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)
<https://sourceforge.net/projects/jmol/files/latest/download?source=files>
On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> 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
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> 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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