Stereochemistry question

In the help of JCHEM, I see that the default sterochemistry is absolute.


But I see nowhere where i can choose relative or centre sterochemistry.





It is strange : the stereochemistry is R for the isomer in my query.


With default stereochemistry (absolute), the isomers results after a substructure search must be all R?


I find some S isomers

Is there any chemaxon tools for checking if a structure is aromatic or not?

Hello,





If you use marvin sketch, then you can aromatize the molecule:


Structure > aromatization > aromatize





Using API calls:


aromatization:


http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/struc/Molecule.html#aromatize(int)


e.g myMol.aromatize();


Than you can check the type of a bond (using aromatization the possible bonds are aromatized, their type has been changed):


http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/struc/MolBond.html#getType()


if (bond.getType() == MolBond.AROMATIC) ....





Best Regards,


Robert

>the exemple of isomer R in a query wich give isomer S in the results is shown in page 1





what do you think about this pb?

Hello,





In jchem if you want to use relative configuration you have to define a molecule with relative stereo information.


e.g. In marvin sketch:


draw molecules with enhanced stereo labels, like:


http://www.chemaxon.com/jchem/doc/user/Query.html#relative_stereo


You can put enanced stereo labels on the chosen atom in the following way:


Pick the atom.


Right click > stereo > enhanced > Choose the label you want.


For a detailed description about how the enhanced labels work read:


http://www.chemaxon.com/jchem/doc/user/Query.html#relative_stereo





Bye,


Robert

Hello,





There are two aromatization methods used, basic and general.


http://www.chemaxon.com/marvin/help/sci/aromatization-doc.html





If you sketch a molecule and aromatize it there you can specify which aromatization you use.


If you draw the previously shown "strange" molecules then using basic aromatization they are not aromatized.





If you search in a database then you have to consider the needed aromatization upon importing the molecules:


http://chemaxon.com/jchem/doc/user/Query.html#standardizationDB


and configure the standardization if needed:


http://chemaxon.com/jchem/doc/user/StandardizerConfiguration.html





Your previous searches were executed on a table which had general aromatization (default) that's why you obtained those results.





Best Regards,


Robert

>the exemple of isomer R in a query wich give isomer S in the results is shown in page 1





what do you think about this pb?

Hi,





Here I would like to point out that the stereo carbon atom has the same spatial arrangement both in the query and the target.


q: Cl and the two C atoms in the plain. The other C is a hatch and the H is a wedge.


If you twist this along the bond between the stereo C and the C which is towards the two C atoms, ten you get the target conformations:


Cl hatch, All C neighbours in the plain and the H is a wedge.





If you draw this twisted molecule, then the C is still labelled R. In the hits they are labelled S because they are a part of a larger molecule.


The important thing to mention is, that only molecules of the same spatial configuration are retrieved.





Hence an S atom can match on an R atom if the surrounding molecule is different, because in this case they may have the same spatial configuration.





Bye,


Robert

(I split this topic into pieces, because more separate questions were dealt with, and it became quite long.)





Just one additional note: the CIP system only describes a stereo configuration unambiguously with R or S when the full environment is defined. When you are comparing substructure and its superstructure configuration, there will be cases where the substructure and superstructure R/S labels are different for the same stereo configuration. The reason is that stereo center ligands in the superstructure may get different priorities than in the substructure. (Because they are bigger and contain more information.)





It all results from the definition of the CIP rule system:


http://en.wikipedia.org/wiki/Cahn-Ingold-Prelog_priority_rules





Best regards,


Szabolcs.