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Axial chirality
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=1065&th=415#msg_1065
Axial chirality is not represented by most of encoding methods, e.g. SMILES, InChi.
Axial chirality can be drawn in ChemDraw and MarvinSketch, but it seems not supported by the built-in sketcher of DataWarrior.
Can you please provide more details on this topic?
]]>zhentg2020-09-09T00:46:29-00:00Re: Axial chirality
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=1066&th=415#msg_1066
As a bit lengthy work-around: I redrew two structures like the one drawn by you outside DW. After their export as .mol (including 3D coordinates), they were converted with openbabel into an .sdf in common. DW apparently recognized the chirality (both.dwar, attached):
]]>nbehrnd2020-09-11T09:37:45-00:00Re: Axial chirality
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=1070&th=415#msg_1070
- For allenes the configuration is assigned to the central atom.
- In case of atropisomers only bi-phenyls with at least three ortho substituents
are considered because of the reliably hindered rotation. Here the central bond
carries the configuration information.
]]>thomas2020-09-13T10:04:05-00:00Re: Axial chirality
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=1078&th=415#msg_1078
I did not know the P/M definition before, and assigning P/M in DW really works.
However, in terms of data exchange feasibility, axial chirality can be represented in MOL format, but not in SMILES. Here you used MOL to transfer data from SDF to DW. That is a nice solution.]]>zhentg2020-09-16T00:03:45-00:00Re: Axial chirality
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=1079&th=415#msg_1079
It will be helpful to add.
By the way, the online Help is not searchable. It would be nice to make it searchable, so that keywords like "axial chirality" will be located easier.]]>zhentg2020-09-16T00:07:54-00:00Re: Axial chirality
https://openmolecules.org/forum/index.phpindex.php?t=rview&goto=1085&th=415#msg_1085
]]>thomas2020-10-02T09:37:19-00:00