Iupac name/structure mismatches

[muthuvenkat]

(CHEBI:3215) 1-butyl-N-(2,6-dimethylphenyl)piperidine-2-carboxamide indicates the butyl is at the 1 position but the structure shows it at the 3 position

(CHEBI:50931) (3Z)-3-(2-chloro-4a,9a-dihydro-9H-thioxanthen-9-ylidene)-N,N-dimethylpropan-1-amine indicates that the 4a, 9a bond is saturated but the structure has it as unsaturated.

(CHEBI:48212) (1R,2R,3R,4S)-11-diazo-4,9-dihydroxy-2-methyl-5,10-dioxo-2,3,4,5,10,11-hexahydro-1H-benzo[b]fluorene-1,2,3-triyl triacetate indicates that the 4b, 10a bond is unsaturated but the structure has it as saturated.

(CHEBI:19891) and (CHEBI:29055) Is it correct to name these as derivatives of pyruvic acid/pyruvate when they are missing a methylene from the the structure of pyruvate/pyruvic acid

(CHEBI:31191) 1-[2-(propen-2-ylphenoxy)]-3-(isopropylamino)propan-2-ol hydrochloride name indicates propen-2-yl whilst structure is propen-3-yl

Reported by: dan2097

[muthuvenkat]

3215: Structure corrected

50931: Name corrected

48212: structure corrected

19891 and 29055: structures corrected

31191: name corrected

Thanks for pointing these errors out.

Steve

Original comment by: stevet7

[muthuvenkat]

(CHEBI:52612) N,N',N''-tris(pyridin-3-yl)benzene-1,3,5-tricarboxamide Name indicates 3 amides but there is only 2 in the structure

(CHEBI:48216) -basically the same as (CHEBI:48212) (1R,2R,3R,4S)-11-diazo-2,3,4,9-tetrahydroxy-2-methyl-5,10-dioxo-2,3,4,5,10,11-hexahydro-1H-benzo[b]fluoren-1-yl acetate indicates that the 4b, 10a bond is unsaturated but the structure has it as saturated.

(CHEBI:39399) (1,3-dioxo-2,3,4,5,6,7-hexahydro-1H-inden-2-yl)methyl (1R)-2,2-dimethyl-3-(2-methylprop-1-en-1-yl)cyclopropanecarboxylate indicates a partially saturated indene, but the structure has a nitrogen like isoindole

Original comment by: dan2097

[muthuvenkat]

(CHEBI:52055) 3,8-diamino-5-{3-[(2-{[3-(3,8-diamino-6-methylphenanthridinium-5-yl)propyl]amino}ethyl)amino]propyl}-6-phenylphenanthridinium dichloride dihydrochloride Structure indicates a positive charge on one of the amines but this is not present in the name

Original comment by: dan2097

[muthuvenkat]

(CHEBI:52163) 5-amino-9-(diethylamino)-6a,12a-dihydrobenzo[a]phenoxazin-7-ium chloride indicates the 6a,12a bond is saturated but the structure has all bonds in the fused ring system unsaturated

Original comment by: dan2097

[muthuvenkat]

52163: Name corrected.

52055: Structure corrected.

52612: Structure corrected

48216: Structure corrected

39399: Structure corrected

Thanks for pointing these out.

Steve

Original comment by: stevet7

[muthuvenkat]

(CHEBI:50031)/(CHEBI:50032)/(CHEBI:50033) thuj-2-ene structure is that of thuj-3-ene

(CHEBI:48214) (1R,2R,3R,4S)-11-diazo-1,3,4,9-tetrahydroxy-2-methyl-5,10-dioxo-2,3,4,5,10,11-hexahydro-1H-benzo[b]fluoren-2-yl acetate indicates that the 4b, 10a bond is unsaturated but the structure has it as saturated. This problem also effects the following (CHEBI:31751), (CHEBI:48211),(CHEBI:48215) (and 2 more which you've already fixed)

Original comment by: dan2097

[muthuvenkat]

(CHEBI:52010)/(CHEBI:4464)/(CHEBI:52013) (3S)-3-(4-chlorophenyl)-N,N-dimethyl-3-pyridin-2-ylpropan-1-amine name says pyridin-2-yl but structure is pyridin-3-yl

(CHEBI:50972) 2-amino-6-{(S)-hydroxy[(4R)-2-hydroxy-2-oxido-1,3,2-dioxaphospholan-4-yl]methyl}-4a,7,8,8a-tetrahydropteridin-4(3H)-one Name has oxido rather than oxo.

(CHEBI:52164) 5-amino-9-(diethylamino)-6a,12a-dihydrobenzo[a]phenoxazin-7-ium perchlorate indicates saturation on the 6a,12a bond but the structure is fully unsaturated

Original comment by: dan2097

[muthuvenkat]

(CHEBI:50031)/(CHEBI:50032)/(CHEBI:50033) This is an odd one. I've seen this compound described as both thuj-2-ene and thuj-3-ene. The structures shown in CHEBI match those shown in both the ChemIDPlus and NIST links. I've also found links where this compound is described as thuj-2-ene: http://www.chemdrug.com/databases/10\_6\_iuycqgupitrsbsvo.html and thuj-3-ene http://lb.chemie.uni-hamburg.de/search/index.php (here, a search for thuj-2-ene gives no hit!)

I've corrected 42814, 31751, 48211 and 48215

Thanks for pointing these out.

Kind regards, Steve

Original comment by: stevet7

[muthuvenkat]

(CHEBI:52010)/(CHEBI:4464)/(CHEBI:52013) - structures corrected

50972: the 'oxido' bit in the name is generated using naming software. The 5-membered cyclic phosphate is named '1,3,2-dioxaphospholan-2-ol 2-oxide'. Not really sure what to do here

52164 - name corrected

Thanks again for pointing these out.

Kind regards, Steve

Original comment by: stevet7

[muthuvenkat]

Hmm the Thuj-3-ene vs Thuj-2-ene case appears to me to be a case of an incorrect name becoming accepted due to repetition. http://www.acdlabs.com/iupac/nomenclature/79/r79\_88.htm is quite clear on the numbering of thujene. This is quite prevalent though e.g. Thuj-3-ene cannot be found on pubchem but thuj-2-ene can (notably 3-thujene is a synonym of this!)

The only thing I would say with some conviction is that thuj-2-ene should not be listed as an IUPAC name for these compounds (they already have a more systematic IUPAC name anyway)

Regarding 50972: https://sourceforge.net/tracker/?func=detail&aid=2821766&group\_id=125463&atid=703819 may be of some use in deciding how to proceed. Oxido is [O-] oxo is [=O] but oxide entirely depends on what you are bonding to e.g. pyridine N-oxide is [O-] sulfoxide is [=O], whilst styrene oxide is [-O-] so 1,3,2-dioxaphospholan-2-ol 2-oxide is a valid name for the non-charge separated form.

If you want the charge separated form using oxido rather than oxo a positive charge should really be on the the P

Are you able to say what naming software you use out of interest?

Original comment by: dan2097

[muthuvenkat]

Yep I agree. I will remove the thuj-2-ene from the IUPAC name as those rules clearly state that position 1 is where the isopropyl substituent is. Its tautomer will be thuj-3-ene. Though if you look at 5-isopropylbicyclo[3.1.0]hex-2-ene just below, this has the isopropyl at the 5-position. Put a 2-methyl substituent in and you get ....... thuj-2-ene. Who knows!!!!!

I admit all the cases of 'oxo' I've seen are =O. We use ACD name. Not entirely flawless but better than some the 'IUPAC' names you see on some sources.

Steve

Original comment by: stevet7

[muthuvenkat]

Indeed on a comparison paper of name generation software I once saw ACD/Name clearly came out the best. It's only a comparatively minor name/structure discrepancy anyway. Are the IUPAC names on Chebi a mixture of ACD/Name generated names and manually submitted names?

Original comment by: dan2097

[muthuvenkat]

Hi Daniel: When about 5 or 6 years ago we were deciding which naming package to use, I did my own survey of what was on the market then and found that ACD/Name was by far the best. This corresponded with the results from other surveys which were around at that time. What happens on ChEBI is that we generally generate a name using ACD/Name and then modify this manually if we deem it necessary. For instance, ACD/Name handles the placement of stereo indicators for steroids differently to how IUPAC recommends: thus ACD/Name will give (3beta,5alpha)-cholestan-3-ol, whereas the IUPAC steroid rules recommend 5alpha-cholestan-3beta-ol. This requires a manual change to be made by a curator. Also, there are still many classes of compounds that ACD/Name cannot handle (fullerene derivatives is one that jumps to mind). In such cases we have to go the IUPAC Recommendations and more or less start from scratch.

(Steve is on holiday this week which is why I'm jumping in on this thread)

Regards Marcus

Original comment by: mennis

[muthuvenkat]

• status: open --> closed

Original comment by: mennis