1. Double-click the Materials Science icon
   • (No icon? See Starting Maestro)

Figure 2-1. Change Working Directory option.

2. Go to File > Change Working Directory
3. Find your directory, and click Choose
4. 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/surfaces_slabs.zip
5. After downloading the zip file, unzip the contents in your Working Directory for ease of access throughout the tutorial

Figure 2-2. Save Project panel.

6. Go to File > Save Project As
7. Change the File name to surface_tutorial, click Save
   • The project is now named surface_tutorial.prj

Figure 2-3. Bulk rutile structure after importing.

We will produce a TiO₂ slab from a previously generated bulk rutile structure. Information on the generation and optimization of bulk crystals is in the Electronic Structure Calculations of Bulk Crystals Using Quantum ESPRESSO tutorial. Let’s import the bulk structure now:

8. Go to File > Import Structures
9. Select bulk_TiO2.mae
10. Click Open
    • A new entry is added to the entry list titled bulk_rutile_TiO2
    • It is both 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 by default

Figure 3-1. Opening the Surface Energy Calculations panel.

1. Ensure that bulk_rutile_TiO2 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 in 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 > Quantum Mechanics > Workflows > Surface Energy
   • The Surface Energy Calculations panel opens

Figure 3-2. Defining the parameters for the slab.

3. Click Load Bulk from Workspace
   • bulk_rutile_TiO2 appears next to the button in the panel
4. Input (1 1 0) for Single plane (hkl)
5. Input 6.000 Å for Vacuum
   • This generates a reasonable vacuum buffer for a small adsorbate; buffers 10 Å or even 15 Å thick may be needed for larger adsorbates
6. Click Add
   • In the table, an entry appears for this (1 1 0) surface orientation with slab settings that can be adjusted

Figure 3-3. Visualizing the cutting planes (after adjusting the Thickness).

7. Click Show Plane
   • Two red planes in the workspace illustrate where the bulk structure will be cleaved in order to generate the slab for the yellow-highlighted entry
8. Returning to the (1 1 0) entry in the table, increase the Thickness to 3.00 layers
   • An extended bulk structure is created in the workspace to show the new cleaving planes  

Integer numbers of layers are generally best, because they preserve the stoichiometry of the bulk. A slab whose stoichiometry is different from that of the bulk will likely have an electronic or redox state that is also different from the bulk, which is usually undesirable. In any case, an integer multiple of the bulk is mandatory for computing the surface energy in this panel.

Figure 3-4. Changing the Slab bottom and visualizing the cutting planes.

It can be seen that this first proposal intersects atoms in the structure, making it a poor choice of cleaving planes. Stable surfaces are generally those that cut the minimum number of bonds. We can check other (1 1 0)-oriented cleavage planes by shifting the planes in the C direction.

Interactively adjust the Bottom, n parameter in the (1 1 0) entry in the table and see what happens to the planes in the workspace:

9. Finally, set Bottom, n  to 0.50
   • At this value the planes cut symmetrically between oxygen atoms
10. Click the Preview Slab button to generate the unoptimized slab structure in a new entry
    • Two new entries are generated, an expanded bulk cell and the slab of interest

Figure 3-5. Previewing the 3-layer (1 1 0) slab.

11. Includethe entry is represented in the Workspace, the circle in the In column is blue the new bulk_rutile_TiO2_110_surface_bottom=0.50_thickness=3.00_vacuum=6.00A entry and check that it looks correct
    • This symmetric choice of cleavage planes has produced a slab with two identical, non-polar slab faces, with overall stoichiometry (TiO₂)₆

Figure 3-6. Generating additional (1 1 0) slabs.

It is of course possible to now run the Surface Energy panel to optimize the bulk and a single slab with QE (see Section 4). However for this tutorial, we would like to construct several additional slabs of varying thicknesses and will use them to test for convergence in the next section:

12. Back in the Surface Energy Calculations panel, Add another (1 1 0) entry with the same Vacuum
13. Set Bottom, n to 0.50
14. Increase the Thickness to 4.00 layers
15. Repeat steps 12-14 to add four further (1 1 0) entries with Thicknesses of 5.00, 6.00, 7.00, and 8.00 layers
16. Ensure your panel matches what is shown in the Figure

Figure 3-7. Generating a 3-layer (1 0 1) slab.

In addition to evaluating several slab thicknesses, we may also want to evaluate slabs generated from other cutting planes

17. Input (1 0 1) for Single plane (hkl)
18. Maintain 6.000 Å for Vacuum
19. Click Add
    • In the table, an entry appears for this (1 0 1) surface orientation, with slab settings that can be adjusted
20. Increase the Thickness to 3.00 layers
21. Click Show Plane and confirm that setting Bottom, n to 0.50 gives good cutting planes
22. Click the Preview Slab button to generate the unoptimized slab structure in a new entry

Figure 3-8. Previewing the 3-layer (1 0 1) slab.

23. Includethe entry is represented in the Workspace, the circle in the In column is blue the new bulk_rutile_TiO2_101_surface_bottom=0.50_thickness=3.00_vacuum=6.00A entry and check that it looks correct
    • This symmetric choice of cleavage planes has produced a slab with two identical, non-polar slab faces

Figure 3-9. Generating all slabs of interest.

24. Repeat these steps to generate additional entries for 4-8 layer thick (1 0 1) slabs

The table in the Surface Energy panel should now match that which is shown in the figure, which contains six (1 1 0) slabs, 3-8 layers thick, and six (1 0 1) slabs, also 3-8 layers thick.

Figure 4-1. Opening the pseudopotential dialog box.

1. Back in the Surface Energy Calculations panel, click Pseudopotentials
   • Quantum ESPRESSO Calculations - Pseudopotentials panel opens

Figure 4-2. Navigating to the pseudopotentials.

2. In Path click Browse
3. Navigate to where you saved the tutorial file and choose the pseudopotentials > all_pbe_UPF_v1.5 directory
   • The Pseudopotentials panel is automatically filled with the paths to the directory and to the Ti and O specific pseudopotential files
4. Click OK to close the Pseudopotentials panel
   • A message appears that the energy cutoffs were not defined. Click OK to close the message as we will define the cutoffs in the next step

Note: Pseudopotentials are not included with the Quantum ESPRESSO installation and must be downloaded separately. There are several libraries available (see this link for more information). The pseudopotentials used in this tutorial can be downloaded from GBRV pseudopotential site.

Figure 4-3. Advanced Theory options.

5. Click Advanced Options
6. In the Theory tab, change Spin treatment to Spin-polarized
7. Change the Density functional type to GGA
   • This should automatically change the Density functional to PBE
8. Change Dispersion correction to DFT-D3
9. Set Grid plane distance to 0.1/Å
10. Check Include Γ-point
    • When computing slabs, this grid plane distance will be applied in the x and y directions, but only one k-point will be used in the z direction
11. Click Update K-point mesh
12. Confirm that the rest of the Theory settings match those shown in the Figure
13. Go to the SCF tab

Figure 4-4. Advanced Theory options, continued.

14. Click Update from pseudopotentials
    • The energy cutoff for wavefunctions is set to 40.0 Ry and the cutoff for charge density to 200.0 Ry
15. Click OK on the Info dialogue
16. Click Save

Figure 4-6. Naming and running the job.

17. Change the Job name to surface_energy_all_slabs
18. Adjust the job settings () as needed
    • This job requires a CPU host and must be run on a Linux machine. The job takes approximately 10 hours on a 12 CPU host
19. If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_04 > surface_energy_all_slabs > surface_energy_all_slabs-out.maegz.
20. Close the Surface Energy Calculations panel

Figure 4-7. Visualizing the output of the surface energy calculation.

21. When the job completes or after importing, a new entry group is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion entitled surface_energy_all_slabs-out containing the 12 DFT-optimized slabs. Feel free to visualize and stylize the outputs as you wish.  

Figure 5-1. The optimized slabs in the entry list with the imported hydroxylated slab included in the workspace.

First, let’s import a hydroxylated 4-layer TiO₂-(1 1 0) slab, functionalized with OH groups, that has been optimized for you:

1. Go to File > Import Structures, navigate to the tutorial files and import Section_05 > optimized_hydroxylated_slab.mae

Your entry list now contains 13 optimized slabs:

• 3-8 layers for (1 1 0)
• 3-8 layers for (1 0 1)
• 1 hydroxylated slab

Figure 5-2. Gas molecules in the entry list after importing.

Here we provide two gas molecules for importing (feel free to draw them yourself if you prefer):

2. Go to File > Import Structures, navigate to the tutorial files and import Section_05 > gas_molecules.mae
   • A new entry group is added to the entry list entitled gas_molecules (3). It contains P(CH₃)₃ and two identical entries of NH₂OH

Figure 5-3. Including the entry.

Depending on the size of the gas molecules, larger surface cells may be needed to provide space for them to adsorb. We will proceed with the (1 1 0) 4-layer cell, the (1 0 1) 4-layer cell and the hydroxylated 4-layer cell. Let’s make larger surface cells:

3. Includethe entry is represented in the Workspace, the circle in the In column is blue surface_energy_all_slabs_110_bott_0.50_thick_4.00_vac_6.00A (the optimized (1 1 0) 4-layer slab)

Figure 5-4. Expanding extents.

4. Click on the button (bottom-right corner of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed) to open the Periodic Structure Tool Window
5. Go to Build Cell
6. Click Extents
7. Insert 1 for the +B direction
8. Click Apply
   • An extended view of the crystal is displayed in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
   • Cell 1 x 2 x 1 is shown in green in the bottom right

Figure 5-5. Making a new P1 Cell.

9. Click on the button to open the Periodic Structure Tool Window
10. Click Make P1 Cell
    • A new entry is added to the bottom of the entry list

Note: If you are not familiar with these cell manipulations, revisit the Building and Manipulating Crystal Structures tutorial.

Note: Rotations and expansions of the cell are also possible via the Redefine Lattice panel.

Figure 5-6. The expanded (1 1 0) cell, renamed in the entry list and shown in the workspace.

11. Rename the new entry bare_TiO2_110_4layer_1x2

Figure 5-7. The three expanded cells are renamed in the entry list. The (1 0 1) cell is shown in the workspace.

12. Repeat Steps 3-11 for the (1 0 1) 4-layer cell and the hydroxylated 4-layer cell, ensuring that you are using the optimized structures. EXCEPT, make the following specifications:
    • Make the (1 0 1) cell 2x2 by inserting 1 for extents in both the +A and +B directions
    • Rename the (1 0 1) cell bare_TiO2_101_4layer_2x2 accordingly
    • Rename the hydroxylated cell hydroxylated_TiO2_110_4layer_1x2

The Figure shows the named entries in the entry list. Feel free to also import Section_05 > expanded_slabs_for_enumeration.mae from the provided files to confirm that your slabs match.

Figure 5-8. Selecting the entries and then loading the substrates into the panel.

13. 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 three expanded substrates in the entry list
14. Go to Tasks > Materials > Enumeration > Adsorption
    • The Enumerate Adsorbates panel opens
15. In the Substrates selection, with Load structures from Selected Entries chosen, click Load
    • The three substrates are loaded into the table
    • The first substrate is shown in the workspace with one atom shown as a ball proposed as the ‘most exposed’

Figure 5-9. Filtering the reactive atom to Ti.

The panel automatically proposes the most exposed atom in each structure as its Reactive Atom.

16. Change the Reactive atom filter to Ti
    • The most exposed titanium atom is selected in the first two substrates
    • Note that whether the atom is at the ‘top’ or ‘bottom’ of the slab is arbitrary and inconsequential, but can be changed manually if desired

Figure 5-10. Changing a Reactive Atom.

The panel cannot identify an exposed titanium atom in the case of the hydroxylated surface. This is, of course, expected given that none of the titanium atoms are exposed.

17. Select (click-to-highlight) the third row in the Substrates table
    • The hydroxylated slab is shown in the workspace
18. Click Pick in WS
19. Click on an exposed H to manually select the hydrogen as the Reactive Atom

The three slabs are now all imported into the panel, and each is tagged with a reactive atom (an exposed Ti for each of the bare slabs and a hydrogen atom for the hydroxylated slab)

Figure 5-11. Selecting the entries and then loading the gases into the panel.

We can now proceed to load the gas molecules:

20. Keep the Enumerate Adsorbates panel open, and return to the entry list to 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 three gas molecules
21. In the Gas molecules selection, with Load structures from Selected Entries chosen, click Load
    • The three gasses are loaded into the table
    • The first molecule is shown in the workspace with one atom shown as a ball proposed as the ‘most exposed’

Figure 5-12. Changing a Reactive Atom.

We have duplicated the hydroxylamine substrate because we could imagine being interested in analyzing adsorption via O-coordination or N-coordination:

22. Select (click-to-highlight) the second row in the Gas molecules table
    • The hydroxylamine_1 molecule is shown in the workspace
23. Click Pick in WS
24. Click on the O to manually select the nitrogen as the Reactive Atom
25. Select (click-to-highlight) the third row in the Gas molecules table
    • The hydroxylamine_2 molecule is shown in the workspace
26. Click Pick in WS
27. Click on the N to manually select the nitrogen as the Reactive Atom

Figure 5-13. Adjusting the adsorption direction settings and running the job.

28. Keep the Adsorption direction set to Automatic
    • The output with the fewest steric interactions will be chosen
29. Check Enumerate and set to 3 rotations around the adsorption axis
    • This will enumerate three rotational orientations of each adsorbate. For hydroxylamine in particular, this will result in a variety of useful starting models
30. Change the Job name to enum_adsorbates_Ti_gas
    • Confirm that your panel resembles that which is shown in the Figure
31. Adjust the job settings () as needed
    • This job requires a CPU host and takes approximately 2 minutes
32. If you would prefer to proceed with pre-generated outputs, go to File > Import Structures, navigate to the tutorial files and import Section_05 > enum_adsorbates_Ti_gas >  enum_adsorbates_Ti_gas-out.maegz. Otherwise, click Run
33. Close the Enumerate Adsorbates panel

Figure 5-14. Viewing the enumeration output.

The output is an entry group entitled enum_adsorbates_Ti_gas (27) containing the 27 possible enumerated outputs from the input (matching each surface, with each gas, in each orientation 3 x 3 x 3 = 27)

34. Includethe entry is represented in the Workspace, the circle in the In column is blue the first entry, entitled trimethylphosphine_on_bare_TiO2_110_4layer_1x2_top-28 which is associated with the adsorption of trimethylphosphine on the (1 1 0) 4-layer slab in one rotated orientation

Figure 5-15. Centering the adsorbate.

The adsorbate atoms may appear to be distributed across the cell boundaries. This is purely visual, but we can make useful adjustments if we like:

35. Right-click on the P atom in the workspace and click Center Cell on Atom
    • The cell adjusts such that the P atom is at the center of the periodic cell

Note: The Manipulate Cell panel can also be used for related adjustments

Figure 5-16. The centered adsorbate, ready for adsorption energy calculations.

Feel free to visualize any of the other enumerated adsorbates as you wish. It is recommended to extend to a 2x2x1 supercell using the periodic structure tools to check for overlap of the adsorbate with its image neighbors (rotation may relieve hindrance here). Always remember to revert back to the 1x1x1 cell afterwards before proceeding to any calculations.

Some of the enumerated structures may be unsatisfactory and can be discarded.  Settings can be adjusted in the Enumerate Adsorbates panel and it can be re-run until you are satisfied with the adsorbate structures. Note that if you want to generate a single adsorbate structure, just import one substrate, one gas molecule and include no directional enumeration.

Each enumerated structure is valid input for the Adsorption Site Finder panel, where the adsorbate can be randomly translated and rotated so as to sample more configurations (Locating Adsorption Sites on Surfaces tutorial).

It is important to note that these are just candidate, unoptimized adsorbate structures. The next step is to run DFT calculations (with Quantum ESPRESSO for periodic slabs or Jaguar for nanoparticles) to optimize the adsorbate structures and compute properties. For this tutorial, we will now proceed to compute adsorption energy for just the trimethylphosphine_on_bare_TiO2_110_4layer_1x2_top-28 system, but feel free to follow the steps in Section 6 for any of the systems.

Figure 6-1. Selecting the adsorbate structure and opening the panel.

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  trimethylphosphine_on_bare_TiO2_110_4layer_1x2_top-28 entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Note: Alternatively, you can select a batch of enumerated entries from some or all of the output of the Enumerate Adsorbates panel.

2. Go to Tasks > Materials > Quantum Mechanics > Workflows > Adsorption Energy
   • The Adsorption Energy Calculations panel opens

Note: We do not need to select the substrate or gas molecule. The adsorbate entry alone includes the requisite information about its components for the calculation.

Figure 6-2. Setting the QE Advanced Options.

The Adsorption Energy Calculations panel allows you to Generate Preview Structures before running the calculation to allow for modifications to be made to the periodic and/ or molecular system. If a job fails, or completes without successfully calculating all of the adsorption energy parameters, we can use the Restart job option to troubleshoot.

For slabs such as this, we will use periodic DFT (Quantum ESPRESSO), but note that the panel can also compute adsorption onto non-periodic systems such as nanoparticles with Jaguar.

The panel also allows adsorption energies to be computed using machine learning force fields (MLFF) and more detail is given in the Atomic Layer Deposition tutorial.

3. Ensure that Periodic with Quantum Espresso is chosen
4. Click Advanced Options
5. Adjust the Advanced Options so that they match those used previously in the tutorial:
   • On the Theory Tab: Spin-polarized, GGA, PBE, DFT-D3, Grid plane distance 0.1, include Γ point, click Update K-point mesh, ensure that there is only one k-point in the z-direction (i.e. 2 x 2 x 1), editing that value manually if necessary
   • On the SCF Tab: custom energy cutoff for wavefunctions 40.0 Ry and custom energy cutoff for charge density 200.0 Ry. Change the Max steps in SCF to 150
   • On the Optimization tab change the Number of steps to 150
6. Click Save

Figure 6-3. Setting the free energy parameters and running the job.

7. Check Adsorption free energy
   • Electronic (internal) energy is always computed and output to 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 by default as well
8. Set the Temperature to Start at 273.15 K, the Number of steps to 5 and the Step increment to 50.0 K
9. Set the Pressure to Start at 0.001 atm, the Number of steps to 3 and the Step multiplier to 10.0
   • These settings specify pressures of 0.001, 0.01 and 0.1 atm
10. Retain the Gas phase entropy lost upon adsorption at 30%
    • The entropy contribution is approximated with Jaguar. For an adsorbate that is mobile on the surface, 30% entropy loss is a good approximation. See the documentation for further discussion
11. Retain the default Jaguar Options, these settings do not need to match the Quantum ESPRESSO settings:
    • The Jaguar calculation is purely for calculating the entropy of the gas molecules (a measurable quantity) via vibrational analysis
    • Quantum ESPRESSO calculations are calculating electronic energies (not a measurable quantity)
    • Since Jaguar and Quantum ESPRESSO are calculating different, relatively independent quantities their settings do not need to match
12. Change the Job name to adsorption_energy_Ti_PMe3
13. Adjust the job settings () as needed
    • This job requires a CPU host and must be run on a Linux machine. The job takes approximately 20 hours on a 12 CPU host
14. If you would prefer to proceed with pre-generated outputs, go to File > Import Structures, navigate to the tutorial files and import Section_06 > adsorption_energy_Ti_PMe3 > adsorption_energy_Ti_PMe3-out.maegz. Otherwise, click Run
15. Close the Adsorption Energy Calculations panel

Figure 6-4. Output entry group with the optimized adsorbate structure shown.

When the job finishes or after importing, a new group of entries is created containing the optimized adsorbate and the individual gas and substrate molecules from which it was derived.

Figure 6-5. Viewing the energies in the Project Table.

16. Open 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 ()

Associated with the adsorbate entry, the Adsorption Energy (as defined in the documentation) is listed as -33.36 kcal/mol, indicative of a strong Lewis acid-base interaction between Ti and P.

Adsorption free energies at the specific temperatures and pressures are also given with the same entry in the Project Table (and can be exported as .csv)

17. Close 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

Figure 6-6. Opening the Thermochemistry Viewer.

18. Open the Thermochemistry Viewer panel via the WAM button () directly in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • Alternatively, access the panel via Tasks > Materials > Quantum Mechanics > Molecular Quantum Mechanics > Thermochemistry Viewer
    • This panel can read any energy output and plot it as a function of pressure or temperature
    • If the panel is not populated with data, select the output and click  Load Data for Selected Entries

Figure 6-7. Tuning the axes.

19. Select Joules for the Base units

The axes can be fine-tuned for easier visualization.

20. Click Axes…
    • The Axes Parameters panel opens
21. For Temperature set the Minimum to 0 and the Maximum to 600
22. For Adsorption Free Energy set the Minimum to -150 and the Maximum to -75
23. Click OK

Figure 6-8. Energy plots.

Note that you can use the Copy button to copy and paste the graph image outside of MS Maestro.

The data shows that adsorption of trimethylphosphine onto bare TiO₂-(1 1 0) at this coverage is thermodynamically favorable (ΔG<0) at all of these temperatures and pressures. In Section 5, we generated 27 adsorbate structures for various molecules on various TiO₂ facets and sites. We can repeat the adsorption energy calculations from this section for any of those other adsorbate structures. Comparing the resulting thermochemistry curves would tell us whether adsorption of those molecules onto the other surfaces is more or less favorable than trimethylphosphine onto bare TiO₂-(1 1 0).