ziprasidone (CHEBI:10119) Incorrect IUPAC name

[muthuvenkat]

5-{2-[4-(1,2-benzisothiazol-3-yl)piperazin-1-yl]ethyl}-4-chloroisoindolin-1-one should be something like: 5-{2-[4-(1,2-benzisothiazol-3-yl)piperazin-1-yl]ethyl}-6-chloroindolin-2-one to describe the correct structure

On an unrelated note for: isoprothiolane sulfoxide (CHEBI:6048) the IUPAC name di(propan-2-yl) (1-oxido-1,3-dithiolan-2-ylidene)malonate should probably be di(propan-2-yl) (1-oxo-1,3-dithiolan-2-ylidene)malonate. My understanding is that oxido is always [O-] and oxo is =O. I havn't got absolute confidence as one name2structure tool still produced the expected structure despite the in my opinion incorrect name.

Reported by: dan2097

[muthuvenkat]

The problem with the use of oxido rather than oxo also applies to: 4-(dioxidosulfanyl)morpholine (CHEBI:36583)

Original comment by: dan2097

[muthuvenkat]

I've changed the name to 5-{2-[4-(1,2-benzothiazol-3-yl)piperazin-1-yl]ethyl}-6-chloro-1,3-dihydro-2H-indol-2-one. We must have omitted the N when creating the name earlier.

Re the use of oxido instead of oxo, I believe this is to reflect the nature of the RR'S=O group as being a sulfoxide, which could also be represented as RR'S(+)-O(-). However I can't find anything about this in any IUPAC recommendations, organic or inorganic. I'll try to find out more and get back to you.

Cheers

Marcus

Original comment by: mennis

[muthuvenkat]

I checked this with Alan McNaught from IUPAC. His comments as follows:
"In naming sulfoxides, one has to decide initially what valence bond representation to use. Many people these days prefer the charge-separated form rather than a double bond, and clearly some of the people who write naming software have taken this view." Hence the use of 'oxido' rather than 'oxo' in our nomenclature software. However Alan assures me that IUPAC is sticking with the S=O representation rather than the S(+)-O(-) one and consequently it would prefer 'oxo' over 'oxido' for our present case. That being the case, I'll make the appropriate changes to our IUPAC Names for both isoprothiolane sulfoxide and 4-(dioxidosulfanyl)morpholine. If you spot any more of these please do let me know.

Cheers

Marcus

Original comment by: mennis

[muthuvenkat]

• status: open --> closed

Original comment by: mennis

[muthuvenkat]

I forgot to mention also that we need to introduce a λ4 immediately after the 1 of 1,3-dithiolan to denote the non-standard bonding number being used for the sulfur at this position. Similarly, we need to include -λ6- in front of the 'sulfanyl' in the name for the morpholine derivative.

Marcus

Original comment by: mennis

[muthuvenkat]

Just to add, if you were going to use the charge separated form then the original name should probably of indicated that a charge was present on the sulfur making it still wrong :-P

I think this is the last of the incorrect names I can currently find. I've been running, OPSIN (the name2structure component of OSCAR3) over an admittedly somewhat out of data version of CHEBI that is used in OSCAR3 as a dictionary. This was primarily actually to spot mistakes that OPSIN was making (there was about 10 times as many true mistakes as mistakes caused by the input names from CHEBI being wrong). Most of the mistakes OPSIN makes are related to more trivial or underspecified names e.g. anthrone, nitroglycerin etc.; not the IUPAC names.

I think you are correct about the lambda convention. I often forget about it as I am used to dealing with names where it is omitted. (I also havn't quite got around to implementing it into OPSIN although it should be simple to do so)

Original comment by: dan2097

[muthuvenkat]

Yes, I've included the charge-separated form as a synonym: 2-[1,3-dioxo-1,3-bis(propan-2-yloxy)propan-2-ylidene]-1,3-dithiolan-1-ium-1-olate

Cheers

Marcus

Original comment by: mennis