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 input and results files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/molecular_deposition.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 molecular_deposition_tutorial, click Save
   • The project is now named molecular_deposition_tutorial.prj

Figure 3-1. Ir(ppy)₂(tmd) in the workspace.

1. To prepare the Ir(ppy)₂(tmd) model, either a) Use the Single Complex Builder or b) go to File > Import Structures, navigate to the provided tutorial files and Open: Section_03 > Ir(ppy)2(tmd).mae
   • If you are unfamiliar with building metal complexes, see the Organometallic Complexes tutorial
   • Ensure that the entry is named Ir(ppy)2(tmd)

This complex will be used as our sole adsorbate in Section 4, and as one of our adsorbates in Section 5. We will return to it later.

Figure 3-2. CBP in the workspace.

2. To prepare the starting CBP molecule, either a) Use the 2D Sketcher or b) go to File > Import Structures, navigate to the provided tutorial files and Open: Section_03 > CBP.mae
   • If you are unfamiliar with using the 2D Sketcher, see the 2D Sketcher Panel documentation
   • Ensure that the entry is named CBP
   • If you drew the molecule yourself, be sure to perform a force-field minimization using the 3D Build palette

We will use this molecule to construct our substrate slab in this section.

Figure 3-3. TSPO1 in the workspace.

3. To prepare the starting TSPO1 molecule, either a) Use the 2D Sketcher or b) go to File > Import Structures, navigate to the provided tutorial files and Open: Section_03 > TSPO1.mae
   • If you are unfamiliar with using the 2D Sketcher, see the 2D Sketcher Panel documentation
   • Ensure that the entry is named TSPO1
   • If you drew the molecule yourself, be sure to perform a force-field minimization using the 3D Build palette

This molecule will be used as one of our adsorbates in Section 5. We will return to it later.

Figure 3-4. Selecting and including CBP and opening the Disordered System Builder.

Now, we need to build a slab of CBP molecules, which will be our substrate in the subsequent molecular deposition steps. If you have already done the Disordered System Building and MD Multistage Workflows tutorial, you will be familiar with the steps needed for constructing this cell:

4. 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 CBP from the entry list
5. Go to Tasks > Materials > Structure Builders > Disordered System
   • The Disordered System Builder panel opens
   • CBP should already be loaded into the table

Figure 3-5. Preparing the Disordered System Builder.

We will build a box of 300 CBP molecules:

6. For Initial state choose Tangled chain
   • Visit the documentation for the differences between the choices. Typically, tangled chain allows for the quickest build
7. On the Components tab, change Number of molecules to 300
   • Because CBP is the only component, it also updates to 300 in the components table

Note: If we wanted to prepare multiple cells, we could do so under the Cells tab. 

Note: We can define different types of builds in the Disorder tab. Here we simply wish to build a starting cell. We will follow this build with a molecular dynamics step. The size of the system is arbitrary, with larger numbers of molecules needed in some cases.

Note: The Cells tab is for specifying the type and number of boxes to create. In this case, we are only generating one replicate, and we (as is almost always the case) intend to use the output for an MD simulation, so the defaults are maintained. It also includes the setting to ensure that the output is ‘prepared’ for MD with a specific force field option. The default option is OPLS4 and is recommended for most systems. OPLS5 with polarizability on select chemical groups is available but it is recommended to confirm first if it is suitable for the system and property of interest given simulation time difference between OPLS5 and OPLS4. It is recommended to use OPLS4 for initial relaxation for any newly built structures. Vacuum or void space may cause OPLS5 convergence failure.

Note: Machine Learning Force Fields (MLFF) are available as an alternative to OPLS force fields. Additional information regarding MLFF can be found in the help documentation, on our website, or in the Disordered System Builder panel documentation.

Figure 3-6. Setting the Initial state, naming and running the job.

8. Change the Job name to CBP_box_DOS
9. Adjust the job settings () as needed
   • This job requires a CPU host. The job can be completed in about 30 minutes on a CPU host
10. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated Section_03 > CBP_box_DOS >  CBP_box_DOS_system-out.cms file from the provided tutorial files
11. Close the Disordered System Builder

Note: In general, always close the Disordered System Builder after use. This panel is interactive with the workspace and leaving it open can cause slowdowns

Figure 3-7. Opening the MD Multistage Workflow panel.

12. When the job is finished or after importing, 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 CBP_box_DOS_all_components_amorphous from the entry list

The system now needs to be densified using molecular dynamics:

13. Use the WAM button () to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

Figure 3-8. Preparing the MD Multistage Workflow.

14. Check Relaxation Protocol
15. Choose Compressive from the dropdown menu
    • The Compressive protocol is a 7 step workflow for densifying the box, including molecular dynamics stages. Read more in the help or revisit the Disordered System Building and MD Multistage Workflows tutorial.
16. Remove the Brownian Minimization step from the workflow using the button
    • The stage is removed from the panel (see the next Figure)

Figure 3-9. Naming and running the job.

17. Change the Job name to multistage_simulation_CBP_box
18. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 60 minutes on a GPU host
19. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated file:Section_03 > multistage_simulation_CBP_box > multistage_simulation_CBP_box-out.cms  from the provided tutorial files/.Close the MD Multistage Workflow panel

Figure 3-10. Output of the MD simulation.

20. When the job is finished or after importing, 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 new CBP_box_DOS_all_components_amorphous entry from the entry list

Note: MD simulations have a number of files associated with the job, for a full description of each file type see the help documentation on Desmond Files

 

Figure 3-11. Preparing the slab.

We next want to prepare a slab (the molecules packed at the bottom of a cell with vacuum above them)

21. Go to Tasks > Materials > Structure Builders > Slabs and Interfaces
    • The Build Slabs and Interfaces panel opens
22. Click Load to import the cell from the workspace
    • CBP_box_DOS_all_components_amorphous appears next to the Load button
23. Check Define slab
24. Maintain Slab thickness of 1.00 n, so as the existing cell is used as the slab
25. Change the Vacuum buffer to 3.00 n
    • This is the multiple (n) of the c-axis length (and in this case the slab thickness) that will be vacuum in the new cell
26. Uncheck Enforce normal C-axis
    • If this option remains checked, there may be some unexpected removal of molecules

The remaining defaults can all be maintained. The (0 0 1) Miller indices for the surface will result in a vacuum layer that is aligned along the z-direction of the original MD cell.

27. Change the Job name to CBP_slab
28. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 2 minutes on a CPU host
29. If you would like to run the job yourself, click Run. If a warning appears, click Continue. Otherwise, import the pre-generated file:Section_03 > CBP_slab > CBP_slab_base_ref_surfaces.mae  from the provided tutorial files
    • If you are running the job, upon launching, press Continue to any pop-up warnings about the cell size
30. Close the Build Slabs and Interfaces panel

Figure 3-12. Output of the slab job.

31. When the job is finished or after importing, 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 new CBP_box_DOS_all_components_amorphous-001-surface entry from the entry list

Figure 3-13. Prepare for MD.

Finally, the system must be equilibrated once more using molecular dynamics. Indeed, the forces on the molecules will be different on the surface than in the amorphous solid. To do so, first the output file type from the slab builder must be augmented.

32. Go to Tasks > Materials > Classical Mechanics > MD Simulations > Prepare for Molecular Dynamics
    • The Prepare for MD Panel opens
33. Click Run
    • The job should complete very quickly

Figure 3-14. MD settings.

34. 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 new CBP_box_DOS_all_components_amorphous-001-surface entry generated from the Prepare for MD step
    • The new entry will have MD in the entry group name and a new WAM button
35. Use the WAM button () to open the MD Multistage Workflow panel
36. Uncheck Relaxation Protocol
37. Click Append Stage
    • A new stage is added
38. Change the Stage type to Molecular Dynamics
39. Change the Ensemble class to NVT and maintain the remaining defaults
    • The default MD parameters are sufficient for this equilibration, except NVT is best to preserve the slab

Figure 3-15. Naming and running the job.

40. Change the Job name to multistage_simulation_CBP_slab
41. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 15 minutes on a GPU host
42. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated file:Section_03 > multistage_simulation_CBP_slab > multistage_simulation_CBP_slab-out.cms from the provided tutorial files
43. Close the MD Multistage Workflow panel

Figure 3-16. The slab after MD.

44. When the job is finished or after importing, 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 new CBP_box_DOS_all_components_amorphous-001-surface entry from the entry list
45. Rename the entry slab_for_deposition
    • We will use this entry in the subsequent sections as our substrate

Figure 3-17. The Manipulate Cell tool as well as the output of the manipulation after Preparing for MD.

Optional: Note that the molecules may have drifted to outside the displayed cell boundaries. This is purely visual, but we can make an adjustment to realign the box if we wish using the Manipulate Cell tool:

46. Go to Tasks > Materials > Tools > Manipulate Cell
    • The Manipulate Cell panel opens
47. For Manipulation choose Align to origin
48. For Axes choose a, b, c
49. Click Run
    • If a dialog box appears, click OK
    • A new entry is created with the same name
50. Close the Manipulate Cell panel
51. Repeat the Prepare for MD procedure (steps 32-33) described above for the aligned slab before proceeding to the deposition sections
    • If you use the output directly from manipulate cell, it is not suitable for proceeding directly to MD

The slab is now aligned better with the displayed cell. For more background on the Manipulate Cell panel, see the help documentation

Figure 4-1. Opening the Molecular Deposition panel.

1. With Ir(ppy)2(tmd) 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, go to Materials > Classical Mechanics > Molecular Deposition
   • The Molecular Deposition panel opens

Figure 4-2. Loading a single adsorbate.

2. Next to Adsorbate 1 isomers click Load selected entries
   • Ir(ppy)2(tmd) (1) appears in the panel

Note: Additional substrates (including isomers of the same substrate) can be loaded into the panel following the same procedure (interactively with the entry list). Remove an adsorbate with the button. You can also define your deposition iterations and intervals here. In this case we are depositing a single molecule once, so the defaults are sufficient. In Section 5 we will cover additional adsorbates.

Figure 4-3. Selecting and including the substrate.

3. Now, with the panel still open, 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 slab_for_deposition entry from the entry list
   • After importing the adsorbates, we must change the selection in the entry list to the substrate before we can run the job

Figure 4-4. Defining molecules for ASL.

During the deposition protocol, there is potential for drifting (i.e. the whole slab changing its position), particularly as the adsorbates impart additional momentum in the z-direction. To prevent this, we can use the Substrate positional restraints section of the panel. This makes the end analysis easier and does not alter the surface of interest.

Here we will choose a few molecules and restrain their movement artificially during the deposition. In general, only select a small number of atoms or molecules near the bottom of the slab.

4. Switch to the Simulation Protocols tab
5. In the Substrate positional restraints section of the panel, click then click Select
   • The Atom Selection window opens
6. Go to the Molecule tab
7. Choose Molecule number in entry
8. In the workspace, select three molecules towards the bottom of the box (click on an atom within each molecule)
   • As you select, the Molecule number in entry will be populated in the window

Figure 4-5. Adding the ASL selection back to the molecular deposition panel.

9. Click Add
   • The ASL box is populated accordingly
   • Note that your molecule numbers may be different than those shown in the Figure
10. Click OK
    • The Atom Selection Set ASL window closes and the Molecular Deposition panel is now populated with the ASL for restraining

Figure 4-6. Setting the simulation protocols.

11. Maintain the Force constant of 500 kcal/mol/Å
12. Uncheck Set random number seed
    • This means that each run will be based on different random numbers, and so will deliver a statistical distribution across the ten depositions that we are going to set up
    • Setting the random number seed to the same value would lead to ten identical simulations

 

There are two molecular dynamics steps. The defaults here for the first step can be maintained. To setup the second step:

13. Check Post-deposition protocols
14. Change the Ensemble class to NVT

Figure 4-7. Setting up the number of iterations and MD runs.

15. Go back to the Adsorbate tab
16. In the Run MD for each iteration after section, choose Each molecule has been added.
17. Set the Iterations to 1
    • This ensures that one MD simulation is run each time a molecule is added to the system. In this case we are running the deposition step only once, therefore, a single deposition step will be followed by a single MD run.

Figure 4-8. Naming and running the job ten times.

We will run this entire deposition job ten times, i.e. ten independent trials, by manually updating the Job name and clicking run each time.

18. Change the Job name to molecular_deposition_Ir_CBP_1
19. Adjust the job settings () as needed
    • This job requires a GPU host. Each job can be completed in about 15 minutes on a GPU host
20. If you would like to run the jobs yourself, click Run, then change the Job name to molecular_deposition_Ir_CBP_2 and so on until _10, clicking Run each time. To save time, we will import the outputs in the next step and assume that you have not run the jobs yourself
21. Close the Molecular Deposition panel

Figure 4-9. The outputs in the entry list.

22. Assuming you did not run the job, go to File > Import Structures, navigate to the provided tutorial files and choose Section_04 > Ir_CBP_all.mae
23. Click Open
    • A new entry group is added to entry list containing the ten outputs from the individual molecular deposition runs

Note that the molecules may have drifted from the displayed cell boundaries. This is purely visual. Feel free to make similar adjustments as we did above, but we will proceed without any cell manipulations.

Figure 4-10. Including all of the outputs.

Let’s improve the visualization of the output. In this example, we wish to inspect the orientations of the iridium complex on the CBP surface across the various trials.

We will begin by stylizing all of the entries:

24. Includethe entry is represented in the Workspace, the circle in the In column is blue all ten entries in the workspace
    • Recall that including means to fill the ‘In’ circle in the entry list (as shown in the Figure)
    • All ten outputs will appear in the workspace simultaneously

Figure 4-11. Element selection.

We are going to change the display so that the Ir and O atoms are easy to see, which will be a clear way to visualize the orientation of the deposited complexes:

25. From the Main Menu, go to Select > Define
    • The Atom Selection panel opens
26. In the Atom tab, choose Element
27. Choose Ir and O from the Element list
28. Click Add
    • The ASL box is populated with the ASL for the iridium and oxygen atoms. For complete documentation on using ASL for selection, see the help

Figure 4-12. Making the selection.

29. Click OK
    • The Atom Selection panel closes
    • The 10 Ir and 20 O atoms are selected in the workspace (you can see Selected 30 atoms in the Status Bar

Figure 4-13. Applying CPK to the Ir and O.

30. Go to the Style palette
31. Click on the CPK Representation ()
    • The Ir and O atoms appear in CPK representation

Figure 4-14. The overlaid outputs after changing the styles.

We can also change the CBP molecules to a more subtle style to make the Ir and O atoms even clearer:

32. From the Toolbar, click the Invert selection button ()
    • The non-Ir and O atoms are selected in the workspace (you can see Selected 179880 atoms in the Status Bar
33. Go to the Style palette
34. Click on the Wire Representation ()
    • The non-Ir and O atoms appear in wire representation
35. Zoom in on the surface to see the orientations of the iridium complexes
    • If you are having trouble stylizing the outputs, you can also import Section_04 > Ir_CBP_all_stylized.mae

Figure 4-15. A single output from the simple iridium complex deposition.

36. To view just one output, includethe entry is represented in the Workspace, the circle in the In column is blue only one of the ten entries in the workspace

 

A quick visual inspection suggests that the tmd ligands are generally oriented toward the vacuum region as opposed to towards the substrate. More advanced statistical analysis can be performed, although that is beyond the scope of this tutorial. For practice analyzing transition dipole moments, see the Calculating Transition Dipole Moments (TDM), TDM Distributions, and Order Parameter tutorial.

Figure 4-16. An overlay of molecules on the surface before (green) and after (blue) the deposition.

Optional: Another possible visual analysis is to compare the alignment of the CBP in the region of the deposited molecule on the surface before and after the deposition.

Extract the nearest CBP molecules from the site of the deposition for one of your ten trials into a new entry. Then extract those same molecules in your original slab. Overlay the two structures to compare. Some alignment at the surface is visible (pi-stacking), and in general, the surface responds to the adsorbate

 

Here are a few tips for performing this comparison in MS Maestro:

• Right-click on an atom or molecule and use the Expand Selection option to select the nearest neighbors to the deposited molecule and then the Create New Entry by option to create a new entry of just the selected molecules
• From the main menu, go to Select > Define to find the ASL for the molecules to then select them in the original slab
• Color the entries using the Style palette
• Overlay the new entries using the Superposition Panel with the Atom pairs method

Figure 5-1. Opening the Molecular Deposition panel.

1. With TSPO1 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, go to Materials > Classical Mechanics > Molecular Deposition
   • The Molecular Deposition panel opens
   • The panel should still be populated with the inputs from Section 4, meaning that Ir(ppy)₂(tmd) should already be loaded as an adsorbate. We will make some adjustments as described in the subsequent steps

Figure 5-2. Loading a second adsorbate.

2. Click Add adsorbate
3. Next to Adsorbate 2 isomers click Load selected entries
   • TSPO1 (1) appears in the panel
4. Now, with the panel still open, 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 slab_for_deposition entry from the entry list
   • As we did before, this signals to the panel the entry to use for the substrate in the calculation
   • Be sure to select the original slab - the last entry before the entries associated with Section 4

Figure 5-3. Setting the constraints  and the simulation protocol.

5. Go to the Simulation Protocols tab
6. In the Substrate positional restraints section of the panel, for Use ASL input atom.entrynum 343, 9279, 8612
   • Here we are fixing 3 atoms instead of 3 molecules to still prevent the system from drifting but also minimize restraints for this more complex system
   • The atoms were selected arbitrarily from near the bottom of the box - if you are using your own outputs you may wish to select different atoms
   • See Section 4 for a refresher on setting the restraints with ASL
7. Keep the Force constant at 500 kcal/mol/Ų
8. Maintain the other MD settings as used in Section 4

Figure 5-4. Setting up and running the job.

9. Go back to the Adsorbate tab.
10. In the Run MD for each iteration after section, choose Each molecule has been added and change Iterations to 30
    • We will deposit one Ir complex and one TSPO1 thirty times
11. Change the Job name to molecular_deposition_Ir_CBP_TSPO1
12. Adjust the job settings () as needed
    • This job requires a GPU host and can be completed in about 4 hours on a single GPU
13. If you would like to run the jobs yourself, click Run. To save time, we will import the outputs in the next step and assume that you have not run the jobs yourself
14. Close the Molecular Deposition panel

Figure 5-4. The output in the entry list after renaming.

15. Go to File > Import Structures, navigate to where you saved the tutorial files and choose Section_05 > molecular_deposition_Ir_CBP_TSPO1 > molecular_deposition_Ir_CBP_TSPO1-out.cms
    • Only the last simulation snapshot is shown. Saving the intermediate .cms and trj files and directories is disk-intensive.
16. Click Open
    • A new entry group is added to the entry list containing the final frame of the deposition protocol
17. Rename the entry deposition_Ir_CBP_TSPO1

 

 

Note that the molecules may have drifted to outside the displayed cell boundaries. This is purely visual. Feel free to make similar adjustments as we did in Section 3. We will proceed without any cell manipulations.

Figure 5-5. Watching the deposition trajectories .mp4 video.

Optional: We did not set the panel to provide the trajectories for each deposition (via the Save intermediate data checkbox), however, to demonstrate the detailed information available from a deposition run, we have saved trajectories from an analogous project. In the tutorial files, a brief .mp4 video is available to view a deposition stepwise.

Open Section_05 > deposition_trajectories.mp4 in a video player to see iterative deposition trajectories strung together.

Figure 5-6. The output in the entry list after stylizing.

18. Follow the analogous Steps in Section 4 to change the Ir and Si atoms to CPK and the remaining atoms to wire
    • Alternatively, import Section_05 > Ir_CBP_TSPO1_stylized.mae which has the style changes incorporated for you

Figure 5-7. The surface after the 60 molecule deposition.

 

A visual inspection of the surface can be performed.

Depending on your research direction, different analyses are possible:

• Analysis of orientation and rotational order of the molecules. See the Calculating Transition Dipole Moments (TDM), TDM Distributions, and Order Parameter tutorial
• Analysis of the distributions of deposited molecules

Moreover, much more complex depositions can be prepared using the Molecular Deposition panel:

• Depositions with pre-defined velocities for adsorbates
• Exclusion or inclusion of certain rotations
• Temperature dependence of deposition
• Substrate temperature dependence
• Iterative depositions to model differing experimental protocols
• Effect of iteration rapidity