Build Nanostructures for MD Simulations
In the last tutorial, generation of gold nanostructures was demonstrated. Here, the focus is on assemble the gold nanostructures and polymers together to form various nanomaterials. The concrete examples are PEO-grafted nanoparticles and nanopores.
General procedures
With the generated nanostructures and the PEO polymer, the next step to assemble them together. There are usually three governing parameters for the assembled system, namely grafting density, polymer chain length and gold size. The general steps to assemble them together is:
- calculate how many polymers are needed for the given grafting density
- determine the grafting site on the gold surface (NPs exterior and PORES inner surface)
- use coordinate rotation and translation to move the given polymer to the desired grafting site
- combine the coordinates of gold and polymers for the final system
To get evenly distributed grafting points, for nanoparticles, one can refer to the Fibonacci sphere split algorithm. The PEO polymer can be just a zig-zag conformation (directly generated by Avogadro using SMILES).
The generated PEO-grafted nanoparticles with radius 2nm and PEO-N20 at the grafting density of 1.50nm-2 (assembled and after equilibration) are rendered below using vmd (not in the same scale):
The PEO-grafted nanopores with radius 5nm and PEO-N20 at the grafting density of 0.46nm-2:
One can see that in order to make the polymer inside the pore and avoid inter-overlapping, a curved PEO chain is employed rather than a straight one as demonstrated in the nanoparticle example which does not have the geometrical restriction. Thus, manual generation of the PEO chain is required so that polymers sit inside the pore in a reasonable shape, instead of going into the gold lattice or staying too close.
References
For further information about the MD simulations or the physics behind the PEO-grafted nanoparticles, one is referred to:
- Macromolecules 53.19 (2020): 8160-8170.
- Macromolecules 51.15 (2018): 5950-5961.