Also check the even more recent: J. Chem. Theory. Comput. vol 2 (2006) 947
They give a nice introduction on the discussion between T-Stacked and Parallel Displaced benzene-benzene structures.
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.
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 ;)
Ciao, Pim
On 7/27/06, [EMAIL PROTECTED] <
[EMAIL PROTECTED]> wrote:
Date: Thu, 27 Jul 2006 09:25:33 +0200
From: "Gerrit Groenhof (RUG)" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] does gromos force field can explain pi-pi
interaction
The most recent paper I read on this is by Piacenza and Grimme (J. AM.
CHEM. SOC. 2005, 127, 14841-14848 ).
They use a very efficient DFT based approach with an empirical
correction to compute accurate stacking energies. At least so they say.
Unfortunately their method DFT-D is not yet available in any of the
quantum chemistry programs that can be linked to gromacs.....
Gerrit
Diane Fournier wrote:
>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-----
>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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