Aromaticity display errors - Marvin 16-4-11

Hi,

The aromaticity of
some molecules I am working with are not properly displaying in MView
16-4-11. Initially, I thought there were valence errors, but
structure checker says there are none. [Marvin sketch – check
structure shows no errors – “the document appears to be
valid”].

If I choose – implicit hydrogens – on all (to
display all hidden H atoms), the structure does not show any extra H
atoms; neither aromatic rings nor double bonds are shown correctly/
where they should be.

But in Maestro (free academic version),
after pasting in the Mview-generated smiles, the aromatic rings
display ok.

Attached is a photo where the
rings equivalent to each other are pointed at by yellow lines (they
differ in appearance).

Here's the smiles:

[H]OC(=O)c1c(O[H])c(OC([H])([H])C2=C([H])[C@]([H])(C(=O)O[H])[C@]([H])(C(=C2[H])C([H])([H])[H])C([H])([H])[H])c([H])c([H])c1C1=C([H])C(=O)c2c(O[H])c([H])c(O[H])c([H])c2O1

Any
suggestions?

Thanks,
Enrique

Hello Enrique,

We know about it, in our backlog to fix. However, if you use the Kekule form (instead of the Aromatic ring) it is all displayed fine. So, until it is fixed please use this workaround. 

Best regards,

K

Thanks. Another thing:

In the attached molecule, only the left ring is displayed with double bonds after "kekule-ization", but the ring on the right is still incorrectly displayed as aromatized (it shouldn't be as the heterocyclic ring's O has only two bonds). Could there be a visualization problem here as well?

Enrique

Dear Enrique,

I assume that the original molecule before 'kekulization' contained aromatic bonds.

As that ring is not aromatic, MarvinSketch can not assign double/single bonds to that,  (see the attached image ).

For more information on aromatic molecule in MarvinSketch please consult our documentation https://docs.chemaxon.com/display/docs/Aromatization.

Should you need any further information, please do not hesitate to contact us.

Best regards,

Nikolett Mihala

Dear Enrique,

 

I am happy to inform you that from version 16.5.23. the problem you reported will be fixed.

Thank you for your patience.

Best regards,

Nikolett Mihala