Otis,

I think you are right about my reloading coinciding with you updating your server.  Today I'm not needing to reload the page.  Ethyl still not flat.  2-propyl is now flat.  Cyclopentyl and cyclohexyl are not flat, even after depicting into JME then reloading into Jmol.


Jeff


***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhansen@depauw.edu
***********************************************


On Apr 27, 2010, at 1:32 AM, Otis Rothenberger wrote:

Jeff,

Your notes were a big help - thanks. By coincidence, I think your page reloading coincided with changes that I was making on the server!

I think the problem involved a Java vs JavaScript string issue that Firefox on Mac ignored but Safari did not. I think I have that fixed. On the other points:

1) C+ - I caused this problem by the way I handle single atom loads from JME. I can fix this.
2) CC+ - I see the same thing. I think this is also fixable.
3) Charges - Unfortunately, the charges are not passed back to JME. This is caused by the fact that I'm passing the extracted molfiles back (not the JME files). The molfiles do not have the charge information.

There are some cases where UFF does not produce a flat BX3. In the cases where it does, I think we are getting a flat "carbocation."

Thanks for the help.

Otis


On 4/26/2010 11:54 PM, Jeff Hansen wrote:
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
*********************************************
-- 
Otis Rothenberger
chemagic.com
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