Re: [AMBER] Benzene Stacking in AMBER

From: Adrian Roitberg <>
Date: Tue, 30 Nov 2010 18:12:53 +0100

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.


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
> _______________________________________________
> AMBER mailing list

                            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.
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Received on Tue Nov 30 2010 - 09:30:03 PST
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