Hello Rinki Arya

Are you talking about creating a slab? Creating model for DFT is still something very tricky and must be done carefully. Nowadays, I recommend BURAI as an input creator for DFT to use Quantum ESPRESSO. Although BURAI has been discontinued, its input creator is the best until now for QE. About other DFT codes, I don't know exactly how to do, but I would pass by the tutorials to create VASP (POSCAR) input, as it seems to be the most common format.

Feel free to reply if you need help

Best regards

Dr. Ricardo Tadeu

Dear friend Rinki Arya

Thank you for raising such an insightful question regarding the creation of surface models for DFT calculations using SEM, TEM, and XRD data. This multidisciplinary approach is indeed crucial for advancing our understanding of cathode catalysts, particularly for ORR studies.

To begin, SEM and TEM provide invaluable structural and morphological details—SEM offers surface topology, while TEM reveals atomic-scale features. These insights are essential for constructing realistic surface models, ensuring that the computational representation closely mirrors the actual catalyst morphology. Meanwhile, XRD data delivers critical information about the crystal structure and phase composition, which are foundational for accurate electronic structure calculations in DFT.

Visualization tools like VESTA and CrystalMaker can bridge the gap between experimental data and computational modeling by enabling the construction and manipulation of crystal structures derived from XRD. These visualizations serve as a starting point for building detailed surface slabs, which can then be imported into DFT packages such as Gaussian, Quantum ESPRESSO, or VASP. These DFT tools are well-equipped to handle complex surface models and can simulate catalytic behaviors, including adsorption and reaction mechanisms.

Integrating SEM and TEM data can further refine your models. Software like ImageJ can help quantify features from TEM images, which can then inform adjustments to your computational models. However, combining data from multiple sources may present challenges, such as aligning scales or reconciling discrepancies between imaging and diffraction data. Nevertheless, this integrative approach can yield a more comprehensive and accurate surface model, ultimately enhancing the reliability of your DFT simulations.

If you would like to discuss specific software workflows or have questions about integrating these datasets, please let me know. I look forward to hearing your thoughts and supporting your research further.

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Best regards,

Kaushik

Ricardo Tadeu Maia and Kaushik Shandilya Sir, firstly, I would like to thank both of you for your valuable response. I have both VESTA and BURAI software, but I don't know how to start developing a model for my study. Essentially, I aim to demonstrate the bonding of metals (Fe, Zn, Cu, Mg) and pyridinic nitrogen adsorption on a graphitic carbon surface. So in this regard, could you give any source or suggestion for this?

Hello Rinki Arya

Is this carbon surface the compound g-C3N4 or any similar structures? g-C3N4 is a layered material which has rings with nitrogen and carbon atoms. If this is the case, you must to do 2 steps:

1 - Build a monolayer

2 - Bind an atom with the monolayer atom

BURAI can make a monolayer easily. And add a single atom binding to it's not that hard, you can add manually. I just don't know what kind of calculation you can do to achieve your objectives. And why did you mention SEM, XRD and TEM in your question?

Hi Rinki Arya

There are many possibilities out there, such as VESTA, Materials Studio, CrystalMaker, and QuantumATK, among others. I personally use VESTA and Materials Studio combined. VESTA is more manual, Materials Studio is more automated (this saves a lot of time, though). In principle, everything you need can be done through VESTA. You can build the graphene sheet through VESTA, following more or less what is discussed here: https://www.youtube.com/watch?v=yP1BREWv6u0

(ensure you have a supercell, like 3x3 or larger, to allow proper modeling).

Maybe you may find the graphene sheet here: https://materialsproject.org/

To create the pyridinic-N site, you can also do this with VESTA (remove adjacent C atoms in a ring and replace them with an N atom, I would say). Finally, still via VESTA, you place the metal atom near the N site, say ~2Å above it. Structure ready for relaxation!

When I say do it all through VESTA, it basically means you make manual changes to the file opened in a notes app and check its changes in VESTA (visual check) ~keep doing this rationally until you find/visualize what you want.

Hope that clarifies a bit,

Best,

Gabriel Vinicius

Gabriel Vinicius thank you so much sir, for your insightful response, i will definitely follow your suggestions.

I also extend my thanks to Ricardo Tadeu Maia sir, for your response and suggestions.