The submitted structure (a) is C3H5O5P, the PubChem shows C3H4O5P+ (b). How did that happen? Why the deposited molecule lost hydride (H–)?
![3-[hydroxy(oxido)phosphoranyl]pyruvic acid](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj4EOt2L_5jcMhNbgn4JaWfKl-49pWwfiawIMueHGFURAD7kBFWozYQr-DrmneMCv2tF-8lST5RFOQZg6w5ncJbfjh5iXS87ZKqo5idU87wsDVn24gxhhyphenhyphentHKwP6d4EmyJPAlXF7A/s320/CHEBI18007.png) |  |
| (a) | (b) |
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In the case of structure C16H36MoN6O4P2 (c), presumably submitted by NIST, it has acquired two hydrons in PubChem to become [C16H38MoN6O4P2]2+ (d).
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| (c) | (d) |
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2 comments:
I have seen a lot of such problems, no clue how they were lost, but I did observe inconsistent behaviour in the ASN and MDL molfiles you can download for entries, the former looking 'chemically better'. File formats are a known source of problems, and it is not uncommon the cheminformatics tools guess wrongly on missing information in those formats.
Regarding hydrogens, as several other Blue Obelisk members advocate too: always use explicit hydrogens! Those are much harder to loose :)
Sure, I always try to draw hydrogens, especially in non-standard cases. However, the second example shows added hydrogens, and this is difficult to prevent!
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