[gmx-users] does gromos force field can explain pi-pi interaction
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Thu Jul 27 11:47:08 CEST 2006
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 ;)
On 7/27/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
> Date: Thu, 27 Jul 2006 09:25:33 +0200
> From: "Gerrit Groenhof (RUG)" <g.groenhof at rug.nl>
> Subject: Re: [gmx-users] does gromos force field can explain pi-pi
> 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.....
> 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.
> >-----Original Message-----
> >Subject: [gmx-users] does gromos force field can explain pi-pi
> >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
> >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
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