3D Clean Up of Atropisomers

Stereochemical assignment for Atropisomers during 3D Clean Up is incorrect.

DISCUSSION:

The most important class of atropisomers are biaryls: specifically, derivatives of biphenyl with a complete set of ortho substituents or dimers of naphthalene derivatives. The ability of axially chiral biaryl compounds (BINAP, QUINAP, BINOL, VANOL) to provide stereoinduction has led to wide use as chiral ligands in assymetric catalysis.

Representation of biaryl atropisomers is achieved not by marking stereochemistry of atoms at the hindered bond, but opposite sides of biaryl rings (BINOL, VD-BetaV21-0010.png). 3D Clean Up doesn't understand such representation and performs stereochemical assignment incorrectly.

Determining the axial stereochemistry of biaryl atropisomers can be accomplished through the use of a Newman projection along the axis of hindered rotation [detailed description of the process can be found here [Stereochemical Assignment]: <https://en.wikipedia.org/wiki/Atropisomer>.

3D Clean Up doesn't understand the stereochemistry of atropisomers (3D CleanUp of Biphenyl Atropisomers.mp4). Additionally, after 3D Clean Up some Bold Bond markings remain (end of video).

EXPECTED BEHAVIOR:

1. 3D Clean Up should perform stereochemical assignment of atropisomers correctly.

2. All Bold Bond markings should be removed.

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FILES:
VD-BetaV21-0010.png
3D CleanUp of Biphenyl Atropisomers.mp4

Windows 10 Pro, version 21H1, 64-bit OS Build 19043.1348,
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Intel HD graphics family (driver version 20.19.15.4642, driver date: 28/03/2017)
Windows OS Display settings for "Scale and layout" are: 250% (Recommended)
ChemDraw Beta v21.0.999.2240