Hi James,
I know that my opinion might sound extreme but I had this discussion
many times (mostly regarding tautomerism which is, however, similar in
some way). The problem is, you can look at a chemical structure in
many different ways - two scenarios are:
1. What can I perceive from a chemical
Hi Greg (and Markus, Peter, et al.),
Personal opinion - my vote would be to always keep the chiral information at
3-valent nitrogen centres...
As Peter pointed-out, there are bridgehead examples (most of which, I guess,
will have additional carbon chiral centres - and offer diastereomeric
consi
Hmm, well - probably not, you mention the always present exception in
chemistry, Peter (Sulfoxides have a similar situation, stereochemistry
from lone pairs). But generally I still think it is more dangerous to
keep or even perceive (from 3D) stereochemistry on three-coordinated N
- you will do mor
"My initial answer, and I would love input on this, is that
three-coordinate N should always have stereochemistry removed."
Umm... even if it's a bridgehead?
-P.
On Thu, Aug 20, 2015 at 10:30 AM, Greg Landrum
wrote:
> This isn't a simple one, so it may take a bit to get to an answer that's
> c
I agree with remove - the chance that you destroy actual information
by this is low - or in other words, the chance that steroinformation
on three-coordinate N is spurious I would expect as high.
Markus
On Thu, Aug 20, 2015 at 4:30 PM, Greg Landrum wrote:
> This isn't a simple one, so it may tak
This isn't a simple one, so it may take a bit to get to an answer that's
comprehensible.
There are two things going on here in the RDKit:
1) Ring stereochemistry
2) stereochemistry about nitrogen centers
Let's start with the second, because it's easier: RDKit does not generally
"believe in" stere
Hi Greg,
I've attached the SDF that Corina generates. I'm not convinced it is a
problem, more an observation that I'm trying to understand.
Looking at the results again today - it seems that from the Corina output
Indigo is interpreting the conformer (including whether the ethyl
substituent on th
Hehe, that is why I keep my computers always really cold when I run RDKit ...
-
| Markus Sitzmann
| markus.sitzm...@gmail.com
> On 20.08.2015, at 04:33, Peter Shenkin wrote:
>
> Maybe when you have a toolkit as blazingly fast as RDKit it captures the
> ch
Hi Rob,
The results below are quite strange. As John has already pointed out: there
really shouldn't be chirality present on either the N+ or the C that has
two methyls attached.
I tried to reproduce the problem by running corina myself using the same
command-line options you provided (from SMILE
Maybe when you have a toolkit as blazingly fast as RDKit it captures the
chirality of N center before it has time to interconvert
-P.
On Wed, Aug 19, 2015 at 10:17 PM, John M
wrote:
> More odd is the carbon stereocentre with two methyls...
>
> Generally trivalent nitrogens are not considere
More odd is the carbon stereocentre with two methyls...
Generally trivalent nitrogens are not considered chiral due to inversion of
the lone-pair. The two usual exceptions are when they are a bridgehead or
in a tight ring (cyclopropane). This is the same in most toolkits, the
InChI technical docum
Dear RDKit community,
I'm trying to use RDKit to read in Corina generated stereoisomers (from a
Mol file), assign chiral tags and stereochemistry to the structure and
output the canonical smiles string for each isomer of a given molecule (in
Python), when I do this, half the canonical smiles strin
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