Locating Adsorption Sites on Surfaces

Tutorial Created with Software Release: 2025-4
Topics: Catalysis & Reactivity, Energy Capture & Storage, Organic Electronics, Thin Film Processing
Methodology: All-Atom Molecular Dynamics, Machine Learning
Products Used: Desmond, MS FF Applications, MS Maestro

Tutorial files

1 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 how to prepare an adsorbate-surface system for use with the Adsorption Site Finder panel. This allows us to identify potential adsorption sites and configurations of adsorbate and surface and to calculate an estimate of the binding energy. We will compare our obtained results (OPLS4 and MLFF) with periodic DFT structures and adsorption energies.

 

Tutorial Content

  1. Introduction

  1. Creating Projects and Importing Structures

  2. Building an Initial Surface-Adsorbate Structure
  3. Running and Analyzing Adsorption Site Finder Calculations

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction

Investigating atomic-scale computational models of surfaces and interfaces is a powerful way to address research questions in application areas such as heterogeneous catalysis, thin film processing, organic electronics, and energy capture and storage.

A crucial first step is to identify possible adsorption sites on surfaces or interfaces. Without prior knowledge of where or how a molecule could bind, identifying a range of potential binding sites and configurations of the adsorbate on the surface is a good starting point for further investigation.

The Adsorption Site Finder panel uses Monte Carlo simulations to sample random configurations of adsorbates on a surface by randomly translating and rotating the rigid adsorbate. Multiple iterations of Monte Carlo simulations are performed in a simulated annealing protocol that goes from high to low temperature. The best configurations are chosen according to an estimated binding energy and then the adsorbate is relaxed while keeping the surface frozen. All the Site Finder simulations make use of force fields, either classical molecular mechanics force fields such as OPLS4 or machine learned force fields (MLFF), and both are demonstrated here.

The aim of this tutorial is to explore how and where an adsorbate could bind to a surface via molecular adsorption. Using the Import Slabs, Disordered System Builder, and Redefine Lattice panels, we will prepare and combine the structures of a surface (SiO2-OH) and an adsorbate molecule (GeMe3F). This will produce the necessary input format for the Adsorption Site Finder panel, which we will subsequently run. Finally, we will analyse the obtained adsorbate configurations on the surface, as well as their estimated binding energies, and compare these to DFT results.

2. Creating Projects and Importing Structures

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/adsorption_site_finder.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 adsorption_site_finder_tutorial, click Save
    • The project is now named adsorption_site_finder_tutorial.prj

Figure 2-3. The imported adsorbate structure.

Now we will import the adsorbate structure.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files (presumably in your working directorythe location where files are saved), and choose Section_02 > adsorbate.maegz
  3. Click Open
    • A new entry is added to your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion named GeMe3F

Note: The structure of this complex can be created from scratch using the Single Complex Builder panel. See the Organometallic Complexes tutorial and the Building Small Molecules video.

3. Building an Initial Surface-Adsorbate Structure

In this section, we will prepare the initial structure as input for the Adsorption Site Finder panel. First we will import the SiO2-OH substrate slab via the Import Slabs panel. Then we will combine the adsorbate and substrate structures and generate the correct input format with the Disordered System Builder panel to generate a randomized initial guess. Finally, we will elongate the unit cell via the Redefine Lattice panel to make room for the adsorbate molecule.

Figure 3-1. Importing the substrate slab.

  1. Go to Tasks > Materials > Structure Builders > Import Slabs
    • Alternatively you can search for the panel in the Tasks menu
    • The Import Slabs panel opens
  2. From the list of options, select the SiO2-OH_Rozanska_101-1 entry
    • We choose this slab because the original publication (see Section For Further Reading) shows that this surface is stable under typical experimental conditions and because the unit cell is small enough to validate with DFT
    • When computing surfaces with MLFF or OPLS force fields but not with DFT, larger and more complex surface cells can be studied
  3. Click Add
    • The table at the bottom of the panel should populate with information about the selected slab
  4. Check the citation agreement option
  5. Click Import Table
    • A new entry is added to your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion named SiO2-OH_Rozanska_101-1
  6. Close the Import Slabs panel

As an alternative to the Import Slabs panel, any surface of any crystalline material can be generated using the Surface Energy Calculations panel, as detailed in the tutorial on Modeling Surfaces.

The next step is to combine the adsorbate molecule and surface slab into one system. In this tutorial we will use the Disordered System Builder to do this. An alternative approach is to use the molecular adsorption function of the Enumerate Adsorbates panel (see the Modeling Surfaces tutorial).

Figure 3-2. The Disordered System Builder panel with only the adsorbate populated in the components table.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the GeMe3F entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  2. Go to Tasks > Materials > Structure Builders > Disordered System

Figure 3-3. Importing the substrate.

  1. Set the Number of molecules to 1
    • Adsorb only one molecule per cell if an Adsorption Energy calculation is to follow afterwards
    • If not, more than one molecule per cell can be specified here for the Adsorption Site Finder, if desired
  2. Includethe entry is represented in the Workspace, the circle in the In column is blue the SiO2-OH_Rozanska_101-1 entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  3. Check the option for Substrate and click Import
    • The SiO2-OH_Rozanska_101-1 is loaded into the panel
  4. Set the Substrate type to Planar interface
  5. Click Define Interface…
    • The Define Interface dialog box opens
    • A red arrow and a yellow plane are shown in the workspace, highlighting the current setting (the crystal vector b)

Figure 3-4. Defining the interface of the surface.

  1. Choose c as the Crystal vector
    • The arrow and plane in the workspace are updated, the surface is now defined as perpendicular to the c vector
  2. Click OK

Figure 3-5. Running the Disordered System Builder job.

  1. Change the Periodic Boundary Conditions (PBC) to Use/expand substrate PBC
  2. Change the Job Name to disordered_system_SiO2-OH_GeMe3F
  3. Adjust the job settings as needed
    • This job requires a CPU host and can be completed in about 1 minute
  4. If you would like to run the job yourself, click Run. Otherwise, import the provided results from the zip file via File > Import Structures: Section_03 > disordered_system_SiO2-OH_GeMe3F > disordered_system_SiO2-OH_GeMe3F_system-out.cms
    • When running the job, a warning will appear related to the extension of the c-axis in the presence of periodic bonds. It can be ignored in this case, just click Continue.
  5. Close the Disordered System Builder panel

Figure 3-6. Elongating the systems unit cell.

In order to make room and accommodate the adsorbate better, we need to elongate the unit cell of the system in c-direction

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includethe entry is represented in the Workspace, the circle in the In column is blue the output entry of the Disordered System Builder (disordered_system_SiO2-OH_GeMe3F_system)
  2. Go to Tasks > Materials > Tools > Redefine Lattice
  3. Check the Set new cell parameters option and change the length of the c direction to 25 Å
    • The transformation matrix will update automatically
  4. In the Transformation mode section select the option for Frame (only cell dimensions may change)
    • We are not trying to change the structure of the slab itself, just increase the space above the slab to have plenty of room for our adsorbate
  5. Click Run
    • This calculation requires a CPU host and will finish almost instantaneously
    • A new entry is added to your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  6. Close the Redefine Lattice panel
 

Figure 3-7. The elongated systems.

  1. Get the output entry ready for use in the next section by double clicking on the entry name and re-naming it to SiO2-OH_GeMe3F
    • A single entry outputted from the Enumerate Adsorbates panel is also valid input for the next section

4. Running and Analyzing Adsorption Site Finder Calculations

In this section, we will use the Adsorption Site Finder panel to locate potential sites of adsorption of our adsorbate molecule on the surface and. We will utilize the OPLS4 and Hybrid_MPNICE MLFF force fields. The latter is part of a class of machine learning force fields called Message Passing Network with Iterative Charge Equilibration (MPNICE). Then, we will look through the generated adsorbate-substrate configurations and check the optimized binding energies. Finally, we will compare our obtained results with structures and adsorption energies from periodic DFT results.

Figure 4-1. The Adsorption Site Finder panel.

  1. Make sure the entry SiO2-OH_GeMe3F is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includedthe entry is represented in the Workspace, the circle in the In column is blue
  2. Go to Tasks > Materials > Structure Builders > Adsorption Site Finder
  3. Keep the Maximum structures at 10
  4. Select the option Minimize
  5. In the Simulation parameters section, keep the Iterations at each temperature at 3000
  6. Select the option to Restrict search to region near surface and set the Distance from surface to 5.0 Å
  7. For our first calculation, we will keep the default OPLS4 Force field
  8. Change the Job Name to adsorption_site_finder_OPLS4
  9. Adjust the job settings as needed
    • This job requires a CPU host and can be completed in about 1 minute
  10. If you would like to run the job yourself, click Run. Otherwise, import the provided results from the zip file via File > Import Structures: Section_04 > adsorption_site_finder_OPLS4 > adsorption_site_finder_OPLS4-mc_sa.maegz.

 

 

We always recommend running a minimization, as in the preceding steps, to find a local minimum. Please note that the geometry of the adsorbate only is minimized, in the presence of the fixed substrate, which is not allowed to relax in response.

We now repeat the site finding process with a machine learning force field (MLFF) that is expected to deliver more accurate geometries and energetics. The system investigated here contains organic and inorganic species, which can be handled simultaneously by Hybrid_MPNICE. Learn more about available MLFF-type force fields, their training, application areas, and limitations in the MLFF documentation, which includes an overview of panels in Schrödinger's Materials Science Suite that have MLFFs available.

Figure 4-2. Running the Adsorption Site Finder panel with MLFF.

  1. Make sure the entry SiO2-OH_GeMe3F is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includedthe entry is represented in the Workspace, the circle in the In column is blue
  2. In case you have closed the Adsorption Site Finder panel, reopen it
  3. In the Simulation parameters section, reduce the Iterations at each temperature to 300
  4. Change the Force field to MLFF
    • An additional option appears below
  5. For Select ML Model, choose Hybrid_MPNICE from the dropdown menu
  6. Change the Job Name to adsorption_site_finder_MPNICE-hybrid
  7. Adjust the job settings as needed
    • This job requires a CPU host and can be completed in about 1 minute
  8. If you would like to run the job yourself, click Run. Otherwise, import the provided results from the zip file via File > Import Structures: Section_04 > adsorption_site_finder_MPNICE-hybrid > adsorption_site_finder_MPNICE-hybrid-mc_sa.maegz

As set in the panel, the ten configurations with the strongest (lowest) binding energy calculated with the selected force field (OPLS4 or Hybrid_MPNICE) are chosen and returned. A minimization is then performed on these ten configurations, which keeps the substrate frozen and only optimizes the adsorbate structure relative to the substrate.

We obtained a variety of different configurations. There is no filter in place to remove nearly identical structures or symmetry-equivalent structures due to the periodicity of the system. A range of different configurations have been generated at different binding sites of the substrate, e.g. with the fluoride or methyl groups pointing towards the surface. The MLFF run seems to have produced more configurations with the molecule binding close to the surface compared to the OPLS4 run.

Figure 4-3. Displaying the optimized binding energy property.

  1. Select adsorption_site_finder groups for both OPLS4 and MLFF. Includethe entry is represented in the Workspace, the circle in the In column is blue the entries in sequence via the arrow keys on your keyboard
    • It could also be helpful to includethe entry is represented in the Workspace, the circle in the In column is blue multiple configurations and tile the workspacethe 3D display area in the center of the main window, where molecular structures are displayed (see workspace toggles in the bottom right corner)
  2. Click on the three dots () in the top right corner of the entry list and click Show Property
    • The Show Properties in Table dialog box opens
  3. Click on Choose
  4. From the dropdown menu, select Binding Energy Optimized kcal/mol
  5. Click OK
    • The values now appear to the right of the entries (you may have to scroll to the right)

Note: All values can also be accessed via 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 instead.

The binding energy is calculated by subtracting the energy of the substrate and the adsorbate from the energy of the combined system. However, all of these energies are absolute energies, which are not particularly meaningful when calculated by a force field. Additionally, only the adsorbate structure was minimized and the substrate was kept fixed.

Any of these output structures from the Adsorption Site Finder panel can be used as input to the Adsorption Energy Calculations panel, which provides a way to accurately compute adsorption (or binding) energies and free energies at MLFF or DFT level - this is detailed in the Modeling Surfaces tutorial.

We now look at output from such a DFT calculation to check the Adsorption Site Finder results.

Figure 4-4. Visualizing the generated configurations of adsorbate on substrate.

We import results of a periodic DFT calculation of the same system.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files, and choose Section_04 > DFT_adsorption-energy_SiO2-OH_GeMe3F.maegz
  3. Click Open
    • A new group is added to your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion named containing two DFT optimized configurations
    • Notice that both substrate and adsorbate have been optimized in the DFT calculation
    • DFT configurations with F pointing towards surface-hydroxyl are consistent with hydrogen bonding and are also found with OPLS and MLFF

Figure 4-5. Displaying the binding and adsorption energies.

  1. Click on the three dots () in the top right corner of the entry list
    • The Show Properties in Table dialog box opens
  2. Click on Choose
  3. From the dropdown menu, select Adsorption Energy (kcal/mol)
  4. Click OK
    • The values now appear to the right of the entries (you may have to scroll to the right)
    • The DFT adsorption energies are of similar magnitude to the MLFF binding energies

Note: All values can also be accessed via 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 instead.

Overall we see that MLFF produces a slightly greater variety in terms of configurations and potential binding site locations than OPLS4. In this example, we found that the optimized binding energies from MLFF are a rough estimate of the DFT adsorption energies, indicating that the MLFF binding energies could be used to identify the most stable structures. However the quality of the MLFF treatment may differ for other chemical systems. Additionally, MLFF (like DFT) does not heed the bonds that are visualized on-screen, which means that intended or unintended reactions on the surface can take place.

The main drawback of using MLFF rather than OPLS is the computational time, which is significantly higher, limiting the size of systems that can be studied. However the computational time required for DFT is orders of magnitude higher again.

If you would like to learn how to study molecular adsorption using periodic DFT, take a look at the Modeling Surfaces and Atomic Layer Deposition tutorials.

5. Conclusion and References

In this tutorial, we learned how to explore how and where an adsorbate could bind to a surface via molecular adsorption using the Adsorption Site Finder panel. We found multiple adsorbate-surface configurations and binding sites with both OPLS4 and an MLFF, which could be good starting points for further investigation.

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 90+ 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 some related practice, proceed to explore other relevant tutorials:

For further reading:
  • Reference for the surface slab: Reconstruction and stability of ß-cristobalite 001, 101, and 111 surfaces during dehydroxylation, DOI:10.1039/C0CP00287A
  • Reference for MLFF and MPNICE: Efficient Long-Range Machine Learning Force Fields for Liquid and Materials Properties, DOI: 10.48550/arXiv.2505.06462

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

Included - the entry is represented in the Workspace, the circle in the In column is blue

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

Recent actions - This is a list of your recent actions, which you can use to reopen a panel, displayed below the Browse row. (Right-click to delete.)

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

Selected - (1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries

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