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
Vojtech >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
<<winmail.dat>>
_______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
