Is this a correct chiral-center count?

Hi,

Using 5.11.2 API, I write the following Java code:

MolHandler mhl = new MolHandler(smiles, false); // if true, import SMILES string as SMARTS

        Molecule mm = mhl.getMolecule();

        Stereochemistry stereo = new Stereochemistry();

        stereo.setMolecule(mm);

        System.out.println("chiral center count = "+stereo.chiralCenterCount());

 java GetChiralCount 'ClC1CCC(Br)CC1'

chiral center count = 0

java GetChiralCount 'Cl[C@H]1CCC(Br)CC1'

chiral center count = 2

The following molecule "ClC1CCC(Br)CC1" has cis trans isomerism in ring. Actually, the chiral center count returns chiral centers, in the case if you change the spatial arrangement of the ligands around the atom and you get a different stereoisomer. 

In this case this you have two center which get meaning just if at least one is specified, so that is why 0 returned.

Thank you for quick response and explanation.  Is there any function/method which I can use that will return "2" for "ClC1CCC(Br)CC1"?

Currently not, but we can implement one in the next 5.12.1 release.

5.12 release commit deadline is over so I cannot add new method there, it is under testing phase.

Is this acceptable for you?

Yes .. thanks .. I think it would be a useful function .. sometimes our chemists draw flat bonds when they don't know the configuration, but we would still like to detect compound has having chiral centers.

You cannot think of any work-around until 5.12.1?  If it is a lot of code, then that is fine with me .. smile.

Thanks again,

Andrew

I have discussed so it can go into 5.12.

The new funcion is :

int[] ccc= Stereochemistry.getPossibleAtomCenteredStereoAtoms(m);

I hope this helps.

best

Andras

Thank you very much!

Hi,

I think we've come up with a work-around that will let us survive until 5.12 is released.  But we have a few questions.

The attached Java code looks for 1) instances of 1,4 disubstituted cyclohexanes with flat substitution bonds, and 2) when it finds them converts the flat substitution bonds to be wiggly bonds.

If you run the code against the attached SDF, the code finds 1,4 disubstituted cyclohexanes with flat bonds in structures 1 and 4, but not 2 or 3.  1 is expected.  2 and 3 are expected failures.  However, 4 is unexpected .. I'm not sure why a wiggly bond should be found?

I also cannot seem to come up with a good standardizer reaction in order to convert the flat substitution bonds into wiggly bonds (see Java code).

Can you offer some help on these items?

Thanks!

Andrew

Oops, these questions are bit out of my scope regarding search and standardizer. My colleagues will respond you soon.

I also cannot seem to come up with a good standardizer reaction in order to convert the flat substitution bonds into wiggly bonds (see Java code).

Currently there is no Standardizer action which can convert flat single bonds into wiggly bonds. Transform action can change the stereo configuration of a chiral center (e.g. from R to S), but it does not change bond types. Bond type changes (e.g. "Single Up"  to "Single Down") are performend automatically when the stereo configuration of a chiral center is changed.

In JChem 6.0 it will be possible to implement your own Standardzier action which can change the bond type.

Hi Andrew,

If you run the code against the attached SDF, the code finds 1,4
disubstituted cyclohexanes with flat bonds in structures 1 and 4, but
not 2 or 3.  1 is expected.  2 and 3 are expected failures.  However, 4
is unexpected .. I'm not sure why a wiggly bond should be found?

It seems to be a problem in the default stereo model, comprehensive, which cannot recognize that it is not a symmetrical case, but a potential cis/trans stereo configuration near the cyclohexane.

The local stereo model will work as expected. So, insert this line into your program:

so.setStereoModel(SearchConstants.STEREO_MODEL_LOCAL);

Best regards,

Szabolcs

Thank you for the helpful replies!

I would like to urge you to avoid using the term "chiral center".  The proper term is "stereocenter" or "tetrahedral stereocenter."  The concepts of chirality and stereogenicity are distinct and should not be conflated.

awrk, you may want to look at this discussion.