Subject: Hyperchem and intermediates

From: Milan Shah <[email-masked]>
Date: Thu, 27 Apr 1995 12:01:05 -0500 (CDT)

Is it possible to model an intermediate for an organic 
reaction through the use of Hyperchem?  Send any observations or
commentary to Milan C. Shah at ( [email-masked] ).  A
summary will be provided.  Thanks beforehand.

---

From: [email-masked] (Joel Polowin)
Date: Thu, 27 Apr 95 15:37:25 -0400

> Date: Thu, 27 Apr 1995 12:01:05 -0500 (CDT)
> From: Milan Shah <[email-masked]>
> Subject: CCL:Hyperchem and intermediates
> 

There are a couple of ways of doing such things.  For example, it is
possible to run semi-empirical molecular dynamics calculations on two
organic units such that they collide and react, giving products that
separate from the site of reaction.  By using the 'snapshot' option,
the coordinates of the atoms are saved periodically during the simulation;
then one can retrieve the configuration of the system at any point,
including the period when the system is rearranging.  The system could
also be set up with a reasonable set of internal vibrations and rotations
at the beginning of the simulation to give an appropriately complex model.

One can also do semi-empirical minimization of the static system, with
bond distances constrained to values that indicate the partial bonds
of an intermediate.  This sort of everything-minimized-but-partial-bonds
model may or may not be a realistic description of a real chemical
species; *I* tend to think not, since I favour a dynamic picture, but
that's merely my personal opinion.

Regards,
Joel
 
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