[gmx-users] Determining the energy of an individual atom

Darrell Koskinen darrellk at ece.ubc.ca
Thu Aug 13 02:16:32 CEST 2009

Hi David,
Thank you for your comments.

The bulk of the graphene sheet is not polarized in the absence of a 
connection to electrodes. In some experiments on graphene adsorption, 
they show significant adsorption of ammonia, but in these experiments 
they connected the graphene sheet to electrodes. Could this be assisting 
in the adsorption of ammonia on the graphene sheet?

The edges of my graphene sheet are polarized since I have terminated the 
edges with hydrogen atoms. I expected to see some adsorption in the bulk 
of the graphene sheet resulting from VdW forces and significantly more 
adorption on the edges due to the polarization. I also expected to see a 
stronger adsorption energy for the adsorption on the edges. However, I 
am not seeing even a single molecule being adsorbed either in the bulk 
or on the edges. Could it be that the binding energy arising from VdW 
forces is much weaker than the vibrational energy of the lattice atoms? 
I should also add that hydrogen atoms attached to the edge of the 
graphene lattice show even greater movement than the carbon atoms in the 
graphene lattice. Is this is to be expected and is it the result of the 
small mass of the hydrogen atoms and could this be impairing the 
adsorption on the edges?

Again, your thoughts and comments are much appreciated.

> Date: Wed, 12 Aug 2009 07:45:11 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Determining the energy of an individual atom.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A8256E7.2030700 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Darrell Koskinen wrote:
>> Dear GROMACS Gurus,
>> In my simulation of a graphene structure surrounded by an ammonia gas, I 
>> am not seeing any adsorption of the ammonia molecules onto the surface 
>> of the graphene structure. I am wondering if the reason I am not seeing 
>> any absorption is because the graphene lattice is vibrating and thereby 
>> imparting too much energy to the ammonia molecule when it comes into the 
>> vicinity of the graphene lattice, thus impairing any adsorption. I 
>> assume that the adsorption energy would have to be significantly greater 
>> than the vibrational energy in order to allow adsorption to occur. If 
>> this is true, then is there some way of determining the translational 
>> (vibrational) energy of an atom in the graphene lattice so that I may 
>> compare it to the adsorption energy?
> If your graphene is not polarizable then the interaction with ammonia is 
> limited to Van der waals interactions. However the induced polarization 
> can be quite strong for such groups, and hence it seems you are missing 
> an important part of the binding energy.
>> Thanks again for your help.
>> Darrell

More information about the gromacs.org_gmx-users mailing list