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dan2097 / opsin

Open Parser for Systematic IUPAC Nomenclature. Chemical name to structure conversion
https://opsin.ch.cam.ac.uk
MIT License
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Dioxidanyliumyl is interpreted as having a single bond #267

Open vaitkus opened 1 week ago

vaitkus commented 1 week ago

Tested with opsin revision 93163ad.

Running opsin revision with the -r flag produces the following outputs for "Dioxidanyliumyl":

The more correct SMILES representation would be [O+]=[O].

dan2097 commented 1 week ago

Dioxidanyliumyl should have a single bond c.f. https://iupac.qmul.ac.uk/BlueBook/P7.html#73020303

I see that Dioxidanyliumyl is associated with https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:29372 and the similar Dioxidanylium brings up https://en.wikipedia.org/wiki/Dioxidanylium. I think these are both misnamed!

Based on IUPAC nomenclature I think this compound [O+]=[O] should be called Dioxideniumyl

vaitkus commented 1 week ago

I must admit that the naming for this specific compound also got me quite confused. IUPAC Red Book (https://iupac.org/wp-content/uploads/2016/07/Red_Book_2005.pdf), pages 302, 320 explicitly list both dioxidanylium and dioxidanyliumyl as cations of dioxydanyl and dioxygen accordingly. Wikipedia/Wikidata, however, seem to prefer the dioxygenyl name for the [O+]=[O](https://en.wikipedia.org/wiki/Dioxygenyl). Wikidata currently has two distinct entries for dioxygen(.1+) [1] and dioxygenyl ion [2] although they seem to refer to the same compound.

The Red Book errata section [3] currently does not seem to list anything related to dioxidanyliumyl, but if it is really a mistake, maybe it is something worth reporting?

[1] https://www.wikidata.org/wiki/Q27110033 [2] https://www.wikidata.org/wiki/Q3028855 [3] https://iupac.qmul.ac.uk/bibliog/RBcorrect.html