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The next most frequent atom types are tri-coordinated and tri-valent oxygen (16.9% of invalid substances), tri-coordinated and penta-valent carbon (8.8% of invalid substances), and tetra-coordinated and penta-valent carbon (8.1% of invalid substances).
The same goes for di-coordinated and tri-valent oxygen (3.9% of invalid substances) and di-coordinated and di-valent fluorine (3.7% of invalid substances).
Di-coordinated and di-valent hydrogen cases (4.7% of invalid substances) are not salvageable by structure standardization.
Penta-coordinated and penta-valent carbon (3.5% of invalid substances) causes the respective substances also to be rejected.
Tri-coordinated, tetra-valent carbon with a positive charge (3.4% of invalid substances) does not exist in the PubChem valence list and is not salvaged by standardization.
The case of tetra-coordinated, tetra-valent and uncharged nitrogen (6.8% of invalid substances) is analogous to the most frequent atom type.
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It will read as invalid disc content.
For the top-3 depositors of substances containing invalid 'organic-only' atom types, the incidence of the respective top-10 most frequent invalid atom types is shown.
The 85,894 substances with "invalid organic-only" atom types provided by ChemSpider contain at least one of 282 offending atom types.
In total, 40 of the 116 (34.5%) invalid atom types identified in substances deposited by IBM occur in only a single substance.
Of the invalid atom types encountered in substances deposited by ChemSpider, 81 of 282 (28.7%) invalid atom types occur in only one substance.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com