Re: [Jmol-users] Jmol 14.14.1 chirality

[Robert Hanson]

argh.  Broke chirality for ketones!

On Fri, Apr 21, 2017 at 11:27 AM, Robert Hanson  wrote:

>
>
> On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall <
> bruce.tattersh...@newcastle.ac.uk> wrote:
>
>> Dear Bob
>>
>>
>>
>> The chirality calculation is clearly useful.
>>
>>
>>
>> I have tried it on my chiral phosphorus compounds, e.g. as in
>>
>> https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
>>
>> and it finds the chiral carbons in the organic ligands and successfully
>> labels them (as R in this case),
>>
>> but it does not find the chirality of the phosphorus atoms to which they
>> are attached.
>>
>>
> It's a work in progress.
>
> Limitations:
>
>  no parallel chirality paths
>  not processing inositols correctly
>  no lone-pair business
>  standard E/Z, R/S, r/s only; no allenes, no planar asymmetry
>
>
>
>>
>> I have no idea of how this works, but would it be possible to extend it
>> easily to phosphorus chirality (for which
>>
>> one uses the same rules but counts the lone pair as lowest priority)?
>>
>>
> Lone pairs wouldn't be too difficult to add, particularly if they are
> limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to
> add imine stereochemistry as well.
>
>
>
>>
>>
>> When I first got into measuring NMR spectra of diastereomers of such
>> compounds about 15 years ago,
>>
>> I found it very hard to get my inorganic chemist’s head around the
>> chirality implications.  It would
>>
>> have been very useful to have a tool to work it out for me.
>>
>>
>>
>> If you are going to elements other than carbon, then I guess that besides
>> phosphorus, the inorganic
>>
>> chemist’s favourite, the chirality at silicon, germanium and arsenic
>> could also be useful to people.
>>
>
> Silicon and ammonium are just like carbon, I think. As and P no problem.
>
> Definitely not going to higher valencies any time soon.
>
> Higher priorities are allenes and getting the darned inositol business
> working  correctly. But maybe P and S and As are so easy I should just do
> them
>
> Bob
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Jmol 14.14.1 chirality

[Robert Hanson]

On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall <
bruce.tattersh...@newcastle.ac.uk> wrote:

> Dear Bob
>
>
>
> The chirality calculation is clearly useful.
>
>
>
> I have tried it on my chiral phosphorus compounds, e.g. as in
>
> https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
>
> and it finds the chiral carbons in the organic ligands and successfully
> labels them (as R in this case),
>
> but it does not find the chirality of the phosphorus atoms to which they
> are attached.
>
>
It's a work in progress.

Limitations:

 no parallel chirality paths
 not processing inositols correctly
 no lone-pair business
 standard E/Z, R/S, r/s only; no allenes, no planar asymmetry



>
> I have no idea of how this works, but would it be possible to extend it
> easily to phosphorus chirality (for which
>
> one uses the same rules but counts the lone pair as lowest priority)?
>
>
Lone pairs wouldn't be too difficult to add, particularly if they are
limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to
add imine stereochemistry as well.



>
>
> When I first got into measuring NMR spectra of diastereomers of such
> compounds about 15 years ago,
>
> I found it very hard to get my inorganic chemist’s head around the
> chirality implications.  It would
>
> have been very useful to have a tool to work it out for me.
>
>
>
> If you are going to elements other than carbon, then I guess that besides
> phosphorus, the inorganic
>
> chemist’s favourite, the chirality at silicon, germanium and arsenic could
> also be useful to people.
>

Silicon and ammonium are just like carbon, I think. As and P no problem.

Definitely not going to higher valencies any time soon.

Higher priorities are allenes and getting the darned inositol business
working  correctly. But maybe P and S and As are so easy I should just do
them

Bob
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Re: [Jmol-users] Jmol 14.14.1 chirality

[Bruce Tattershall]

Dear Bob

The chirality calculation is clearly useful.

I have tried it on my chiral phosphorus compounds, e.g. as in
https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
and it finds the chiral carbons in the organic ligands and successfully labels 
them (as R in this case),
but it does not find the chirality of the phosphorus atoms to which they are 
attached.

I have no idea of how this works, but would it be possible to extend it easily 
to phosphorus chirality (for which
one uses the same rules but counts the lone pair as lowest priority)?

When I first got into measuring NMR spectra of diastereomers of such compounds 
about 15 years ago,
I found it very hard to get my inorganic chemist’s head around the chirality 
implications.  It would
have been very useful to have a tool to work it out for me.

If you are going to elements other than carbon, then I guess that besides 
phosphorus, the inorganic
chemist’s favourite, the chirality at silicon, germanium and arsenic could also 
be useful to people.

Best wishes

   Bruce

Bruce Tattershall
School of Chemistry
Newcastle University
England

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 20 April 2017 16:47
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.14.1

OK - this is better:  Looking for the latest version? Download 
Jmol-14.14.1-binary.zip (69.7 MB) 


On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson 
> wrote:
hmm. something is missing there. I had to delete that and will upload again.

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson 
> wrote:
Jmol.___JmolVersion="14.14.1" // released 4/19/17

new feature: CALCULATE CHIRALITY {atom set}
  -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
  -- continues with Rules 3-5, which require full-molecule analysis.
  -- work in progress:
 -- Rules 1 and 2 complete
 -- Rule 3 (E/Z) implemented
 -- Rule 4 partially implemented
-- simple linear sequences of R/S ok
 -- Rule 5 not implemented
  -- caveates
 -- no pseudochirality
 -- not cyclitols
 -- does not distinguish rings, so inserts "Z" into ring bonds
 -- only validated on

  -- optionally limited to the given atom set (or the currently selected atoms 
by default)


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