Band Shape

Tutorial Created with Software Release: 2025-3
Topics: Organic Electronics
Methodology: Molecular Quantum Mechanics
Products Used: Jaguar, MS Maestro

Tutorial files

0.6 MB
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 calculate and visualize band shape in the Materials Science Suite.

 

Tutorial Content

  1. Introduction to Band Shape

  1. Creating Projects and Importing Structures

  1. Preparing a Band Shape Input for Anthracene

  1. Visualizing and Analyzing the Band Shape Results

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Band Shape

Ultraviolet-visible (UV/Vis) spectroscopy is a key analytical technique for understanding electronic transitions in organic molecules and transition metal-containing compounds. Accurate and efficient computational prediction of UV/Vis spectra is challenging due to a large number of vibrational and rotational states available; nonetheless, the precise prediction of band shape of such spectra is significant for several applications, including but not limited to:

  • Comparison to or prediction of experimental UV/Vis spectra
  • Molecular design for optoelectronic or OLED materials
  • Color prediction and analysis of color purity
  • Detailed analysis of transitions

In this tutorial, we will learn to use the Calculate Band Shape panel to compute the UV/Vis spectrum for a prototypical organic electronic material, anthracene (Figure 1). Anthracene is a conjugated organic molecule with a diagnostic emission spectrum. We will use the Band Shape Results panel to visualize and analyze the predicted spectrum.

Figure 1: anthracene

For detailed information about the workflow and associated panels described herein, visit the help documentation. For an overview of the organic electronics project area in the Schrödinger Materials Science suite, see a summary on our website.

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 the Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. 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/band_shape.zip
  4. 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.

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

3. Preparing a Band Shape Input for Anthracene

First, we will draw our molecule of interest, anthracene, and then we will run a band shape calculation with anthracene.

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, in the 2D Sketcher window, go to the icon Edit > Paste in Text and use the following string for anthracene: C1=CC=C2C=C3C=CC=CC3=CC2=C1. Name the entry anthracene and proceed to Step 5.

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

  1. Draw anthracene
  2. 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 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 entriesin the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

The 2D sketcher functions like many standard 2D molecular drawing tools. For a complete overview of using the sketcher panel, see the 2D Sketcher Panel documentation or watch the Building Small Molecules video in the Getting Going with Materials Science Maestro Video Series.

Figure 3-3. Changing the style.

  1. Close the 2D Sketcher

The 3D anthracene 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

  1. Switch to a ball-and-stick representation by clicking Style () > Apply ball-and-stick representation

Often at this step, it would be recommended to perform a Conformational Search for the molecule. This is particularly important because several properties are quite sensitive to conformation. However, in this case, the starting geometry is suitable to proceed.

Figure 3-4. The Calculate Band Shape panel.

  1. Ensure that anthracene 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 and 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.
  2. Select Tasks > Materials > Quantum Mechanics > Band Shape  > Band Shape Calculations

Let’s familiarize ourselves a bit with some of the options in the Calculate Band Shape panel. For a complete description, visit the detailed help documentation.

  • Structure(s) can be loaded from 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 or from a file.
  • The job restart capabilities are useful for running band shape calculations at non-zero temperatures or restarting failed jobs.
  • Charge can be set, allowing for band shape calculation for cationic and anionic species.
  • You can calculate either emission or an absorption spectrum using the dropdown in the Transition>Type section of the panel.
    • By definition, an emission spectrum will always have a final state of S0, whereas an absorption spectrum will always have an initial state of S0.
    • The corresponding initial or final state can be selected from S1 and T1 depending on whether you are interested in the first excited singlet or triplet state.

    

  • Two methodologies are available for TD-DFT: Tamm-Dancoff or Linear response.
  • Two methodologies are available for obtaining the excited state geometries and vibrational frequencies: Adiabatic and Vertical.
    • The adiabatic methodology provides more accurate results but takes more time to run. The difference between the options is outlined in the help as well as in a tool-tip visible by hovering over the checkboxes.
  • Other options are available such as scaling Franck-Condon intensities, calculating intersystem and reverse intersystem crossing rates, and performing the spectrum prediction at various temperatures.
  • Finally, band shape calculations can be computationally expensive with respect to both time and memory, so two additional considerations are worth noting:
    • To minimize the computation of low-intensity transitions, you can use the Limit normal modes and Min intensity capabilities.
    • Be cautious when using Print information for intense transitions as this option requires storing information on all vibrational states, which can occupy significant memory.

Figure 3-5. Setting the parameters for the job in the Calculate Band Shape panel.

For this tutorial, we will utilize almost all of the default settings, which are designed to function very well in most typical use cases:

  1. For Excited State: select Vertical
    • This approximation greatly reduces the computational expense, which in this case does not detract from the qualitative accuracy significantly.
  2. Change the Job name: to bandshape_anthracene

Otherwise, maintain all of the panel defaults. This job takes ~30 minutes on a single CPU core. If you’d like to skip running the job and use a pre-generated output, proceed to Section 4, Step 1 now. If you’d like to run the job, adjust Job settings () as needed, click Run and then proceed to Section 4, skipping Steps 1 and 2

4. Visualizing and Analyzing the Band Shape Results

The output of the band shape calculation can be visualized and analyzed, as shown in this section.

Figure 4-1. Importing the pre-generated results file.

  1. Go to File > Import Structures
    • The Import panel opens
  2. Navigate to the downloaded tutorial files and select Section_04 > bandshape_anthracene > bandshape_anthracene_out.mae file and click Open
    • A new entry group is added to the entry list titled bandshape_anthracene_out (3), which contains three entries: initial, final and bandshape_anthracene

Figure 4-2. Output of the band shape job.

The output of the job includes three entries:

  • initial: the geometry optimized initial state, which in this case is the S1 state. If you wish, you can view the structure and analyze the vibrations ()
  • final: the geometry optimized final state, which in this case is the S0 state. If you wish, you can view the structure and analyze the vibrations ()
  • bandshape_anthracene: this entry, if 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, is the final geometry as well. Most importantly, this entry is associated with the spectrum and data of interest

Figure 4-3. Accessing the results via the WAM.

  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 In column is blue the third entry in the entry group, bandshape_anthracene.
    • The anthracene molecule (optimized in the S0 state) is displayed in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  2. To open the results panel, either:
    • Use the Workflow Action Menu (WAM) button () to directly access the spectrum viewer
    • Go to Tasks > Materials > Quantum Mechanics > Band Shape  > Band Shape Results

Figure 4-4. Loading the UV/Vis spectrum.

  1. If you accessed the panel from the Tasks menu, change Type: to UV/Vis and click Load
    • If you used the WAM button, these selections should be made by default
    • The UV/Vis spectrum appears in the plot display

Let’s familiarize ourselves a bit with some of the key features in the Spectrum Plot panel for UV/Vis. For a complete description, visit the detailed help documentation.

  • Multiple spectra can be loaded simultaneously, and they can be overlaid or stacked for convenient comparison.
  • The Line shape: options include Gaussian and Lorentzian, and the energy units can be toggled between nm and cm-1.
  • Normalize will scale the intensities such that the maximum absolute value of the displayed intensity is 1.
  • The Bin band shape spectral lines using a width of: function allows you to consolidate lines by a binning technique, which can greatly speed up the generation of the spectrum depending on the number of lines computed. Be mindful that improper binning can result in the visualization of artifacts. 
  • Within the Spectrum: section of the panel, you can use the dialog box or slider to set the scale factor (scales the frequencies of the spectral lines) or the half-bandwidth for the spectral lines. These adjustments can be key for properly visualizing key features of the band shape output.

  • On the right side of the panel, there is a data table which includes the frequency, intensity and symmetry of the spectral lines.

Figure 4-5. Normalized spectrum for anthracene with adjusted half-bandwidth.

  1. Select Normalize ()
    • The intensities are scaled such that the maximum absolute value of the displayed intensity is 1
  2. Set the Half-bandwidth: to 7 (using the slider or entering 7 into the dialog box and pressing enter)
    • The spectrum sharpens to reveal the key features

Figure 4-6. Labeling a transition on the UV/Vis spectrum.

The data table on the right side of the panel includes the frequency, intensity and symmetry of the spectral lines. Specifically, oscillator strengths corresponding with the energy bins (in this case, 400 cm-1 bins) are shown

  1. Select the row corresponding with the largest intensity (356.1 nm, 0.371)
    • The row is highlighted
  2. Click Label Selected Transitions
    • The peak is labeled on the spectrum

Note: The Offset column can be used to shift individual lines, or you can use the Offset Selected By: button to shift several selected lines simultaneously

5. Conclusion and References

In this tutorial, with a prototypical example of anthracene, we learned how to calculate and visualize band shape in the Materials Science Suite.

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 related learning, proceed to explore other relevant tutorials:

For further reading:

6. 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

Recent actions - This is a list of your recent actions, which you can use to reopen a panel, displayed below the Browse row. (Right-click to delete.)

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