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Axial chirality [message #1065]

Wed, 09 September 2020 02:46

zhentg
Messages: 25
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

Attachment: dw1.png
(Size: 56.29KB, Downloaded 918 times)

Datawarrior is a good tool

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Re: Axial chirality [message #1066 is a reply to message #1065]

Fri, 11 September 2020 11:37

nbehrnd
Messages: 224
Registered: June 2019

Senior 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):

index.php?t=getfile&id=271&private=0

Attachment: diff.png
(Size: 41.12KB, Downloaded 818 times)
Attachment: both.dwar
(Size: 2.21KB, Downloaded 373 times)
Attachment: then3D.png
(Size: 34.81KB, Downloaded 939 times)
Attachment: both.sdf
(Size: 7.32KB, Downloaded 379 times)

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Re: Axial chirality [message #1070 is a reply to message #1066]

Sun, 13 September 2020 12:04

thomas
Messages: 711
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

Attachment: axialChirality.png
(Size: 12.56KB, Downloaded 871 times)

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Re: Axial chirality [message #1078 is a reply to message #1066]

Wed, 16 September 2020 02:03

zhentg
Messages: 25
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

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Re: Axial chirality [message #1079 is a reply to message #1070]

Wed, 16 September 2020 02:07

zhentg
Messages: 25
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

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Re: Axial chirality [message #1085 is a reply to message #1079]

Fri, 02 October 2020 11:37

thomas
Messages: 711
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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