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

Spiwok Vojtech Vojtech.Spiwok at vscht.cz
Thu Jul 27 10:39:43 CEST 2006

Dear Diane

You might check this:
Unexpectedly Strong Energy Stabilization Inside the Hydrophobic
Core of Small Protein Rubredoxin Mediated by Aromatic Residues:
Correlated Ab Initio Quantum Chemical Calculations
J Vondrasek, L Bendova, V Klusak, P Hobza
J. Am. Chem. Soc.; 2005; 127(8) pp 2615 - 2619;
DOI: 10.1021/ja044607h


>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.

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