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Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to

Yuya Nakajima1, Takuto Ohmura2, Junji Seino1,2

  • 1Waseda Research Institute for Science and Engineering, Tokyo, Japan.

Journal of Computational Chemistry
|April 30, 2024
PubMed
Summary

We developed a machine learning method to group atoms based on their environments, improving the accuracy assessment of density functional theory (DFT) functionals for predicting 13C NMR chemical shifts.

Keywords:
DFT functionalNMR chemical shiftcarbon atomsclusteringdensity functional theory

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Area of Science:

  • Computational Chemistry
  • Materials Science
  • Machine Learning

Background:

  • Density Functional Theory (DFT) is crucial for predicting material properties.
  • Accurate evaluation of DFT functionals is essential for reliable predictions.
  • Existing methods may not capture the nuances of local atomic environments.

Purpose of the Study:

  • To develop a detailed method for evaluating DFT functional accuracy.
  • To leverage machine learning for atomic clustering based on descriptors.
  • To enhance the assessment of 13C NMR chemical shift predictions.

Main Methods:

  • Utilized a machine learning-based clustering approach.
  • Employed structural and electronic descriptors for atom grouping.
  • Analyzed 30,436 carbon atoms from the QM9 dataset, forming 36 intuitive clusters.
  • Evaluated 84 DFT functionals for 13C NMR chemical shift calculations.

Main Results:

  • Successfully generated 36 distinct atomic clusters reflecting similar chemical environments.
  • Demonstrated that grouping atoms by environment reduces prediction errors.
  • Showcased the capability of the method to provide detailed accuracy insights.
  • Identified variations in DFT functional performance across different atomic clusters.

Conclusions:

  • Atomic clustering based on machine learning offers a refined approach to DFT functional evaluation.
  • This method provides more granular insights into the accuracy of DFT calculations for specific chemical environments.
  • The developed technique enhances the reliability of predicting 13C NMR chemical shifts.