I am trying to find chiral centers of molecules in QM9 dataset. Browsing their SMILES representation, I noticed SMILES yield using

datasets.get_qm9(GGNNPreprocessor(), return_smiles=True)

don't have @ or @@, but it seems that some of these molecules have alternative representations. For instance, both 'Cc1ccoc1C(C)O' and 'CC@Hc1c(C)cco1' represent the same molecule, but of course the latter one outputs the chiral center:

[(1, 'S')]

while only the former is available in the dataset. I found this at https://github.com/chemspacelab/qm9-C7O2H10. Does anyone know if this can be generalized to all the molecules in the QM9 dataset? Thanks!

  • 1
    $\begingroup$ I'd be very, very careful using random versions of QM9. The original files are available albeit a bit non-standard - but your problem is based on incorrect stereo-stripped SMILES - however you got them. $\endgroup$ Commented Sep 21, 2019 at 20:14
  • $\begingroup$ @GeoffHutchison Cc1ccoc1C(C)O is from chainer_chemistry package. CC@Hc1c(C)cco1 is from github account above, which I realized that belongs to one of QM9 authors (von Lilienfeld). $\endgroup$
    – Blade
    Commented Sep 24, 2019 at 15:02

1 Answer 1


I don't know about that particular GitHub archive, although I'll point out that the smiles.csv contains several kinds of SMILES - the final column containing the correct SMILES.

IMHO, this is an unfortunate result of people mis-using SMILES. As you note, it's perfectly possible to take a chiral molecular structure and output a SMILES with no stereochemical information.

Take alanine - to a chemist, if you simply say 'alanine,' they immediately think 'amino acid' and translate to L-alanine, or C[C@@H](C(=O)O)N as the so-called "isomeric SMILES":

enter image description here

Unfortunately, if you go to PubChem for L-Alanine, you'll see a "canonical SMILES" which sounds official and is CC(C(=O)O)N - no stereochemistry!

The official version of QM9 can be found on FigShare based on the corresponding publication.

While the official files are in a somewhat non-standard XYZ format, they do have the stereochemically-correct SMILES at the end of the file, e.g. C1N2[C@H]3[C@@H]4[C@@H]5O[C@]13[C@H]2[C@H]45 Just watch that some numbers are formatted like -8.0386*^-6 (i.e., $-8 \times 10^{-6}$) and can sometimes be misinterpreted by programs like Open Babel or RDKit .. practically everything I've seen.

  • $\begingroup$ Thanks for sharing the original source. Although I was familiar with the publication, I never checked their original dataset for some reason, maybe never thought it would be any different. I'll try see if the results improve with this. $\endgroup$
    – Blade
    Commented Sep 24, 2019 at 15:05

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.