Elemental Enumeration

Tutorial Created with Software Release: 2024-4
Topics: Catalysis & Reactivity, Consumer Packaged Goods, Organic Electronics, Pharmaceutical Formulations, Polymeric Materials
Methodology: Molecular Quantum Mechanics
Products Used: MS Maestro
This tutorial is written for use with a 3-button mouse with a scroll wheel.
Words found in the Glossary of Terms are shown like this: Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

Tip: You can hover over a glossary term to display its definition. You can click on an image to expand it in the page.
Abstract:

 

In this tutorial, we will learn to use the Elemental Enumeration panel to create a set of N-substituted tetracene isomers.

 

Tutorial Content

  1. Introduction to Elemental Enumeration

  1. Creating Projects and Importing Structures

  1. Preparing N-Substituted Tetracene Isomers

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Elemental Enumeration

Calculating the properties of a collection of similar molecules is incredibly useful for tuning a particular property of a substance, such as the binding affinity for a ligand. However, creating a large selection of similar molecules can be a tedious process if one were to create each molecule by hand. Materials Science Maestro includes several structure building tools, however the Elemental Enumeration panel is particularly useful for this purpose.

In this tutorial we will show how to easily make a set of isomers using the Elemental Enumeration panel. Specifically we will show how to automate the following transformation:

Figure 1: Transforming tetracene into diazatetrazene isomers.

The panel can also be used to create a set of molecules with various vacancies and transform atoms into multiple different choices of molecules to create large molecular libraries to run further calculations with. For more information on the capabilities of this panel, see the associated documentation.

For more types of enumeration tools see the For Further Learning section at the end of this tutorial.

2. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location where files are saved in MS Maestro to make file navigation easier. Each session in MS Maestro begins with a default Scratch Projecta temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project, which is not saved. A MS Maestro project stores all your data and has a .prj extension. A project may contain numerous entries corresponding to imported structures, as well as the output of modeling-related tasks. Once a project is saved, the project is automatically saved each time a change is made.

Structures can be built in MS Maestro or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. The Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion is located to the left of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data can be accessed by Ctrl+T (Cmd+T) or Window > Project Table if you would like to see an expanded view of your project data.

  1. Double-click the Materials Science icon

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose

 

Figure 2-2. Save Project panel.

  1. Go to File > Save Project As
  2. Change the File name to _tutorial, click Save
    • The project is now named elemental_enumeration_tutorial.prj

3. Preparing N-Substituted Tetracene Isomers

In this section, we will use the Elemental Enumeration panel to create a set of N-substituted tetracene isomers.

Figure 3-1. Opening the 2D Sketcher

We will begin by sketching tetracene.

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

Figure 3-2. Drawing tetracene.

  1. Draw tetracene

If you are unfamiliar with using the 2D Sketcher panel, visit the Introduction to Materials Science Maestro tutorial, the 2D Sketcher help documentation, or watch the Building Small Molecules video in the Getting Going with Materials Science Maestro Video Series.

  1. Click Save as New and name the entry: tetracene, then click OK
    • The 3D tetracene 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
  2. Close the 2D Sketcher

 

Note: To skip manual drawing, go to Import () > Paste in Text and use the following string for tetracene: C1=CC=C2C=C3C=C4C=CC=CC4=CC3=CC2=C1 Name the entry tetracene and proceed to Step 5.

Figure 3-3. Changing the visualization style.

  1. With tetracene 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, switch to a ball-and-stick representation by clicking Style > Apply ball-and-stick representation

Note: Often at this step, it might be recommended to perform a Conformational Search. However, in this case, the molecule is rigid so there is not a substantial conformational space to be explored.

Figure 3-4. Setting the parameters for the elemental enumeration.

  1. Go to Tasks > Materials > Enumeration > Elemental
  2. In the Transmute atoms to section, for Element: input N for nitrogen
  3. In the Atoms to transmute section, check Pick atoms in Workspace
    • A banner will appear in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  4. Click on all of the carbons that have a hydrogen bond (see the selected atoms in the Figure for reference)
    • The Transmute Atoms table in the panel is populated
    • There should be a total of 12 atoms selected
  5. Set the minimum and maximum transmutations to 2
    • All of the outputs will replace exactly two C-H fragments with two nitrogen atoms
    • The total combinations defined will be 66

Let’s quickly take a closer look at the features of this panel.

In the Transmute atoms to section there are two options:

  • Element allows the user to select the element(s) that any specified atoms can be transmuted into. Multiple elements can be selected using the Periodic Table menu or by putting commas between entries in the text box.
  • Vacancy allows the user to delete any specified and the hydrogens bonded to them. The remaining bonds are not adjusted, but instead left as unsatisfied vacancies.

In the Atoms to transmute section the atoms that are to be altered or removed can be specified:

  • All atoms of element allows one to select all atoms of a particular element to transmute or remove.
  • Pick atoms in Workspace allows you to interactively select atoms in the included workspace entry to be transmuted or deleted. The table underneath is updated with the selected atoms. Remove Selected Rows can be used to remove any atoms that were mistakenly picked in the workspace selection.

The remaining options in the panel help specify how the vacancies or transmutations are performed:

  • Minimum transmutations per structure allows the user to specify the minimum number of specified atoms are transmuted or deleted per structure.
  • Maximum transmutations per structure allows the user to specify the maximum number of specified atoms are transmuted or deleted per structure.
  • Eliminate duplicates based on unique SMILES strings automatically removes duplicate molecules produced by the enumeration.
  • Randomly choose selects a random subset - the size of the subset depends on the percentage set by the user - of the total number of structures that can be created by the specified settings and only produces those structures.

Figure 3-5. Submitting the elemental enumeration calculation.

  1. Change the Job name to elemental_enumeration_tetracene
  2. Adjust the job settings () as needed and click Run
    • This job can be completed in a minute on a CPU host
    • The job takes less than 10 minutes
  3. Close the Elemental Enumeration panel

Figure 3-6. Deleting the non-transmuted tetracene entry from the group.

Once the calculation has finished you should see a new group in the entry list with 22 structures. One of these structures is the original tetracene structure, the other 21 are the results of the enumeration procedure. The duplicates within 66 structures that could have been created from the enumeration were eliminated because we left ‘Eliminate duplicates based on unique SMILES strings’ selected in the panel.

 

  1. Remove tetracene from the elemental_enumeration_tetracene_out group by:
    • 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 only the tetracene entry
    • Right-click
    • Choose delete from the menu that appears
  2. When prompted to permanently delete, choose OK
    • The original tetracene entry is still accessible in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

 

Figure 3-7. Tiling the entries via the workspace configuration panel.

We can visualize all 21 molecules at once by using the tiling features in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue all 21 isomers in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed by including the first entry, holding shift, and including the final entry
    • A warning appears about including > 10 entries. Click Continue
    • All 21 isomers appear in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed simultaneously; because they are stacked, they cannot be distinguished well
  2. Go to the Workspace Configuration Panel () and click Tile
    • All of the isomers appear tiled in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  3. Close the Workspace Configuration Panel ()

Figure 3-8. Viewing the tiled entries.

  1. You can turn off tiling by going back to the Workspace Configuration Panel () and clicking Tile by

4. Conclusion and References

In this tutorial, we learned how to use the Elemental Enumeration panel to create a set of structures by transmuting atoms from a single entry.

For further learning:

For introductory content, focused on navigating the Schrödinger Materials Science interface, an Introduction to Materials Science Maestro tutorial is available. Please visit the materials science training website for access to 70+ tutorials. For scientific inquiries or technical troubleshooting, submit a ticket to our Technical Support Scientists at help@schrodinger.com.

For self-paced, asynchronous, online courses in Materials Science modeling, including access to Schrödinger software, please visit the Schrödinger Online Learning portal on our website.

For some related practice, proceed to explore other relevant tutorials:

5. Glossary of Terms

Entry List - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

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

Project Table - displays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data

Scratch Project - a temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project

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

Working Directory - the location where files are saved

Workspace - the 3D display area in the center of the main window, where molecular structures are displayed