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How to Create a Gold Nanoparticle with a Self Assembled Monolayer?

As the title suggests, I am trying to create a gold nanoparticle (20 nm diameter) with 1,4-Benzenedimethanethiol covering the surface.

I haven’t been successful yet, and I was hoping that someone with more experience on the matter could give me some advice.

Hi, @Paanta. Could you be more specific about the problems you met? I guess, you can start with cutting a nanoparticle from .cif structure of bulk gold, and then you will have to cover it by organic molecules manually, and after that you will need to optimize the organic layer to make it more realistic.

Thank you @Iamkaant, right now I have managed to create a gold nanoparticle (sphere of pure gold, 2 nm in diamter). What I am asking is: how can I cover the surface of my gold nanoparticle with organic molecules?

I see you have suggested that I do it manually, but I haven’t been able to open the .cif file of the nanoparticle in Avogadro. Also, even if I could, wouldn’t there be a better way to cover the surface than doing it manually? Doing it manually would be extremely time consuming and tedious, so I would much rather avoid it.

Generally for creating nanoparticles, I’d suggest using pymatgen

For placing ligands, I generally suggest Packmol which lets you place ligands (in PDB format) around a sphere.

It’s possible that someone has created utilities for pymatgen to place ligands too, but a search didn’t turn anything up.

I did see a website for creating nanoparticles using Wulff construction:

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Although not an OP, I highly appreciate your reply. Never heard of Packmol before… I used to write Python scripts for similar tasks, but having a program at hand should be much faster. Saving that to my notes!