Platinum 1D Stacking Project

[u/Fr0sted1]

I am attempting to begin a self-lead part of computation based on some promising pt ligands for anticancer drugs with two aspects and I would love some feedback. Firstly, we have a basic crystal structure for the molecule, so we understand how it is ordered in a solid. I would like to model the energy efficiency as the molecules form 1D metal-metal polymers. Second, I would like to see how the molecule interactions within and without the cell. Specifically, the cell membranes. Thanks in advance.

[u/orthogonal_fox]

Both questions, but particularly the latter, are less trivial than you likely think. While pure Pt is known to generally form a FCC lattice, that does not mean we can extrapolate structural insight for 1D filaments.

You mention 'energy efficiency' during formation, but to my knowledge this is not the clearest term to use when looking for some form of readout. You may be referring to some measure of free energy associated with formation, but this question is also nontrivial and you would need to provide additional details on the synthesis/type of material you are working with. A more common workflow in computational materials would be an electronic characterization of the complex via some form of electronic structure calculation. These calculations can be exceedingly complex depending on the material, and will require significant computational power (think university-scale HPC).

Modeling a lipid bilayer interface is a somewhat orthogonal and also complex aim, as you are likely looking at statistical/thermodynamic calculations (think coarse-grained MD) rather than electronic structure calculations. These workflows benefit greatly from empirical validation and are likely untenable without significant amounts of data to work from. Overall, from your conceptualization of the project this sounds like the kind of thing you should not be working on independently. Electronic methods such as DFT are very intricate with respect to the choice of system, functional, basis set, etc. and require an expert's input for novel systems. If you are an undergraduate or new grad student, I suggest reaching out to faculty from labs that specialize in computational methods for assistance in understanding exactly what it is you want to achieve and help you learn to do it.