Incorrect stereo label

User a11e9761d6

23-01-2014 16:55:50

Hi ChemAxon,


We recently encountered a situation where Marvin/JChem appear to assign the incorrect stereo label.


As an example, for the following CXSMILES, from this paper


OCCC1=CC=C(C=C1)N(C[C@@H](O)CN1CCN(CC1)C(C1=CC=CC=C1)C1=CC=CC=C1)S(=O)(=O)C1CCC(Cl)CC1 |c:5,7,25,27,32,34,t:3,23,30|


The ChemAxon tools assign the S label, but Chemdraw assigns the R label, which we think is correct based on the literature.


We are using JChem/Marvin 6.1.4.


 


Thanks,


Krishna

ChemAxon fc046975bc

24-01-2014 09:27:52

Hi Krishna,


Unfortunately, I cannot reproduce the problem you reported. I imported that SMILES to Marvin and ChemDraw, and I found that in both cases the stereocentre is (S). Also, in daylight's depict, it is imported as (S).


Can you specify the problem in more detail?


Thanks,
Peter

User a11e9761d6

29-01-2014 01:45:17

Hi Peter,


Thank you for looking into this.


Unfortunately the structure that does exhibit this problem is proprietary, and the chemist who reported it has not been able to come up with a non-proprietary structure that reproduces the issue. He thought this one did (I didn't have access to ChemDraw to verify), but as you demonstrated it does not.


You can consider this issue closed for now; thank you again for your assistance.


Krishna