how to build and calculate following structure

ShiyuWang781

Currently, I need to perform DFT calculation on following structure, whict is pretty complex. There is a crystal which is a restricted area material with negative charge. The crystal provides 2D restricted area channels in which polymers are located. However, the polymer don't have the PBC which makes it not appropriate to perform fist principle calculation. But there is crystal. What approach is appropriate for the structure which is mixed by PBC structure and none PBC structure?


The goal of the calculation is to calculate the combining energy of Al ion and polymer and calculate the polarities of C=O before and after the combinaiton of Al ion and polymer.

Uus/pMeC6H4-/キ

I do not understand the purpose of uploading a compressed file for merely an image; giving the article link Angew. Chem. Int. Ed. 2021, 60, 22265 –22269 (https://doi.org/10.1002/anie.202108801) in plaintext and pointing to Figure 1 is way simpler and saves server space. (Note: this is yet another typical experiment-centric article putting all computational details in supporting information; the methods in "binding energy calculation" does not look rigorous and is of questionable reproducibility.)

Regarding the modelling issue itself, it is unclear how large the system would be or what scheme would be used (a few static calculation or molecular dynamics simulation, ab initio/DFT methods or classical force field). But it may be possible to construct a periodic poly(sodium 4-styrene sulfonate) structure that aligns with periodicity of MXene with, for example, the fix bond/create functionality in LAMMPS.

ShiyuWang781

Uus/pMeC6H4-/キ 发表于 2025-5-29 17:17
I do not understand the purpose of uploading a compressed file for merely an image; giving the artic ...

Just because someone gave me the picture to briefly illustrate the structure of the material, I didn't know if it was from an article. We want to use DFT method for the calculation. But the actural structure of the polymer isn't periodic, if it will lead to mistake of building a periodic polymer?

Uus/pMeC6H4-/キ

ShiyuWang781 发表于 2025-5-29 19:07
Just because someone gave me the picture to briefly illustrate the structure of the material, I di ...

Please clarify your concerns - what is a "mistake", in your opinion, that is distinct from some acceptable approximation and needs to be avoided? Indeed the real-life polymer is macroscopic and non-periodic, and of course using it directly for theoretical computation is not possible due to its sheer scale. It is only possible to work with a scaled-down microscopic model system and hope it is representative enough to capture the key features of the polymer. Your choice is building it either as (1) an isolated, non-periodic, cluster-like system of finite size, or (2) a periodic, condensed-phase-like system represented by some unit cell, also of finite size; in either case there is a balance between (a) sufficient size to avoid significant boundary/surface effect, and (b) feasible size within capabilities of limited computational resource. Speaking of which, do you have a sense about the spatial and temporal magnitude that varioud methods (DFT, classical force fields, etc) can deal with?

ShiyuWang781

Uus/pMeC6H4-/キ 发表于 2025-5-29 21:27
Please clarify your concerns - what is a "mistake", in your opinion, that is distinct from some ac ...

I got the reason for such way, thanks a lot.