Dear Eliac,
This is just my personal opinion on this.
First, the ONLY possible definition of stacking energy I can imagine is
what one would call dimerization energy. Basically, it is the energy of
the dimer, minus the energy of a single benzene alone (this last one
multiplied by two of course). This could be done in solution or
in-vacuo, etc
I am not sure what the values really are, but there is not 'stacking'
energy per se anywhere in the force field.
Another point of importance. It is a common misunderstanding to think of
a benzene dimer as 'stacked'. In fact, in vacuum, the most stable
conformation is a T-shape, not the stacked one. The second most stable
is a displaced stacked conformation, and what one usually calls 'staked'
comes in third place. The T-shaped conformation is around 2 kcal/mol
stable at most.
See recent paper by David Sherill on this issue. It requires some very
heavy QM calculation to get it right.
Adrian
On 11/30/10 6:04 PM, Eliac Brown wrote:
> Dear All
> I was wondering if you could direct me to how the stacking energy of the benzene rings implemented in AMBER? all what I need is a start point.
> Thanks
> Eliac
>
>
>
>
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--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
Senior Editor. Journal of Physical Chemistry.
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Tue Nov 30 2010 - 09:30:03 PST
