Machine Learning CO Oxidation on Pt(111)

MLPotential Catalysis Surface Science CO oxidation Adsorption Nudged Elastic Band (NEB)

Note: This tutorial is intended for AMS2026 with access to the UMA-S-1.2-OC25 machine learning potential.

This tutorial will teach you how to:

• construct a Pt(111) surface,

• identify the common adsorption sites on Pt(111),

• build and relax adsorbed O*, O₂, CO, and CO* + O₂* structures,

• set up a simple NEB reaction path for CO* + O₂* → CO₂+ O*.

We will focus on 2 typical research questions in oxidative catalysis:

• Can co-adsorbed CO stabilize molecular oxygen on Pt(111)?

• Which co-adsorbed geometry is the most plausible precursor for oxidation?

A machine learning potential will be used to carry out these calculations. These models allow simulations to be performed more quickly, without significant loss of accuracy compared to the reference DFT data.

Fig. 28 Calculated reaction pathways corresponding to CO* + O₂* → CO₂+ O* with O₂ adsorbed at different surface sites. The reaction energies are relative to the binding energy of CO and O₂ on Pt(111).

Note

A Python notebook is also available for download. This notebook follows the same procedure outlined in this tutorial. Considering how surface reactions can require analyzing a large number of adsorption sites, adsorbate structures and reaction pathways, scriptable workflows are highly recommended to speed up more extensive studies.

Introduction

Pt(111) is a standard model surface for heterogeneous catalysis, and CO oxidation on Pt is one of the classic benchmark reactions in surface science. A useful way to study such a reaction system is to break the problem into a sequence of smaller steps:

• optimize the bulk reference,

• build the surface model,

• identify adsorption sites,

• compare the stability of adsorbate and co-adsorbate geometries,

• compare reaction pathways between candidate reactant and product states.

In this tutorial, we use a 2 x 2 Pt(111) surface and examine:

• atomic O at fcc and hcp sites,

• CO at top and bridge sites,

• molecular O₂ in two adsorption motifs, and

• two CO* + O₂* co-adsorbed structures.

The final section shows how to define a practical reaction pathway from the relaxed co-adsorbed states.

Bulk Pt Reference

Before building the surface, we optimize the bulk fcc Pt structure in order to determine the correct lattice parameters.

1. Open AMSinput: SCM → New Input

2. Choose Builders → Crystal Structure → Cubic → fcc

3. Choose Pt in the Presets menu and press OK

4. Switch to the machine learning engine: →

5. Set Model to UMA-S-1.2-OC25

6. Set Task to Geometry Optimization

7. Go to Details → GeometryOptimization

8. Set Optimize lattice to Yes

9. Save the job using File → Save as with the name Pt_bulk

10. Start the job using File → Run

Build the Pt(111) Surface

Next, we cut a Pt(111) surface from the optimized crystal structure.

1. Choose Update Molecule once the calculation is finished to load the optimized coordinates

2. Go to Details → GeometryOptimization and uncheck Optimize lattice

3. Choose Edit → Crystal → Generate Slab and select Convert to Conventional Cell

4. Set the number of layers to 4 and the Miller indices to (1,1,1). Click Generate the Slab and then Close

5. Go to Edit → Crystal → Generate Supercell. Set the diagonal matrix elements to 2 and click OK

6. Save the job using File → Save as with the name Pt111_2x2_empty

7. Start the job using File → Run

Build the Adsorbates

The common adsorption sites on Pt(111) are top, bridge, threefold fcc, and threefold hcp.

Our next step will be to create a small library of adsorbate structures for these sites:

• CO adsorption on the top site

• CO adsorption on the bridge site

• O adsorption on the fcc site

• O adsorption on the hcp site

• O₂ adsorption on the fcc site

• O₂ adsorption on the bridge site

These are considered to be the most likely candidates for stable adsorption on the basis of simplified MO models. We also consider 2 co-adsorbate structures:

• Co-adsorption of CO (top) and O₂ (fcc)

• Co-adsorption of CO (top) and O₂ (bridge)

A full study could be extended to consider other combinations of adsorption sites, but we will limit our selection here for the sake of brevity.

The structure editor in AMSinput can be used to easily construct these adsorbate structures. To build the top-adsorbed CO:

1. Open Pt111_2x2_empty with AMSinput

2. Click on the button and select Ligand → CO. Click on a point above the surface to add a CO molecule

3. Go to Edit → Tune Geometry

4. Select a surface Pt atom from the first layer. Then, click on the ⬭ button next to Above atoms

5. Set Distance to Plane to 2.0 A

6. Select the carbon atom. Use Select → Select Molecule to highlight the CO molecule. Click the Orient ⟂ button to orient the CO molecule upright. Then click the Move button to position the CO molecule over the top site

7. Save the job using File → Save as with the name Pt111_2x2_CO_top

To build the bridge-adsorbed CO:

1. Select 2 adjacent surface Pt atoms from the first layer. Then, click on the ⬭ button next to Above atoms

2. Select the CO molecule and click the Move button to position the CO molecule over the bridge site

3. Set Distance to Plane to 1.6 A

4. Save the job using File → Save as with the name Pt111_2x2_CO_bridge

To create the fcc-adsorbed O:

1. Open Pt111_2x2_empty with AMSinput

2. Click on the O button and click on a point above the surface to add an O atom

3. Go to Edit → Tune Geometry

4. Select the 3 surface Pt atoms surrounding an fcc site. Then, click on the ⬭ button next to Above atoms

5. Set Distance to Plane to 1.2 A

6. Select the oxygen atom, then click the Move button to position the atom over the fcc site

7. Save the job using File → Save as with the name Pt111_2x2_O_fcc

To create the hcp-adsorbed O:

1. Select the 3 surface Pt atoms surrounding an hcp site. Then, click on the ⬭ button next to Above atoms

2. Set Distance to Plane to 1.2 A

3. Select the oxygen atom, then click the Move button to position the atom over the fcc site

4. Save the job using File → Save as with the name Pt111_2x2_O_hcp

To build the bridge-adsorbed O₂:

1. Open Pt111_2x2_empty with AMSinput

2. Click on the button and select Ligand → CO. Click on a point above the surface to add a CO molecule

3. Select the carbon atom and use Atoms → Change Atom Type → O to create an O₂ molecule

4. Go to Edit → Tune Geometry

5. Select 2 adjacent surface Pt atoms from the first layer. Then, click on the ⬭ button next to Above atoms

6. Set Distance to Plane to 1.6 A

7. Select the O₂ molecule. Click the Orient ∥ button to orient the O₂ molecule parallel to the surface. Then click the Move button to position the O₂ molecule along the bridge site

8. Save the job using File → Save as with the name Pt111_2x2_O2_bridge

To build the fcc-adsorbed O₂:

1. Open Pt111_2x2_O2_bridge with AMSinput

2. Go to Edit → Tune Geometry

3. Select a surface Pt atom from the first layer. Then, click on the ⬭ button next to Above atoms

4. Set Distance to Plane to 1.2 A

5. Select the O₂ molecule. Click the Orient ∥ button to orient the O₂ molecule with the fcc base. Then click the Move button to position the O₂ molecule over the fcc site

6. Save the job using File → Save as with the name Pt111_2x2_O2_fcc

To build the co-adsorbed CO (top) / O₂ (bridge) system:

1. Open Pt111_2x2_O2_bridge with AMSinput

2. Click on the button and select Ligand → CO. Click on a point above the surface to add a CO molecule

3. Go to Edit → Tune Geometry

4. Select a surface Pt atom opposite from the O₂ adsorption site. Then, click on the ⬭ button next to Above atoms

5. Set Distance to Plane to 2.0 A

6. Select the carbon atom. Use Select → Select Molecule to highlight the CO molecule. Click the Orient ⟂ button to orient the CO molecule upright. Then click the Move button to position the CO molecule over the top site

7. Save the job using File → Save as with the name Pt111_2x2_O2_bridge_CO

To build the co-adsorbed CO (top) / O₂ (fcc) system:

1. Open Pt111_2x2_O2_fcc with AMSinput

2. Click on the button and select Ligand → CO. Click on a point above the surface to add a CO molecule

3. Go to Edit → Tune Geometry

4. Select a surface Pt atom opposite from the O₂ adsorption site. Then, click on the ⬭ button next to Above atoms

5. Set Distance to Plane to 2.0 A

6. Select the carbon atom. Use Select → Select Molecule to highlight the CO molecule. Click the Orient ⟂ button to orient the CO molecule upright. Then click the Move button to position the CO molecule over the top site

7. Save the job using File → Save as with the name Pt111_2x2_O2_fcc_CO

You should now have a set of 8 jobs corresponding to the structures shown below. Run the calculations through AMSjobs, then proceed to the next step once the results are in.

Gas-phase References

In order to compute adsorption energies, we need to obtain the energy of the reactant/product molecules in the gas phase (the reaction mixture).

To set up the calculation for CO:

1. Open AMSinput: SCM → New Input

2. Switch to the machine learning engine: →

3. Set Model to UMA-S-1.2-OC25

4. Set Task to Geometry Optimization

5. Click on the button and select Ligand → CO. Click on the drawing area to add the CO molecule.

6. Save the job using File → Save as with the name CO_gas

7. Start the job using File → Run

To set up a calculation for O₂:

1. Open CO_gas with AMSinput

2. Select the carbon atom and use Atoms → Change Atom Type → O to create an O₂ molecule

3. Save the job using File → Save as with the name O2_gas

4. Start the job using File → Run

To set up a calculation for CO₂:

1. Open CO_gas with AMSinput

2. Select the carbon atom and use the O tool to add another oxygen atom

3. Save the job using File → Save as with the name CO2_gas

4. Start the job using File → Run

Analyze Adsorption and Binding Energies

After the jobs finish, we can collect the energies for each of the structures. These can be found by opening the results with SCM → Output and requesting the section AMS → Energy.

Tip

It can be helpful to construct a table with the energies of the individual calculations, as we have done below, to keep track of the different states.

We can now obtain the binding energies of the different adsorbate configurations:

\[E_\mathrm{bind}(\mathrm{CO}) = - \left[E(\mathrm{Pt+CO}) - E(\mathrm{Pt}) - E(\mathrm{CO})\right]\]

\[E_\mathrm{bind}(\mathrm{O}_2) = - \left[E(\mathrm{Pt+O}_2) - E(\mathrm{Pt}) - E(\mathrm{CO})\right]\]

\[E_\mathrm{bind}(\mathrm{O}) = - \left[E(\mathrm{Pt+O}) - E(\mathrm{Pt}) - 0.5 E(\mathrm{O})\right]\]

We report below the calculated binding energies together with reference calculations obtained from literature. The main difference here originates from the absence of dispersion corrections in the literature PBE data, highlighting the role of dispersive interactions in the stabilization of adsorbates.

Table 10 Binding-energy comparison for adsorbates on Pt(111)

Structure	Calculated binding energy (eV) - PBE(D3)	Ref. [1] (eV) - PBE
O (fcc)	1.468	1.65
O (hcp)	1.090	–
CO (top)	1.721	1.58
CO (bridge)	1.732	–
O2 (fcc)	1.462	0.68
O2 (bridge)	1.521	0.72
CO (top) + O2 (fcc)	3.160	2.30
CO (top) + O2 (bridge)	3.284	2.36

The lateral interactions between the co-adsorbates can be calculated by referencing the isolated adsorbates:

\[E_\mathrm{lat} = E_\mathrm{bind}(\mathrm{CO+O}_2) - E_\mathrm{bind}(\mathrm{CO}) - E_\mathrm{bind}(\mathrm{O}_2)\]

This yields a lateral binding energy of -0.023 eV for the top/fcc configuration and +0.042 eV for the top/bridge configuration. The presence of CO is thus seen to affect the stability of co-adsorbates in different ways. The O₂ (bridge) is stabilized (stronger binding) while the O₂ (fcc) is destabilized (weaker binding). For this system, the steric interaction of the CO is the most likely cause for this difference, with a closer CO-O₂ proximity in the top/fcc state. However, in general, inductive surface-mediate interactions should also be considered, which may play a role when other metals, adsorbates or surface terminations are considered.

Build the Product States

So-far, we have focused on the stability of the surface species. In order to understand the effect of co-adsorbates on the reactivity of the catalyst, we need to analyze the stabilization of the transition state complex.

We will use the co-adsorbed CO + O₂ structures as candidates for the initial state of the oxidation reaction. Next, we proceed to generate structures for the final states containing CO₂ + O.

For the top/fcc configuration:

1. Open Pt111_2x2_O2_fcc_CO with AMSinput

2. Go to Edit → Tune Geometry

3. Select the carbon atom and click on the ⬭ button next to Translate atoms, target

4. Set the Step (fraction) to 0.5. This will place the transition state at the midpoint between the initial and final states

5. Click the ▶ button to move the oxygen atom

6. Save the structure using File → Save as with the name Pt111_2x2_O2_fcc_CO2

Repeat this process for the top/bridge configuration:

1. Open Pt111_2x2_O2_bridge_CO with AMSinput

2. Go to Edit → Tune Geometry

3. Select the carbon atom and click on the ⬭ button next to Translate atoms, target

4. Set the Step (fraction) to 0.5

5. Click the ▶ button to move the oxygen atom

6. Save the structure using File → Save as with the name Pt111_2x2_O2_bridge_CO2

We will set up a NEB calculation to search for the transition states. Normally, we would perform an optimization of the final states first. However, we skip this step here due to the tendency of CO₂ to desorb from the substrate.

Note

It is important that the atom order of the final and initial states remains the same. (A change in the atom order can occur by deleting atoms from the structure.) When generating the final state for a NEB calculation, restrict yourself to using move or tune operations only.

Run the NEB Calculations

Using our initial and final state structures, we can define a transition state search using the NEB method in AMSinput.

1. Open Pt111_2x2_O2_fcc_CO with AMSinput

2. Change Task → NEB

3. In Model → Nudged Elastic Band (NEB) set the Number of images to 6

4. Set the Initial system to Pt111_2x2_O2_fcc_CO

5. For the Final system select New Molecule. This will create a new panel in the molecule editor

6. Use File → Import Coordinates → From File → Pt111_2x2_O2_fcc_CO2 to load the final state

7. Save the job using File → Save as with the name Pt111_2x2_O2_fcc_CO_TS

8. Start the job using File → Run

Repeat this process for the top/bridge configuration:

1. Open Pt111_2x2_O2_bridge_CO with AMSinput

2. Change Task → NEB

3. In Model → Nudged Elastic Band (NEB) set the Number of images to 6

4. Set the Initial system to Pt111_2x2_O2_bridge_CO

5. For the Final system select New Molecule. This will create a new panel in the molecule editor

6. Use File → Import Coordinates → From File → Pt111_2x2_O2_bridge_CO2 to load the final state

4. Disable Optimize reactants/products as this step has already been done

7. Save the job using File → Save as with the name Pt111_2x2_O2_bridge_CO_TS

8. Start the job using File → Run

After the NEB jobs finish, we can visualize the energy landscape of the reaction using AMSmovie (SCM → Movie).

This gives a first reaction-path comparison for the two co-adsorbate motifs. The top/fcc configuration is seen to yield the lower barrier, and hence the faster rate, for CO oxidation. Lateral destabilization of the initial state aids the reaction rate by slightly lowering the barrier. The opposite effect is noted for the top/bridge configuration. This is a common phenomenon, where stability of the reactants is often inversely proportional to their reactivity.

Summary

In this tutorial, we have shown how to perform a reaction pathway analysis for a surface reaction on a heterogeneous catalyst. The role of co-adsorbate interactions was discussed, and we have highlighted the procedure for setting up transition state searches. A machine learning model was used to accelerate the energy calculations.

For this example, we have limited ourselves to a single reaction. The full microkinetic network for CO oxidation involves multiple steps, and can also include alternative routes such as CO/O₂ dissociation. For co-adsorption, there are a large number of possible initial states. In our discussion, we have used arguments from MO theory to determine a reasonable set of configurations. High-throughput screenings could alternatively be performed to more thoroughly evaluate possible reaction coordinates, especially when considering higher surface coverages.

References

[1]

1. Eichler and J. Hafner, Reaction channels for the catalytic oxidation of CO on Pt(111), Phys. Rev. B 59, 5960 (1999). DOI: 10.1103/PhysRevB.59.5960