Stereochemical assignment for Atropisomers during "Convert Name To Structure"

Bold Bonds vs Wedged/Hashed-Wedged bonds:

Historically, Wedged/Hashed-Wedged bonds are not used for stereochemical assignment of biaryl atropisomers [using Bold Bonds is more popular] AND not always involve marking stereochemistry of atoms immediately at the hindered bond (see Vanol, VD-BetaV21-0013.png). Some of the reasons are that Wedged/Hashed-Wedged bonds cannot be used on double bond, but Bold Bond tool can. Piere, in your sample [file with Vanol stereoisomers] exact choice of Wedged/Hashed-Wedged bond combination for stereochemical assignment around hindered bond location is influenced by positions of double bonds:

1. What combination of hashed-wedged bond will be used;

2. Will they be at one (E) or opposite sides (Z) of the bond [red bonds, VD-BetaV21-0030.png]?

When Bold Bond tool is used, the position of double bonds in the structure are irrelevant for stereochemical assignment AND a single representation for each stereoisomer can be used independently of double bond locations to the hindered bond (yellow rectangles, VD-BetaV21-0030.png).

There are some molecules when you can't do simplistic stereochemical assignment using Wedged/Hashed-Wedged bonds approach. For instance, [6+]helicenes. Unfortunately, I cannot draw a stereomeric pair for [6+]helicenes using either Bold Bond approach or Wedged/Hashed-Wedged bonds, that would have a correct appearance after 3D Clean Up (Atropisomers-3.mp4).

"Convert Name To Structure" for atropisomers:

Unfortunately, "Convert Name To Structure" for atropisomers with Bold Bond marking approach gives mixed success rate:

1. If it includes only one atom of the hindered bond, only one stereoisomer is correctly assigned:
   (S), but not (R) in VD-BetaV21-0011.png
   (S), but not (R) in VD-BetaV21-0012.png

2. If it DOES NOT include atoms of the hindered bond - no R/S stereochemical designation is issued [Vanol, VD-BetaV21-0013.png] or [Vanol in yellow rectangles, VD-BetaV21-0030.png].

Additionally, I disagree with Mike's conclusion about ambiguity if only ONE atom of the hindered bond of Vanol atropisomers has wedged or hashed-wedged bond assignment. My understanding is that stereochemistry is complete and NOT ambiguous [one stereocenter is defined with wedged or hashed-edged bond, there is no rotation around hindered bond and a naphtalene part on a side with no assignment is flat meaning there is no ambiguity in position of each part attached to the hindered bond]. R/S stereochemical designation during "Convert Name To Structure" should be issued and is issued correctly (VD-BetaV21-0031.png).

Regarding 3D Clean Up:

1. 3D Clean Up of (S)-Vanol with Wedged/Hashed-Wedged bond assignment on both atoms of hindered bond [two possible variants] DOES NOT give a correct 3D structure. Refer to my video (Atropisomers-1.mp4). Observe, that 3D Clean Up of your wedged/hashed-wedged (S)-Vanol [second structure from the left in a video] gives a structure where Ph-C-C*-C-OH parts are non-planar AND not rotated around hindered bond to give (S)-stereochemical representation. As you can see, it's different from 3D model you provided for (S)-Vanol after 3D Clean Up [probably, you are using a different Beta version of ChemDraw].

2. On contrary, using Bold Bond assignment approach gives a correct 3D model for both Vanol atropisomers [Vanol in yellow rectangles, VD-BetaV21-0030.png].

3. I tried to explore 3D Clean Up of Vanol atropisomers with all possible stereochemical presentations [Wedged/Hashed-Wedged bond assignment on both atoms of a hindered bond, or only one side, or Bold Bond assignment] (VD-BetaV21-0033.png). The end result of 3D Clean Up - VD-BetaV21-0032.png. See video as well [Atropisomers-2.mp4].

I do not see the same behaviour as Pierre (MacBook Air M1).

When I draw the structures as Pierre does and do 'name to structure' it arrives without the R and S labels. 3D Clean up gives the correct 3D structure (Image 1)

When I change one of the wedged or hashed-wwedged bonds to a single bond the R and S labels appear. But when I do 3D Clean up (three times in a row for each) it seems to arrive to the same 3D structure. (Image 2)

In the first example it should give R and S labels and does not.

In the second, I think the stereochemistry is ambiguous and it should not label them. The fact that it arrives at the same thing after 3D clean up seems to mean that Chemdraw is ambiguouos about them too.

The wedged and hashed-wedged bonds allow for proper recognition of the atropoisomers

I may be saying the same thing, but it appears to depend on how you draw it - ie placement of double bonds in a benzene ring.