I've tried several variations now and can report the following: t-butyl gives a flat structure. Using depict model creates a structure in JME with a boron. Loading that structure creates a flat boron structure. 2-propyl cation does not result in a flat model. Depicting that model in JME makes the boron structure. Loading that structures results in still not flat. ethyl behaves same as 2-propyl. methyl is very interesting. It is not flat. Depicting the model in JME doesn't give a structure containing boron. Loading in back into Jmol it still isn't flat.
Just to further explore I made a cylopentyl cation in JME and loaded it into Jmol. Behaved like 2-propyl. When I made 1-methyl-1-cyclopentyl cation and tried to load it into Jmol it displayed nothing. Depicting that back into JME showed methylcyclopentane with no charge. This was weird so I reloaded the page and started over. Now the methylcyclopentyl cation loaded into JMol fine but flat. Depicted in JME fine (with boron). Loaded back to Jmol now flat. A few more experiments and I determined that if I just cleared the JME and built a new molecule it was a problem. Either it didn't display or the molecule wasn't ever flat. If I reload the web page and build the molecule then loaded into JMol etc. It seemed to behave better. 2-propyl cation still wasn't flat, but now after depicting back to JME where it changes to boron then reloading into Jmol, it now becomes flat. No matter what, though ethyl and methyl always behaved as described above. I also tried benzyl (after reloading the page) and the cation was definitely not flat and the hydrogens were rotated almost perpendicular to the plane of the ring. After depicting into JME (changed to boron) then reloading into JMol, it flattened out nicely. *********************************************** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *********************************************** On Apr 26, 2010, at 9:24 PM, Philip Bays wrote: > I see the flat structure with the t-butyl cation. > > > On Apr 25, 2010, at 10:06 PM, Otis Rothenberger wrote: > >> This is a request for a Mac user test of a page. I'm trying to create >> the appearance of a JME to Jmol loading of a planar carbocation. >> Admittedly, this is a work around, but it's a work around of UFF not >> Jmol. The following works on Windows (MSIE, Firefox, and Chrome), but >> apparently there are Mac issues: >> >> On http://www.che.ilstu.edu/osrothen/web_molecules/script_page_large.aspx >> >> 1) Click Display Molecular Editor. >> 2) On the subsequent control screen click Draw. >> 3) Draw a simple carbocation - e.g. 2-propyl cation. >> 4) Click Load Model. >> >> On Windows, I consistently see a planar carbocation. On Mac, I have a >> problem report. >> >> Again, I admit that this is all smoke and mirrors, but on Windows it >> accomplishes our objective - A "carbocation" model JME --> Jmol with a >> planar geometry: >> >> jmolScript("load INLINE '" + >> document.getElementById(jme1).jmeFile().replace("C+", "B+") + "';color >> {boron and formalCharge = 1} '#909090';hover off;{boron and formalCharge >> = 1}.element='C';calculate hydrogens;{carbon and formalCharge = >> 1}.element='B';color {boron and formalCharge = 1} '#909090';", "01") >> >> The above is followed by a minimize. Are any Mac users seeing the planar >> result? >> >> Otis >> >> -- >> Otis Rothenberger >> chemagic.com >> >> >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > J. Philip Bays > Professor of Chemistry > Department of Chemistry and Physics > Saint Mary's College > Notre Dame, IN 46556 > (574) 284-4663 > pb...@saintmarys.edu > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users
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