Thanks, Greg!
So, "C[C@H](O)C(O)[C@@H](O)C" --> [(1, 'S'), (3, '?'), (5, 'S')]
and "C[C@H](O)C(O)[C@H](O)C" --> [(1, 'S'), (3, '?'), (5, 'R')]
and therefore I understand that changing the configuration at position 5
does not informs me
about the change of status of atom 3, even though it changes from
"non-asymmetric carbon" to "asymmetric carbon".
As you suggested, imposing a definite configuration to carbon 3 leads to:
"C[C@H](O)[C@H](O)[C@@H](O)C" --> [(1, 'S'), (3, '?'), (5, 'S')] C-3 is
non-asymmetric but appears as asymmetric-but-undefined
"C[C@H](O)[C@H](O)[C@H](O)C" --> [(1, 'S'), (3, 's'), (5, 'R')] OK
"C[C@H](O)[C@@H](O)[C@H](O)C" --> [(1, 'S'), (3, 'r'), (5, 'R')] OK
I will change my question for an another one.
Having created molecule m as Chem.MolFromSmiles("C[C@H](O)C[C@@H](O)C")
of from a MOL file,
with a CH2 in the middle of the molecule, how would it be possible to
create molecules m1 and m2 from m
with a substitution H -> OH (or H->D) at the central position with the 2
possible configurations, so that I can reproduce the three examples
here-above?
Best,
Jean-Marc
Le 17/05/2021 à 13:09, Greg Landrum a écrit :
Hi Jean-Marc,
In that particular configuration:
image.png
the central atom is not a chiral center since atoms 1 and 5 have the
same absolute stereo.
However, if you change the stereo of either atom 1 or 5, then the
central atom can be a chiral center:
image.png
This possibility is why FindMolChiralCenters() flags that atom as a
possible stereocenter.
-greg
On Mon, May 17, 2021 at 12:09 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear all,
The determination of the absolute configuration of chiral centres is
certainly not an easy problem.
Even recognizing that a carbon atom is an asymmetric one is not that
trivial, even for humans.
I tried:
>>> smi = "C[C@H](O)C(O)[C@@H](O)C"
>>> m = Chem.MolFromSmiles(smi)
>>>
Chem.FindMolChiralCenters(m,force=True,includeUnassigned=True,useLegacyImplementation=False)
[(1, 'S'), (3, '?'), (5, 'S')]
but the central carbon atom of this compound, indexed "3", is not an
asymmetric one, is it?
Best regards,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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