Catalytic Selectivity Through Microkinetic Modeling

Tutorial Created with Software Release: 2026-1
Topics: Catalysis & Reactivity, Energy Capture & Storage, Metals, Alloys & Ceramics, Thin Film Processing
Methodology: Molecular Quantum Mechanics, Periodic Quantum Mechanics
Products Used: MS Maestro, MS Reactivity, Quantum Espresso

Tutorial files

0.3 MB
This tutorial is written for use with a 3-button mouse with a scroll wheel.
Words found in the Glossary of Terms are shown like this: Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

Tip: You can hover over a glossary term to display its definition. You can click on an image to expand it in the page.
Abstract:

 

In this tutorial, we will learn to analyze the selectivity of the catalytic oxidation of CO and H2 on a Pd(111) surface using Microkinetic Modeling (MKM) calculations.

Tutorial Content

  1. Introduction to Microkinetic Modeling Selectivity Analysis

  1. Creating and Saving Projects

  1. Performing a Microkinetic Modeling Calculation

  1. Analyzing a Microkinetic Modeling Calculation

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Microkinetic Modeling Selectivity Analysis

Microkinetic modeling (MKM) is a powerful tool for determining a surface's outcome of coupled kinetics in a reaction network, especially useful for heterogeneous catalysis and vapor-based processes like atomic layer deposition.

Gas-surface processes involve a series of competing, sequential elementary steps (adsorption, diffusion, reaction, and desorption) that occur over varying timescales. A single overall reaction typically proceeds through multiple potential reaction channels (pathways), collectively forming a reaction network.

To run an MKM simulation, you need:

(i) initial concentrations (coverages) of surface species

(ii) partial pressures of gases

(iii) temperature, and

(iv) a fully defined reaction network,

where the kinetics for each elementary step (forward and reverse) in the reaction network are specified by reactants, products, activation energies, and pre-exponential factors (from experiment, empirical estimates, or quantum mechanical (QM) calculations).

An optimally performing catalyst is expected to maximize the rate of reactions leading to the desired products, i.e., exhibit high selectivity. Selectivity is quantified as a fraction (or percentage) of a specific product with respect to the total reaction products.  The degree of selectivity control (DSC) analyzes how strongly each elementary step influences the selectivity of this product in the overall reaction. DSC is closely related to the degree of rate control (DRC) introduced in our Microkinetic Modeling tutorial.   

MKM solves coupled kinetic equations to determine rates and surface coverages of all species, revealing the process's overall effectiveness. Key insights include: turnover frequency (TOF) for each elementary step, factors controlling the reaction, such as rate-determining steps and optimal reactor conditions, and for thin film deposition, growth rate over time.

By providing these insights, MKM offers a powerful approach for optimizing reactor conditions, catalysts, and gaseous reactants or precursors.

In this tutorial, we will learn to use the Microkinetic Modeling and Microkinetic Viewer panels to investigate the preferential oxidation of CO in excess H2 (CO-PROX), a crucial catalytic process. Our primary focus will be on analyzing the CO2 selectivity by examining the competitive formation of CO2 and H2O on a Pd(111) surface. As inputs, we provide a reaction network for the catalytic oxidation of CO and H2 on a Pd(111) surface and corresponding forward and reverse activation free energies.

The key elementary reactions involved in this reaction network are (* denotes a free surface site):

  1. CO Molecular Adsorption: CO(g) + * → CO*
  2. O2 Dissociative Adsorption: O2(g) + 2* → 2O*
  3. CO Oxidation: CO* + O* → CO2(g) + 2*
  4. H2 Dissociative Adsorption: H2(g) + 2* → 2H*
  5. Hydroxyl Formation: H* + O* → OH* + *
  6. Water Associative Desorption: OH* + H* → H2O(g) + 2*

An overview of the workflow is shown below:

For additional practice in solid-state modeling with Schrödinger, see the Microkinetic Modeling, Electronic Structure Calculations of Bulk Crystals Using Quantum ESPRESSO, Modeling Surfaces and Activation Energies for Reactivity in Solids and on Surfaces tutorials.

2. Creating and Saving Projects

At the start of the session, change the file path to your chosen Working Directorythe location where files are saved in MS Maestro to make file navigation easier. Each session in MS Maestro begins with a default Scratch Projecta temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project, which is not saved. A MS Maestro project stores all your data and has a .prj extension. A project may contain numerous entries corresponding to imported structures, as well as the output of modeling-related tasks. Once a project is saved, the project is automatically saved each time a change is made.

Structures can be built in MS Maestro or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. The Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion is located to the left of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data can be accessed by Ctrl+T (Cmd+T) or Window > Project Table if you would like to see an expanded view of your project data.

  1. Double-click the Materials Science icon

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. Pre-generated files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/mkm_selectivity.zip
  4. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

  1. Go to File > Save Project As
  2. Change the File name to MKM_selectivity_tutorial, click Save
    • The project is now named MKM_selectivity_tutorial.prj

3. Performing a Microkinetic Modeling Calculation

In this section, we will set up the calculation using the Microkinetic Modeling panel.

Figure 3-1. Opening the Microkinetic Modeling panel.

  1. Go to Tasks > Materials > Quantum Mechanics > Surface Science > Microkinetic Modeling

Figure 3-2. The Reactor Settings tab.

The Reactor Settings tab is used to specify the Physical conditions to model.

  1. Change the Temperature to 623 K
    • For this example, we will explore the kinetics at this specific temperature

Figure 3-3. The Reaction Network tab.

  1. Go to the Reaction Network tab
  2. Click New Reaction
    • The New Reactions Editor panel opens. This panel allows you to type or copy in the reaction workflow.
  3. Add all six reactions for our reaction workflow:
    • CO+*:Cat->CO:Cat;0 0.137
    • O2+2*:Cat->2O:Cat;0 1.151
    • CO:Cat+O:Cat->CO2+2*:Cat; 0.717 999
    • H2+2*:Cat->2H:Cat;0 0
    • O:Cat+H:Cat->OH:Cat+*:Cat;0.96 1.18
    • OH:Cat+H:Cat->H2O+2*:Cat;0.64 999

 

Note: The forward and reverse free energy barrier values, measured in eV, are provided at the end of these reactions. These energy values are sourced from the works of Tiburski et al and Wang et al. Please refer to the References.

Figure 3-4. Viewing the imported reactions.

The panel is now populated with the six reactions, their stoichiometries, the energy barriers, the molecular weight, and the catalyst (populated in the Reactor Settings tab). These six reactions have been named rxn_n, where n=1-6 in the order they were added in the panel.

 

Figure 3-5. Adjusting the Partial Pressures.

  1. Change the Partial Pressure of CO, O2 and H2 to 0.02, 0.08 and 0.02 bar, leave all other pressures as zero

Figure 3-6. Setting up the Reaction Network tab.

  1. Set the Adsorbate-adsorbate interactions to Simple quadratic
  2. Set the Lateral Scaling Parameter for H:Cat to 0
  3. Change the Collision Factor to Hertz-Knudsen for reactions 1, 2, and 4. Note that we assume adsorption in these steps to be barrierless.

Figure 3-7. Viewing the reaction network.

  1. Click View Reactions
    • A window depicting the reaction network opens. The reaction network can be exported as an image.
  2. Close the window.

Figure 3-8. The Steady State tab.

  1. Go to the Steady State tab
  2. Check Calculate degree of rate control
    • The degree of rate control is an important feature in analyzing the rate-limiting step(s) in the overall reaction
  3. Check Calculate degree of selectivity control
    • The degree of selectivity control measures the influence of a particular elementary reaction step on the selectivity.

Figure 3-9. The Solver Settings tab.

  1. Go to the Solver Settings tab
  2. Set the Jacobian to Numerical
    • Numerical is recommended when computing the degree of rate control (DRC) and the degree of selectivity control (DSC) with lateral interactions
  3. Change the Job name to microkinetic_modeling_selectivity
  4. Adjust the job settings () as needed. The job can be completed in 5 minutes on a CPU host
  5. If you would like to run the job yourself, click Run. Otherwise, we will proceed with imported results files in the next section
  6. Close the Microkinetic Modeling panel

4. Analyzing a Microkinetic Modeling Calculation

In this section, we will use the Microkinetic Viewer panel to analyze the output of the previous calculation.

Figure 4-1. Loading the output file.

We will proceed to import the results (in this case from the provided files).

  1. Go to File > Import Structures
  2. Navigate to the provided files and choose microkinetic_modeling_selectivity.mae via Section_04 > microkinetic_modeling_selectivity
  3. Click Open

 

Note: When running the job yourself, after  successful completion, it will be incorporated into the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. The entry will have a WAM (workflow action menu) button () for loading the results. If the calculation fails, you can still manually import the .mae output into MS Maestro and then manually into the panel. All results for failed jobs are reported to enable analysis of the failure.

Figure 4-2. Opening the Microkinetic Viewer panel.

An entry group containing a dummy structure is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. This contains all of the data for loading the Microkinetic Viewer panel.

  1. Use the WAM (workflow action menu) button () to access the Microkinetic Viewer panel
    • Alternatively, go to Tasks > Materials > Quantum Mechanics > Surface Science > Microkinetic Modeling and use the Import from Workspace button to load the panel
    • The Microkinetic Viewer panel opens

The output data is organized into two main tabs, Time Profile and Final State, each with various subtabs. The Time Profile tab includes data across the various integration steps, whereas the Final State tab provides the data at the last step of the simulation. Complete descriptions of each tab are available in the help documentation.

Feel free to explore all of the tabs of interest. For this example, we will only highlight the outputs most relevant to this specific case.

Figure 4-3. The Coverage plot in the Time Profile tab.

  1. Go to the Time Profile tab
  2. Go to the Coverage subtab
  3. Check Plot log10, increasing small values to this power -20
    • In this case with very small coverage values, log conversion helps visualize the data

The plot shows the log10(Coverage) versus integration step. The plot indicates that a steady state solution is achieved (constant coverages, evidenced by plateaus on the plot).

Figure 4-4. The Coverage plot in the Final State tab.

  1. Go to the Final State tab
  2. Go to the Coverage subtab

Note, that the predicted total coverage by all intermediates at the steady state is ~0.45 while  coverage of the hydroxyl intermediate is almost negligible

Figure 4-5. The Selectivity plot in the Final State tab.

  1. Go to the Selectivity subtab

As shown in the plot, the calculated CO2 selectivity is around 98%, indicating the insignificance of H2O formation over flat Pd(111) catalyst.

Figure 4-6. The Degree of Rate Control plot.

  1. Go to the Derivative Properties subtab
  2. Select Net formation rate of species and pick CO2 from the dropdown menu

This bar plot illustrates the degree of rate control for each specified reaction. A higher degree of rate control signifies a greater influence of that reaction on the overall turnover frequency. For instance, the high degree of rate control observed for CO2 in reactions 1 (CO molecular adsorption) and 3 (CO oxidation) emphasizes that these elementary steps are key factors in determining the total catalytic activity.

Figure 4-7. The Degree of Selectivity plot.

  1. Go to the Degree of Selectivity Control subtab

The bar plot illustrates the degree of selectivity control (DSC) for all specified reactions. The DSC quantifies the influence of a particular elementary step on the overall selectivity toward the desired CO2 product. Importantly, the DSC values for all species must sum to zero.

 

5. Conclusion and References

In this tutorial, we learned how to use the Microkinetic Modeling panel to investigate the preferential oxidation of CO in excess H2 (CO-PROX). The primary focus was on analyzing the CO2 selectivity by examining the competitive formation of CO2 and H2O on a Pd(111) surface. Calculations predicted a very high selectivity of CO2 oxidation with almost negligible H2O formation. It must be noted that MKM predictions are only as accurate as the underlying model (e.g reaction channels and their kinetic parameters). It is important to critically examine the results, understand the most critical parameters, and reassess their reliability. In doing so, one should try to answer the following questions:

  1. Are all the important reactions included in the model?
  2. Are the activation barriers of the forward and reverse reactions accurate?
  3. What are rate-limiting or selectivity-limiting reactions?
  4. How would the results change if some reactions were excluded from or added to the reaction network?
  5. How would the results change if some kinetic parameters were modified?   

The examination of the case of CO2 oxidation shows that the high CO2 selectivity is due to the very low rate of H2O formation, which is controlled by the formation of the hydroxyl intermediate (reaction 5). This conclusion is also reflected in a high value of the Degree of Selectivity Control for this reaction (Fig. 4-7). The high activation barrier of this reaction (0.96 eV) leads to a very low coverage of OH groups (Fig 4.4) and low reaction rate. We note that the activation barrier for OH formation used in our study is the DFT-derived value for the ideal Pd(111) surface cited in literature. Further investigations reveal that (at least in the less reducing atmosphere) the experimental activation barrier for OH formation on Pd(111) is estimated at ~0.4 eV. The literature suggests that such a low activation barrier may originate from the active sites located at other (less stable) Pd surfaces, the surface steps, or other defects. Such arguments were not included in the present study. So, the next logical step of the investigation would be to see how the CO2 selectivity is affected by reducing the activation barrier for OH formation.          

For further learning:

For introductory content, focused on navigating the Schrödinger Materials Science interface, an Introduction to Materials Science Maestro tutorial is available. Please visit the materials science training website for access to 100+ tutorials. For scientific inquiries or technical troubleshooting, submit a ticket to our Technical Support Scientists at help@schrodinger.com.

For self-paced, asynchronous, online courses in Materials Science modeling, including access to Schrödinger software, please visit the Schrödinger Online Learning portal on our website.

For related practice, proceed to explore other relevant tutorials:

For further reading:

6. Glossary of Terms

Entry List - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Microkinetics - an approach to determining the properties of a reaction network by studying the elementary reactions that compose it

Project Table - displays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data

Reaction Channels - The possible pathways of elementary reactions that can link a product and reactant

Reaction Network - A collection of reaction channels

Scratch Project - a temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project

Working Directory - the location where files are saved

Workspace - the 3D display area in the center of the main window, where molecular structures are displayed