On 23 Feb 2011, at 01:33, Robert Hanson wrote: > Well, at least I think so.... > > http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flot-energy.htm?model=data/cyclohexaneFlip.jmol > > Please let me know if that does not work for you.
Bob, The issue of whether the path passes through a boat transition state or not is an interesting one. The pathway you show is chiral at all points except the first and the last (D3d symmetry there, with planes of symmetry). In particular, point 18, the twist boat and the half way point, is itself chiral (C2 symmetry). The half chair transition states (10 and 25) are also chiral, but 10 is the enantiomer of 25. The alternative, shown in many texts, is of a mirror-symmetric potential, involving an achiral boat transition state (C2v) at the mid point, with the left of the potential a mirror image of the right. Thus we have chair-chair interconversion happening via either a pathway which has a mirror symmetric geometry at its mid point, or via a pathway which is chiral at every point except the start and end. This latter type of potential has been described by Patrick Fowler as "chiral connectedness" (although it does not quite match). See Symmetry: Culture and Science, Vol. 16, No 4, 321-334, 2005. An animation which purports to be derived from a molecular dynamics simulation can be seen at http://www.youtube.com/user/DokeDJ#p/u/4/bPLREpfZ63I and it does seem to support the intermediacy of a boat transition state at the "mid point" rather than passing directly from a twist boat to the half chair on one side of the potential. What I am trying to find here is whether the species either side of the mid point should be symmetric at each point of the potential or not. http://www.youtube.com/user/DokeDJ#p/u/4/bPLREpfZ63I seems to show this, but > http://chemapps.stolaf.edu/jmol/docs/examples-12/jmol-flot-energy.htm?model=data/cyclohexaneFlip.jmol does not. 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! ------------------------------------------------------------------------------ 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
