Chemical Space Exploration with Artificial “Mindless” Molecules

We introduce MindlessGen, a Python-based generator for creating chemically diverse, "mindless" molecules through random atomic placement and subsequent geometry optimization. Using this framework, we constructed the <i>MB2061</i> benchmark set, containing 2061 molecules with high-level PNO-LCCSD(T)-F12 reference data for H<sub>2</sub>-promoted decomposition reactions. This set provides a challenging benchmark for testing, validating, and training density functional approximations (DFAs), semiempirical methods, force fields, and machine learning potentials using molecular structures beyond conventional chemical space. For DFAs, we initially hypothesized that highly parametrized functionals might perform poorly on this set. However, no consistent relationship between the fitting strategy and accuracy was observed. A clear Jacob's ladder trend emerges, with ωB97X-2 achieving the lowest mean absolute error (MAE) of 8.4 kcal·mol<sup>-1</sup> and r<sup>2</sup>SCAN-3c offering a robust cost-efficient alternative (19.6 kcal·mol<sup>-1</sup>). Furthermore, we discuss the performance of selected semiempirical methods and contemporary machine-learning interatomic potentials.

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Publication Details

Journal
Journal of Chemical Information and Modeling
Published
2025-09-02
DOI
https://doi.org/10.1021/acs.jcim.5c01364
Citations
3
Primary Topic
Machine Learning in Materials Science
Type
article
Field-Weighted Citation Impact
1.55

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Chemical Space Exploration with Artificial “Mindless” Molecules

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Journal of Chemical Information and Modeling
Machine Learning in Materials Science
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article

Chemical Space Exploration with Artificial “Mindless” Molecules

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article en
3 citations

Abstract

We introduce MindlessGen, a Python-based generator for creating chemically diverse, "mindless" molecules through random atomic placement and subsequent geometry optimization. Using this framework, we constructed the <i>MB2061</i> benchmark set, containing 2061 molecules with high-level PNO-LCCSD(T)-F12 reference data for H<sub>2</sub>-promoted decomposition reactions. This set provides a challenging benchmark for testing, validating, and training density functional approximations (DFAs), semiempirical methods, force fields, and machine learning potentials using molecular structures beyond conventional chemical space. For DFAs, we initially hypothesized that highly parametrized functionals might perform poorly on this set. However, no consistent relationship between the fitting strategy and accuracy was observed. A clear Jacob's ladder trend emerges, with ωB97X-2 achieving the lowest mean absolute error (MAE) of 8.4 kcal·mol<sup>-1</sup> and r<sup>2</sup>SCAN-3c offering a robust cost-efficient alternative (19.6 kcal·mol<sup>-1</sup>). Furthermore, we discuss the performance of selected semiempirical methods and contemporary machine-learning interatomic potentials.

Journal of Chemical Information and ModelingVol. 65(18)
University of Bonn (DE), Center for Theoretical Physics (PL), Microsoft (Germany) (DE)
Microsoft Research, Fonds der Chemischen Industrie
Openalex Percentile: Top 16%
Machine Learning in Materials Science
1.55
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