I have read a lot on this subject since I wanted to prove one such interaction myself (between inhibitor and enzyme).
Generally, authors who talk of such interaction never give proof using
simulation, but use a simple geometric criteria (benzene rings are superposed
in T-shape or face-to-face staggered configuration at a given distance) to
describe them in crystal structures.
For modeling, there are a few papers (beginning 1990s, not quite recent) which
used a point charge model to model pi-pi stacking (Hunter-Saunders model). In
this model, charges are distributed onto the hydrogens and in the middle of the
benzene ring (with a dummy atom) and their results (geometry optimization)
showed some similarity to experimental results seen in crystals. I can give you
the references if you like.
However, pi-pi interactions have some polarization component, and so they have
been best modeled with quantum mechanics; this would involve doing a QMMM
simulation. I have not seen yet a paper talking about QMMM simulation of pi-pi
stacking (if somebody has seen one please give me the reference)
I have also heard of polarizable force fields, but I don't know if they can
model pi-stacking properly.
If somebody has heard of a proven method of modeling pi-stacking, energy- and
geometry-wise, I would also be very interested in it.
Diane
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Wei Fu
Sent: Wed 7/26/2006 11:44 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] does gromos force field can explain pi-pi interaction
Dear gmx users,
My simulation shows that the aromatic ring of ligand forms stacking
pi-pi interaction with the side chain of Phe of receptor during MD
simulation.
One reviewer of my manuscript questions that such pi-pi interaction can
not accurately accounted for by the employed force field.
I do not know how to answer this question, any idea is highly appreciated!
Linda
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