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Home » DataWarrior » Functionality » Axial chirality (Does DataWarrior support Axial chirality?)
Axial chirality [message #1065] Wed, 09 September 2020 02:46 Go to next message
zhentg is currently offline  zhentg
Messages: 15
Registered: March 2020
Junior Member
Hi DW developers,

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?
index.php?t=getfile&id=263&private=0
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Datawarrior is a good tool
Re: Axial chirality [message #1066 is a reply to message #1065] Fri, 11 September 2020 11:37 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 54
Registered: June 2019
Member
Possibly the scrutiny for P/M in simpler biphenyls differs from the one in larger systems with axial chirality when structures are drawn in the sketcher from scratch:

index.php?t=getfile&id=269&private=0

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):

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Re: Axial chirality [message #1070 is a reply to message #1066] Sun, 13 September 2020 12:04 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 362
Registered: June 2014
Senior Member
Axial chirality (indicated as M or P) is covered to some extend:

- 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.

index.php?t=getfile&id=273&private=0
Re: Axial chirality [message #1078 is a reply to message #1066] Wed, 16 September 2020 02:03 Go to previous messageGo to next message
zhentg is currently offline  zhentg
Messages: 15
Registered: March 2020
Junior Member
Thanks for your comprehensive answer.
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.


Datawarrior is a good tool
Re: Axial chirality [message #1079 is a reply to message #1070] Wed, 16 September 2020 02:07 Go to previous messageGo to next message
zhentg is currently offline  zhentg
Messages: 15
Registered: March 2020
Junior Member
Thanks Thomas. Is this Axial chirality introduction covered in the online help of DW?
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.


Datawarrior is a good tool
Re: Axial chirality [message #1085 is a reply to message #1079] Fri, 02 October 2020 11:37 Go to previous message
thomas is currently offline  thomas
Messages: 362
Registered: June 2014
Senior Member
Thanks for the recommendation. I will look into search functionality. I know and regret that online help is always much behind the actual functionality. I could need some support here...
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