[CHM Research] The Struggles with Tinker

[Andrew Pounds]

So, as you are learning, you have to know something about chemistry to 
really use the programs effectively.  Tinker, for example, is really 
meant to be run on organic (biological) molecules that are arlready 
pretty close to their minimum configuration.  For that reason you 
sometimes have to "finesse" it to make it do what you want.

Here is something for you to try --

1. Open molden, and then the Z-matrix editor.  Click immediately on 
replace by fragment and select the methyl fragment

2.  This should put a Cabon atom in the center of the screen with three 
hydrogens attached

3. Optimize this with Tinker.  You should get a trigonal planar structure

4. Put a phenyl groups on two of the hydrogens.  If two of the hydrogens 
are very close it will cause Tinker to fail, so locate a carbon on one 
of the rings that has a Z-matrix dihedral angle that is related to the 
first carbon on the other ring.  Change the value of this coordinate 
from 180 degrees to 60 degrees.  Then optimize with tinker

5. Add a third phenyl ring by replacing the hydrogen that it attached to 
the central carbon.  You will most likely also have to also change the 
dihedral on this one so that the hydrogens on adjacent rings are not too 
close.  Do this and reoptimize.

At this point you should have three phenyl rings attached to a central 
carbon atom and then rings are each slightly tilted to minimize steric 
hindrance.

6.  Try replacing the central carbon with a nitrogen (just chage the 
appropriate C to an N in the Z-matrix editor).  Try top optimize this -- 
it should fail for several reasons.


Let me know if it fails for you.

-- 
Andrew J. Pounds, Ph.D.  (pounds at theochem.mercer.edu)
Professor of Chemistry and Computer Science
Mercer University,  Macon, GA 31207   (478) 301-5627