Some more Iupac name/structure mismatches

(CHEBI:5107) {2-(2-{2-[bis(carboxylatomethyl)amino]-5-(2,7-dichloro-6-oxido-3-oxo-3H-xanthen-9-yl)phenoxy}ethoxy)-4-methylphenylamino}acetic acid (name indicates negative charges on carboxylic acids) (CHEBI:29055) (3,4-dihydroxyphenyl)(oxo)acetate (name has no methylene between the benzene and the carbonyl) (CHEBI:37759) boranediide (InChI is wrong: 3 hydrogen rather than 1) (CHEBI:58991) (p-hydroxyphenyl)glycinamide (Could be renamed to 2-(p-hydroxyphenyl)glycine to be clear) (CHEBI:35762) 2,2'-([(carboxymethyl)imino]bis{ethane-2,1-diyl[(carboxymethyl)imino]})diacetate (name is a bit unclear how about :2,2'-([(carboxymethyl)imino]bis{ethane-2,1-diyl}bis[(carboxymethyl)imino])diacetate or 2,2'-([(carboxymethyl)imino]bis{ethane-2,1-diyl[(carboxymethyl)azandiyl]})diacetate) (CHEBI:2425) (3R,3aS,9aS,9bS)-3,6,9-trimethyl-3,3a,4,5,9a,9b-hexahydroazuleno[4,5-b]furan-2,7-dione (Structure has an extra methyl at position 9b) (CHEBI:51619) 2',7'-dichloro-3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-6-carboxylic acid (should this be two seperate molecule entries?) (CHEBI:29345) azanebis(ylium) (InChI is wrong: 3 hydrogen rather than 1) (CHEBI:17448) and (CHEBI:16314) For both compound substituents locant 'N' is used to locant onto the L-glutamine but in the structure they are connected to different Nitrogen Assuming the structure to be correct it should be made more clear which nitrogen is being referred to. (CHEBI:17056) name should be 1-carboxyethenyl hydrogen carboxyphosphonate (CHEBI:38476) name should be 2,2-dimethyl-2,3-dihydro-1-benzofuran-7-yl (dibutylamino)sulfanylcarbamate to be clear as to what the methyl attaches to. Bracketing the methyl is definitely the current IUPAC recommendation. Do you know whether the IUPAC has any guidelines as to how to interpret names where clarification is not given? Currently the key heuristic I use is whether there is a hyphen between the substituents e.g. sulfanyl]-methylcarbamate would of given the intended structure (CHEBI:52185) Name indicates that the nitrogen opposite the O+ is NH (the 8a, 9 bond is saturated) (CHEBI:30580) InChI is completely wrong, should be InChI=1/HSi/h1H (CHEBI:35325) diazanediium and hydrazinediium in my opinion are formally ambiguous (should specify 1,2-) (CHEBI:48005) The N must be specified more exactly e.g. N(5)-(4-aminobutyl)-L-glutamine (CHEBI:15838) A bit pendantic, but the IUPAC name should end with "carboxylic acid" not "carboxylate" as the compound is not charged (CHEBI:28004) The locant of the atom the N is attached to should be specified to avoid ambiguity (CHEBI:52929) Change dimethylammonio to dimethylazaniumdiyl and I think the first of the IUPAC names is acceptable (CHEBI:53752) Structure describes a diester but the name describes a diether (CHEBI:29765) InChI should be InChI=1/AsH/h1H/q+2 (CHEBI:51821) Name is missing a methyl at the 4 position (CHEBI:20745) Name has a methyl instead of a hydroxy (CHEBI:16274) Name says 5-oxo but structure has a hydroxy at that position

If you can find: 5-{[(4-{bis[(acetoxymethoxy)carbonyl]amino}-3-[2-(2-{bis[(acetoxymethoxy)carbonyl]amino}phenoxy)ethoxy]phenyl)amino]sulfonyl}-2-(2,3,6,7,12,13,16,17-octahydro-1H,5H,11H,15H-pyrido[3,2,1-ij]quinolizino[1',9':6,7,8]chromeno[2,3-f]quinolin-4-ium-9-yl)benzenesulfonate in ChEBI (it's too long for your search dialog) it should contain two methylenes less than the structure. My hunch in this case is that the structure is actually at fault.

(CHEBI:41983) One of the hydroxys is an iodine in the name (CHEBI:48386) Structure is wrong. Name says cyano but structure has an alkyne instead (CHEBI:39397) Structure is a cyclic imide i.e. has nitrogen but there is no nitrogen indicated in the name

Reported by: dan2097

Hi Daniel

Changes made as detailed below will be incorporated into our next release (July 7). Many thanks for reporting these errors.

Regards, Marcus

(CHEBI:5107) {2-(2-{2-[bis(carboxylatomethyl)amino]-5-(2,7-dichloro-6-oxido-3-oxo-3H-xanthen-9-yl)phenoxy}ethoxy)-4-methylphenylamino}acetic acid (name indicates negative charges on carboxylic acids)

* Name is now {2-(2-{2-[bis(carboxymethyl)amino]-5-(2,7-dichloro-6-hydroxy-3-oxo-3H-xanthen-9-yl)phenoxy}ethoxy)-4-methylphenylamino}acetic acid

(CHEBI:29055) (3,4-dihydroxyphenyl)(oxo)acetate (name has no methylene between the benzene and the carbonyl)

* Name is now 3-(3,4-dihydroxyphenyl)-2-oxopropanoate.

(CHEBI:37759) boranediide (InChI is wrong: 3 hydrogen rather than 1)

* I can't get our drawing software to calculate this correctly, so until I get a developer to look at this problem I've turned off the InChI generation option for the compound (on the basis that it's preferable to show no information at all than to show wrong information).

(CHEBI:58991) (p-hydroxyphenyl)glycinamide (Could be renamed to 2-(p-hydroxyphenyl)glycine to be clear)

* Agreed and done (but I assume that you mean rename to 2-(p-hydroxyphenyl)glycinamide (i.e. not ...glycine)

(CHEBI:35762) 2,2'-([(carboxymethyl)imino]bis{ethane-2,1-diyl[(carboxymethyl)imino]})diacetate (name is a bit unclear how about: 2,2'-([(carboxymethyl)imino]bis{ethane-2,1-diyl}bis[(carboxymethyl)imino])diacetate or 2,2'-([(carboxymethyl)imino]bis{ethane-2,1-diyl[(carboxymethyl)azandiyl]})diacetate).

* I agree with the use of 'azanediyl' instead of 'imino' so have substituted your second suggestion (but with 'azanediyl' instead of 'azandiyl') into this entry.

(CHEBI:2425) (3R,3aS,9aS,9bS)-3,6,9-trimethyl-3,3a,4,5,9a,9b-hexahydroazuleno[4,5-b]furan-2,7-dione (Structure has an extra methyl at position 9b).

* I've removed the offending methyl.

(CHEBI:29345) azanebis(ylium) (InChI is wrong: 3 hydrogen rather than 1)

* Same problem as for boranediide above. Here as well I've removed the offending InChI pending solution of this problem by our developers.

(CHEBI:51619) 2',7'-dichloro-3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-6-carboxylic acid (should this be two seperate molecule entries?)

* I've created two new entries, CHEBI:59677 and CHEBI:59678, for the 5- and 6-carboxylic acid isomers respectively and linked these to the parent 51619 in the ontology by 'has_part' relationships. The structures in the parent have now been deleted in favour of those in the new entries.

(CHEBI:17448) and (CHEBI:16314) For both compound substituents locant 'N' is used to locant onto the L-glutamine but in the structure they are connected to different Nitrogen. Assuming the structure to be correct it should be made more clear which nitrogen is being referred to.

* For each case I've added superscript numerals to the locant 'N's to indicate which of the nitrogens are the sites of substitution.

(CHEBI:17056) name should be 1-carboxyethenyl hydrogen carboxyphosphonate.

* Agreed and changed.

(CHEBI:38476) name should be 2,2-dimethyl-2,3-dihydro-1-benzofuran-7-yl (dibutylamino)sulfanylcarbamate to be clear as to what the methyl attaches to. Bracketing the methyl is definitely the current IUPAC recommendation. Do you know whether the IUPAC has any guidelines as to how to interpret names where clarification is not given? Currently the key heuristic I use is whether there is a hyphen between the substituents e.g. sulfanyl]-methylcarbamate would of given the intended structure.

* Agreed that addition of brackets removes ambiguity. As far as I'm aware, IUPAC gives no guidance on interpretation of other systems of nomenclature: they are much too concerned with their own system. Personally, I would advise caution when basing interpretation on the presence or absence of a hyphen, as some naming software packages can introduce these even when there is no need.

(CHEBI:52185) Name indicates that the nitrogen opposite the O+ is NH (the 8a, 9 bond is saturated).

* The diagram is correct, the name wrong. I have changed the name to ...-2,3,6,7-tetrahydro-1H,5H-....

(CHEBI:30580) InChI is completely wrong, should be InChI=1/HSi/h1H.

* Another one for the developers. Again, for the meantime I've disabled the InChI generator while this is sorted out.

(CHEBI:35325) diazanediium and hydrazinediium in my opinion are formally ambiguous (should specify 1,2-).

* Locants are not needed. According to IUPAC recommendations to be published later this year (available in draft form on the IUPAC website), multiplying locants ‘di’, ‘tri’, etc., are used to denote the multiplicity of identical cationic centres. Thus if there are only two N atoms, then use of 'di' indicates that each of these is identically charged, negating any need for locants 1,2-.

(CHEBI:48005) The N must be specified more exactly e.g. N(5)-(4-aminobutyl)-L-glutamine.

* Agreed. I've added a superscript 5 to the N.

(CHEBI:15838) A bit pendantic, but the IUPAC name should end with "carboxylic acid" not "carboxylate" as the compound is not charged

* Of course! I've made the change.

(CHEBI:28004) The locant of the atom the N is attached to should be specified to avoid ambiguity.

* Superscript 5 added, as for 48005.

(CHEBI:52929) Change dimethylammonio to dimethylazaniumdiyl and I think the first of the IUPAC names is acceptable

* Agreed. I've changed dimethylammonio to dimethylazaniumdiyl and deleted the second of the two IUPAC Names.

(CHEBI:53752) Structure describes a diester but the name describes a diether.

* The oxo groups were left off the structure when this was named, hence the naming as a diether. I have now renamed the compound as a diester:
1-anilino-2-[(9Z)-octadec-9-enoyloxy]ethyl (9Z,12Z)-octadeca-9,12-dienoate

(CHEBI:29765) InChI should be InChI=1/AsH/h1H/q+2

* Another one for the developers. I've temporarily removed the InChI.

(CHEBI:51821) Name is missing a methyl at the 4 position

* Agreed. Name changed to ...-2,2,4,8,10,10-hexamethyl-...

(CHEBI:20745) Name has a methyl instead of a hydroxy

* Name changed from ...-2,4,5-trimethyl-... to ...-2-hydroxy-...

(CHEBI:16274) Name says 5-oxo but structure has a hydroxy at that position

* I've changed the structure to that of the keto tautomer, and also in the name changed 12,12a-dihydro to 6,12-dihydro. Structure and name now agree.

* This is ChEBI:51923 (so-called 'calcium crimson'). The structure is correct and I have changed the name to match it.

(CHEBI:41983) One of the hydroxys is an iodine in the name.

* Error corrected. I've now also given this entity a carbohydrate-based name.

(CHEBI:48386) Structure is wrong. Name says cyano but structure has an alkyne instead.

* Error in structure now corrected.

(CHEBI:39397) Structure is a cyclic imide i.e. has nitrogen but there is no nitrogen indicated in the name.

* Name now changed to one based on isoindole instead of indene.

Original comment by: mennis

ebi-chebi / ChEBI

Some more Iupac name/structure mismatches #477