Crosslinking Polymers

Tutorial Created with Software Release: 2025-4
Topics: Consumer Packaged Goods, Pharmaceutical Formulations, Polymeric Materials
Methodology: All-Atom Molecular Dynamics
Products Used: Desmond, MS Maestro

Tutorial files

0.2 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 Crosslink Polymers Calculation and Results panels to build and analyze an epoxy-amine thermosetting composite material.

 

Tutorial Content

  1. Introduction to Crosslinking

  1. Creating Projects and Importing Structures

  1. Building and Equilibrating a Multi-Component Disordered System

  1. Building and Analyzing a Crosslinked Polymer System

  1. SMARTS Patterns

  1. Conclusions and References

  1. Glossary of Terms

1. Introduction to Crosslinking

The Crosslink Polymers Calculation and Viewer panels allows you to build polymers from a periodic cell of monomers by linking monomers according to a predefined reaction scheme. In Schrödinger’s Materials Science (MS) Maestro suite, a periodic cell of monomers can be polymerized following a straightforward workflow as summarized here:

The Crosslink Polymers module is commonly used for simulating the formation of thermosetting polymer materialssynthetic materials that strengthen while being heated and cannot be remolded after their initial heat-forming. The procedure alternates between two steps: 1) the detection of potential new bonds (using cutoffs based on interatomic distances) and their formation and 2) short molecular dynamics (MD) simulations at elevated temperatures. The high-temperature MD simulations serve to equilibrate the system and to move the molecules such that the reactive groups can move into linking distance of their reaction partners. The procedure is terminated when either no new bonds can be formed, or a target percentage of possible links is reached. While not explored in this tutorial, the Crosslink Polymers panel can also incorporate an impermeable or semi-permeable potential barrier. For more information about this capability, see the Applying Barrier Potentials for Molecular Dynamics Simulations tutorial.

Crosslinking simulations allow us to build and explore the properties of crosslinked systems. The Crosslink Polymers panel is one of many in Materials Science Maestro that allows us to explore the design space of polymeric materials.

In this tutorial, we will build a thermosetting composite polymeric material from a periodic cell consisting of N,N,N′,N′-tetraglycidyl-4,4'-diaminodiphenylmethane (TGDDM) and 3,3'-diaminodiphenyl sulfone (3,3-DDS) monomers. The structure of the monomers and their crosslinking reaction is described in more detail in Section 4.

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 files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/crosslink_polymers.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 crosslink_polymers_tutorial, click Save
    • The project is now named crosslink_polymers_tutorial.prj

3. Building and Equilibrating a Multi-Component Amorphous System

In this section, we will build a randomized multi-component box with the Disordered System Builder panel containing 32 molecules each of TGDDM and 3,3-DDS. We will then use the MD Multistage Workflow panel to perform a molecular dynamics (MD) simulation. This workflow can be utilized for preparing a box containing any mixture of molecules. For a more in depth explanation of building and equilibrating disordered systems, see the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial. In the next section, we will crosslink this epoxy-amine system. If you are already comfortable building and equilibrating disordered systems, feel free to skip to Section 4 and begin crosslinking the system.

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

We will proceed to import the components that we will use in this section: TGDDM and 3,3-DDS. If you would prefer to draw or build these components yourself using the 2D Sketcher feel free to do so following similar steps outlined in the Introduction to Maestro for Materials Science tutorial. Otherwise:

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided files (presumably in your Working Directory), and choose the input_structures.mae file
  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 entitled Components (2) containing the two entries
  4. 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 TGDDM and 33DDS entries from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • Please see the Glossary of Terms for definitions of underlined terms such as “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”
  5. Go to Tasks > Materials > Structure Builders > Disordered System

Figure 3-2. Setting the Component parameters.

To satisfy stoichiometry, the total number of reactive groups of the epoxy resin (TGDDM) and the curing agent (3,3-DDS) must be equal. The crosslinking reaction scheme with reactive groups highlighted is shown in Section 4. There are four epoxy groups in TGDDM and four N-H bonds in 3,3-DDS that can react with one another. This means that we should build our system with a 1:1 stoichiometry of TGDDM:3,3-DDS.

We will keep most of the default settings in the Disordered System Builder panel, but let’s look into what these defaults are. For a more in depth explanation of the Disordered System Builder, see the Disordered System Building and Molecular Dynamics Multistage Workflows tutorial

  1. For Initial state, choose Tangled chain
  2. Ensure the Number of molecules is set to 64 in the Components tab
    • The Components tab is used to specify the structures to be included in the box, as well as their quantities and proportions
    • We will construct a cell containing 32 molecules of each monomer. This system size is relatively small, but practical for instructive purposes
  3. Go to the Cells tab

Figure 3-3. Setting the Cells parameters.

  1. We will leave the default options selected in the Cells tab. One cell containing both TGDDM and 33DDS will be created and prepared for a subsequent MD simulation
    • If we were interested in creating several cells, we could increase the Number of cells of each type
  2. Go to the Disorder tab to see the parameters for how the 64 molecules will be packed into an orthorhombic cell

Figure 3-4. Setting the Disorder parameters and running the Disordered System Builder.

The default parameters will quickly build a box that is a good starting point for subsequent MD. Other options may be more useful when building a more complex disordered system

 

  1. Change the Job name to disordered_system_TGDDM_33DDS
  2. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in less than 2 minutes on one CPU core
  3. If you would like to run the job, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_03 > disordered_system_TGDDM_33DDS > disordered_system_TGDDM_33DDS_system-out.cms
  4. Close the Disordered System Builder

 

Note: In general, always close the Disordered System Builder after use. This panel is interactive with the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and leaving it open can cause slowdowns

Figure 3-5. Viewing the disordered system.

  1. Once the job is successfully completed or imported, a new disordered_system_TGDDM_33DDS_system (1) group, with a single entry titled disordered_system_TGDDM_33DDS_all_components_amorphous, 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 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
    • The components are colored by default, but feel free to stylize as you wish

Note: If the system you are building requires an impermeable or semi-permeable barrier, it can be created before performing the molecular dynamics simulation. See our tutorial on Applying Barrier Potentials for Molecular Dynamics Simulations for more details.

Figure 3-6. Opening the MD Multistage Workflow panel 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 the output of the disordered system builder, disordered_system_TGDDM_33DDS_all_components_amorphous

MD simulations in MS Maestro are performed with the MD Multistage Workflow panel.

  1. Use the WAM (workflow action menu) button () to open the MD Multistage Workflow panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow
    • The MD Multistage Workflow panel opens

Here we will use a relatively standard simulation protocol to equilibrate the system. First, the Compressive relaxation protocol will be applied, 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 compress the system. Subsequently, we will implement an MD stage at constant temperature and pressure to equilibrate the cell and gather trajectory data for analysis. Finally, we will perform bulk analysis on the system for a variety of standard properties. Note that protocols for MD simulations always depend on the system at hand as well as computational resources available.

For a more in depth explanation of MD Multistage Workflows, see the Disordered System Building and Molecular Dynamics Multistage Workflow tutorial and the help documentation.

Figure 3-7. Setting and running the MD Multistage Workflow stages.

  1. Check Relaxation protocol and choose Compressive from the dropdown menu
  2. Change the next stage (Stage 8) to Molecular Dynamics
  3. Set the Simulation time (ns) to 5
  4. Click Append Stage
    • A 9th stage appears in the workflow
  5. Change the new stage (Stage 9) to Analysis
  6. Change the Job name to multistage_simulation_TGDDM_33DDS
  7. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 45 min on a GPU host
  8. If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open  Section_03 > multistage_simulation_TGDDM_33DDS > multistage_simulation_TGDDM_33DDS-out.cms
    • 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
  9. Close the MD Multistage Workflow panel

Figure 3-8. Visualizing the 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_TGDDM_33DDS_all_components_amorphous entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Figure 3-9. Viewing the trajectory.

  1. Click on the T button () next to this entry and select Load Trajectory
    • The trajectory is now loaded into the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Each frame in a trajectory is a snapshot of the system at a specific time period (as designated in the MD parameters by the simulation time and recording interval). The Trajectory Player enables us to examine individual frames or play the frames sequentially to visualize the course of the MD simulation. Feel free to explore the trajectory visualization if you wish.

Figure 3-10. Loading the trajectory into the MS MD Trajectory Analysis panel.

Finally, we can view bulk properties of the system over the course of the trajectory. Before we proceed to the crosslinking, it is recommended to confirm that the starting system is fairly well equilibrated. We can view the density over time to confirm this:

  1. Go to Tasks > Materials > Classical Mechanics > Trajectory Analysis > MS MD Trajectory Analysis
  2. Click Load from Workspace
    • The Simulation Details tab fills with information about the MD job and system
  3. Go to the Bulk Properties tab

Figure 3-11. Viewing bulk properties of the system.

  1. Use the dropdowns to view the various properties as a function of time from the MD stage. Select Density from the first property option menu
    • Click Final 20% to view the last 20% of the trajectory
    • It is good practice to check the density of the equilibrated system to ensure that the system has densified and equilibrated

Note: The Specific Heat Capacity (Cp for NPT, Cv for NVT) is printed at the top of the display as seen in the Figure.

  1. When you are finished, close the MS MD Trajectory Analysis panel

In the following section, we will use the optimized TGDDM-3,3-DDS cell to simulate the formation of thermosetting materials

4. Building and Analyzing a Crosslinked Polymer System

In this section, we will use the Crosslink Polymers panel to prepare a thermosetting composite polymer from our equilibrated cell containing our epoxy and amine building blocks, TGDDM and 3,3-DDS. It is good practice to use an equilibrated cell of monomers as we have provided here. The crosslinking reaction that we will model in this section is shown here:

On a mechanistic level of bond breaking and making, this epoxy curing reaction consists of breaking one NH bond in 3,3-DDS and one CO bond in TGDDM. Two new bonds are formed, a hydroxyl (OH) and an NC bond, shown in red above. Each monomer can undergo the reaction at four sites as shown in the Figure with blue circles. Indeed, the reaction will occur at multiple sites for each monomer if the conditions set in the Crosslink Polymers panel are met.

Figure 4-1. Opening the Crosslink Polymers panel.

Here, we will use the Crosslink Polymers panel on the equilibrated TGDDM-3,3-DDS system.

  1. If you followed Section 3 of this tutorial, skip ahead to Step 2. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open  Section_03 > multistage_simulation_TGDDM_33DDS >  multistage_simulation_TGDDM_33DDS-out.cms
  2. 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 equilibrated disordered_system_TGDDM_33DDS_all_components_amorphous entry
  3. Go to Tasks > Materials > Classical Mechanics > Crosslink Polymers > Crosslink Polymer Calculations

The Crosslink Polymers panel is a powerful tool that allows you to build polymers from a box of monomers by linking the monomers according to a reaction scheme. The reaction scheme must include breaking and forming two bonds, generally represented as:

A—B + C—D → A—C + B—D

The reaction occurs when the atoms involved in the bond forming are within a specified distance. There is then a short MD simulation to move the molecules around and allow for another round of bond breaking and forming. Let’s familiarize ourselves with how the Crosslink Polymers panel is operated and navigated.

  • Ensure that Use structures from points to the entry that you wish to perform the crosslinking on. If you wish to run the same protocol on several entries, select multiple from the entry list.
  • The Define Reactions tab allows you to define one or more reactions according to the general scheme above. For each reaction, two bonds are broken, labeled AB and CD, and exchanged to form two new bonds, labeled AC and BD. The bonds can be located on the same molecule or on different molecules.
    • The Reaction label in the top-left corner will display the reaction once the parameters are populated
    • The bonds participating in the reaction must be defined using SMARTS patterns. The panel will always bond A with C and B with D, according to the order of the atoms in the reactive group SMARTS strings. The SMARTS Index Panel can be used to help define SMARTS patterns for atoms of interest. Also, see Section 5 for more guidance on using SMARTS patterns
    • The search radius for forming new bonds is defined here
    • Kinetics can be defined in the Rate box if there are multiple reactions occurring
  • In the Crosslinking tab, parameters for crosslinking completion are specified. Best practice is to react the system slowly (1-5% maximum per iteration) so that it has a chance to equilibrate after forming a few new bonds
  • The Simulation Protocol tab allows us to specify parameters for the high-temperature MD simulations between crosslinking steps

Here we use the Crosslink Polymers panel to perform a single reaction, N—H + C—O → N—C + H—O, in our TGDDM-3,3-DDS system. A similar procedure, as seen in Section 5, can be followed for a system in which multiple crosslinking reactions occur simultaneously.

Read more in the detailed help documentation

Figure 4-2. Setting the Define Reactions parameters.

Now, let’s specify our crosslinking parameters:

  1. In the Define Reactions tab enter N[H] for AB reactive group SMARTS
    • In the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, all N-H groups are highlighted in yellow. We do not have to worry about specifying which N-H bonds should be broken because only 3,3-DDS has N-H bonds and they participate in the reaction
  2. For CD reactive group SMARTS, enter [C;r3;H2]O
    • In the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, all C-O groups that are part of a three membered ring and bonded to two H atoms are highlighted in blue. Here, the SMARTS pattern is specific to target only these C-O bonds as there are many others in our structure
  3. Check Reaction Threshold next to Forming AC bond: N-C and set the Max to 5.0 Å
    • N-C bonds will be formed if the two atoms are between 3.0-5.0 Å of each other in a given iteration of the crosslinking process
  4. Go to the Crosslinking tab

 

Note: The panel will always bond A with C and B with D, according to the order of the atoms in the reactive group SMARTS strings. For more on SMARTS patterns, please visit Section 5

 

Note: Use the Delete molecule checkbox if you wish for one of your products to be removed from the system. This may be useful, for example, if the reaction generates water or a gas that you do not need as a component in any subsequent study

There are three crosslinking modes available. In Standard mode, short molecular dynamics (MD) simulations are run between crosslinking iterations. This allows the monomers to move after an unsuccessful crosslinking attempt, potentially coming within bonding distance during a subsequent iteration. It also allows the system to relax after a successful crosslinking event involving the formation and breaking of bonds. This is the most time consuming mode, but is also expected to yield the highest conversion.

To speed up crosslinking jobs, the Fast mode only runs MD simulations in iterations without successful crosslinking events. After successful crosslinking iterations, only local minimization is performed. This drastically speeds up crosslinking jobs, typically at the expense of a modest decrease in crosslinking conversion compared to the Standard mode.

The High-Throughput mode displays equivalent behavior in terms of MD simulations to the Fast mode, but also skips structure checks after every crosslinking event to get rid of ring-spear. This allows for further speedup relative to the Fast mode. However, this mode can produce poor structures with new bonds formed from crosslinking through tight rings. Final structures from this mode should be verified using the Locate Rings and Spears panel.

Figure 4-3. Setting the Crosslinking parameters.

  1. For Crosslinking mode, choose Standard
  2. For Target crosslink saturation, choose applies to Rxn: 1 Group CD Count=128 ([C;r3;H2]O) from the dropdown menu
    • Here we specify that 100% of the C-O bonds identified are available to be broken and reacted
  3. Set Limit number of crosslinks per iteration to 2
    • This will limit the number of crosslinks per iteration to 2, even if more reactive groups are within the reaction threshold
    • Best practice is to set Limit number of crosslinks per iteration to a number between 1-5% of the total number of possible crosslinks
  4. Go to the Simulation Protocol tab

 

Note: Here we leave the Maximum bond order for crosslinked bond as the default of 3. This setting can be changed to prevent the formation of bonds with higher bond orders.

Figure 4-4. Setting the Simulation Protocol parameters.

  1. Set Temperature to 800.0 K
    • The MD simulations will be run at 800 K. This high temperature is utilized to ensure the molecules can move enough per iteration to ensure complete crosslinking

Note: We retain the default Ensemble class of NPT which works well for our epoxy curing reaction of interest. In general, we have the option of using either NPT or NVT for our crosslinking simulation. NVT can be useful in cases where major phase separation or pores occur during crosslinking or when a particular volume or box dimensions need to be maintained. If crosslinking with compaction as allowed in NPT ensemble is not successful, it is suggested to crosslink using the NVT ensemble.

Note: If using a barrier potential, a message will appear at the bottom of the panel in the Simulation Protocol tab indicating that a barrier has been found. If a barrier is found but you do not want to use it in the crosslinking calculation you can remove it in the Set Barrier Potential for MD panel.

  1. Change the Job name to polymer_crosslink_TGDDM_33DDS
  2. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in 4 hours on a GPU host
  3. If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open  Section_04 > polymer_crosslink_TGDDM_33DDS > polymer_crosslink_TGDDM_33DDS-out.cms
  4. Close the Crosslink Polymers panel

Figure 4-5. Viewing the crosslinked system.

  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_TGDDM_33DDS_all_components_amorphous entry from the polymer_crosslink_TGDDM_33DDS_sysbuild_system (1) entry group
    • Feel free to visualize the output system in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. You can see that we have generated a single composite output

Figure 4-6. Opening the Crosslink Polymers Viewer panel. 

We can analyze the Crosslink Polymers calculation further using the Crosslink Polymers Results panel:

  1. Use the WAM (workflow action menu) button () to open the Crosslink Polymers Results panel
    • Alternatively, access the panel via Tasks > Materials > Classical Mechanics > Crosslink Polymers > Crosslink Polymer Results
    • The Crosslink Polymers Viewer panel opens
    • Note that when the Viewer panel is opened, the individual crosslinking iterations load in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and the last entry 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. The results panel opens with a view of the plain text log file

Figure 4-7. Coloring the crosslinked system by candidate and formed bonds.

Let’s explore the different tabs in this panel to display and analyze the crosslinking calculation. The Reactivity tab allows us to visualize the components of the box involved in the crosslinking process.

  1. Click on Color for Color Candidate Cross-link Bonds AB Bonds
    • All N-H bonds that did not react are highlighted in orange
  2. Click on Color for Color Candidate Cross-link Bonds CD Bonds
    • All C-O bonds on the epoxy ring that did not react are highlighted in blue
  3. For Color Crosslinked Bonds Iteration, select All iterations
  4. Click on Color for Crosslinked Bonds
    • The crosslinked bonds formed in all iterations during the calculation are highlighted in yellow

 

The tools here help us gain a better understanding of the reaction we have just modeled. Feel free to explore these coloring schemes further if you are interested.

 

  1. Go to the Time Series tab

Figure 4-8. Viewing properties of the crosslinking calculation.

The Time Series tab facilitates visualizing properties of the crosslinking calculation as a plot. For example, we can view how the molecular weight and density of the system as a function of crosslinking saturation:

  1. Click Y Properties
  2. From the option-menu, select First Largest Reduced MW and Second Largest Reduced MW and deselect Density
    • The reduced molecular weight (RMW) is determined by dividing the molecular weight (first largest or second largest) by the total molecular weight
  3. Check Second Y property
  4. For Second Y property, choose Density g/cm3

 

This analysis can give us insight to a property called gel point. It is difficult to measure the gel point experimentally, but it can be estimated as the inflection point of the largest RMW or as the maximum in RMW of the second largest MW. Here we can extract it from the plot of the First Largest Reduced MW and %xlink saturation. It can be difficult to estimate the inflection point, so in this example we estimate the gel point as the %crosslink where the first largest molecular weight reaches 50%. Here that value is ~45% crosslink saturation. At this point, the system suddenly transitions from liquid type behavior to solid type behavior.

Figure 4-9. Viewing the saturation of formed crosslinks.

  1. Change the X property to Iteration
  2. Click Y Properties
  3. From the option-menu, select Total # xlinks
  4. Deselect the Second Y property

Plotting the Total # xlinks (cummulative number of crosslinks formed) shows that a saturated state (plateau) was reached within 80 crosslink iterations.

  1. Go to the Molecular Weight tab

Figure 4-10. Viewing the Molecular Weight.

The Molecular Weight tab shows a histogram of Frequency of occurrence or Max # Xlinks as a function of molecular weight for individual iterations in the cross-linking process. The view of iteration 129 shown in the figure shows that all the crosslinked molecules are forming one composite molecule with a molecular weight of 21466.7 g/mol.

  1. Close the Crosslink Polymers Viewer panel

Figure 4-11. Selecting the output of the crosslinking calculation.

If we are satisfied with the output of the crosslinking simulation, it is next recommended to set up and run another MD Multistage Workflow to equilibrate our crosslinked system. We will use the same settings as our initial MD simulation

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue and 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 output from the crosslinking calculation, disordered_system_TGDDM_33DDS_all_components_amorphous entry from the polymer_crosslink_TGDDM_33DDS_sysbuild_system (1) entry group
  2. Go to Tasks > Materials > Classical Mechanics > MD Simulations > MD Multistage Workflow

Figure 4-12. Setting and running the MD Multistage Workflow stages.

  1. Revisit Section 3 to set up the MD Multistage Workflow as shown in the Figure here
  2. Change the Job name to multistage_simulation_crosslinked_system
  3. Adjust the job settings () as needed
    • This job requires a GPU host. The job can be completed in about 1 hour on a GPU host
  4. If you would like to run the job yourself, click Run. Otherwise, go to File > Import Structures, navigate to the provided tutorial files and Open Section_04 > multistage_simulation_crosslinked_system > multistage_simulation_crosslinked_system-out.cms
  5. Close the MD Multistage Workflow panel

Figure 4-13. Visualizing the 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_TGDDM_33DDS_all_components_amorphous entry from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

We now have a crosslinked and equilibrated TGDDM-3,3-DDS system. This model is of high interest as a thermosetting material and can be further used in the Penetrant Loading and Polymer Property Prediction tutorials. Proceed to explore this crosslinked epoxy-amine system or others depending on your interests.

5. SMARTS Patterns

SMILES ARbitrary Target Specifications (SMARTS) is a language used for describing molecular patterns such as bonds, motifs and functional groups that builds off of the SMILES language. SMARTS allows us to efficiently identify substructures of interest and pass them along to further calculations. For an introduction to SMARTS, examples of SMARTS patterns, visualization and practice questions see the linked resources. The Crosslinking Polymers panel relies on SMARTS to run a reaction. In this section, we will learn about SMARTS patterns using a few examples of crosslinking reactions. The structures shown in this section can be found in the provided files. The first example is the reaction between TGDDM and 3,3-DDS modeled in Section 4:

Reaction 1:

A reaction scheme for the epoxy curing reaction between TGDDM and 3,3-DDS is shown in Section 4. To describe this reaction in the Crosslink Polymers panel, we need to specify which two bonds break (denoted AB and CD) and the panel will then cause two new bonds to form (AC and BD).  The bonds are specified with SMARTS strings. Here the bond breaking and forming can be expressed by the following reaction, N—H + C—O → N—C + H—O. In the Figure below, the red arrow points to the two bonds that will be broken.

Figure 5-1. The epoxy curing reaction between TGDDM and 3,3-DDS. Red arrows identify bonds that could be broken in the reaction. The blue arrow identifies the CH-O bond which will not be broken.

Let’s begin with the N-H bond in the 3,3-DDS molecule. For the NH2 group in the molecule, it is unimportant which N-H bond participates in the reaction. The SMARTS pattern to represent this N-H bond is simply N[H]. N refers to any nitrogen, H refers to hydrogen, and [ ] tells us that this refers explicitly to a hydrogen atom. In the panel, inputting the AB reactive group as N[H] specifies that A is nitrogen and B is hydrogen.

We can take a similar approach to define the SMARTS string for the C-O bond of interest in TGDDM. In order to distinguish between the multiple C-O bonds in this system, we define the carbon as being a CH2 carbon in a 3-membered ring, i.e. [C;r3;H2], connected to an oxygen atom. The C atom in the other C-O bond (marked by a blue arrow) is also part of the three membered ring but is only attached to one hydrogen atom. Here we use [C;r3;H2]O to target a C-O bond ([ ]) in which the C atom is part of a three membered ring (r3) and (;) is attached to two hydrogens (H2). Using this SMARTS string as the CD reactive group in the panel means that C is carbon and D is oxygen; recall that C always reacts with A and D with B to form the products.

SMARTS are flexible strings, so there can be more than one unique way to refer to a group. For example, the C-O bond of interest could also be specified by [CH2X4][O], a carbon (C) atom connected to exactly four other atoms (X4), two of which being hydrogen (H2) and connected to an oxygen atom ([O]). The symbol X includes implicit bonds to hydrogen while the symbol D does not. The bond breaking could be easily controlled to instead occur in the CH-O bond (marked by the blue arrow) by changing the SMARTS to [CHX4][O].

 

 

Reaction 2:

Using the Crosslink Polymers panel, we can model a complex and realistic representation of a l-lactide/trimethylene carbonate (TMC) polymerization reaction. The panel facilitates forming polymers with (i) a higher degree of interlocking as a larger range of degrees of freedom can be accessed by monomers than by the interweaving of larger chains, and (ii) a diversity of chain sizes as it gets more and more difficult to find available bonds to break/form within a cutoff radius as the reaction progresses. This will generate a distribution of polymer chains with larger and smaller chain sizes which are more representative of experimental polymeric systems. This can be extremely useful for polymers of high rigidity.

The polymerization reaction we consider here consists of breaking one O-(C=O) bond of one l-lactate and one O-(C=O) bond of TMC to form two new O-(C=O) bonds, thus forming a linear chain of poly-(l-lactide-co-TMC). Here the bond breaking and forming can simplistically be expressed by the following reaction, C—O + O—C → C—O + O—C. In the Figure below, the red arrows point to the bond types that can be broken.

Figure 5-2. The l-lactide/TMC polymerization reaction. Red arrows identify bond types that can be broken in the reaction.

The SMARTS for these two groups are as follows:

AB reactive group SMARTS: [CX3;r6][OD2][CHX4]

CD reactive group SMARTS: [OD2][CX3;r6][OD2][CH2X4]

Let’s look at each of these terms more closely:

[CX3;r6] a carbon atom (C) attached to three other atoms (X3) and (;) is part of a six membered ring (r6)

[OD2] an oxygen (O) atom explicitly attached to two other groups (D2), also known as an ether. D2 refers to an atom with 2 explicit bonds in which implicit H's do not count

[CHX4] a carbon (C) atom connected to exactly four other atoms (X4), one of which being hydrogen (H)

[CH2X4] a carbon (C) atom connected to exactly four other atoms (X4), two of which being hydrogen (H2)

We ensure that one and only one l-lactide molecule and one and only one TMC molecule participate in the polymerization by using specific SMARTS patterns. The first two atoms described for the AB and CD reactive groups, [CX3;r6][OD2] and [OD2][CX3;r6] are the same for both molecules. However, we can specify which molecule the C-O bond is located in by adding terms to this SMARTS pattern. [CX3;r6][OD2][CHX4] indicates the bond being broken is in the l-lactide molecule as this combination of atoms does not exist in the TMC molecule. [OD2][CX3;r6][OD2][CH2X4] indicates the bond being broken is in the TMC molecule as this combination of atoms does not exist in the l-lactide molecule.

 

 

Reaction 3:

Similarly, using the Crosslink Polymers panel, we can model a realistic representation of a l-lactide/l-lactide polymerization reaction. The polymerization reaction we consider here consists of breaking one of the O-(C=O) bonds of each of two cyclic l-lactate molecules, opening the ring, making two new O-(C=O) bonds between them, and thus forming a linear chain of poly-l-lactide. Here the bond breaking and forming can simplistically be expressed by the following reaction, C—O + O—C → C—O + O—C. In the Figure below, the red arrows point to the bond types that can be broken.

Figure 5-3. The l-lactide/l-lactide polymerization reaction. Red arrows identify bond types that can be broken in the reaction.

 

The SMARTS for these two groups are as follows:

AB reactive group SMARTS: [CX3;r6][OD2][CHX4]

CD reactive group SMARTS: [OD2][CX3;r6][CHX4]

Reaction 4:

In crosslinking simulations involving radical polymerization, we typically manage the radical species by substituting them with a dummy atom, such as fluorine. For example, when crosslinking acrylates, we can use an initiated monomer with a fluorine dummy atom. The reaction for bond breaking and forming is: C—F + C=C → C—C + C—F. The target crosslink saturation should be based on the C=C group since it is consumed as the reaction proceeds. This process decreases the double bond order and forms new C—C bonds between molecules. After the crosslinking run, delete all fluorine atoms and they will automatically be replaced with hydrogen atoms. The force field will need to be reassigned if additional simulations are to be performed with the output structures. Shown below is the crosslinking of bisphenol-A epoxy acrylate with an initial monomer. Either of the C=C bonds in the acrylate molecule is capable of reacting. Specific fragments for the reaction can be selected using SMARTS patterns.

Figure 5-4. Radical polymerization of bisphenol-A epoxy acrylate and an initiated monomer. Red arrows identify bonds that could participate in the reaction.

The SMARTS for these two groups are as follows:

AB reactive group SMARTS: [C][F]

CD reactive group SMARTS: [C;X3H2]=[C;X3H1]

 

 

 

 

6. Conclusion and References

In this tutorial, we learned how to build and analyze a crosslinked polymer system. Additionally, we learned how to use SMARTS to specify bonds of interest in a molecule.  

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 100+ 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

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

Thermosetting polymer materials - synthetic materials that strengthen while being heated and cannot be remolded after their initial heat-forming

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