Excited State Analysis

Tutorial Created with Software Release: 2025-2
Topics: Organic Electronics
Methodology: Molecular Quantum Mechanics
Products Used: Jaguar, MS Maestro

Tutorial files

0.4 GB
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 Excited State Analysis panels to visualize and quantify charge transfer in several example systems. 

 

Tutorial Content

  1. Introduction to Excited State Analysis 

  1. Creating Projects and Importing Structures

  1. Excited State Analysis for an Organic Molecule

  1. Excited State Analysis for a Metal Complex

  1. Excited State Analysis for a Molecular Dimer

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Excited State Analysis

Defining the nature of an electronic excited state is significant for characterizing molecules with respect to their spectroscopic, photochemical or photophysical properties. In this tutorial we will be studying charge transfera type of excited state in which electron density is moving from one part of a molecule to another (intramolecular charge transfer) or from one molecule to another (intermolecular charge transfer) (CT) excited states in organometallic structures. This category of excited state can be further divided into CT states that are metal-centered, ligand-centered (intra-ligand), metal-to-ligand (MLCT), ligand-to-metal (LMCT), or ligand-to-ligand (inter-ligand). Traditionally, visual inspection of natural transition orbitalsa depiction of molecular orbitals that is known for showing the transfer of electron density between orbitals. This depiction comes from a diagonalization of the electronic transition density matrix. (NTOs) is employed to perform this classification. Beyond visual inspection, quantification of excited states based on fragmentation of a molecule (whether atom-wise, connectivity-based or metal-ligand-based; vide infra) is most informative. The workflow described herein allows the user to input a molecule for excited state analysis. The output can be studied by visualization of NTOs, but also based on fragmenting the molecule and then assessing charge transfer character quantitatively.

Figure 1: molecules of interest in this tutorial

In this tutorial, we will learn to utilize the Excited State Analysis panel. First, we will look at a simple organic molecule, 4-(dimethylamino)benzonitrile (DMABN) to demonstrate running an Excited State Analysis job in full, fragmenting the molecule for analysis, and quantification and classification of the excited states. For DMABN, or any monomeric organic molecule, only ligand-to-ligand (fragment-to-fragment) and intra-ligand (intra-fragment) excitations are possible. Then, we will look at the prototypical organometallic phosphor, Ir(ppy)3, in which the excited states include metal character, which includes analysis of MLCT and LMCT. Finally, we will analyze the excited states in a dimer system composed of the electron acceptor, 2,4,6-tris[3-(diphenylphosphinyl)phenyl]-1,3,5-triazine (PO-T2T), and the electron donor, tris(4-carbazoyl-9-ylphenyl)amine (TCTA). This demonstrates intermolecular behavior that can be described with the excited state analysis tools.

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 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/excited_state_analysis.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 excited_state_analysis_tutorial, click Save
    • The project is now named excited_state_analysis_tutorial.prj

Figure 2-3. Importing optimized structures.

 

The Excited State Analysis panel takes a molecule as input. For this tutorial we use three examples that have been pre-optimized in the ground state multiplicity, and we will import the structure files.

  1. Go to File > Import Structures
  2. Select esa_optimizedmolecules.mae and click Open

Figure 2-4. Imported optimized structures.

Three structures appear in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion in an entry group titled esa_optimizedmolecules (3) containing DMABN, Ir(ppy)3, and PO-T2T_TCTA, which have been pre-optimized

The molecules were optimized with B3LYP-D3 // 6-31G**, B3LYP-D3 // LACVP** and wB97X-D // LACV3P**, respectively. For background on optimizations, functionals and basis sets, see:

3. Excited State Analysis for an Organic Molecule

We will first perform the Excited State Analysis on DMABN.

Figure 3-1. Setting the parameters and noting the keywords.

  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 only DMABN in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • The DMABN molecule appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  2. Go to Tasks > Materials > Quantum Mechanics > Excited State Analysis > Excited State Analysis
  3. Click Jaguar Options
  4. For Theory: select M06
  5. For Basis set: select LACVP**
  6. Otherwise, we will keep the default settings, but to understand a bit more about the panel, note that several Additional keywords: are included by default
    • nroot = 5 indicates the amount of excited state roots
    • rsinglet and rtriplet allow calculation of the singlet and triplet states. These can be toggled off or on with 0 or 1. The default is to calculate both
    • With tddft_nto = 1, the NTOs will be calculated and displayed
  7. Without changing any of these Additional keywords, click OK
  8. Change the Job name: to es_analysis_DMABN

This job takes ~3 minutes on a CPU host. Adjust Job settings () as needed

  1. Click Run and close the Excited State Analysis panel

These files are also available for importing in the provided tutorial files: go to File > Import Structures, navigate to where you downloaded the tutorial files, and Open Section_03 > es_analysis_DMABN > es_analysis_DMABN_out.mae

Note: If you elect to increase nroot significantly, you may wish to turn off NTOs generation (tddft_nto = 0) to save disk space

Figure 3-2. Output from the Excited State Analysis job.

When the job is complete, a new entry group appears in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled es_analysis_DMABN_out (1) containing one entry titled DMABN

  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 DMABN from the new entry group
    • The DMABN molecule appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, with all of the NTOs simultaneously overlaid

Figure 3-3. Hiding all NTOs.

The surfaces () button allows you to (un)display NTOs

  1. Click on the surfaces () button and click Hide All
    • All of the surfaces are removed from the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 3-4. Visualizing a specific NTO.

  1. From the list of surfaces, display an NTO, by clicking on any of the orbitals in the surfaces list, for example, Singlet Excitation 1, hole from NTO1
    • The NTO appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Feel free to visualize any of the NTO outputs

Figure 3-5. The results panel, the new entry and the workspace prior to fragment defining.

  1. To open the results panel, either:
    • Use the Workflow Action Menu (WAM) button () in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to directly access the Excited State Analysis Results panel
    • Go to Tasks > Materials > Quantum Mechanics > Excited State Analysis > Excited State Analysis Results

Note: upon loading the panel, a new entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled excited_state_analysis_viewer_structure. This entry should be includedthe entry is represented in the Workspace, the circle in the In column is blue while parameterizing the Excited State Analysis Viewer

We want to quantify charge transfer from one fragment to another (or to itself). By default, the fragments to be used for the excited state characterization are the individual atoms in the molecule. Because there are 21 atoms in this structure, analyzing atom-to-atom charge transfer is not very informative. Instead, we want to partition the molecule into fragments to analyze the intra- and inter-fragment charge transfers. Several options, both automated and manual, are available for defining the fragments.

Figure 3-6. Defining fragments and updating the plots.

For DMABN, we simply wish to separate the electron-donating and electron-withdrawing groups in the molecule into separate fragments. This can be achieved using the Rotatable bonds redefining parameter:

  1. Select Redefine fragments and By molecule
  2. Select Rotatable bonds
  3. Deselect Metal-ligand bonds
  4. Click Update Plots
    • The DMABN molecule is colored in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed by fragments. In this instance, two fragments were defined, colored orange and blue

Figure 3-7. Charge transfer heat map for the S1 excitation.

  1. Go to the Charge Transfer Heat Map tab
  2. Maintain Excited State Multiplicity: as Singlet, Index: as 1 and select Annotate cells
    • The Heat Map is updated to include the composition quantities

The heat map shown is for the S1 excited state.

 

 

Note: The exact quantities may vary depending on the version of Materials Science Maestro that you are using and/or if you use different Jaguar Options

The heat map for any of the other singlet or triplet calculated excited states can be displayed by changing the multiplicity and index. The quantities in the cells, associated with the heat map shown on the right, indicate the composition of the S1 excited state, where the electron resides on the x-axis, and where the hole resides on the y-axis with the fragments color-coded to match the workspacethe 3D display area in the center of the main window, where molecular structures are displayed (fragment 1, blue, associated with the ring and the nitrile group; fragment 2, orange, associated with the dimethylamino group)

In this case, the S1 excited state is composed predominantly of π->π* excitation within the benzonitrile fragment (0.65), with a significant contribution from a 2->1 charge-transfer transition (0.32)

Note that the energy of the excited state and the oscillator strength are shown above the heat map

Feel free to explore heat maps for other excited states by changing the multiplicity and the index

Figure 3-8. Charge transfer bar graph.

  1. Go to the Charge Transfer Bar Graph tab

The bar graph shows similar information to the individual heat maps, but all at once for all of the excited states. Each bar represents an excitation, ordered from left to right from lowest to highest energy. Each bar is colored by the character of the excitation. Note that intra-fragment character is excluded from the graph, but it can be toggled on by selecting the Include intra-fragment characters check box

The graph by default includes the bars for all of the singlet and triplet states calculated, but you can choose to display only the singlet or only the triplet data using the dropdown

Feel free to explore toggling the intra-fragment characters and viewing only singlet or triplet states individually. The heat map for any given bar can be visualized back in the Charge Transfer Heat Map tab by selecting the multiplicity and index accordingly

  1. Close the Excited State Analysis Viewer

4. Excited State Analysis for a Metal Complex

We will next perform the Excited State Analysis on Ir(ppy)3.

Figure 4-1. Selecting and including the Ir. complex.

  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 Ir(ppy)3 in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • The Ir(ppy)3 molecule appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  2. Go to Tasks > Materials > Quantum Mechanics > Excited State Analysis > Excited State Analysis

Figure 4-2. Renaming the job.

  1. Maintain the parameters from the previous job (see Section 3)
  2. Change the Job name: to es_analysis_Irppy3

This job takes ~10 minutes on a CPU host. Adjust Job settings () as needed

  1. Click Run and close the Excited State Analysis panel
    • If you prefer not to run the job yourself the project files can be imported from Section_04 > es_analysis_Irppy3 > es_analysis_Irppy3_out.mae

Figure 4-3. Output from the Excited State Analysis job.

When the job is complete or the file have been imported, a new entry group appears in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled es_analysis_Irppy3_out (1) containing one entry titled Ir(ppy)3

  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 Ir(ppy)3 from the new entry group
    • The Ir(ppy)3 molecule appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, with all of the NTOs simultaneously overlaid.
  2. Click on the surfaces () button and click Hide All
    • All of the surfaces are removed from the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Feel free to explore visualizing the NTOs for this complex. Identify those NTOs which have predominantly intra-ligand excitations and those which have significant metal character

Figure 4-4. The Viewer panel and the viewer structure. 

  1. To open the results panel, either:
    • Use the Workflow Action Menu (WAM) button () in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to directly access the Excited State Analysis Results panel
    • Go to Tasks > Materials > Quantum Mechanics > Excited State Analysis > Excited State Analysis Results

Note: upon loading the panel, the excited_state_analysis_viewer_structure entry is updated to the Ir complex. Make sure it is 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 when parameterizing the Excited State Analysis Viewer

Figure 4-5. Defining metal-ligand, connectivity-based fragments.

For this example, we will want to assess metal-metal, metal-ligand, ligand-metal and ligand-ligand charge transfer. Thus, we want to define fragments by the metal-ligand bonds, such that the Ir center will be one fragment, and each ppy ligand will be another fragment

  1. In the Define Fragments tab, select Redefine fragments
  2. Select By molecule and Metal-ligand bonds only

Figure 4-6. Updating plots and color-coding the molecule by fragment.

  1. Click Update Plots
    • The structure shown in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed (excited_state_analysis_viewer_structure) is updated with color-coding to depict the fragmentation
    • There are four fragments, as expected

Figure 4-7. Charge transfer heat map.

  1. Go to the Charge Transfer Heat Map tab

Note that there are now four rows and columns corresponding with the four fragments, numbered 1 through 4, and color-coded to correspond with the representation in the workspace

  1. Change Excited State Multiplicity: to Triplet, keep the Index: as 1 and select Annotate cells
    • The Heat Map is updated to show the T1 Excited State
    • The character of the T1 state is composed of 3 equal ligand-ligand excitations, each ~16%, and 3 equal MLCT each comprising ~13%. Given the symmetry of the system. T2 and T3 have a similar distribution, although not exactly equal as symmetry was not imposed on the molecule during geometry optimization

Figure 4-8. Charge transfer bar graph.

  1. Go to the Charge Transfer Bar Graph tab

A similar analysis is possible here. Note that the first three low energy excitations (T1, T2 and T3) are almost degenerate (differing by 0.02 eV), as expected from the symmetry of the system

  1. Close the Excited State Analysis Viewer

5. Excited State Analysis for a Molecular Dimer

Finally, we will look at an interesting case of a molecular dimer composed of PO-T2T and TCTA (drawn in Figure 1 of Section 1), in which charge separation is largely intermolecular. This emissive exoplex is an instructive model for a film that may be constructed of a donor and acceptor molecule.

Figure 5-1. Selecting and including the PO-T2T/TCTA system.

  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 PO-T2T_TCTA in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • The two molecules appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

To better visualize this pair of intertwined molecules, the hydrogens are hidden in the provided input (Style menu > hide hydrogens)

Rotating the molecules (left-click and drag) in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed allows for clearer visualization

Figure 5-2. Setting the Jaguar Options.

  1. Go to Tasks > Materials > Quantum Mechanics > Excited State Analysis > Excited State Analysis
  2. Keep the Jaguar Options the same as in the first two examples, except change tddft_nto=1 to tddft_nto=0
    • This means that the NTOs will not be calculated in order to save on the computational cost of the calculation
  3. Click OK

Figure 5-3. Preparing the Excited State Analysis panel.

  1. Change the Job name: to es_analysis_PO-T2T_TCTA

This job takes ~60 minutes on a CPU host, so instead of running the job, we will import pre-generated data

  1. Close the Excited State Analysis panel

Figure 5-4. Importing the Jaguar output file.

  1. Go to Tasks > Materials > Quantum Mechanics > Excited State Analysis > Excited State Analysis Results
  2. Click Import from Jaguar Output File
  3. Navigate to where you downloaded the tutorial files, and select Section_05 > es_analysis_PO-T2T_TCTA > es_analysis_PO-T2T_TCTA_jaguar_PO-T2T_TCTA.out
  4. Click Open

Figure 5-5. Updating plots by molecule. 

Here, we would like the fragments to simply be the two molecules, to evaluate intermolecular charge transfer

  1. Select Redefine fragments
  2. Select By molecule
  3. Ensure Rotatable bonds and Metal-ligand bonds are not selected
  4. Click Update Plots
    • The structure shown in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed is updated with color-coding to depict the fragmentation
    • There are two fragments, as expected

Figure 5-6. Charge transfer heat map.

  1. Go to the Charge Transfer Heat Map tab

There are now two rows and columns corresponding with the two fragments, numbered 1 and 2, and color-coded to correspond with the representation in the workspace

  1. Select Annotate cells
    • The Heat Map shows the S1 Excited State
    • The character of the S1 state is almost entirely molecule-to-molecule charge transfer (0.96).

Feel free to explore other singlet and triplet states

Figure 5-7. Charge transfer bar graph.

  1. Go to the Charge Transfer Bar Graph tab

All of the first five singlet and triplet excited states are 2 → 1 charge transfers, clearly visualized here

  1. Close the Excited State Analysis Viewer

6. Conclusion and References

In this tutorial, we learned to use the Excited State Analysis panels to visualize and quantify charge transfer in three example systems. 

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:

For further reading:

 

7. Glossary of Terms

Charge transfer - a type of excited state in which electron density is moving from one part of a molecule to another (intramolecular charge transfer) or from one molecule to another (intermolecular charge transfer)

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

Natural transition orbitals - a depiction of molecular orbitals that is known for showing the transfer of electron density between orbitals. This depiction comes from a diagonalization of the electronic transition density matrix.

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