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/optoelectronics.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 optoelectronics_tutorial, click Save
   • The project is now named optoelectronics_tutorial.prj

Figure 3-1. Launching the 2D Sketcher.

1. From the main menu, go to Edit > 2D Sketcher
   • The 2D sketcher opens

Note: To skip manual drawing, go to Import () > Paste in Text and use the following strings for anthracene and 2-phenylpyridine: C1=CC=C2C=C3C=CC=CC3=CC2=C1 and C1=CC=C(C=C1)C2=CC=CC=N2. Name the entries anthracene and ppy and proceed to Step 5.

Figure 3-2. Saving and naming a 2D Sketch.

2. Draw anthracene
3. Click Save as New and name the entry: anthracene, then click OK.
   • The 3D anthracene molecule will be both includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and 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

Figure 3-3. Saving and naming a 2D Sketch.

4. Keep the 2D sketcher open, erase the anthracene molecule and sketch 2-phenylpyridine (shown in the Figure)
   • To do so, use the eraser, the benzene ring, the line tool, and the N atom
5. Click Save as New and name the entry: ppy, then click OK

Note: Clicking Update Entry will overwrite the anthracene molecule. While this can be a useful way for editing a molecule in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed, in this instance, we want to draw another molecule, so Save as New should be used

Figure 3-4. Selecting both molecules and opening the Group panel.

6. Close the 2D Sketcher.

Now the 3D ppy molecule will be includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and 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

7. 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 both molecules in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion (Shift + click) and right click on either name in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
   • A menu opens
8. From the menu, click Group
   • The Group Selected Entries & Groups panel opens

Figure 3-5. Selecting both molecules and opening the Group panel.

9. Change New group title to organics
10. Select At top level for the Location of new group
11. In the corresponding option menu select Top of table
12. Click Create Group
    • The two molecules in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion are grouped under a common group called organics (2)

Note: While this grouping step is by no means required or necessary, it is a convenient way to keep your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion organized and to make multiple selections later, especially if you are developing a large project

Figure 3-6. Changing the style.

Optionally, stylize the molecules in the workspace by including the entries and switching to a ball-and-stick representation by clicking Style () > Apply ball-and-stick representation

Figure 3-7. Selecting the entry group and opening the Optoelectronics Calculations panel.

13. Ensure that the organics (2) group 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
14. Go to Tasks > Materials > Quantum Mechanics > Optoelectronics > Optoelectronics Calculations
    • The Optoelectronics Calculations panel opens

Figure 3-8. Setting the parameters in the panel.

15. For Use structures from, choose Project Table (2 selected entries)
16. For Mode, select Screening
17. Choose the following from the Property section: oxidation potential, reduction potential, hole reorganization energy, and triplet energy
18. Change the Job name to optoelectronics_organics
19. Adjust the job settings depending on your available resources, and click Run
    • This job takes ~6 minutes on a 12 CPU host
    • Pre-generated results are also available for proceeding
20. Close the Optoelectronics Calculations panel

Figure 3-9. Viewing the output files.

21. If you ran the job, 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 entry group from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion: optoelectronics_organics-opto1 (10) and proceed to Step 22
22. Otherwise, to import the pre-generated results, from the main menu, choose File > Import Structures
23. Navigate to where you downloaded the tutorial files and choose the optoelectronics_organics-opto.maegz file
24. Click Open
    • 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. The entry is automatically 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

Note: Ten outputs should be in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion (five for each molecule). The requested optoelectronics properties are calculated from a minimum number of calculations with relatively inexpensive but accurate basis sets due to the efficiency of Screening mode

Figure 3-10. Data analysis in the project table.

In Section 4 of the tutorial, we will practice using the more advanced optoelectronics analysis tools. For now, let’s simply look at some of the data for anthracene and 2-phenylpyridine in 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.

25. 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
    • Data from the job is available for perusal. Notice that in addition to the requested values, some additional output is provided, including dipole moment (D)

Figure 4-1. Viewing the imported files.

1. From the main menu, choose File > Import Structures
2. Navigate to where you downloaded the tutorial files and choose the provided Section_04 > optoelectronics_enum-opto.maegz file
3. Click Open
4. 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. The group is automatically 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
   • The group is titled optoelectronics_enum-opto (825)

Figure 4-2. Accessing the results panel via the WAM button.

The most convenient method to access the Optoelectronics Results panel is by using the Workflow Action Menu (WAM) button which appears next to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

5. Click on the WAM button and select Optoelectronics Results
   • The Optoelectronics Results panel opens

Optoelectronics data for the 165 enumerated compounds is presented in the table. In addition to the requested properties, several additional outputs are provided that are generated from the calculation at no additional computational expense

Note: The results panel can also be accessed from the tasks menu via Tasks > Materials > Quantum Mechanics > Optoelectronics > Optoelectronics Results

Figure 4-3. Enlarging a 2D structure.

Hovering the mouse over any of the structures, you can see a larger 2D image

6. Hover the mouse over any of the structures
   • A larger 2D inset appears

Figure 4-4. Optoelectronics results plot of oxidation potential, reduction potential and dipole moment.

A practical approach to sifting through a large data set is to use the plotting tool to visually identify target molecules. For this exercise, let’s suppose we are interested in identifying a 2-phenylpyridine derivative with the following attributes: oxidation potential between 1.35 and 1.50 eV, reduction potential above -2.6 eV, and a low dipole moment

7. From the X-axis dropdown menu, select Oxidation Potential (eV)
8. From the Y-axis dropdown menu, select Reduction Potential (eV)
9. From the Color by dropdown menu, select Dipole (D)
   • A results plot is immediately generated with the requested data

Figure 4-5. Clicking and dragging the dashed filter bars.

The dashed bars can be used to filter a set of target compounds.

10. Click and drag on the blue vertical dashed lines to approximately enclose the target oxidation potential region of 1.35-1.50 eV
    • The range outside of the dashed lines turns grey
11. Click and drag on the bottom red horizontal dashed line to approximately enclose the target reduction potential above -2.6 eV
    • The range outside of the dashed lines turns grey
12. Scroll in the above table and you will notice that the compounds matching the gating criteria are highlighted in yellow

Six compounds appear to fit the criteria based on oxidation and reduction potentials. Analyzing the dipole moment coloring indicates that four of the compounds have relatively lower dipole moments

Figure 4-6. Selecting the target compounds in the project table.

13. Click on the Select in PT (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) checkbox
    • The six compounds that fit the criteria are 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 in the entry list. These entries are highlighted in blue in the entry list
14. Close the Optoelectronic Results panel

Note: The Include in Workspace and Select in PT checkboxes are convenient tools for communicating between 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 and the optoelectronics results

Figure 4-7. Duplicating into a new group.

15. Back in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, right click on any of the six 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 compounds (highlighted in blue)
16. Click Duplicate > Into New Group
    • The Duplicate into New Group panel opens

Figure 4-8. Naming and creating the group.

17. Set the group title to target_compounds
18. Click the At top level radio button
19. In the corresponding option menu select Top of table
20. Click Duplicate
    • A new group is created in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled target_compounds containing the six molecules of interest
    • The group 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 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
21. Includethe entry is represented in the Workspace, the circle in the In column is blue all 6 molecules in the target_compounds group in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-9. Opening the workspace configuration panel.

To view the subset of compounds simultaneously, use the Tile option

22. Open the Workspace Configuration Panel 
23. Click on Tile
    • The six target compounds are tiled in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 4-10. Accessing Workspace Properties.

To see the exact values for the parameters of interest, you can reopen the Optoelectronics Results panel or 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 at any time and cross-reference the molecule name.

Alternatively, you may wish to include some properties in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed directly.

24. Right click on the Title in the upper-left corner of the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
25. Click Edit Workspace Properties
    • Change Workspace Properties appears

Figure 4-11. Adding Workspace Properties.

26. Click Add and select optelec oxidation potential, optelec reduction potential and optelec Dipole (D)
27. Click Close
    • Each tile now contains the title as well as the three properties of interest

Figure 4-12. Identifying a target molecule.

Based on the hypothetical criteria, the substituted 2-phenylpyridine with the lowest dipole moment (1.44) within the ideal oxidation and reduction potential ranges is identified and might be considered for further exploration