Is polyply suitable for the construction of carbon quantum dots?

[ludan0719]

Currently, there is a model for carbon quantum dots (based on a VMD plugin). I would like to ask if Polyply can be used to build carbon quantum dots of different sizes and with different functional groups.

[fgrunewald]

Hi @ludan0719,

Polyply cannot build quantum dots. Perhaps @ricalessandri has an idea

[ricalessandri]

@ludan0719 atomistic or coarse-grained?

[ricalessandri]

@ludan0719 for CG, you could use the Martini 3 graphene model we published here as a starting point: https://doi.org/10.26434/chemrxiv-2024-6s1wj. The preprint links to a code that allows you to generate graphene sheets of arbitrary dimensions. You can stack a few of them, tight them together with some bonds, and that could be it? I guess like this you'd get a "crystalline carbon dot". But polyply won't be of help here. Hope this helps

[ludan0719]

I noticed this work, which is very helpful to me. It makes the establishment of graphene structures possible and also helps me study the interaction between polysaccharides and graphene quantum dots (without functional groups). I have another question: for the structure in the image below, where carbon cores bind to edge positions with various functional groups (mainly hydroxyl, carboxyl, and amino groups), how can polyply be used to parameterize and study coarse-grained simulations with cellulose?

[ludan0719]

and if polyply can not be of help here，i just need to parameterize myself. I first use polyply to construct cellulose coordinates and topology, and then use insert-molecules to add this small molecules (similar to one single layer of carbon dot). In this workflow, the effect of functional groups on the self-assembly of cellulose could be studied. Am i on the right track?

[ricalessandri]

missed your follow ups, apologies. A M3 model of cellulose has been developed by @fgrunewald in https://doi.org/10.1021/acs.jctc.2c00757 so you should be able to use that and polyply would be of help - but I think that's missing from the polyply library @fgrunewald ?

[ricalessandri]

@ludan0719 cellulose is available, see: https://github.com/marrink-lab/polyply_1.0/blob/master/polyply/data/martini3/cellulose.martini3.ff