-MOF database, the model achieves a test-set R2 of 0.985, with a mean absolute error (MAE) of 0.0314 e and a species-averaged MAE (SMAE) of 0.0527 e. Subsequent grand canonical Monte Carlo and Widom insertion simulations demonstrate that CO2, N2, and water adsorption properties calculated using DeGAT charges closely match those derived from standard REPEAT charges. These results demonstrate that DeGAT enables efficient and accurate prediction of partial atomic charges in MOFs while maintaining charge neutrality and physical consistency, providing a scalable parametrization scheme for high-throughput screening and molecular simulations of porous materials.
Predicting the electronic properties of transition metal complexes (TMCs) from 2D molecular graphs remains challenging; organic-trained property models lack TMC transferability, universal interatomic potentials require 3D coordinates rather than SMILES, and tools providing holistic electronic property prediction with atom-level explainability and calibrated uncertainty remain limited. We present tmGNN-XAI, a multitask relational graph convolutional network that predicts seven quantum-chemical properties of TMCs directly from SMILES strings and produces perturbation-based atom-level attributions for each prediction. The model encodes dative coordination bonds as a dedicated edge type distinct from covalent bonds and is trained on 100,703 complexes from the tmQM data set spanning 30 transition metals. Test-set performance is competitive with a Chemprop D-MPNN baseline, achieving R2 = 0.979 for metal partial charge and R2 = 0.964 and 0.949 for HOMO and LUMO energies. Across all 100,703 complexes, donor atoms (N, O, S, P) appear among the top-five most important atoms in more than 99.8% of complexes for every property, a large-scale data-driven result consistent with ligand field theory. A trust framework combining ensemble agreement with attribution direction separates predictions into four reliability scenarios; confident predictions achieve 1.6 to 2.5 times lower mean absolute error than uncertain ones for five of seven properties. The framework generalizes to cross-level DFT validation, phototherapy candidate screening (area under the ROC curve (AUC) = 0.735), and indirect redox prediction via Koopmans' theorem. An interactive web application makes property predictions, atom-level attributions, and trust labels accessible without programming or DFT expertise. tmGNN-XAI is designed as an explainable, first-tier screening tool for TMC electronic property estimation.
Abdulmujeeb T. Onawole· Journal of Chemical Informat...· 2 citations
Coupled-cluster theory defines the accuracy standard for molecular electronic-structure properties but scales too steeply for routine application, whereas density-functional theory is affordable yet systematically biased. We resolve this trade-off with a single equivariant network, MEHnet-MG, that predicts an effective one-electron Hamiltonian from one inexpensive B3LYP/def2-SVP calculation and derives a broad suite of properties from it (energy, optical gap, dipole, quadrupole, polarizability, Mulliken atomic charges, and Mayer bond orders) at coupled-cluster accuracy across nine main-group elements, including the under-served phosphorus, sulfur, and chlorine chemistries. The model is trained on a new in-house dataset of multi-property labels computed at the CCSD(T) level for all nine elements. On a held-out test set, it reduces the error of every property by a factor of 3.8 to 230 relative to semi-local, hybrid, and double-hybrid DFT (referenced to composite CCSD(T)/cc-pVTZ; Methods), while adding only ~25 ms wall time per molecule, delivering coupled-cluster-quality predictions at the cost of a single DFT calculation. Critically, deriving every property from a predicted Hamiltonian rather than pooling per-atom features builds the correct size-scaling into the model architecture: on pi-conjugated oligothiophenes it matches finite-field CCSD polarizability and the EOM-CCSD optical gap to ~2% at the largest sizes where those references remain affordable (44 and 37 atoms, where a single CCSD field point already costs ~500x the model's entire inference) and extrapolates the corrected trends to 58-atom chains, a regime where pooling-based architectures fail by construction. Accurate extrapolation is therefore set by the model's inductive bias rather than by the training data.
This work bridges the gap between data-driven and physics-based approaches, providing a scalable solution for pesticide discovery when target-specific data are limited, and incorporating meta-learning and MD insights improves cross-species transferability and yields interpretable attention patterns based on biophysical principles.
Haroon· Journal of Molecular Modelin...· 0 citations
Density functional theory (DFT) serves as a reliable tool for atomistic molecular simulations, while machine learning potentials have become powerful complements to balance accuracy and efficiency. In this work, we release OpenGEM26 (Open Generated Ensemble of Molecules, 2026), a large-scale dataset comprising 200,000 unique molecules and 4.4 million conformations composed of H, C, N, O, S and Cl with up to ten heavy atoms. All calculations are carried out at the {\omega}B97X-D/Def2-SVP and Def2-TZVP levels with dispersion corrections, and complete structural optimization trajectories and abundant non-equilibrium structures are recorded. Statistical analyses confirm that this dataset covers a broader conformational space than QM9 in terms of energy, bond lengths and bond angles. A graph neural network-based potential GPTFF-mol is trained using the new dataset, achieving an energy mean absolute error of 16 meV/molecule, which is equivalent to 0.82meV/atom, and superior force prediction performance compared with ANI-2x. Validated by butane rotation and keto-enol tautomerization tests, the model accurately describes molecular dynamical behaviors and reaction barriers at distorted geometries. This work provides a high-quality resource and robust ML potential for efficient simulations of sulfur- and chlorine-containing organic molecules.
Yifan Huang, Fankai Xie, Jiangnan Zheng et al.· 0 citations
An adaptation of the Δ-ML strategy for quantum property prediction of transition metal complexes is presented, which consistently achieves higher accuracy in the prediction of high-fidelity targets, while demonstrating improved data efficiency and out-of-domain transferability.
Hannes Kneiding, David Balcells· Chemistry· 0 citations
A data-driven framework combining explainable machine learning (ML) with large-scale virtual library generation with large-scale virtual library generation is presented, establishing a practical route from experimental data to actionable catalyst designs.
Xuefeng Li, Haoke Qiu, Hanwen Pei et al.· Journal of Physical Chemistr...· 0 citations
