Re: [Rdkit-discuss] stereochemistry of S with degree 3

Interesting discussion, never decided myself whether it was worth handling two implied neighbors: C[S@H](=O) Probably v. low barrier to inversion for this example but thought I'd share. John -- Site24x7 APM Insight:

Re: [Rdkit-discuss] stereochemistry of S with degree 3

On Feb 10, 2016, at 6:09 AM, Greg Landrum wrote: > I agree that this is a bug. Glad to hear. I was wondering how I would get my code to handle that case otherwise. On Feb 10, 2016, at 4:19 PM, David Cosgrove wrote: > As chiralities go, this one has turned out to be quite valuable! You can

Re: [Rdkit-discuss] stereochemistry of S with degree 3

Not sure that the anything[S@H](=O) molecules exist... Jean-Marc Le 11/02/2016 11:04, John M a écrit : Interesting discussion, never decided myself whether it was worth handling two implied neighbors: C[S@H](=O) Probably v. low barrier to inversion for this example but thought I'd

Re: [Rdkit-discuss] stereochemistry of S with degree 3

Hi Andrew, As chiralities go, this one has turned out to be quite valuable! https://en.wikipedia.org/wiki/Esomeprazole Dave On Mon, Feb 8, 2016 at 3:05 PM, Andrew Dalke wrote: > Hi! > > Could someone explain to this non-chemist what the chirality means in > the

Re: [Rdkit-discuss] stereochemistry of S with degree 3

I agree that this is a bug. Here's a simpler reproducible: In [11]: Chem.CanonSmiles("C[S@](Cl)=O") Out[11]: 'C[S@@](=O)Cl' In [12]: Chem.CanonSmiles("C[S@]2=O.Cl2") Out[12]: 'C[S@](=O)Cl' Note that it seems to have something to do with the special handling of the S=O, because this looks fine:

Re: [Rdkit-discuss] stereochemistry of S with degree 3

The other thing to remember is that at room temperature and pressure, small sulphoxides will be able to interconvert forms from R to S rapidly. It's only when the groups on the sulphur get big enoough (or interconnected, like in a 3 or 4 member ring) that they actually can be resolved and

Re: [Rdkit-discuss] stereochemistry of S with degree 3

On Feb 8, 2016, at 7:03 PM, Paolo Tosco wrote: > ... there is a "ghost" atom involved in determining the sulfur chirality, > which is the sulfur lone pair. Even if this is not in the Daylight specs, the > lone-pair is usually treated as an implicit hydrogen, and therefore > considered as the

Re: [Rdkit-discuss] stereochemistry of S with degree 3

Dear Andrew, that functional group is a sulfoxide, and it is indeed chiral because has a lone pair on the sulfur, which is pyramidal; there is a short description here: https://en.wikipedia.org/wiki/Sulfoxide So it is the same (R,S) chirality you would have on a tetrahedral carbon. The carbon

Re: [Rdkit-discuss] stereochemistry of S with degree 3

Thanks Paolo and Hannes for pointing me to sulfoxide. I am enlightened! I assume this is something that every chemist knows, but it's not mentioned in the Daylight SMILES documentation (or the OpenSMILES documentation), so I had no clue. I wonder how many more cases there are like that. Any

Re: [Rdkit-discuss] stereochemistry of S with degree 3

On Mon, 8 Feb 2016 16:05:46 +0100 Andrew Dalke wrote: > Hi! > > Could someone explain to this non-chemist what the chirality means > in the following? > > CN[S@@](=O)C1=CC=CC=C1 > > It comes from PubChem id 12194260 at >

[Rdkit-discuss] stereochemistry of S with degree 3

Hi! Could someone explain to this non-chemist what the chirality means in the following? CN[S@@](=O)C1=CC=CC=C1 It comes from PubChem id 12194260 at https://pubchem.ncbi.nlm.nih.gov/compound/12194260 . Isn't this a symmetric structure, which can't have an orientation at that point? Even

Re: [Rdkit-discuss] stereochemistry of S with degree 3

De : Andrew Dalke <da...@dalkescientific.com> Envoyé : lundi 8 février 2016 16:05 À : rdkit-discuss@lists.sourceforge.net Discuss Objet : [Rdkit-discuss] stereochemistry of S with degree 3 Hi! Could someone explain to this non-chemist what the chirality

Re: [Rdkit-discuss] stereochemistry of S with degree 3

Sorry for the noise, this is the same message as before, just with less typos and repetitions. I couldn't help re-sending it after reading what I had written! Dear Andrew, the reason why Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1") returns 'CN[S@@](=O)c1c1' and

Re: [Rdkit-discuss] stereochemistry of S with degree 3

Dear Andrew, the reason why Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1") returns 'CN[S@@](=O)c1c1' and Chem.CanonSmiles("CN1.[S@@]1(=O)C1=CC=CC=C1") returns 'CN[S@](=O)c1c1' is that there is a "ghost" atom involved in determining the sulfur chirality, which is a lone pair, which is the