curatedQM9 dataset

The QM9 dataset [Ref-1] comprises structures and properties of 133,885 stable, synthetically feasible small organic molecules with up to 9 C, N, O and F atoms. The geometries and structures are calculated using density functional theory (DFT) at the B3LYP/6-31G(2df,p) level. The initial geometries of these molecules were generated from SMILES strings reported in the GDB17 chemical universe [Ref-2]. Out of 133885 molecules in the QM9 set, 3054 have been labeled as ‘uncharacterized’ because these molecules rearranged during geometry optimization. This 3054 set has been curated [Ref-3] using a high-throughput workflow that performs CONNectivity preserving Geometry Optimization (ConnGO) with the same DFT method as in [Ref-1]. With ConnGO, 2830 molecules (out of 3054) are successfully converged to geometries with correct connectivities as encoded in their original SMILES. The resulting curatedQM9 dataset contains 130831 + 2830 = 133660 molecules.

Download link: 133660_curatedQM9_outof_133885.zip, 208 MB.

The zip contains 133660 xyz files, where atomic coordinates are augmented with additional molecular properties as outlined in Table-2 and Table-3 of [Ref-1].

---

References

[Ref-1] Quantum chemistry structures and properties of 134 kilo molecules
Raghunathan Ramakrishnan, Pavlo Dral, Matthias Rupp, O. Anatole von Lilienfeld
Scientific Data 1, Article number: 140022 (2014).

[Ref-2] Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17
Lars Ruddigkeit, Ruud van Deursen, Lorenz C. Blum, and Jean-Louis Reymond
J. Chem. Inf. Model. 52 (2012) 2864-2875

[Ref-3] Troubleshooting unstable molecules in chemical space
Salini Senthil, Sabyasachi Chakraborty and Raghunathan Ramakrishnan
Chemical Science 12 (2021) 5566-5573
Supplementary Information to the article (PDF)