Chemical Space Exploration with Artificial ”Mindless” Molecules

13 June 2025, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

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 MB2061 benchmark set, containing 2061 molecules with high-level PNO-LCCSD(T)-F12 reference data for dissociation reactions. This set provides a challenging benchmark for testing, validation, and training of density functional approximations (DFAs), semiempirical methods, force fields, and machine learning potentials using molecular structures beyond the conventional chemical space. For DFAs, we initially hypothesized that highly parameterized functionals might perform poorly on this set. However, no consistent relationship between 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−1 and r²SCAN-3c offering a robust cost-efficient alternative (19.6 kcal·mol−1). Furthermore, we discuss the performance of selected semiempirical methods and contemporary machine learned interatomic potentials.

Keywords

DFT
benchmarking
MLIP
FF
SQM

Supplementary materials

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ESI1
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Additional technical details and supporting fig- ures
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ESI2
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Calculated reaction energies with SQM, DFT, and MLIPs
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Benchmark Set
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Geometries (XYZ files), reference energies, and reaction energy coefficients of the MB2061 benchmark set
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