<br>
Also check the even more recent: J. Chem. Theory. Comput. vol 2 (2006) 947<br>
<br>
They give a nice introduction on the discussion between T-Stacked and Parallel Displaced benzene-benzene structures.<br>
It appears that the actual conformation of liquid benzene (crystalline
benzene can be a whole different story altogether), is a still ongoing
point of discussion (from ab-initio, experimental, and MD point of
view) and therefore there can currently be no conclusively correct
forcefield that would describe benzene-benzene orientations.<br>
The referee makes a fair point of course, but it would be rather
far-fetched if you would have to first parametrize such a
real-ultimate-power benzene forcefield before you could publish your
study ;)<br>
<br>
Ciao, Pim<br><br><div><span class="gmail_quote">On 7/27/06, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>Date: Thu, 27 Jul 2006 09:25:33 +0200
<br>From: "Gerrit Groenhof (RUG)" <<a href="mailto:g.groenhof@rug.nl">g.groenhof@rug.nl</a>><br>Subject: Re: [gmx-users] does gromos force field can explain pi-pi<br> interaction<br><br>The most recent paper I read on this is by Piacenza and Grimme (J. AM.
<br>CHEM. SOC. 2005, 127, 14841-14848 ).<br>They use a very efficient DFT based approach with an empirical<br>correction to compute accurate stacking energies. At least so they say.<br>Unfortunately their method DFT-D is not yet available in any of the
<br>quantum chemistry programs that can be linked to gromacs.....<br><br>Gerrit<br><br>Diane Fournier wrote:<br><br>>I have read a lot on this subject since I wanted to prove one such interaction myself (between inhibitor and enzyme).
<br>><br>>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.<br>><br>>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.<br>><br>>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)<br>><br>>I have also heard of polarizable force fields, but I don't know if they can model pi-stacking properly.<br>><br>>If
somebody has heard of a proven method of modeling pi-stacking, energy-
and geometry-wise, I would also be very interested in it.<br>><br>>Diane<br>><br>>-----Original Message-----<br>>Subject: [gmx-users] does gromos force field can explain pi-pi interaction<br>><br>>Dear gmx users,
<br>><br>> My simulation shows that the aromatic ring of ligand forms stacking<br>>pi-pi interaction with the side chain of Phe of receptor during MD<br>>simulation.<br>>One reviewer of my manuscript questions that such pi-pi interaction can
<br>>not accurately accounted for by the employed force field.<br>><br>>I do not know how to answer this question, any idea is highly appreciated!<br>><br>>Linda</blockquote></div><br>