Hi Marco,
Sorry I wasn't clear in the original question. I was asking about the
cis/trans stereochemistry of the C=P bond. I agree that it's not generally
useful to think of bonds as being chiral.[1]
-greg
[1] There's an argument to be made here about the best way to represent
atropisomers, but that's for a different discussion
On Fri, Mar 11, 2016 at 9:22 AM, Giuseppe Marco Randazzo <
gmranda...@gmail.com> wrote:
> 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 <greg.land...@gmail.com> 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
> Here's the corresponding substance record (which is how PubChem received
> the structure):
> 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
>
> Best,
> -greg
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
