Subject: CCL:Hydrogenation reaction path

From: "George P. Ford" <[email-masked]>
Date: Tue, 10 Oct 95 16:24 CDT

Dave Close writes:

>   I would like to use MOPAC to investigate the reaction of H2 with a
> planar molecule.  Since one is allowed just one reaction coordinate,
> I set up the problem as follows:
>  
>   XX
>   XX  2.5 -1  0.0              1
>   H   .5  1  90.0  1  0.0 0    2  1
>   H   .5  1  90.0  1  180.0  0 2  1  3
>    etc.
>  
>   The planar molecule is fastened to the first dummy atom.  My idea
> was to shorten the distances between to the two dummy atoms to study
> the reaction.  My output is very strange.  The H2 hardly moves.  Each
> cycle of the reaction shows the shortened distance I've selected, but
> the xyz coordinates show the H2 out at approximately the 2.5 A starting
> distance.

The trouble is you have too many degrees of freedom. You will notice that as the
reaction coordinate changes the distances and angles defining the hydrogen atoms
(which you have defined as variables) simply change to allow the H2 to remain in
its minimum energy position.

Mopac does allow the equivalent of two reaction coordinates via the GRID
keyword. However, unless you restrict yourself to special symmetrical situations
even that is not enough.

In the absence of symmetry this is at least a three "reaction coordinates" 
problem. There are two C-H distances and the H-H distance, all of which change
substantially along the reaction path. Any "reaction path" treatment using less
than this number must employ some kind of arbitrary relationship between them.

Do you really want to visualize the potential surface in this much detail? If
you are simply trying to locate approximate transition state geometries you
could probably make estimates that are good enough to use with one of the 
several refinement options in MOPAC (NLLSQ, EF, etc) in other ways.

Withough knowing what reaction you are studying its hard to suggest exactly
how to go this. If, for exmaple, you are adding H2 to a multiple bond you could
probably generate a good enough trial t.s. by interpolating between the 
geometries of the product and one with an intact H2 above the double bond at 
about the van der Waals distance. This could be done manually, or via the SADDLE
option. Some experimentation might be required. However, with one t.s. in hand
it could be used as a template for the remainder.

Hope this helps.

============================================================================
George P. Ford                          |      email:  [email-masked]
Department of Chemistry                 |  telephone:  (214)768-2479
Southern Methodist University           |        fax:  (214)768-4089
Dallas, Texas 75275                     |
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