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I've been taught that in a wedge-dash diagram, the wedge represents a bond above the plane of the paper, and the dash represents a bond below the plane.

Accordingly, I expected the structure of this particular conformer of 1,2-dichloro-1,2-difluoroethane to have the fluorine groups in a trans orientation. I am aware that conformers can interconvert, but my question is about the wedge-dash representation of this particular conformer; the representation obviously cannot interconvert.

enter image description here

In other words, I was expecting the structure to have the following sawhorse projection:

enter image description here

But when I ran it through MolView, I got the following structure, in which both fluorine groups seem to be above the plane.

enter image description here

That is, the structure had the following sawhorse projection:

enter image description here

Am I missing something? Or is the 3D structure from MolView wrong? I am not referring to the R/S configurations here; my doubt is only in the wedge-dash representation.

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  • $\begingroup$ I think you should check out how conformers work, particularly interconvert... $\endgroup$
    – Mithoron
    Commented Jun 24, 2022 at 15:23
  • $\begingroup$ The molecule can rotate freely around the C-C axis. But I would interchange one $\ce{H}$ and one $\ce{F}$ atom on the left (lower) carbon atom on the picture. $\endgroup$
    – Maurice
    Commented Jun 24, 2022 at 16:10
  • $\begingroup$ @Mithoron I know that there an infinite number of possible conformers of this molecule, and that they interconvert. I wanted to know about this specific conformer, because my question is about the representation itself. $\endgroup$
    – Righter
    Commented Jun 24, 2022 at 17:24
  • $\begingroup$ @andselisk My question is not about the R/S configurations, but the wedge-dash notation. $\endgroup$
    – Righter
    Commented Jun 24, 2022 at 17:30
  • $\begingroup$ Get the stereochemistry right before dealing with conformation. follow the advice of @Maurice regarding H and F. $\endgroup$
    – user55119
    Commented Jun 24, 2022 at 18:59

1 Answer 1

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MolView has issues with preserving stereochemistry when converting 2D to 3D. Do not expect accurate conversion of the drawn wedge-and-dash projection into the three-dimentional model because the structure is converted to the proprietary SMILES format first, and despite SMILES having support for stereochemistry, there is no uniform open standard.

MolView sends generated SMILES to third-party services such as PubChem and CID, and numerous things may break (and they do) along the way, for example, since there is no hydrogen atoms in the SMILES generated within MolView if none explicit hydrogens were drawn, the stereochemistry interpreted by PubChem has nothing to do with the intended one because their API expects an isomeric SMILES string with explicit hydrogen atoms.

If you still want to use MolView to depict stereoisomers, use the search function with one of the following queries:

In your case you were getting wrong structure for (1S,2S)‐1,2‐dichloro‐1,2‐difluoroethane with SMILES string F[C@@H](Cl)[C@@H](F)Cl, which had nothing to do with your drawing, rather with interconversion process. Always check how the software operates and don't blindly rely on technology without understanding its limitations.

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