Henry, so you are saying you think something is wrong with that pathway. From what I can see, there are two possible pathways from the chair -- one with a twist to the "left"; one with a twist to the "right."  The enatiomeric twist is not depicted. (Although I think you could invert the configuration of all models and see it!) So from the get-go, symmetry is broken. Nothing wrong with that.... The entire sequence is chiral!

Bob

On Wed, Feb 23, 2011 at 1:29 PM, Rzepa, Henry <h.rzepa@imperial.ac.uk> wrote:
>Hens! Good to hear from you. I hope you don't mind my co-opting your model -- reminds me that I need to put a link to WeTChe there.
>
>I'd love a little discusson of this, because I'd like to get this out there. My understanding is that both are "correct" -- the boat transition state is lower than the twist chair (though I don't see exactly why)


Because the angles are opened up beyond  109 in the half chair

>, and so statistically the molecule will find itself more often in a boat than a twist chair anyway, I think the "synthetic organic chemist"  should realize that what is
>shown is not a potential surface, but one degree of freedom singled out.


Surely a molecular dynamics trajectory is more accurate, since a degree of freedom can only be harmonic and you cannot have harmonic modes connecting the entire surface? The MD trajectory seems to show a boat transition state being involved at the half way point, not a twist boat minimum?

My concern is that a single degree of freedom singled out does not marry with group theory!


--

+44 (020) 7594 5774 (Voice); Blog: http://www.ch.ic.ac.uk/rzepa/blog/
 Dept. Chemistry, Imperial College London, SW7  2AZ, UK.

(Voracious anti-spam filter in operation for received email.
If expected reply not received, please phone/fax).


------------------------------------------------------------------------------
Free Software Download: Index, Search & Analyze Logs and other IT data in
Real-Time with Splunk. Collect, index and harness all the fast moving IT data
generated by your applications, servers and devices whether physical, virtual
or in the cloud. Deliver compliance at lower cost and gain new business
insights. http://p.sf.net/sfu/splunk-dev2dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users



--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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