Oxazepin aromaticity (canonize mode)

[fredludlow]

Hi there,

I think I've found a small bug (the first one in many happy years of using JME and JSME, so thank you!)

Oxazepine (C1=CC=CON=C1) - a 7-membered ring with an O, an N and 3 double bonds - is not an aromatic compound (at least, my electron counting and a quick DFT geometry optimization suggest it's not aromatic or flat).

If I sketch it, or paste the SMILES into the JSME demo here: https://jsme-editor.github.io/dist/JSME_minimal.html it displays fine:

But if I click the smiles button it gives me back something aromatic: c1ccnocc1.

The nocanonize option forces it to avoid aromaticity detection but in this particualar case I would like aromatic molecule as lower-case so I'd rather not use that option.

[peter-ertl]

Hello Fred, JSME does not contain any aromaticity detection, like 4n+2 rule. It generates aromatic SMILES for all conjugated rings. So if you need correct aromatic or non-aromatic SMILES, you need to process JSME SMILES output with some special cheminformatics tool.

…

On Wed, May 7, 2025 at 12:13 PM Fred Ludlow ***@***.***> wrote: *fredludlow* created an issue (jsme-editor/jsme-editor.github.io#59) <#59> Hi there, I think I've found a small bug (the first one in many happy years of using JME and JSME, so thank you!) Oxazepine (C1=CC=CON=C1) - a 7-membered ring with an O, an N and 3 double bonds - is not an aromatic compound (at least, my electron counting and a quick DFT geometry optimization suggest it's not aromatic or flat). If I sketch it, or paste the SMILES into the JSME demo here: https://jsme-editor.github.io/dist/JSME_minimal.html it displays fine: image.png (view on web) <https://github.com/user-attachments/assets/7912b045-1fc4-41de-90f2-dc58e0e55e7d> But if I click the smiles button it gives me back something aromatic: c1ccnocc1. The nocanonize option forces it to avoid aromaticity detection but in this particualar case I would like aromatic molecule as lower-case so I'd rather not use that option. — Reply to this email directly, view it on GitHub <#59>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACNDUUD2B7ZZGPWJEDX6IAL25HMCZAVCNFSM6AAAAAB4TOOCKCVHI2DSMVQWIX3LMV43ASLTON2WKOZTGA2DKNBWGI4TENY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[fredludlow]

Thanks for the reply!