Dear Greg,
as i know from organic/inorganic and physical chemistry courses a
stereochemistry like that is unreal and i think it’s a bug of the pubchem
depiction generator.
Atoms can be chiral.
Bonds are not chiral.
Why bonds are not chiral? The answer is given by the molecular orbital theory
(MO), which says that when you make a bond between two atoms, orbitals need to
be “in phase”, and aligned one along the other. MO use the linear combination
of atomic orbitals, which says that from N orbitals which are combined, where
generated N new orbitals:
N/2 boding and N/2 antibonding. These orbitals bonding and anti bonding, are
not chiral because the direction of these is given by the resolution of the
schroedinger equations so… and they have a well “defined” direction in the 3D
space (probability to find an electron in that space). So the concept of phase
between the orbitals which are combined is very important and can’t be chiral
because of the well defined direction in the 3D space.
I’m available if you need something else.
Best regards
Marco
> On 11 Mar 2016, at 05:11, Greg Landrum <[email protected]> wrote:
>
> Dear all,
>
> Here's a question for the chemists in the group: do we need to be concerned
> about representing the stereochemistry of the P=C bond in substructures like
> O=P(/O)=C/C under normal circumstances?
>
> Here's a pubchem compound example that has the double bond crossed (possibly
> leading one to believe that it could have stereochemistry):
> https://pubchem.ncbi.nlm.nih.gov/compound/56981965
> <https://pubchem.ncbi.nlm.nih.gov/compound/56981965>
> Here's the corresponding substance record (which is how PubChem received the
> structure):
> https://pubchem.ncbi.nlm.nih.gov/substance/135741697
> <https://pubchem.ncbi.nlm.nih.gov/substance/135741697>
>
> Another example, this time without the crossed bond in the compound record:
> https://pubchem.ncbi.nlm.nih.gov/compound/87396055
> <https://pubchem.ncbi.nlm.nih.gov/compound/87396055>
>
> Best,
> -greg
>
>
>
>
>
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