[gmx-users] does gromos force field can explain pi-pi interaction

[Gerrit Groenhof (RUG)]

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-----
>From: gmx-users-bounces at gromacs.org on behalf of Wei Fu
>Sent: Wed 7/26/2006 11:44 AM
>To: gmx-users at 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
>
>
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>  
>
>------------------------------------------------------------------------
>
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>