Possible problems with Marvin Molfile parsing

Hi,





We've been importing structures from some Vendor chemical libraries, and have discovered what might be problems Marvin and JChemBase when parsing the Molfiles, in each case ChemAxon software is not detecting the differences between the various structures.





Case 1: Propranolol Hydrochloride





I've attached three mol files: racemic, R and S. If you copy and paste these Molfiles into Marvin, it does not detect the stereochemistry and displays each structure as racemic. Inserting these structures via JChemBase does the same thing.





Case 2: Endrin and Dieldrin have different connectivity, and if you paste these Molfiles into Marvin, they are different in 2D but when you open up MarvinSpace the 3D structures are the same. Also, when inserting these structures via JChemBase, they are considered the same structure. Molfiles attached.





Please let me know if there's something wrong with the Molfiles, or if this is a ChemAxon bug.





Thanks!





Moses

We will check it.

Hi Moses,





Case 1 (propanolol)





This is an ambiguous stereo center configuration, which is therefore not assigned. This configuration is also mentioned in





"Graphical representation of stereochemical configuration (IUPAC Recommendations 2006)"


http://www.iupac.org/publications/pac/78/10/1897/


(page 1916):

Quote:

These depictions are formally ambiguous and cannot be interpreted with certainty. They should never be used.

Case 2 (Endrin and Dieldrin)





I could see no stereo designation in the two files. If I add the missing wedges, the two molecules are recognized as different. See attached files.





Best regards,


Szabolcs

Hi Szabolcs,





Great answer to #1, and thanks for the paper reference, I'll read it. My fault with case #2, I was fooled by the 2D coordinates, but I see now that the stereocenters are not specified.





Thanks again,





Moses