Re: [Rdkit-discuss] explicit H atoms

[Ling Chan]

Hello Mark,

I thought you could depict it like the attached, since only the narrow end
of a wedged bond counts. Sure, it is confusing, but it is doable. Except
that in section ST-0.5 of the IUPAC guidelines pointed out by Greg
https://www.degruyter.com/document/doi/10.1351/pac200678101897/html
it says that "stereobonds between stereocenters should be avoided at all
costs".

Just that there are times when "stereobonds between stereocenters" are not
avoidable, if all four neighbours of a chiral carbon are themselves chiral.

I guess for practical purposes having H's could make things clearer, but in
theory you may not need them for chiral atoms.

Ling


Mark Mackey via Rdkit-discuss  於
2021年3月10日週三 上午2:33寫道：

> I believe it's not possible to represent the chirality of the attached
> molecule's ring fusion carbons without using an explicit H.
>
> Regards,
> Mark
>
> --
> Mark Mackey
> Chief Scientific Officer
> Cresset
> New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8
> 0SS, UK
> tel: +44 (0)1223 858890mobile: +44 (0)7595 099165fax: +44 (0)1223
> 853667
> email: m...@cresset-group.comweb: www.cresset-group.comskype:
> mark_cresset
>
>
>
> -Original Message-
> From: Jean-Marc Nuzillard 
> Sent: 08 March 2021 13:55
> To: RDKit Discuss 
> Subject: [Rdkit-discuss] explicit H atoms
>
> Dear all,
>
> my question of the day is more general than directly related to RDKit but
> the link is indirect.
>
> Is it always possible to represent an organic molecule in 2D with all
> necessary configuration hints (bond wedges pointing to the front or to the
> back) without introducing any explicit hydrogen atom?
>
> May be my question is very naive, all my apologies in advance for that.
>
> Best,
>
> Jean-Marc
>
> --
> Jean-Marc Nuzillard
> Directeur de Recherches au CNRS
>
> Institut de Chimie Moléculaire de Reims
> CNRS UMR 7312
> Moulin de la Housse
> CPCBAI, Bâtiment 18
> BP 1039
> 51687 REIMS Cedex 2
> France
>
> Tel : 03 26 91 82 10
> Fax : 03 26 91 31 66
> http://www.univ-reims.fr/icmr
> http://eos.univ-reims.fr/LSD/CSNteam.html
>
> http://www.univ-reims.fr/LSD/
> http://www.univ-reims.fr/LSD/JmnSoft/
>
>
>
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Re: [Rdkit-discuss] two molecules in mol object

[Jason Biggs]

Have you looked at GetMolFrags?

if you define
>m=MolFromSmiles('CCC.CC')

then

>rdmolops.GetMolFrags(m,asMols=True)

returns two molecules, keeping any coordinates or non-computed properties
in the process.

Jason Biggs



On Wed, Mar 10, 2021 at 9:42 AM Shani Zev  wrote:

> Hi all,
> I have mol object that contains two molecules, I want to delete one of the
> molecules but without going through smiles (if I will go through smiles it
> could be easy but I need to do it directly for the mol object.)
> There is a way to get to each molecule while they are in the same mol
> object?
> just for a simple example:
> [image: image.png]
> I finally want to write from mol object to coordinates file and when I
> have it together it overlapping.
> thank you very much,
> Shani
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[Rdkit-discuss] two molecules in mol object

[Shani Zev]

Hi all,
I have mol object that contains two molecules, I want to delete one of the
molecules but without going through smiles (if I will go through smiles it
could be easy but I need to do it directly for the mol object.)
There is a way to get to each molecule while they are in the same mol
object?
just for a simple example:
[image: image.png]
I finally want to write from mol object to coordinates file and when I have
it together it overlapping.
thank you very much,
Shani
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Re: [Rdkit-discuss] explicit H atoms

[Jean-Marc Nuzillard]

Dear Mark,

Many thanks for this nice example !

Best,

Jean-Marc


Le 10/03/2021 à 09:52, Mark Mackey a écrit :

I believe it's not possible to represent the chirality of the attached 
molecule's ring fusion carbons without using an explicit H.

Regards,
Mark

--
Mark Mackey
Chief Scientific Officer
Cresset
New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK
tel: +44 (0)1223 858890mobile: +44 (0)7595 099165fax: +44 (0)1223 853667
email: m...@cresset-group.comweb: www.cresset-group.comskype: 
mark_cresset



-Original Message-
From: Jean-Marc Nuzillard 
Sent: 08 March 2021 13:55
To: RDKit Discuss 
Subject: [Rdkit-discuss] explicit H atoms

Dear all,

my question of the day is more general than directly related to RDKit but the 
link is indirect.

Is it always possible to represent an organic molecule in 2D with all necessary 
configuration hints (bond wedges pointing to the front or to the back) without 
introducing any explicit hydrogen atom?

May be my question is very naive, all my apologies in advance for that.

Best,

Jean-Marc

--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/



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BioMolecular Discovery Limited for any loss or damage arising in any way from their 
receipt, opening or use. Privacy notice



--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/




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Re: [Rdkit-discuss] explicit H atoms

[Mark Mackey via Rdkit-discuss]

I believe it's not possible to represent the chirality of the attached 
molecule's ring fusion carbons without using an explicit H.

Regards,
Mark

--
Mark Mackey
Chief Scientific Officer
Cresset
New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK
tel: +44 (0)1223 858890mobile: +44 (0)7595 099165fax: +44 (0)1223 853667
email: m...@cresset-group.comweb: www.cresset-group.comskype: 
mark_cresset



-Original Message-
From: Jean-Marc Nuzillard 
Sent: 08 March 2021 13:55
To: RDKit Discuss 
Subject: [Rdkit-discuss] explicit H atoms

Dear all,

my question of the day is more general than directly related to RDKit but the 
link is indirect.

Is it always possible to represent an organic molecule in 2D with all necessary 
configuration hints (bond wedges pointing to the front or to the back) without 
introducing any explicit hydrogen atom?

May be my question is very naive, all my apologies in advance for that.

Best,

Jean-Marc

--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/



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Re: [Rdkit-discuss] explicit H atoms

[Jean-Marc Nuzillard]

Dear Greg, Jason, and Maciek,

many thanks for your feedback.
The reading of the IUPAC guidelines will certainly bring useful information.

Best,

Jean-Marc


Le 10/03/2021 à 09:28, Greg Landrum a écrit :


On Wed, Mar 10, 2021 at 9:05 AM Jean-Marc Nuzillard 
mailto:jm.nuzill...@univ-reims.fr>> wrote:



Your answer about tetragonal carbons goes in the same direction as
my initial feeling did,
but my feeling was only a feeling, just like yours.
I was wondering whether someone had some more formal view about
this question.


If you're looking for formal, I find the IUPAC guidelines really 
helpful for stuff like this:

https://www.degruyter.com/document/doi/10.1351/pac200678101897/html

Again I don't always agree with them, but they are pretty clear and 
include a bunch of examples of both good and bad representations.


-greg




--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/

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Re: [Rdkit-discuss] explicit H atoms

[Greg Landrum]

On Wed, Mar 10, 2021 at 9:05 AM Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:

>
> Your answer about tetragonal carbons goes in the same direction as my
> initial feeling did,
> but my feeling was only a feeling, just like yours.
> I was wondering whether someone had some more formal view about this
> question.
>

If you're looking for formal, I find the IUPAC guidelines really helpful
for stuff like this:
https://www.degruyter.com/document/doi/10.1351/pac200678101897/html
Again I don't always agree with them, but they are pretty clear and include
a bunch of examples of both good and bad representations.

-greg
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Re: [Rdkit-discuss] explicit H atoms

[Jean-Marc Nuzillard]

Dear Ling,

Your answer about tetragonal carbons goes in the same direction as my 
initial feeling did,

but my feeling was only a feeling, just like yours.
I was wondering whether someone had some more formal view about this 
question.


Many thanks!

Jean-Marc


Le 09/03/2021 à 20:42, Ling Chan a écrit :
This is the continuation of the previous reply, to elaborate on "the 
stripped structure can always be represented using wedged bonds".


One potential problem is that a bond is required to be wedged from 
both ends. But this should not happen. For an atom to be chiral, it 
needs to be attached to at least 3 other atoms. If it is attached to 3 
atoms, its chirality can be specified by using a wedge on any one of 
the three bonds. Hence there should always be enough possibilities to 
avoid the potential problem.


I could be wrong. I can't proof it. But this is what it feels like to 
me, especially if no atom is bonded to more than 4 other atoms.



Ling Chan mailto:lingtrek...@gmail.com>> 於 
2021年3月9日週二 上午11:32寫道：


Hello Jean-Marc,

This is a very interesting question.

Given any molecule, consider its structure stripped of all H's.
There is no reason why this stripped structure cannot be
represented using wedged bonds etc. (Will continue on the next
reply.) Hence potential problems can only arise when the added Hs
themselves introduce new chirality / stereochemistry, or that the
position of the added H itself is not uniquely defined by the
stripped structure.

One example I can think of is the secondary amine, if you only
consider one state  (say if the temperature is so low that it is
locked in that geometry). But if there is a rule saying that "the
implicit hydrogen is understood to lie in the plane of the paper",
then everything will still be fine. Just that the drawings may
look a bit strange, as attached.

But for stereo bonds, perhaps there is no escape. You will need to
draw the explicit hydrogen. See attached.

But then how about the orientation of hydroxyl groups in general?
They are usually neglected in chemical representations, aren't they??

Ling




Jean-Marc Nuzillard mailto:jm.nuzill...@univ-reims.fr>> 於 2021年3月9日週二
上午1:04寫道：

Sure, testosterone may be drawn as



Jean-Marc


Le 08/03/2021 à 18:26, Rocco Moretti a écrit :

On Mon, Mar 8, 2021 at 11:17 AM Paul Emsley
mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:

On 08/03/2021 13:55, Jean-Marc Nuzillard wrote:
>
> Is it always possible to represent an organic molecule
in 2D with all necessary
> configuration hints (bond wedges pointing to the front
or to the back)
> without introducing any explicit hydrogen atom?

No. Testosterone.


Is that "not possible" or simply "against convention"? One
could certainly imagine someone attempting to put the dashed
and wedged designations on the ring bonds, and leaving the
hydrogens implicit. (Flagrantly ignoring how much it would
mess with steroid chemists' brains.)


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Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr  
http://eos.univ-reims.fr/LSD/CSNteam.html  


http://www.univ-reims.fr/LSD/  
http://www.univ-reims.fr/LSD/JmnSoft/  


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--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/

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