Evidence map›Paper›PMID 38049389›Full record

ArticleJournal of chemical information and modeling2023

Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Data Set.

Aaron G Garrison, Javier Heras-Domingo, John R Kitchin, Gabriel Dos Passos Gomes, Zachary W Ulissi, Samuel M Blau

Abstract read
In one paragraph

Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed.

  1. AI-EXAFS: Physics-Informed Prediction of EXAFS from Atomic Structure.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
    Article
  2. Article
  3. tmQM-RDF Data Set: A Knowledge Graph Representing Transition Metal Complexes.Journal of chemical information and modeling · 2026
    Article
  4. Article
  5. Article
  6. Review
  7. Review
  8. tmQMg* Data Set: Excited State Properties of 74k Transition Metal Complexes.Journal of chemical information and modeling · 2025
    Article
  9. Article
  10. Graph neural networks for predicting metal-ligand coordination of transition metal complexes.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  11. Article
  12. Article
  13. Article
  14. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Aaron G GarrisonDepartment of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.ORCID 0000-0001-8011-2704
Javier Heras-DomingoDepartment of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.
John R KitchinDepartment of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.ORCID 0000-0003-2625-9232
Gabriel Dos Passos GomesDepartment of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.ORCID 0000-0002-8235-5969
Zachary W UlissiDepartment of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.ORCID 0000-0002-9401-4918
Samuel M BlauLawrence Berkeley National Laboratory, Berkeley, California 94720, United States.ORCID 0000-0003-3132-3032

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Machine learning (ML) methods have shown promise for discovering novel catalysts but are often restricted to specific chemical domains. Generalizable ML models require large and diverse training data sets, which exist for heterogeneous catalysis but not for homogeneous catalysis. The tmQM data set, which contains properties of 86,665 transition metal complexes calculated at the TPSSh/def2-SVP level of density functional theory (DFT), provided a promising training data set for homogeneous catalyst systems. However, we find that ML models trained on tmQM consistently underpredict the energies of a chemically distinct subset of the data. To address this, we present the tmQM_wB97MV data set, which filters out several structures in tmQM found to be missing hydrogens and recomputes the energies of all other structures at the ωB97M-V/def2-SVPD level of DFT. ML models trained on tmQM_wB97MV show no pattern of consistently incorrect predictions and much lower errors than those trained on tmQM. The ML models tested on tmQM_wB97MV were, from best to worst, GemNet-T > PaiNN ≈ SpinConv > SchNet. Performance consistently improves when using only neutral structures instead of the entire data set. However, while models saturate with only neutral structures, more data continue to improve the models when including charged species, indicating the importance of accurately capturing a range of oxidation states in future data generation and model development. Furthermore, a fine-tuning approach in which weights were initialized from models trained on OC20 led to drastic improvements in model performance, indicating transferability between ML strategies of heterogeneous and homogeneous systems.

Indexed as

Coordination ComplexesHydrogenMachine LearningNeural Networks, ComputerThermodynamicsCoordination ComplexesHydrogen

Identifiers

PMID38049389
PMCPMC10751796

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.