Polymer Electrolyte Analysis

Tutorial Created with Software Release: 2026-1
Topics: Energy Capture & Storage, Polymeric Materials
Methodology: All-Atom Molecular Dynamics
Products Used: MS Maestro

Tutorial files

0.7 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:

 

As an ion diffuses through an electrolyte, it will interact with various functional groups present in the system. In this tutorial, we will learn how to use the Electrolyte Analysis panels in Materials Science Maestro to analyze and visualize the coordination environment of lithium ions diffusing through a polymer electrolyte.

 

Tutorial Content

  1. Introduction to Polymer Electrolyte Analysis

  1. Creating Projects and Importing Structures

  1. Building and Running Molecular Dynamics for a Multi-Component Box

  1. Preparing Polymer Electrolyte Analysis Calculations

  1. Analyzing the Results of the Polymer Electrolyte Analysis

  1. Conclusion and References

  1. Glossary of Terms                

1. Introduction to Polymer Electrolyte Analysis

Battery performance is impacted by how well the electrolyte can transport ions between the cathode and anode. One key chemical aspect in understanding transport is to study how the electrolyte shuttles ions, which often depends on the coordination between the two. Looking at the coordination helps to understand if the electrolyte will accept the ions, as well as how effectively the ions can diffuse through the electrolyte. The coordination count shows how well the electrolyte is filling the ion shell and how easily the ions can pass through the polymer electrolyte. Indeed, measuring and monitoring the number and origin of coordinated species around the transference ion is important to understanding the battery electrolyte performance. The most diffusive ions will frequently shift between multiple polymer electrolytes and have a higher coordination number than the ions that may oscillate between a few polymer electrolyte chains.

In this tutorial, we will learn to use the Electrolyte Analysis Calculations and Viewer panel, which are key Schrödinger capabilities for studying battery and energy storage materials and polymeric materials.

Specifically, we will study a molecular dynamics trajectory of a system containing lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt in polyethylene glycol (PEG) and calculate the coordination of oxygen around the lithium ions. We will also visualize the coordination clusters around the lithium ions to study the movement of ions (or ionic conductivity). Note that the trajectory used by the Electrolyte Analysis workflow can be created using the MD Multistage Workflow or the Diffusion workflow.

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/polymer_electrolyte_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 electrolyte_tutorial, click Save
    • The project is now named electrolyte_tutorial.prj      

Figure 2-3. The entry list after importing (the TFSI anion is included in the workspace).

We will construct a typical system containing three components: lithium cations, TFSI anions and amorphous polyethylene glycol (PEG). These components are provided:

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files (presumably in your working directorythe location where files are saved), choose inputs_electrolyte.mae
  3. 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 containing three entries

If you would prefer to practice preparing the components yourself, draw the ions in the 2D Sketcher and be sure to include charge. Generate the PEG 50-mer using the polymer builder. For background on using these tools, see the Introduction to Maestro for Materials Science and Building, Equilibrating and Analyzing Amorphous Polymers tutorials.

Note: The PEG 50-mer was prepared with the polymer builder and is linear. Because we will use the Tangled chain setting in Section 3, it is no problem to build the starting model in this way. If you are using Snapped to grid or Amorphous states, you should generate a more reasonable starting model.

3. Building and Running Molecular Dynamics for a Multi-Component Box

In this section, we will build a multi-component box with the Disordered System Builder panel. Then we will use the MD Multistage Workflow panel to perform a molecular dynamics simulation. Our simulation box will contain lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt in polyethylene glycol (PEG).

Figure 3-1. The entries selected and the Disordered System Builder panel open.

  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 the TFSI, Li and PEG entries from the entry list

Note: Please refer to the Glossary of Terms for the difference between 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 entries.

 

Note: For systems containing charged particles, it is generally a best practice to separate the anion and cation components into separate entries, as we have done here. To be sure that charges are assigned, you can open the 2D Sketcher or add charge labels in the workspace.

  1. Go to Tasks > Materials > Structure Builders > Disordered System
    • The Disordered System Builder panel opens
    • The three selected components are by default loaded into the panel
    • If you see different components or additional components, revisit Step 1

Figure 3-2. Setting the component table in the Disordered System Builder.

  1. For Initial state, choose Tangled chain
  2. Change Number of molecules to 450
  3. Change the number of TFSI and Li molecules to 200
    • The number of PEG molecules should update automatically to 50

Figure 3-3. Setting the Disorder and running the job.

  1. Change the Job name to disordered_system_Li_TFSI_PEG

 

  1. This job will take about 5 minutes on a CPU host. To adjust job settings, click on the gear () button next to the Job name. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated Section_03 > disordered_system_Li_TFSI_PEG > disordered_system_Li_TFSI_PEG_system-out.cms file from the provided tutorial files via File > Import Structures
  2. Close the Disordered System Builder

Figure 3-4. Output of the Disordered System Builder in the workspace.

When the job is complete, a new entry group will be incorporated titled MD: disordered_system_Li_TFSI_PEG_system (1) containing one entry titled disordered_system_Li_TFSI_PEG_all_components_amorphous

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the new entry
    • The box is visible in the workspace
    • Feel free to stylize as you wish. Here we show coloring by element with the ions ‘ball-and-stick’ and the polymer chains ‘wire.’
  2. Use the WAM button () to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

Here we will use a relatively standard simulation protocol to equilibrate the system, similar to that used in the Diffusion tutorial. For this example we choose the Compressive relaxation protocol, which is a seven step workflow that is effective for compressing systems that are built to low density. This relaxation protocol includes a high pressure stage intended to densify the system. Subsequently, we will implement various stages to heat up the system (for this example, we will study a model at ~500 K ) and perform molecular dynamics in three different thermodynamic ensembles. Note that protocols for MD simulations always depend on the system at hand as well as computational resources available.

The Compressive relaxation protocol is carried out at 300 K. We want to study the system at 500 K, which is an experimentally relevant condition. As a result, before further equilibration, we will use an annealing procedure to heat the system to 500 K.

We follow the annealing procedure with an MD protocol using the following steps:

  • Equilibration in the NPT ensemble to ensure that equilibrium density is obtained
  • Equilibration in the NVT ensemble, using the average equilibrated box vectors from the NPT simulation to equilibrate the temperature for a structure at average density
  • A production run in the NVE ensemble using the output of the NVT simulation to focus the simulation only on unperturbed movement of the molecules

Interesting to note, during the production run in the NVE ensemble a thermostat is not used. Therefore, it is good practice to run an NVT ensemble then switch to an NVE ensemble to ensure the system will remain close to the desired temperature when dynamics are added.

Figure 3-5. Setting up the MD Multistage Workflow (Stages 1-9).

  1. Check Relaxation protocol and choose Compressive from the dropdown list
  2. For Stage (8), change to Simulated Annealing
  3. Change the Number of stages to 2
  4. Set the Time to 0, 2000 and the Temperature to 300, 500
  5. Change the Simulation time to 2 ns and the Trajectory Recording interval to 50 ps
    • The system temperature will be linearly ramped from 300 to 500 K over the course of 2 ns
  6. Change the Ensemble class to NPT
  7. Click Append Stage
  8. For Stage (9), change to Molecular Dynamics
  9. Change the Simulation time to 10 ns and the Trajectory Recording interval to 200 ps
    • This recording interval was chosen to give a sufficient number of samples to the Average Cell stage that follows
  10. Change the Temperature to 500 K
  11. Click Append Stage

Figure 3-6. Setting up the MD Multistage Workflow (Stages 10-12).

  1. For Stage (10), change to Average Cell
  2. Click Append Stage
  3. For Stage (11), change to Molecular Dynamics
  4. Change the Simulation time to 10 ns and the Trajectory Recording interval to 1000 ps
  5. Change the Ensemble class to NVT
  6. Change the Temperature to 500 K
  7. Click Append Stage
  8. For Stage (12), change to Molecular Dynamics
  9. Change the Simulation time to 20 ns
  10. Change the Ensemble class to NVE
  11. Change the Job name to multistage_simulation_Li_TFSI_PEG
  12. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 7 hours on a GPU host
  13. If you would like to run the job yourself, click Run. Otherwise, import the pre-generated multistage_simulation_Li_TFSI_PEG-out.cms file from the provided tutorial files via File > Import Structures
  14. Close the MD Multistage Workflow panel

Figure 3-7. Output of the MD simulation.

  1. When the job is finished or after importing, 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 new disordered_system_Li_TFSI_PEG_all_components_amorphous entry from the entry list
    • MD simulations have a number of files associated with the job, for a full description of each file type see the help documentation on Desmond Files

Feel free to visualize the trajectory and stylize as you wish. Shown in the Figure is the Maestro Default preset with the ions in ball-and-stick styling.

 

4. Preparing Polymer Electrolyte Analysis Calculations

To use the Electrolyte Analysis panel, we must always begin with a trajectory from an MD simulation that contains a transference ion and a counterion. Now that we have generated a trajectory in the previous section,we can proceed to the Electrolyte Analysis workflow.

Figure 4-1. Launching the Electrolyte Analysis panel.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue disordered_system_Li_TFSI_PEG_all_components_amorphous in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  2. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > Electrolyte Analysis Calculations

 

Before we prepare this job submission, let’s learn a bit more about the general capabilities of the Electrolyte Analysis Calculations panel. For a comprehensive overview, refer to the help documentation.

The input for this panel is a trajectory from an MD simulation. All frames are loaded into the panel from the workspace. Clicking the Trajectory Frames button opens a slider that can be used to truncate the analysis to a smaller section of the trajectory, or introduce a step size to specify some interval of trajectory frames. For the most complete data set, it is recommended to use the entire trajectory range during which the system is at equilibrium for the MD simulation. Otherwise, consider using the latter region of the range (if the system is not well-equilibrated at the start) or performing another MD simulation.

The panel contains various menus:

  • Transference ion menu: Choose the cationic species which is the transport ion. In this example, it is the Li ions. If a polyatomic species is selected, the user needs to select an atom in the workspace as an example molecule of the species.
  • Counterion menu: Choose the anionic species or the counterion. In this example, it is the TFSI ions.
  • Coordination elements menu: Here we choose the coordination element(s) from the specified counterion. This chosen element (or elements) is what we wish to analyze interacting with the transference ions. Note that multiple elements can be selected except for C and H.  In the tutorial example, the oxygens in TFSI are the coordinating atoms of interest.
  • Chain coordination element menu: Choose the coordination element (or elements) from any species that are not the transference ion or counterion, for example polymers or other additives in the simulation box. Multiple elements can be selected except for C and H. Here, again, we specify oxygen, but this choice now refers to the oxygen atoms on the PEG chains.
  • Coordination cutoff menu: The maximum coordination distance between the transference ion and coordination element, in angstroms. Changing the coordination cutoff value will directly alter the output quantities. The default values are reasonable for studying the Li-O interactions herein.
  • Visualization cutoff menu: The size of the coordination sphere around the transference ions (Li) for visualization, in angstroms. This cutoff value does not need to be the same value as the coordination cutoff. Changing the visualization cutoff will alter the subsequent output images but will have no impact on the output quantities. It is simplest to select the same quantities for coordination cutoff and visualization cutoff unless you are interested in perhaps visualizing a larger coordination sphere.

Figure 4-2. Loading data into the Electrolyte Analysis panel.

  1. Click Load from Workspace
    • Next to the button, disordered_system_Li… will appear

Figure 4-3. Setting the Electrolyte Analysis parameters.

  1. For Trajectory Frames, use the entire span 0.00-20.02 ns
  2. Ensure that the Transference ion is Li and the Counterion is C2F6NO4S2 (TFSI)
    • The alternative choice in the dropdown menu, which should not be chosen, is the PEG polymer
  3. Select only O for the Coordination element
  4. Select O for the Chain coordination element
  5. Maintain 3.30 for the Coordination cutoff
  6. Maintain 3.30 for the Visualization cutoff
  7. Change the Job name to electrolyte_analysis_LiTFSI
  8. Adjust the job settings () as needed
  9. Click Run
    • This job takes ~2 minutes on a 12 CPU host
  10. Close the Electrolyte Analysis panel

5. Analyzing the Results of the Polymer Electrolyte Analysis

We will now proceed to analyze the output visually and quantitatively using the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and the Electrolyte Analysis Viewer panel.

Figure 5-1. Visualizing all clusters.

Once incorporated, a banner appears and a new group titled electrolyte_analysis_LiTFSI-out1 (201) appears in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the entry titled All clusters in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • All of the coordination spheres around the 200 lithium ions in the final frame of the trajectory are shown

Note: Molecules will be broken for ease of visualization, leaving only the atoms within the visualization cutoff radius 

Figure 5-2. Visualizing a single cluster.

Each of the subsequent entries in the group after the “All clusters” entry is associated with a unique lithium ion and its corresponding individual cluster

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue atom_3196 in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • The coordination sphere about this lithium ion is shown. The lithium ion is the soft red larger ion but feel free to change the color.

Figure 5-3. Identifying the repeat unit associated with an atom.

Because some molecules are broken, it may be helpful to see from which repeat unit an atom originates. Information about an individual atom can be noted by hovering the mouse over any atom in the visualization sphere.

  1. Hover the mouse over one of the oxygens bonded to carbon in the visualization sphere.
    • The toolbar at the bottom of the screen indicates A for repeat unit, indicating that this fragment is part of a PEG chain (the rest of the chain is outside of the visualization cutoff)

Note: In this example, TFSI is associated with TFSI, UNK with lithium, and A with PEG.

Figure 5-4. Selecting tile from the Workspace Configuration panel.

Tiling lithium ion coordination spheres is a useful approach for visualizing several environments simultaneously

  1. Click on the icon (bottom-right corner of your screen) to show the Workspace Configuration Panel
  2. Click Tile

Figure 5-5. Viewing the nine tiles.

  1. In the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, includethe entry is represented in the Workspace, the circle in the In column is blue multiple lithium ions. For example, includethe entry is represented in the Workspace, the circle in the In column is blue atom_3077 and the next five entries (Shift + Click)
    • The eight visualization spheres associated with the corresponding lithium ions appear tiled in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 5-6. Opening the Electrolyte Analysis Results panel.

Feel free to continue exploring the visualization capabilities on your own. When you are ready:

  1. Exit the tile layout by repeating Steps 4 and 5 of this section (toggling the tile option off)
  2. Includethe entry is represented in the Workspace, the circle in the In column is blue All clusters in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, as we did previously
  3. Use the WAM button () to open the Electrolyte Analysis Viewer panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Trajectory Analysis > Electrolyte Analysis Results
    • The Electrolyte Analysis Viewer panel opens
  4. Click Load from Workspace
    • So long as “All clusters” was 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, the aggregate coordination graph should populate and All clusters should appear next to the button

Figure 5-7. The Aggregate Coordination graph.

  1. Ensure that the Element is O

The graph shows the distribution of the number of oxygen atoms within the coordination cutoff of each individual lithium atom throughout the entire trajectory range. The oxygen source can be either PEG or TFSI. To view the graph for just PEG or TFSI oxygen coordination separately, toggle the Coordination source dropdown menu. This option lets you determine if the PEG is displacing the TFSI effectively and filling the coordination points. A coordination of 4-5 is considered standard coordination for the Li ions.

Figure 5-8. Chain Coordination graph.

  1. Click on the Chain Coordination tab
    • The chain coordination graph appears with Ion atom number 3001 selected

The graph shows which chain molecule(s) (identified by molecule number on the y-axis) an individual lithium atom (in this case 3001) is coordinated with over time during the course of the trajectory range (ns on the x-axis). In this example, lithium atom 3001 interacts with chain 435 for about 20 ns. The graph gives information about how often the lithium ion hops between chains, where more hopping generally means more diffusion which increases the battery electrolyte performance.

  1. Click on another lithium ion from the menu on the left to view its corresponding chain coordination plot
    • The filter search can be used if you are interested in data regarding a specific lithium ion

Figure 5-9. Number of Chains graph.

  1. Select ion atom number 3002 and click the Number of chains radio button still within the Chain Coordination tab
    • The Number of Chains graph appears

The graph shows the number of chains (count on the y-axis) an individual lithium atom (in this case 3002) is coordinating with over time during the course of the trajectory range (ns on the x-axis). In this example, lithium atom 3002 interacts with one chain for most of the trajectory, but with occasional periods in which it is interacting with two or no chains.

  1. Click on another lithium ion from the menu on the left to view its corresponding Number of Chains plot
    • The filter search can be used if you are interested in data regarding a specific lithium ion

Using the visual tools in tandem with the quantitative data analysis tools, you are able to analyze lithium ion diffusion through the polymer electrolyte system.

Note that this workflow is typically recommended to be performed in tandem with Diffusion calculations for a more comprehensive study of the electrolyte behavior. 

6. Conclusion and References

In this tutorial, we learned how to analyze the coordination environment of lithium ions diffusing through a polymer electrolyte. We learned to utilize the Electrolyte Analysis panel to set parameters for the calculation, and then practiced using the workspace to visualize the output. Finally, various data representation tools were used in the analysis viewer to examine the output from the calculation. 

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

Electrolyte - a substance that releases ions. For this tutorial, electrolyte refers to the small molecule fluid or polymer that is the carrier for battery ions.

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