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), and so statistically the molecule will find itself more often in a boat than a twist chair anyway, whether you consider the boat a "dead end" or not; what you miss in the standard 2D representation is that the system does not HAVE to go through the boat, and can instead smoothly transition between the two chairs without it. One of the interesting things I've found is that this particular pathway is fun to demonstrate. See this lousy-resolution YouTube video, for instance: http://www.youtube.com/watch?v=38YKPG1r30Q If you do this, you can actually FEEL in your hands the model going over the twist-chair transition state, because all you are doing is pressing with the palm sides of your thumbs, and as soon as the transition state is passed, the model stops pushing back, and just sort of slides into place. In terms of Jmol, what is interesting here is that we can use the COMPARE command to align frames that otherwise would be difficult to align. Hens, did you ever think about aligning the frames this way? Bob On Wed, Feb 23, 2011 at 7:06 AM, Hens Borkent <[email protected]> wrote: > > > Op 23-2-2011 10:12, Rzepa Henry schreef: > > > > > > I appreciate a debate on this topic may or may not be suited for the > > Jmol list, but if anyone wants to add their opinion, I would welcome > > this, if only because my "synthetic organic chemistry" colleagues > > need to know what the "most realistic" description of this iconic > > potential surface is! > > > I think the "synthetic organic chemist" should realize that what is > shown is not a potential surface, but one degree of freedom singled out. > To put it crudely: the molecule is wobbling all the time, hopping from > one possible path to the other, distorting any symmetry all the time. > More realistic, although not so appealing maybe as the animations shown. > My original was based on a series MOPAC IRC calculations starting from > selected transition state maxima. > Hens > > > > ------------------------------------------------------------------------------ > 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 > [email protected] > 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
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