ahhh :-) now i understand. Ok it’s an other point of question so…
if the oxygen bonded to the Phosphor of the group C=P is in Cis or Trans. Yes,
describe this feature make sense.
The bond C=P is blocked, so the oxygen is not free to be rotated along the bond
C=P.
Finally, i think is important to describe this kind of isomerism.
However about atropisomerism i’m a bit unconvinced to be added into a SMILES
notation, because this kind of isomerism it depends on the conformation of the
molecule and not in the configuration as in the case of the oxygen in Cis/Trans
of the C=P group.
Marco
> On 11 Mar 2016, at 09:48, Greg Landrum <greg.land...@gmail.com> wrote:
>
> 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 <mailto: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
>> <mailto: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
>> <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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