[gmx-users] Silica monolayer with Martini force field

André Farias de Moura moura at ufscar.br
Wed Oct 29 15:05:27 CET 2014

Dear Ramon,

we did something like that last year, except that our system was a ZrO2
nanoparticle and the chains were carboxylic acid instead of alkanes, but
the ideas are similar:

Nanocrystals self-assembled in superlattices directed by the
solvent–organic capping interaction, Nanoscale 5 (12), 5602-5610, 2013.

I would summarize as follows:

(1) if the grafting density is high (say, nearly 100% surface sites are
covered) and chain length is large enough (say, 3-4 beads), then the direct
interaction of the solvent with the solid substrate is neglible, because
surface becomes protected by a dense organic monolayer.

(2) the fact that alkanes are going to be exposed to water will lead to a
very high interfacial energy and this will be the dominant interaction
defining the packing of the hydrocarbon chains (the so-called hydrophobic
effect), not the weak, attractive dispersion interaction between alkyl
chains and the substrate or between alkyl chains, so again the interactions
involving the solid are not so important.

in short, I think you may set a polar site to the glass units and freeze
them and then check if these assumptions hold in your simulated system.

(which polar site to choose depends on the properties of the glass you are
interested in: if you have contact angle data for the glass-water and
glass-alkane you might in principle choose the best parameters)

I hope it helps.



On Tue, Oct 28, 2014 at 5:22 PM, RAMON REIGADA SANZ <reigada at ub.edu> wrote:

> Hi Gromacs users,
>    I want to simulate a monolayer of alkane molecules attached to a solid
> glass surface. I wonder if anyone has experience with these kinds of
> systems with the Martini force field. My idea is to add water to the
> surface and I am interested in what happens between water and the fixed
> alkanes, so I will freeze the solid beads and the first carbon of the
> alkane chain.
> My question is what kind of beads would correspond to glass (silica)
> surface? Somewhere I found that 'Na' beads could be used to simulate a Pt
> surface, but I do not know if this would work in my case.
> Did anyone has experience simulating solid surfaces with Martini?
>   thank you,
>   Ramon
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090

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