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Tutorial for Adsorption tool

Tutorial for Adsorption tool. The adsorption tool operates on two objects: -- The P1 description of a slab, currently stored as the periodic object -- The current finite object. This Tutorial details two examples: -- Deposit a methanol molecule on Pt and (Pt,Ru)

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Tutorial for Adsorption tool

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  1. Tutorial for Adsorption tool

  2. The adsorption tool operates on two objects: -- The P1 description of a slab, currently stored as the periodic object -- The current finite object This Tutorial details two examples: -- Deposit a methanol molecule on Pt and (Pt,Ru) -- Deposit a nanotube on Pt(111)

  3. Create a molecule of methanol Choose “Edit molecule”

  4. For the time being, let’s view the methane molecule. Methane is the editable default content at startup. If that is not suitable, just paste Cartesian coordinates for the startup molecule you had in mind. Alkanes are built by substituting H by methyl, staggered or eclipsed. Alcohols are built from alkanes by substituting H by OH. New chemical nature for any atom is typed in the editable window. Bond lengths and torsion angles are interactively adjustable.

  5. We wish to substitute an OH ligand at H2 Cartesian axes graduated in Angstroms The atom numbering is the sequence # in the editable window

  6. Substitute H2 by OH The software generates staggered OH with C-O = 1.43 and O-H = 1.029A If eclipsed OH is desired, just rotate by 60 degs about the C-O bond.

  7. An oxygen appears at 2, with C1-O2 = 1.43A H6 appears, staggered with O2-H = 1.029A Let’s view results

  8. we would like the molecule to sit on Pt atoms at O2, H3 and H5 This is methanol Let’s then make a Pt(111) surface

  9. Create a 8 A thick (111) Pt surface This dialog is accessed from the “Surfaces” button

  10. Fine so far. What is needed is a 4x4x1 supercell of this, to avoid interactions between neighbouring molecules. c

  11. The resulting slab represented with metal-radius spheres Sounds OK now! c

  12. select “Adsorption”

  13. Let’s first have a look at the surface

  14. This could do, but things would be clearer if we only plotted the top layer

  15. The top Pt layer is at z=0.633 After adjusting the z plot limits from 0.6 to 1.1, we get:

  16. We will try to position O2 over Pt58, H3 toward Pt 59, H5 toward Pt55, all at 2.1 A dist. That’s more legible!

  17. This will position O2 at 2.1A above Pt58

  18. It sounds like O2 is indeed above Pt58

  19. This should aim H3 toward Pt 59

  20. In this combined picture of methanol over the Pt 64 slab, H3 is called H(64+3=67) Success! The “Adsorption” dialog accepts all of 3, 67, H3 and H67 to designate “molecule atom #3”

  21. This will pivot the molecule around its C2-H3 vector and bring C5-Pt55 to 2.1A

  22. Plotting Pt green clarifies the plot. It may not be the best, but this is exactly the orientation we asked for. Anyway, it’s good enough to be optimized

  23. The interatomic distances for the three atoms involved are precisely what was requested. H3 (=H67) was requested to aim at a point 2.1A above Pt59, not to achieve such a bonding distance with it. It ends up at 2.21A distance from this atom. Energy optimization should fix that…

  24. Contacting-sphere view of model of methanol adsorbed on Pt (111) Let’s relax it!

  25. Relax atom coordinates with VASP

  26. First a quick-and-approximate relaxation job

  27. Energy convergence of methanol adsorbed on Pt64 slab (eV) cycles Minor ripples through Pt layers major bond-length adjustments About 1 cycle per hour on 1.8GHz 32-bit Athlon

  28. Relaxed structure ready to be cut in JOBreport

  29. The picture is qualitatively the same, but Pt-O is now 2.33 A while Pt-H is ~2.7 A That huge change came about in a day of computing by a PC. Let’s change the oxygen Pt to Ru

  30. Things are similar on Ru, but the Ru-O distance is now only 2.22 A. This H is now 3A from this Pt Let’s fix O above Ru and pull on H

  31. Optimization still running. Results will be added here later.

  32. Create a nanotube and lay it flat on Pt (111)

  33. End of Adsorption tool tutorial

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