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#70 A few more Iupac name/structure mismatches

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nobody
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5
2010-05-20
2010-05-20
Daniel Lowe
No

(CHEBI:29943) The InChI for this record, oddly, seems to describe a different structure to the names/SMILES. The InChI appears to be for PH3(2+). For PH(2+) I think the InChI is InChI=1/HP/h1H/q+2

(CHEBI:17706) The name describes a structure with 2 rather than 1 phenols

(CHEBI:17728) I'm not keen on the name S-methyl-L-methionine due to the lack of indication of a charge on the sulfur although valency 4 sulfur with a hydrogen is also unlikely so I can see how that might be how it is named

(CHEBI:52298) Similar problem to some of the other dyes. The fix is the same as for (CHEBI:52219) . I think the replacement name for CHEBI:52219 is still not quite right though and should actually be:
2,2'-{propane-1,3-diylbis[(dimethylazaniumdiyl)propane-3,1-diylpyridin-1-yl-4-ylidenemethylideneyl]}bis(3-methyl-1,3-benzoxazol-3-ium) tetraiodide
To be clear which bonds are single and which are double.

(CHEBI:7719) N-{[(3R)-5-chloro-8-hydroxy-3-methyl-1-oxo-3,4-dihydro-1H-2-benzopyran-7-yl]carbonyl}-L-phenylalanine The name has a hydroxy, at the 8 position the structure does not.

(CHEBI:30876) Structure is that of 4-oxalobenzoic acid

Discussion

  • Marcus Ennis

    Marcus Ennis - 2010-05-21

    Hi Daniel

    Changes made as follows:

    CHEBI:29943. The InChI now correctly reflects the structure. Our structure drawing package does tend to add in extra hydrogens automatically which then require manual adjustment.

    CHEBI:17706. IUPAC Name now changed from 8-benzyl-2-(4-hydroxybenzyl)-... to 2,8-dibenzyl-...

    CHEBI:52298. Afraid you'll need to remind what the problem was for CHEBI:52219 and what the fix was so that I can do the same for 52298, as I can't find any record of correspondence about this.

    CHEBI:7719. The OH has been inserted into the structure.

    CHEBI:30876. The structure has been corrected to 3-oxalo.

    The next ChEBI release is scheduled for June 2nd.

    Thanks again for your input.

    Regards,
    Marcus

     

  • Daniel Lowe

    Daniel Lowe - 2010-05-21

    Thanks for the quick fixes.
    Regarding CHEBI:52298, a problem with the naming of 52219 and a few other related compounds was identified in this thread relating to the way the central part of the molecule was described:
    https://sourceforge.net/tracker/?func=detail&aid=2979638&group_id=125463&atid=703819
    I cannot currently find a reference in the IUPAC organic guidelines as to whether or not I am correct in my criticism of your replacement names for the identified compounds.
    In methylylidene. yl does take priority over ylidene (and ylidyne) for citation, but I was under the impression that to clarify multiplicative names that the ordering of these suffixes should reflect their relation to substituents they are intended to form bonds with. In this case the ylidene is used with the previous substituent and the yl with the following substituent. This rule is definitely present in IUPAC polymer nomenclature e.g. you get things like pyridin-4,2-diyl to indicate it connects by the 4 position to the previous substituent and to next substituent by the 2 position.