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/builders_organometallic.zip
5. 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.

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

Figure 3-1. Complex information.

1. Go to Tasks > Materials > Structure Builders > Single Complex
   • The Build Single Complex panel opens

First we will define the metal and its coordination geometry in the Complex information section:

2. Change Metal to Al
3. For Geometry, choose Trigonal planar
4. Nuclearity should be Monomer
5. Isomer will default to none

Figure 3-2. Using the Ligand Template dropdown.

Now we will define the ligands:

6. Use the Template dropdown menu to choose methyl (Me)

Note: You can narrow down the options by clicking the funnel icon and filtering for “Family: alkyl.” Remember to untick the filter before searching for the next ligand.

 

Note: In the Build Single Complex panel, we use R groups to designate the attachment point to the metal center. The methyl ligand is ‘monodentate,’ as it attaches to the metal via one atom. Multidentate ligands can be prepared by using multiple R groups. We will see this later in the tutorial.

 

Note: The Template dropdown includes ~400 standard organometallic ligands. The sketcher can also be used to define any ligand. If you draw ligands that you are going to use frequently, use the Save New Template and Manage Templates buttons to save ligands.

Figure 3-3. Adding two methyl ligands.

The Ligands section of the panel is used to define the coordination numbers and sites.

7. Change Copies to 2
   • The panel updates  Ligands will occupy: 2 of 3 available sites on each metal

Figure 3-4. Choosing a chloride ligand.

8. Click on the add button () to add a ligand row.
9. Choose chloro (Cl) from the Template dropdown
10. Maintain Copies: 1 for the new ligand
    • The panel updates  Ligands will occupy: 3 of 3 available sites on each metal

 

Note: The ligands demonstrated in this example are monoanionic ligands. Neutral ligands forming dative bonds should be drawn in the same way. Generally, there is no need to specify the M-L bond type.

Figure 3-5. Adding one chloride ligand and generating the complex.

We have now defined AlMe₂Cl in the Build Single Complex panel.

 

11. For Project Entry Title, type Al_Me_2_Cl
12. For Clean geometry with, choose xTB
    • This will optimize the input geometry of the complexes with GFN2-xTB
13. Click Create
14. Close the Build Single Complex panel

Figure 3-6. AlMe₂Cl in the entry list and workspace after building.

A new entry is added to the entry list titled Al_Me_2_Cl. Feel free to stylize the structure however you prefer. In the Figure, the representation is updated to ball-and-stick.

 

It is important to note that this structure is only optimized using GFN2-xTB. We will, however, optimize the structure using DFT as part of the workflow in Section 5. For additional introductory concepts regarding QM geometry optimizations, the following tutorials are recommended:

• Introduction to Geometry Optimizations, Functionals and Basis Sets
• Introduction to Multistage Quantum Mechanical Workflows

Figure 4-1. Complex information for dimer.

Our first target complex is Mn₂(CO)₁₀.

1. Go to Tasks > Materials > Structure Builders > Single Complex
   • The Build Single Complex panel opens
2. Reset the panel to remove the AlMe₂Cl complex information from the previous section.

First we will define the metal and its coordination geometry in the Complex information section:

3. Change Central atom to Mn
4. For Geometry, choose Octahedral
5. For Nuclearity, choose Dimer
   • In this option, the two metal atoms are directly bonded to one another

Figure 4-2. Using the Ligand Template dropdown.

Now we will define the ligands:

6. Use the Template dropdown menu to choose carbonyl (CO)

 

Figure 4-3. Adding five carbonyl ligands.

The Ligands section of the panel is used to define the coordination numbers and sites.

7. Change Copies to 5
   • This is the number of terminal ligands per metal.
   • The panel updates Ligands will occupy: 5 of 5 available sites on each metal

Figure 4-4. Generating the complex.

We have now defined Mn₂(CO)₁₀ in the Build Single Complex panel.

8. For Project Entry Title, type Mn_2_CO_10
9. For Clean geometry with, choose xTB
   • This will optimize the input geometry of the complexes with GFN2-xTB
10. Click Create
11. Close the Build Single Complex panel

Figure 4-5. Mn₂(CO)₁₀ in the entry list and workspace after building.

A new entry is added to the entry list titled Mn_2_CO_10. Feel free to stylize the structure however you prefer. In the Figure, the representation is updated to ball-and-stick.

 

It is important to note that this structure is only optimized using GFN2-xTB. We will demonstrate how to optimize a structure using DFT in  Section 5, using AlMe_xCl_y as an example.

Figure 4-6. Complex information for bridged dimer.

Next, we will build a bridged dimer Au₂(OAc)₂Me₄. Here, the Au atoms are not directly bonded, but rather are connected via the bidentate acetato ligand.

12. Go to Tasks > Materials > Structure Builders > Single Complex
    • The Build Single Complex panel opens
13. Reset the panel to remove the Mn₂(CO)₁₀ complex information.

First we will define the metal and its coordination geometry in the Complex information section:

14. Change Central atom to Au
15. For Geometry, choose Square planar
16. For Nuclearity, choose Bridged dimer

Figure 4-7. Adding ligands to bridged dimer

Now we will define the ligands:

17. Under Bridged Ligand Name add 2 copies of acetato (OAc)
    • This is the number of bridging ligands for the entire complex
18. Under Terminal Ligand Name add 2 copies of methyl (Me) per metal center.
    • This is the number of terminal ligands per metal
    • The panel updates: Ligands will occupy: 4 of 4 available sites on each metal

Figure 4-8. Generating the complex

We have now defined Au₂(OAc)₂Me₄ in the Build Single Complex panel.

17. For Project Entry Title, type Au_2_OAc_2_Me_4
18. For Clean geometry with, choose xTB
    • This will optimize the input geometry of the complexes with GFN2-xTB
19. Click Create
20. Close the Build Single Complex panel

Figure 4-9. Au₂OAc₂Me₄ in the entry list and workspace after building.

A new entry is added to the entry list titled Au_2_OAc_2_Me_4. Feel free to stylize the structure however you prefer. In the Figure, the representation is updated to ball-and-stick.

 

It is important to note that this structure is only optimized using GFN2-xTB. We will demonstrate how to optimize a structure using DFT in  Section 5, using AlMe_xCl_y as an example

Figure 5-1. Opening the Complex Enumeration and Stability Analysis panel and changing to Project Table ligand selection.

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 the Al_Me_2_Cl entry in the entry list and workspace
2. Go to Tasks > Materials > Enumeration > Complexes
   • The Complex Enumeration and Stability Analysis panel opens
3. Choose Project Table for Select ligands from
   • The panel updates to match that which is shown in the Figure

Figure 5-2. Choosing Stability analysis.

4. Check Stability analysis with DFT
   • Below the checkbox, Up to 8 structures will be optimized with DFT appears, indicating that this enumeration will generate up to 8 structures
5. Ensure the Central atom is set to Al
6. Click Jaguar Options

Figure 5-3. Setting the Jaguar Options.

7. Change the Theory to B3LYP-D3
8. Change the Basis set to LACVP**
9. Click OK
   • The panel updates to show the selected functional and basis set

For more detailed discussion of Jaguar options, see the Introduction to Geometry Optimizations, Functionals and Basis Sets tutorial. For metal-containing systems, B3LYP-D3/LACVP** is a reasonable default for balancing accuracy and computational expense. Of course, many other combinations of functional and basis set will give good results.

Figure 5-4. Naming and running the job.

10. Change the Job name to complex_enum_stability_Al
11. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 10 minutes on a 12 CPU host
12. If you would like to run the job yourself, click Run. Otherwise, import the provided Section_05 > complex_enum_stability_Al > complex_enum_stability_Al-out.maegz file
13. Close the Complex Enumeration and Stability Analysis panel

Figure 5-5. The output of the enumeration and stability analysis.

When the job is complete or after importing, four new entries are added to the entry list for the four enumerated complexes (AlMe₃, AlMe₂Cl, AlMeCl₂, AlCl₃)

Because the Stability analysis with DFT option was chosen, these complexes have been optimized. Feel free to visualize the various structures in the workspace.

Figure 5-6. The Project Table with the Ligand exchange stability property shown.

14. To view the relative energies of the complexes, go to the Project Table ()
15. Scroll until you see the Ligand exchange stability (kcal/mol) property

 

By definition, all homoleptic complexes are assigned a stability value of zero, as is evident for AlMe₃ and AlCl₃ in this example.  Heteroleptic complexes may be more stable (stability < 0) or less stable (stability > 0) with respect to exchanging ligands with the homoleptic complexes.  In this example, the two heteroleptic complexes are more stable than the two homoleptic ones.  The most stable combination of ligands has the lowest (i.e. most negative) ligand exchange stability - AlMeCl₂ in this example, albeit only slightly more favored than AlMe₂Cl. See the help documentation for more detail on this calculation.

 

 

Note: These data are for monomeric gas phase structures. In solution and in the solid state, aluminum complexes such as these are known to form dimers or other clusters, and the exchange energies can be expected to be different.

Figure 6-1. Opening the Complex Enumeration and Stability Analysis panel, resetting and changing to Ligand Library selection for ligands.

1. Go to Tasks > Materials > Enumeration > Complexes
   • The Complex Enumeration and Stability Analysis panel opens
2. Reset the panel by clicking the button in the bottom left corner of the panel () or using the job settings () dropdown
3. Choose Library for Primary ligand source
   • The panel updates to match that which is shown in the Figure, though you may have different Ligand library options in your dropdown menu depending on your previous use of MS Maestro

Figure 6-2. Choosing the Anionic CVD Ligands library and opening the ligand creator.

In this mode, a ligand library is used for enumeration. Several ligand libraries are provided by default with MS Maestro.

 

4. For this tutorial, start by selecting Anionic CVD ligands for the Ligand library
   • This library may in principle be used as is, but will produce a very large set of enumerated complexes.  We will therefore modify the library to make it smaller.
5. To view and modify the ligands in the Ligand Library, next to Libraries, click Modify
   • The Ligand Creator panel opens with a 2D sketcher window

Figure 6-3. Managing Ligand Libraries.

6. Switch to the Manage Ligands tab
   • A list of all the ligands in all available libraries is shown
7. Uncheck all the ligand libraries except Anionic CVD ligands
   • Only the ligands in that library are shown
   • As before, the dummy atom R₁ indicates where the ligand will be coordinated to the metal center
   • R₂ is used for bidentatea single ligand which binds to a metal center via two atoms (e.g. ethylenediamine) ligands, and so on

 

Note: To read more about the Ligand Creator panel options, check the panel help documentation

Figure 6-4. Selecting and copying ligands from the existing library.

8. For this tutorial, select the following four ligands from Anionic CVD ligands with Ctrl+Click (Cmd+Click on Mac): chloro, methyl, acetylacetonato, and diethylacetamidinato
   • Note that the ligands can be monodentatea single ligand which binds to a metal center via one atom (e.g. -CO, -Cl) (chloro, methyl here), bidentatea single ligand which binds to a metal center via two atoms (e.g. ethylenediamine) (acetylacetonato, diethylacetamidinato here) or haptic , etc. (e.g. cyclopentadienyl).
9. Click More Actions and select Copy
   • The selected ligands are copied to the clipboard. We will add them to a new library shortly

Figure 6-5. Creating a new Ligand Library.

10. At the top of the panel, click New…
    • New R-Group Library panel appears
11. For Library name, input anionic_modified then click OK
    • A new library is created that is initially empty of any ligands

Figure 6-6. Pasting copied ligands to a new library.

12. Click More Actions again and select  Paste

Figure 6-7. A new ligand library is created.

The four chosen ligands from Anionic CVD ligands are copied to the new library.

 

The new library is saved automatically.

 

13. Close the Ligand Creator panel and go back to the Complex Enumeration and Stability Analysis panel

 

Note: Chemically, each of these ligands has a single negative charge (monoanionic). However, this panel does not keep track of molecular charge. The line drawings sometimes show positive charge (e.g. N on dimethylacetamidinato), but this does not in fact affect the charge state of the complex. 

 

Note: In addition to creating ligand libraries by copying and pasting from the provided libraries, new ligands can be drawn on the Create Ligands tab and added to custom libraries.

Figure 6-8. Refreshing and then choosing a custom Ligand library.

14. Back in the Complex Enumeration and Stability Analysis panel, click Refresh to update the Ligand libraries
    • The newly created anionic-modified (4) ligand library is now visible in the dropdown list of libraries
15. Select anionic_modified (4) as the chosen Primary ligand source

Figure 6-9. Setting the complex tab.

In the Complex tab:

16. Select Ti from Periodic Table and click OK
    • Another option is to type Ti in the Central atom textbox

 

Coordination sites can be specified by a number of ligands or by a geometry. Number of ligands will generate complexes with four ligands from the library, regardless of denticitythe number of donor groups through which a single ligand binds to a metal. Kappa notation is used to describe denticity. (monodentatea single ligand which binds to a metal center via one atom (e.g. -CO, -Cl), bidentatea single ligand which binds to a metal center via two atoms (e.g. ethylenediamine) etc.). Geometry will enumerate only complexes that satisfy the geometry from the dropdown. Here we will use Number of ligands, because we would like to arrange four monoanionic ligands around the tetravalent Ti center, and allow various geometries for multidentate coordination.

 

17. Set Number of ligands to 4
18. Maintain Clean geometry with and select xTB
19. Ensure that Stability analysis with DFT is unchecked

Figure 6-10. Setting the isomers tab.

20. Go to the Isomers tab
21. Maintain Tetrahedral as 4-coordinate geometry
    • Ti complexes are typically tetrahedral
22. For Bidentate ligands, choose Do not flip
    • In this example, flipping ligands is pointless, as the bidentatea single ligand which binds to a metal center via two atoms (e.g. ethylenediamine) ligands are both symmetric
23. For Octahedral isomer, maintain Facial
    • Even with just four ligands per complex, effectively octahedral isomers may be generated if two of the four ligands are bidentatea single ligand which binds to a metal center via two atoms (e.g. ethylenediamine)
24. Make sure that Remove duplicates is checked

Figure 6-11. Naming and running the job.

25. Change the Job name to Ti_anionic_modified_enumeration

 

The compute time depends on the size of the ligand library and the speed of the computer; this example takes a few minutes using a CPU localhost. Also note that in this case, unlike in Section 5, we are not running QM calculations on the complexes. The output complexes will be unoptimized structures. We will perform a geometry optimization in Section 7.

26. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 10 minutes on a 12 CPU host
27. If you would like to run the job yourself, click Run. Otherwise, to proceed with pre-generated files, go to File > Import Structures, navigate to where you downloaded the tutorial files and import Ti_anionic_modified_enumeration-out.maegz
28. Close the Complex Enumeration and Stability Analysis panel

Figure 6-12. Output of the enumeration.

When the job finishes or after importing, a new entry group titled Ti_anionic_modified_enumeration-out is added to the entry list. Feel free to visualize and stylize the complexes as you wish.

 

The enumeration job generates dozens of structures, but some of them are identical isomers.  For example, Ti(Cl)(Cl)(Cl)(CH₃) is identical to Ti(Cl)(Cl)(CH₃)(Cl). We do not need to maintain both entries. We can conveniently find and keep only the chemically-unique isomers.

Figure 6-13. Selecting the entry list group.

29. In the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, select the entire output group by clicking on the title of the entry group Ti_anionic_modified_enumeration-out
    • The entire list of complexes is selected

 

Note: The total number of enumerated complexes might vary with different versions of MS Maestro depending on the thresholds being used for the enumeration.

Figure 6-14. Filtering duplicates.

30. With the group selected, go to Tasks and search for Filter Duplicates
    • Filter Duplicates appears in the Displaying Results area
    • Another option is to select Browse All > Project Table and Project Operations > Filter Duplicates
31. Click the Filter Duplicates task item
    • A window with a message appears indicating the number of unique entries identified (in this case, it detects 35)
    • Only the 35 unique isomers are now selected in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

 

Note: Allowing repetition, the number of unique combinations of ligands chosen from a library of ligands is . We therefore expect 35 complexes when combining 4 ligands from a library of 4 ligands. 

 

32. Click OK to close the message

Figure 6-15. Duplicating into a New Group.

33. Right-click on any of the 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, unique, isomers in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
34. Select Duplicate > Into New Group
    • The Duplicate into New Group panel opens

Figure 6-16. Naming and placing the group.

35. For the New group title, input Ti_complexes_unique
36. For Location of new group, select At top level and choose End of table
37. Click Duplicate

Figure 6-17. The new group of unique complexes.

A new group appears in entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion: Ti_complexes_unique (35) containing the unique complexes from the enumeration

Figure 7-1. Selecting the entry group and opening the QM Multistage Workflow panel.

1. In the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, 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  Ti_complexes_unique (35) group
   • All of the entries in the group are selected
2. Go to Tasks > Materials > Quantum Mechanics > Molecular Quantum Mechanics > QM Multistage Workflow…
   • The QM Multistage Workflow panel opens

Figure 7-2. Setting the QM Multistage Workflow panel.

3. For Use structures from ensure Project Table (35 selected entry) is chosen
4. For Stage type select Optimization
   • We will perform a single stage workflow where an optimization is performed on each complex
5. Change the basis set by clicking on the icon next to Basis set. Choose LACVP** from the list
   • The basis set for every structure in this job is also set to LACVP**
6. Ensure that B3LYP-D3 is selected for the Theory (functional)

 

Note: As before, many other functionals would also give good results. For more background, see: Introduction to Geometry Optimizations, Functionals and Basis Sets

 

Note: For a more complete introduction to the QM Multistage Workflow panel, see: Introduction to Multistage Quantum Mechanical Workflows

Figure 7-3. SCF tab settings.

7. Switch to the SCF tab
8. Set Maximum iterations to 200
   • For metal complexes, SCF convergence may require more iterations than the default

Figure 7-4. Optimization tab settings.

9. Switch to the Optimization tab
10. Set Maximum steps to 250
    • For metal complexes, optimization may require more steps than the default

Figure 7-5. Properties tab settings.

11. Switch to the Properties tab
12. From the Properties list, check Atomic electrostatic potential charges (ESP) and Polarizability and hyperpolarizability    

Note: Click on a property row to see more specific settings below. The default property method for polarizability is alpha, beta / analytic

Figure 7-6. Naming and running the job.

13. Change the Job name to Ti_complexes_QM_workflow
14. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 12 hours on a 12 CPU host
15. If you would like to run the job yourself, click Run. Otherwise, to proceed with pre-generated files, go to File > Import Structures, navigate to where you downloaded the tutorial files and import Ti_complexes_QM_workflow-out.maegz
16. Close the QM Multistage Workflow panel

Figure 7-7. Output of the QM job with one example entry shown in the workspace.

When the job finishes or after importing, a new entry group is added to the entry list titled Ti_complexes_QM_workflow-out (35) which contains all of the geometry optimized complexes.

 

Feel free to visualize any of the output entries in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 7-8. Polarizability data in the Project Table.

17. To view the Polarizability values, go to the Project Table ()
18. Scroll down to the 35 output files from the QM Multistage job
    • Various data will be displayed, e.g. QM Method, QM Basis, Number of canonical orbitals, Gas Phase Energy, etc.
19. If Polarizability appears as a data column, view the values for the complexes. If it is not showing, choose Window > Property Tree from the menu bar. Then, in the Property Tree, expand All > Jaguar > Secondary and check Polarizability
    • Polarizability appears as a data column in the Project Table
    • You can see the units (au) by hovering over the header of the data column
    • This data can be sorted, plotted and/or exported depending on your next directions

 

The enumerated complexes can now be ranked based on their computed polarizability.  Those with lower polarizability are likely to have lower melting and boiling points, which may be relevant for CVD and ALD applications.

 

20. Close the Project Table

Figure 7-9. Including an entry and accessing the Edit Custom Label panel.

The atomic electrostatic potential charges can be viewed in the workspace.

21. Includethe entry is represented in the Workspace, the circle in the one of the entries from the calculation (in the Figure, we include TiCl₂Me₂)
22. Go to the Style palette, click the dropdown next to Apply Labels and choose Edit Custom Label
    • The Edit Custom Label panel opens

Figure 7-10. Including an entry and accessing the Edit Custom Label panel.

23. From the label fields list, choose ESP Charges
    • If ESP Charges is not listed, use the button to add it
24. Click OK

Figure 7-11. The TiCl₂Me₂ entry with ESP charges labeled in the workspace.

The charges will be labeled in the workspace. To turn labels on and off, use the Annotations Toggle () in the bottom-right of the GUI.

Figure 7-12. Comparing ESP charges for several tiled complexes.

Optional: To compare the atomic charges across many of the complexes, tile several complexes of interest in the workspace and apply the labeling scheme.

 

Note: The polarizabilities and atomic charges can also be found in the .out file associated with each QM job.