I want to make structure of DBT (C12H8S) adsorbed TiO2 (100) surface. I have made TiO2 (100) surface from material studio, now I want to adsorb DBT molecule. How can make such type of structure in material studio ?
Shilendra
Dear Shilendra :
0,06 g TiO2 spread in 20 g 2wt.% DBT in toluene solution. Mixture stirr under ultrasonic condition. Samples filter under suction till almost dry.
Best regards.
Dear Prof. Yuri Mirgorod ,
Thank you for reply but my question is regarding how does make structure based on computational simulation using material studio software.
Shilendra
Hi Shilendra,
Based on my esperience, you can just open both TiO2 (100) surface and DBT (C12H8S) structures in MS. And then copy the gas phase DBT (C12H8S) structure and paste it on TiO2(100) surface. Then you can move the absorbate to your desire site on the surface. Does it make sense? Hope it helps!
Best,
Nannan
Dear Nannan Shan,
Thank you for your answer. I will try to implement your suggestion.
Shilendra
Hi Shilendra,
If you want to do DFT calculation on a unit cell of TiO2 see the tutorials on Adsorption of CO on Pd (110) surface. if you want to use a periodic TiO2 super cell then you can see the tutorials on the interaction of polymer with Al203 surface using MD. just go to quick tutorial and then search. Hope that these help!
Zahed.
Dear Nannan Shan,
Your suggestion is working, I have resolved my problem. Now I am able to make molecule adsorbed structure. I can use this structure in any DFT code.
Thank you again !
Shilendra
Dear Shilendra,
If you want to investigate physorption on TiO2, copy and past the structure will work but it will not work to explore chemisorption because you need construct a ban between molecule and TiO2 atoms.
Dear Zahed Ghelichkhah thank you for your answers and suggestions !
So in case of chemisorption how does construct input structure and what precautions we should take account ? Can you much elaborate about chemisorption and its input structure ?
Shilendra
Dear Shilendra,
Really, it depends on the type of Module you want to use, for example if you want to use of Castep Module you need to use of periodic structures.( see the tutorial on castep). If you want to use of Dmol3 just construct the bonds between your compound through desire atom with TiO2 and then optimize the final structure (you can use Gauss view 09 to do your project too).
Dear Zahed Ghelichkhah, I am using VASP code which also need periodic structure. I want to use material studio for making input structures for VASP code.
MS does not give VASP input structure file directly but we can save in other format CIF and PDB format after that we can visualize these files in VESTA.
VESTA gives VASP input structure format.
Shilendra
Dear all, I have a similar problem. I have two distinct file one is metal surface and another is a molecule configuration in material studio. When I paste the molecule on the metal surface, I can not move it to a desirable position and the molecule is very close to the surface. How can I change the position of molecule?
Dear Dear Nannan Shan,
When we paste molecule then so many symmetric molecule paste simultaneously in material studio. It creates confusion, how does remove symmetric molecules in materials studio.
Shilendra
Dear Nannan ,
As one guy asked if chemisorption is considered then will your solution be helpful? Also how we can move the pasted molecule on the surface?
Best
You can move the molecule up, down, right or left by pressing alt+shift+up(down etc keys) but first you need to select your molecule with the Select Fragment option in the shortcut menu. Also you can rotate your selected molecule by pressing shift+up(down etc) keys of your keyboard.
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