Re: [Jmol-users] R: Jmol 14.15.2 -- chirality work complete: exception?

[Robert Hanson]

ps -- if you issue for that second sample:

MINIMIZE

(maybe twice? Don't know; I did that.) Then it works:

print {chirality != ""}.label("%a%[chirality]").join(",").replace("C","")

1Z,2Z,3E,4E,5Z,6Z,7Z,8Z,9Z,10Z

(carbon numbering, not naming)






On Fri, May 5, 2017 at 3:57 PM, Robert Hanson  wrote:

> Pino,
>
> The first structure shows no designations because designations are
> specifically removed for all ring sizes less than 8, and you have
> 7-membered rings there.
>
> In the second case, you have highly twisted double bonds, so the cis/trans
> determination cannot be made. They have to be planar.
> ​
>



-- 
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] R: Jmol 14.15.2 -- chirality work complete: exception?

[Robert Hanson]

Pino,

The first structure shows no designations because designations are
specifically removed for all ring sizes less than 8, and you have
7-membered rings there.

In the second case, you have highly twisted double bonds, so the cis/trans
determination cannot be made. They have to be planar.
​
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[Jmol-users] R: Jmol 14.15.2 -- chirality work complete: exception?

[pinostricc...@alice.it]

Hi Bob, can you check this new page I did on E/Z stereochemistry ? Annulene 
seems not working well. 
 The first structure doesn't show stereochemistry, while the second doesn show 
the double with E
http://pinostriccoli.altervista.org/?p=8967
Pino


Messaggio originale

Da: hans...@stolaf.edu

Data: 29-apr-2017 22.30

A: "jmol-users@lists.sourceforge.net"

Ogg: [Jmol-users] Jmol 14.15.2 -- chirality work complete



Jmol 14.15.2 https://sourceforge.net/projects/jmol/files

fully implements all IUPAC 2013 Blue Book 
(http://pubs.rsc.org/en/content/ebook/9780854041824) involved in:

   -- simple R/S and E/Z, with small-ring removal of E/Z
   -- odd and even cumulenes (E/Z, M/P)
   -- atropisomers (M/P)
   -- pseudochiral r/s and m/p
   -- P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
   -- imine and diazine E/Z chirality
(In case "M/P" is new to you,  M(inus) and P(lus) are the preferred 
designations now for axial and planar chirality rather than Ra and Sa, 
respectively. I like this a lot, because it is simply the sign of the 
associated torsion angle.)

Jmol does not implement hypervalent chirality (trigonal bipyramidal, octahedral)

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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