Drawing tricky structures

It seems MarvinSketch does not allow a wedge bond to be used (red circle) (I draw it use ChemDraw), because it does not think there is a chiral center. Suggestions? Thanks.

Hello,

We have a long weekend due to our national holiday here, but my colleagues will answer you soon.

Regards,
Erika.

Hi,

This is an allene like chirality type which is not handled correctly in the checker.

Andras

Do you mean you cannot draw a wedge bond there or you just get the wedge bond highlighted as error (by the WedgeErrorChecker)?

Sorry for the confusion. I can draw, but The SMILES obtained from the drawing does not contain stereo information, i.e., the wedge information is lost upon subsequent operations.

Hi,

This allene like chirality is not yet supported in SMILES.

Until we support it please use an other format (like mrv) to save the molecule.

Thank you

Andras

Thanks. Just tried it. Yes, mrv format will preserve the wedge. jc_equals, however, will treat the two isomers (solid wedge and hashed wedge) as identical structure. I understand this is a difficult case, so I just want to check on forum, in case there is sth. else I missed. Thanks.

Hi Yingyao,

 

I just confirm here that this kind of stereochemistry is not supported in JChem, that is why jc_equals reported that the two stereoisomers are the same.

 

Best regards,

Szabolcs