Re: [Rdkit-discuss] Stereochemistry question

On Mon, Mar 14, 2016 at 6:39 AM, Jean-Marc Nuzillard < jm.nuzill...@univ-reims.fr> wrote: > > You might want also to consider nitrones > https://en.wikipedia.org/wiki/Nitrone > that are sometimes written (CAS does it!) with > a nitrogen atom surrounded by a C=C and a C=O double bond. >

Re: [Rdkit-discuss] Stereochemistry question

Dear all, for sure, having a double bond surrounded by four single bonds makes the assignment of the E/Z configuration simpler. You might want also to consider nitrones https://en.wikipedia.org/wiki/Nitrone that are sometimes written (CAS does it!) with a nitrogen atom surrounded by a C=C and a

Re: [Rdkit-discuss] Stereochemistry question

Dear all, for sure, having a double bond surrounded by four single bonds makes the assignment of the E/Z configuration simpler. My might want also to consider nitrones https://en.wikipedia.org/wiki/Nitrone that are sometimes written (CAS does it!) with a nitrogen atom surrounded by a C=C and a

Re: [Rdkit-discuss] Stereochemistry question

Im agree with you but if you consider triphenylphosphorane such as ethoxycarbonylmethylene triphenylphosphorane you will have different equilibrium between the cis and trans form function of the organic solvent. If you increase the polarity of the solvent, the equilibrium shifts in the

Re: [Rdkit-discuss] Stereochemistry question

Le 11/03/2016 10:38, Giuseppe Marco Randazzo a écrit : An example can be the case of this isomerism is given by triphenylphosphorane (Witting reagents). Wittig reagents with their three identical phenyl groups on the phosphorus atom do not present any intriguing configuration problem around

Re: [Rdkit-discuss] Stereochemistry question

I think these are all different. The substructure in question here is R1O/P(=O)=C/R2 I think I managed to convince myself that stereochemistry here is reasonable by rewriting the structure as: R1O/[P+]([O-])=C/R2 but I would still certainly like some real examples. -greg On Fri, Mar 11, 2016

Re: [Rdkit-discuss] Stereochemistry question

I do not have the feeling that the handling of a C=P bond should be different of the one of a C=C bond. Jean-Marc Le 11/03/2016 10:12, Greg Landrum a écrit : On Fri, Mar 11, 2016 at 10:05 AM, Jean-Marc Nuzillard > wrote:

Re: [Rdkit-discuss] Stereochemistry question

On Fri, Mar 11, 2016 at 10:05 AM, Jean-Marc Nuzillard < jm.nuzill...@univ-reims.fr> wrote: > > Le 11/03/2016 05:11, Greg Landrum a écrit : > > > 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

Re: [Rdkit-discuss] Stereochemistry question

Dear all, Le 11/03/2016 05:11, Greg Landrum a écrit : 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? It has a meaning to write that

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

[Rdkit-discuss] Stereochemistry question

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