Adsorption

• In this section, we will see how to calculate the adsorption energy.
• When we considering the catalytic reaction using surface, adsorption is the first event.
• Chemical species adsorbed on a surface is called adsorbates.
• Adsorbates will undergo the surface reaction, which is a reaction that employes the surface. Usually, a surface reaction is easier to occur than the corresponding gas-phase reaction.
• There are two types of the surface reaction; one is called Langmuir-Hinshelwood type and the other is Eley-Rideal type. The former is the reaction that occurs between the adsorbed species. In the latter, the reaction occurs between the adsorbed species and the gas-phase species.

• Therefore, we need to consider following four types of reactions along the adsorption event (the asterisk means the surface, and species with asterisk is the adsorbate).

• Adsorption

$$\ce{A + surf -> A-surf}$$

1. Surface reaction (Langmuir-Hinshelwood)

$$\ce{A-surf + B-surf -> C-surf}$$

1. Surface reaction (Eley-Rideal)

$$\ce{A-surf + D -> E}$$

1. Desorption

$$\ce{F-surf -> F + surf}$$

Calculating adsorption energy

• As an example, we will see how to calculate the hydrogen adsorption energy on the Ru surface.
• This reaction is important, for example, in the ammonia (NH3) formation reaction.
• We use the ASE to build the bare, adsorbate, and adsorbed surface.

ASE scripts

• The followings are the Python script using ASE.

1. Simplest approach

from ase import Atom
from ase.io import write
from ase.build import hcp0001, add_adsorbate, molecule
from ase.visualize import view

surf = hcp0001(symbol="Ru", size=[3, 3, 4], a=2.7, c=4.2, vacuum=10.0, periodic=True)
clean_surface = surf.copy()

add_adsorbate(slab=surf, adsorbate=Atom("H"), height=1.2, position="fcc")

# output H2 POSCAR
h2 = molecule("H2")
h2.cell = [10, 10, 10]
h2.center()
write("POSCAR1", h2)

# output surface POSCAR
write("POSCAR2", clean_surface)

# output H-adsorbed surface POSCAR
write("POSCAR3", surf)

• Advantage: easy
• Disadvantage: non-generalizable (especally for high Miller index surfaces)

2. General approach

from ase import Atom
from ase.io import write
from ase.build import bulk, surface, add_adsorbate, molecule
from ase.visualize import view

bulk = bulk(name="Ru", crystalstructure="hcp", a=2.7, b=2.7, c=4.2)
surf = surface(lattice=bulk, indices=[0, 0, 1], layers=2, vacuum=10.0)

# make surface a little bigger
surf = surf*[3, 3, 1]

add_adsorbate(slab=surf, adsorbate=Atom("H"), height=1.2, offset=(0.22, 0.11))
...

• Advantage: a bit complex
• Disadvantage: general

Executing VASP

• After generating the POSCAR files (here POSCAR1, POSCAR2, and POSCAR3), the VASP calculation can be done.
• Do not forget to make directories for each calculations, setup the KPOINTS and POTCAR files (by copying VASP potentials files; see previous sections).
• Geometry optimization calculation should be done.
• After the calculation, get the energies by takeing the value of energy(sigma->0).
• Then the adsorption energy ($E_{\rm ads}$) can be calculated as

$$E_{\rm ads} = E_{\rm surf-ads} - \left(E_{\rm surf} + E_{\rm adsorbate}\right)$$

• Therefore in this case, the adsortion energy is

$$E_{\rm ads} = E_\ce{Ru-H} - \left(E_\ce{Ru} + \frac{1}{2}E_\ce{H2}\right)$$

• The reference adsorption energy is -0.63 eV (fcc hollow). Compare with your calculated value. https://www.researchgate.net/figure/Adsorption-sites-for-H-on-the-Ru0001-surface-with-corresponding-energies-of-adsorption_fig1_340125395

Advanced topic

• You can load several files using ase.io.read, to make a variety of surface-adsorbate pairs.
• In the following, we consider the benzene adsorption on the Si surface.
• Assuming that we have the coordinate of benzene ("benzene.xyz") and that of bulk Si ("si.cif"). There are available from many sources (such as PubChem, Materials Project).

from ase import Atom
from ase.io import read, write
from ase.build import bulk, surface, add_adsorbate, molecule
from ase.visualize import view

bulk = read("./files/si.cif")
surf = surface(lattice=bulk, indices=[0, 0, 1], layers=2, vacuum=10.0)
surf = surf*[2,2,1]

adsorbate = read("benzene.xyz")
add_adsorbate(slab=surf, adsorbate=adsorbate, height=2.0, offset=(0.5, 0.5))

view(surf)

Exercise

1. Calculate the adsorption energy on other sites. The "hollow" keyword in add_adsorbate for hcp0001 puts adsorbate on the fcc hollow site. Use other keywords such as "ontop" or "bridge", and compare with the reference.
2. Adjust the offset value in the add_adsorbate, and put the H atom to the hcp hollow site. Then calculate the $E_{\rm ads}$.