Author Topic: HOMO-LUMO of a slab+molecule system  (Read 277 times)

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Offline hadi9827

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HOMO-LUMO of a slab+molecule system
« on: December 16, 2020, 11:30 »
Dear QuantumATK family,

I am trying to investigate the interactions between a molecule with ZnO surface. To do this I use a ZnO crystal and use the "cleave surface" and make a normal slab of ZnO with a vacuum on the top of the surface and relax it. Then I put the relaxed molecule on the vicinity of the surface and optimize the system and observe the trajectory to see what . You can see the system attached to this message.

Now I want to calculate the HOMO-LUMO of the whole system (ZnO +absorbed molecule). I read all the posts about HOMO-LUMO in the forum and I know that HOMO-LUMO are defined for a non-periodic isolated system but I think my system is periodic in A and B direction. I used "change the configuration to molecule" to eliminate the periodicity of the slab but when I try to relax it the whole structure of the ZnO will be changed (see the second attached pic). Do you have any idea how I can build up a system so I can investigate the interactions of a molecule with ZnO surface and also see the homo-lumo in the whole system?

Thank you in advance

Offline hadi9827

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Re: HOMO-LUMO of a slab+molecule system
« Reply #1 on: December 16, 2020, 15:31 »
Dear all,
I am in an urgent situation. Would you please help me? Thanks
Best regards,
Hadi

Offline mlee

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Re: HOMO-LUMO of a slab+molecule system
« Reply #2 on: December 16, 2020, 16:25 »
I am not sure what is your purpose to simulate it finally.

In the slab model, you can analyze the BandStructure, DensityOfStates, or MolecularEnergySpectrum related to homo and lumo energy.
In the molecular model, cluster model is commonly used to analyze the homo-lumo energy or adsorption energy. You need to assume the cluster as a surface.

If you would like to obtain the adsorption energy between molecule and surface, one probe device model (using surface NEGF) or slab model will be good starting because it will be more realistic than cluster as a surface.

Offline hadi9827

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Re: HOMO-LUMO of a slab+molecule system
« Reply #3 on: December 16, 2020, 16:52 »

Dear mlee,

Thank you very much for your response. I am going to  investigate adsorption energy, binding energy, homo-lumo and charge transfer.
You mentioned two methods. Would you please elaborate on them?
You wrote "In the slab model, you can analyze the BandStructure, DensityOfStates, or MolecularEnergySpectrum related to homo and lumo energy." slab (the structure I sent you in my former message) is periodic from two sides, isnt it? is it possible to calculate HOMO-LUMO for a periodic structure in ATK?
You also wrote me "In the molecular model, cluster model is commonly used to analyze the homo-lumo energy or adsorption energy. You need to assume the cluster as a surface." May I ask you explain me how I can do it? I have no idea what you mean by cluster? How can I make it?
Generally, if I want to investigate the interactions of a molecule with the surface of a crystal in ATK for calculating some parameters like adsorption energy, binding energy, homo-lumo and charge transfer, how would you recommend me to set the structure? making a slab and putting the molecule above it was the only idea I could come up with. What is the best option in your opinion? The cluster? would you elaborate on it please?
Sorry for asking many questions? Thank you for your help.

Best regards,
Hadi

Offline mlee

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Re: HOMO-LUMO of a slab+molecule system
« Reply #4 on: December 17, 2020, 06:42 »
I recommend to search papers. You can easily find cluster model, periodic model for adsorption energy and charge transfer.
(For instance, J. Phys. Chem. B 2005, 109, 38, 17943–17950, International Journal of Molecular Sciences 10(10):4310-29  ...)
« Last Edit: December 17, 2020, 09:32 by mlee »

Offline hadi9827

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Re: HOMO-LUMO of a slab+molecule system
« Reply #5 on: December 17, 2020, 14:26 »
Thank you very much for your response.
Considering this that I am using the slab method (the structure I attached to the first message) and I am interested in calculating the homo-lumo and visualizing them, would you please guide me how to do that?
Best regards,
Hadi

Offline mlee

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Re: HOMO-LUMO of a slab+molecule system
« Reply #6 on: December 17, 2020, 19:37 »
You can analyze the MolecularEnergySpectrum.
It shows the energy levels and homo-lumo gap.
The below manuel will be useful.
https://docs.quantumatk.com/manual/Types/MolecularEnergySpectrum/MolecularEnergySpectrum.html

Offline hadi9827

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Re: HOMO-LUMO of a slab+molecule system
« Reply #7 on: January 5, 2021, 12:49 »
Thank you very much.
And what about charge transfer? How I can calculate the charge transfer between the absorbed molecule and the slab?
Thanks alot.

Offline mlee

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Re: HOMO-LUMO of a slab+molecule system
« Reply #8 on: January 6, 2021, 17:02 »
MullikenPolulation in analysis will be one of options to see the charge transfer between the absorbed molecule and surface.

Offline hadi9827

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Re: HOMO-LUMO of a slab+molecule system
« Reply #9 on: January 7, 2021, 11:24 »
Thank you very much for your valuable responses. May I ask some other questions?
I used MolecularEnergySpectrum and since it also represents the orbital occupations I could find HOMO and LUMO orbitals. Then I used Eigenstate and plotted HOMO and LUMO. I attached the output file.
- HOMO is 388 and LUMO is 389, am I right?
- My next question is about choosing the suitable isovalue when I want to plot HOMO and LUMO. For different isovalues I will get a totally different plots. How can I make a relevant choice of isovalue for visualizing HOMO and LUMO orbitals?
Thank you for your responses.

Offline hadi9827

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Re: HOMO-LUMO of a slab+molecule system
« Reply #10 on: January 7, 2021, 13:46 »
Sorry an another important question. I am using SemiEmprical (Slater-Koster, dftb.org option) for calculating MullikenPopulation, charge transfer, HOMO-LUMO and binding energy for my system. Is it okay or I have to use Extended Huckel option? Thank you very much.

Offline hadi9827

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Re: HOMO-LUMO of a slab+molecule system
« Reply #11 on: January 8, 2021, 09:22 »
Anyone to answer my questions please? :(

Offline mlee

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Re: HOMO-LUMO of a slab+molecule system
« Reply #12 on: January 8, 2021, 10:54 »
I can confirm that HOMO is 388 and LUMO is 389.
« Last Edit: January 8, 2021, 10:58 by mlee »

Offline hadi9827

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Re: HOMO-LUMO of a slab+molecule system
« Reply #13 on: January 8, 2021, 13:05 »
Thank you very much
Would you mind responding to my next questions about isovalue and Salter-Koster method please?
Thank you for your patience  :)