AMBER Archive (2002)

Subject: Re: C60 parameter

From: Pascal Bonnet (pascal.bonnet_at_man.ac.uk)
Date: Thu Nov 28 2002 - 06:12:19 CST

Hi Vanna,

During my Ph.D. I studied a complex formed by a gamma-cyclodextrin dimer
and a fullerene (C60) using AMBER force field. (P. Bonnet et al.
Supramolecular Chemistry, 2002, in press).

We started with a major problem: as C60 has an Ih symmetry, all the
carbon atoms are identicals, so their atomic charges are 0 and the
electrostatic interactions can not be calculated.

For the simulation we used CA as atom types for all the carbon atoms.
The diameter of the fullerene was 7.03 A during the simulation and was
well comparable to the experimental value (7.09 A).
To introduce the effect of the electrostatic interaction, we have
introduced dummy atoms having atomic charges and no vdW parameters (it
was a real nightmare with the use of the modules of Amber5 like prep and
link).

C60 have 12 pentagons and 20 hexagons, so two different bond lenghts.
One similar to a sp3-sp3 bond lenght (1.432 A obtained by RX) and the
other one near a sp2-sp2 bond lenght (1.389 A). So in our methodology,
we have introduced dummy atoms in the center of these bonds (we obtained
90 dummy atoms). We have calculated the atomic charges with Gaussian
(optimization at HF/STO-3G followed by HF/6-31G* to obtained the ESP)
and obtained two different values: positive on the center of the sp3-sp3
bonds (0.03) and negative on the sp2-sp2 bonds (-0.06).
There are different ways to introduce dummy atoms: on the center of each
ring, above and below each bond, on the center of the bond, etc.

But I think it is important to introduce polarizability, and the
semi-empirical methods are more appropriate (when the number of atoms is
not a problem).

Please, send me an email if you want more informations.

Pascal

 

vannajan_at_chiangmai.ac.th wrote:
>
> Does anyone have the force field parameter for C60?
> Thanks,Vanna
>
> -------------------------------------------------
> This mail sent through : Chiangmai University 

-- 
***************************************************
 Dr. Pascal Bonnet
 School of Pharmacy and Pharmaceutical Sciences,
 University of Manchester, Oxford Road,
 Manchester, M13 9PL, U.K
 Tel:(+44) (0)161 275 2431
 http://www.man.ac.uk/~mbpsspb3