Subject: conjugation in molecular mechanics

From: Bob Funchess <[email-masked]>
Date: Tue, 5 Oct 1993 14:04:32 -0400

On Oct 4, [email-masked] (Neil S. Ostlund) wrote:

> Subject: conjugation in mol mech
> 
> The standard molecular mechanics methods (MM2, Amber, CHARMm, etc) 
> assign parameters on the basis of the "atom type" of the relevant 
> atoms involved (4 atoms,in the case of a torsion) without consideration
> of the bond type.  This results in the same torsional constants for the 
> SINGLE BOND in biphenyl at for the AROMATIC RING BONDS of Benzene!!

I can't comment about MM2 or Amber; however, the currently released version
of CHARMm does not predict that biphenyl _in vacuo_ is planar.  The actual
angle given by a short test minimization is near 37 degrees; a vapor phase
study has indicated an angle of "about 45 degrees".

It's possible that an outdated version of the forcefield did predict a planar
structure, or that the atoms were improperly typed, but the default typing
from QUANTA with the current forcefield does produce planar phenyl rings with
a 37 degree 'twist' in the single bond.

     Regards,
                Bob Funchess

-- 
Dr. Robert B. Funchess                           Molecular Simulations Inc.
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