RxnProfiler for Polyethene Insertion

Tutorial Created with Software Release: 2025-2
Topics: Catalysis & Reactivity, Energy Capture & Storage, Polymeric Materials
Methodology: Molecular Quantum Mechanics
Products Used: AutoTS, Jaguar, MS Maestro, MS Reactivity

Tutorial files

28 MB
This tutorial is written for use with a 3-button mouse with a scroll wheel.
Words found in the Glossary of Terms are shown like this: Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

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

In this tutorial, we will calculate and analyze the energetics of ethene insertion into a Zr-ethyl bond with a novel Ziegler-Natta homogeneous catalyst using the Reaction Network of a different catalyst.

Tutorial Content

  1. Introduction to RxnPofiler

  1. Creating Projects and Importing Structures

  1. Visualizing the Structures and Energy Profile of the Reference Reaction

  1. Creating Reaction Network Profiler Input Files for the Reference Reaction

  1. Building a Novel Catalyst with the Single Complex Builder

  1. Swapping Fragments

  1. Running and Analyzing Reaction Network Profiler

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to RxnProfiler

A Chemical Reaction Network (CRN) is a collection of all possible chemical transformations connecting molecular species (nodes) through elementary steps (edges). The Free Energy Surface (FES) being a multidimensional function of atomic coordinates is the fundamental energetic landscape that determines how a CRN evolves and thus provides direct insight into the reaction mechanism. CRNs are naturally derived from the FES: by exploring the FES, one can map out all possible reaction pathways, defining nodes (species) and edges (elementary reactions). However, construction and subsequent global mapping of FESs is prohibitively computationally expensive, and the quantum-chemical solution quickly becomes impossible for systems with more than ~10 heavy atoms even on the best supercomputers in the world. In the opposite approach, an FES can be constructed from a predefined CRN by optimizing and computing the Free energies of all relevant stationary points at a chosen level of theory. In the context of molecular reactivity, the FES provides a thermodynamic and kinetic map of the reaction mechanism—capturing the relative Free energies of intermediates and transition states, including those that govern selectivity. Here we introduce the Reaction Network Profiler (RxnProfiler), MS Maestro module which accepts any predefined reaction network as input and converts it into (lowest-energy or Boltzmann-averaged) FES based on a specified quantum-mechanical level of theory.

The RxnProfiler supports any type of reaction network ranging from general case A), and including special cases B) and C) as input such as:

In previous tutorials, we have learned to perform geometry optimization for equilibrium geometries and transition states (minima and 1st order saddle points on the potential energy surface, respectively). For review, visit: Introduction to Geometry Optimizations, Functionals and Basis Sets, Locating Transition States: Part 1 and Part 2. These structures (XYZ) can be used as input structures to construct a reaction network.  For such a case, RxnProfiler can be used to re-optimize these structures under a different level of theory, perform conformational sampling (/force fields Monte Carlo or xTB metadynamics sampling techniques), and/or add QM multistage and automatically plot the resultant(lowest-energy or Boltzmann-averaged) FES. Complementing these is the swapping fragments functionality, which can be used for “deep” structure modification, paving the way for rational reactivity optimization.

In this tutorial, you will learn how to use RxnProfiler to model a single-step polyethylene insertion reaction for a novel Ziegler–Natta homogeneous catalyst (L2, Figure 2). The starting point is a reference reaction network representing the same step for a related system (L1, Figures 3 and 4). You will be provided with Cartesian coordinates for the reactant, transition state, and product, along with their corresponding Free Energy Surface (FES), calculated separately for reference. Using RxnProfiler’s editing tools, you will modify the structures to substitute catalyst L1 with L2—while keeping the rest of the molecular framework intact. This approach provides chemically reasonable starting geometries for subsequent optimization and FES calculations for the L2 system.

Figure 2: ‘Novel’ Zr structure with L2 ligands

Figure 3: Reference reaction with L1 ligands

Figure 4: Free energy diagram for the reference reaction with L1 ligand

Using the results of the Reaction Network Profiler calculations for the L2 system, we will be able to create a similar reaction profile diagram as shown in Figure 4. This will allow us to easily compare the ability of the two catalysts to perform the reaction via studying the differences between their Gibbs free energy barrier heights.

The process demonstrated herein uses several panels in MS Maestro: Create Reaction Network Profiler Input Structures, Single Complex Builder, Swap Fragments, Reaction Network Profiler Calculations and Reaction Profile Viewer.

The overall approach utilizes both molecular mechanics for conformational searching and quantum mechanics for geometry optimization, transition state searches, and frequency calculations. The full tutorial workflow can be summarized as follows:

Figure 5: Tutorial workflow. The gray text in each box is the panel name that is used in each step.

In addition to Reaction Network Profiler, another tool is available for developing a set of Reaction Networks for multiple potential catalysts, Reaction Network Enumeration Profiler, which is described in detail in the Design of Asymmetric Catalysts with Reaction Network Enumeration Profiler tutorial.

2. Creating Projects and Importing Structures

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

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

  1. Double-click the Maestro 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: https://www.schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/rxnprofiler.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 reaction_profiler_tutorial, click Save
    • The project is now named reaction_profiler_tutorial.prj

Jaguar optimizations and transition state calculations have been performed in advance on the three states (reactant, transition state, product) for the L1 reference reaction (see Figure 1 in the Introduction). The calculations were performed at the B3LYP-D3 / LACVP* level of theory following similar procedures to those demonstrated in the Introduction to Geometry Optimizations, Functionals and Basis Sets, Locating Transition States: Part 1 tutorials. We will proceed to import the pre-run files.

Figure 2-3. Entry list after importing. The [L1Zr(C=C)Et]+ complex is shown in the workspace.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files, choose jag_batch_opt_B3LYP-D3_LACVPs_Et-Ethene_nBu > Et-Ethene_isomer1.01.mae and click Open
  3. Repeat the import step for the jag_batch_opt_B3LYP-D3_LACVPs_Et-Ethene_nBu > nBu_isomer2.01.mae and jag_Et-Ethene-TS_ts_B3LYP-D3_LACVPs > jag_Et-Ethene-TS_ts_B3LYP-D3_LACVPs.01.mae files
    • Three new entry groups are added to the entry list, corresponding with the reactant, transition state and product of the reference reaction

3. Visualizing the Structures and Energy Profile of the Reference Reaction

Before we proceed with the Reaction Network Profiler, let us take a moment to view the input structures and the corresponding reaction profile. If you are already comfortable with these operations, you can proceed directly to Section 4.

Figure 3-1. Animating the negative frequency associated with the transition state.

Quantum mechanical calculations have already been performed on three imported structures. We can confirm that the [L1Zr(C=C)Et]+ and [L1ZrnBu]+ complexes are minima and that the transition state is a maximum by confirming that only the transition state structure has a negative imaginary frequency.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue. the Et-Ethene-TS entry in the workspace
  2. Click the button to view the vibrations
  3. With the negative frequency row highlighted, click the play button ()
    • The vibration associated with the transition state is shown in the workspace
  4. Close the Vibrations viewer

Optional: Feel free to confirm that the reactant and product complexes have no imaginary frequencies.

Figure 3-2. Opening the Reaction Profile Viewer and loading the reactant.

We can now generate the free energy reaction profile using the Reaction Profile Viewer

  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 Et-Ethene ([L1Zr(C=C)Et]+) entry
  2. Go to Tasks > Materials > Quantum Mechanics > Reaction Network > Reaction Profile Viewer
  3. In the Reactant row, click Selected Entries in the Import column
    • The Et-Ethene complex is loaded into the panel

Figure 3-3. Adding the transition state.

  1. Click Add New Step
    • A new row, labeled Product is added
  2. Double-click Product and change the Title to TS
  3. 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 Et-Ethene-TS entry from the entry list
  4. In the TS row, click Selected Entries in the Import column
    • The Et-Ethene-TS complex is loaded into the panel

Figure 3-4. Adding the product.

  1. Click Add New Step
    • A new row, labeled Product is added
  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. the nBu ([L1ZrnBu]+) entry from the entry list
  3. In the Product row, click Selected Entries in the Import column
    • The nBu complex is loaded into the panel

Figure 3-5. Viewing the energy profile.

Various energies can be viewed. Here we will look at the free energy under standard conditions

  1. Next to Jaguar at the top of the panel, choose Free Energy at 298.15K 1atm from the dropdown menu
  2. Click Plot
    • The energy profile (as shown in Figure 2 of the Introduction) is generated
  3. Close the Reaction Profile Viewer

 

Now we know the thermodynamics associated with our reference reaction. In the subsequent sections, we wish to efficiently determine the same information for a new ligand.

4. Creating Reaction Network Profiler Input Files for the Reference Reaction

In this section of the tutorial, the input structures and files for the Reaction Network Profiler are prepared for the reference reaction using the Create Reaction Network Profiler Input Structures panel. This panel sets up structures for the reaction network profiler via specifying the various reactants, transition states, intermediates and products, as well as the possible groups of conformers associated with each of these steps, in our reaction profile. In addition, we use this panel to specify restraints on atoms or geometric parameters in the process of finding the various minima (reactants, products, and intermediate structures) or the transition states. These restraints (and other settings) are stored as entry properties in the output structures. The groups of conformers are also organized into parent and sibling stages to specify the order of steps and allow branching when needed. Visit the help documentation for a complete overview of the panel.

Figure 4-1. Selecting the reactant and opening the Create Reaction Network Profiler Input Structures panel.

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries. and includethe entry is represented in the Workspace, the circle in the In column is blue. the Et-Ethene entry in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. and workspacethe 3D display area in the center of the main window, where molecular structures are displayed., respectively
  2. Go to Tasks > Materials > Quantum Mechanics > Reaction Network > Create Reaction Network Profiler Input Structures

Figure 4-2. Preparing the reactant group.

In this example, we have a fairly straightforward linear reaction with three species (reactant, transition state, product), in which each structure is the parent of the subsequent structure.

  1. In the Groups of Conformers (1) section of the panel, click Import Selected Entries
  2. Change the Conformer group name to Et-Ethene
  3. Change the Sibling group name to reactant
    • Click inside the white box to edit the option, clicking the blue arrow will show the option menu
  4. Ensure that the Charge is 1 and the Multiplicity is 1
    • The structures are cationic singlets
  5. Click Define next to Indices of atoms to keep

Figure 4-3. ASL for atoms to keep in the swap.

  1. For the ASL, input atom.entrynum 1-14
  2. Click OK
    • The Indices of atoms to keep updates in the panel to include a list of 1-14

Here we are specifying the atom numbers that we wish to keep when we swap to the novel catalyst. In this example, this is the Zr center as well as the ethene and ethyl substituents. In addition to ASL, these atoms can be specified using a workspace selection. Hovering over the atoms in the workspace will show its entry number.

Figure 4-4. Indices of superposable atoms.

  1. For Indices of superposable atoms, input 20,1,15
    • These atom numbers correspond to a Cp bridging Carbon linked to zirconium, the zirconium metal center and an opposite Cp bridging carbon

Here we are specifying the atom numbers that will be used to orient the swapped ligand later on. Note that the selection order of the superimposable atoms is critical, so it is recommended that you keep the same order of superposable atoms between all reaction network groups.

We will not apply any restraints. For reactants, products, and intermediates, only a single optimization step is performed, so it is usually not recommended to apply restraints.

  1. Click Add Group
    • A new Group of Conformers (2) is added

Figure 4-7. Defining the sibling and parent group of the transition state.

  1. With the panel still open, 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 Et-Ethene-TS entry in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  2. Click Import Selected Entries
  3. Change the Conformer group name to Et-Ethene-Ts
  4. Change the Sibling group name to transition_state
  5. Keep Add parent group name set to reactant and click Add
    • Reactant is added to the dialog box indicating that the parent for this step will be the reactant step
  6. Ensure again that the Charge is set to 1 and the Multiplicity to 1

Figure 4-8. Create Reaction Network Profiler Input Transition State Structure.

  1. Now for this Et-Ethene-TS structure, Repeat Steps 7-10 of this section
    • We will keep the same atoms in the swap, and as mentioned  above, we want to use the same superposable atoms
    • In this example the atoms that match between the reactant and transition state structures happen to be the same, this might not always be the case

Figure 4-9. Defining restraints for the transition state group.

With transition state steps, pre-optimization is performed. If restraints are defined, these coordinates become the active coordinates used to guide the transition state search. See the Locating Transition States: Part 2 tutorial for more on pre-optimization and restraints

  1. For Indices of atoms to restrain, input 1,2,3,8
    • These are the four atoms associated with the bond breaking and forming step of the transition state (Zr and three carbons)
  2. For Atom index pairs of distances to restrain, input (3,1);(1,2);(2,8);(8,3)
    • These are the distances associated with the four key bonds of the transition state. Note that the order of index pairs does not matter
  3. Check Transition state
    • This ensures that this Conformer group is treated as a transition state

 

Figure 4-10. Adding the product.

  1. Click Add Group
    • A new Group of Conformers (3) is added
  2. With the panel still open, 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 nBu entry in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  3. Click Import Selected Entries
  4. Change the Conformer group name to nBu
  5. Change the Sibling group name to product
  6. Change Add parent group name to transition_state and click Add
    • transition_state is added to the dialog box indicating that the parent for this step will be the transition_state step
  7. Ensure again that the Charge is set to 1 and the Multiplicity to 1
  8. Repeat Steps 7-10 of this section
    • We will keep the same atoms in the swap, and as mentioned above, we want to use the same superposable atoms

Figure 4-11. Naming and running the job.

  1. Change the Reaction network name to rxnwf_input_L1_reference
  2. Check Ensure mass is conserved
    • Doing so is optional, but this is a good check to be sure that mass is conserved
  3. Click Run
    • The panel does not require any host
    • The job will finish immediately
  4. Close the Create Reaction Network Profiler Input Structures panel

Figure 4-12. Output of the job.

This job should finish almost instantly. A new rxnwf_input_L1_reference (3) group 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 the first group entry, Et-Ethene, 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 structures match our inputs, but are now coded with the necessary information for swapping fragments and running the reaction network profiler in the next sections.

5. Building a Novel Catalyst with the Single Complex Builder

In this section, we will use the Single Complex Builder to construct the L2 ligand precursor (shown in the Introduction Figure 2). If you are new to building organometallics, visit the Organometallic Complexes tutorial. If you are familiar and wish to skip to the swapping fragments step, simply import L2Zr_precursor.mae from the provided tutorial files and skip to Section 6.

Figure 5-1. Open the Single Complex Builder and define the Complex information.

  1. Go to Tasks > Materials > Structure Builders > Single Complex
  2. Change the Metal to Zr either by direct input or by selecting the element from the periodic table
  3. Change the Geometry to Tetrahedral
  4. Click on the Ligand Name (none) in the table and open the sketcher dialog by clicking the pencil symbol

Figure 5-2. Drawing and adding the bidentate ligand.

  1. In the Ligand sketcher, draw the bidentate ligand as shown in the figure
    • Be sure to use R1 and R2 to specify that the ligand is bidentate
    • Be sure to assign a negative charge to the singly-bonded carbon in the Cp ring
  2. Click OK

Figure 5-3. Adding the methyl ligand from the template list.

  1. Click the plus sign to add a new row to specify another ligand structure
  2. Click the ligand list and search the templates for methyl to select the methyl (Me) ligand
  3. Change Copies for the methyl ligand to 2

Figure 5-4. Creating the new project entry.

Now the bidentate and monodentate ligands are specified and occupied coordination sites should be updated to 4 of 4.

  1. Select the radio button for xTB to clean the geometry
    • xTB has been shown to give good geometries for organometallic substances
  2. For Project entry title, input L2Zr_precursor
  3. Click Create
    • After a few seconds, a new entry is added to the list of entries titled L2Zr_precursor.
  4. Close the Build Single Complex panel

Feel free to stylize the complex however you prefer.

If you are having difficulties building the complex, or to be sure that your complex matches the tutorial, import L2Zr_precursor.mae (Section_05 > L2Zr_precursor.mae) from the provided tutorial files.

6. Swapping Fragments

Now that we have the ligand for our new catalyst as well as all of the key indices and restraints for the reference system, this information can be used to easily swap atoms to generate the reaction network profiler input for the new system using the Swap Fragments panel. Specifically, we will swap the two methyl groups attached to the zirconium atom for the ethyl and ethene groups that are involved in the reaction we wish to model. The panel uses both the structure we created in the previous section along with the output of the Create Reaction Network Profiler Input Structures panel to ensure the swap will preserve the other components of the reactant, product, and intermediate structures.

Figure 6-1. Opening the Swap Fragments panel and importing the reference structures.

  1. In the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion., 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 rxnwf_input_L1_reference (3) entry group
  2. Go to Tasks > Materials > Quantum Mechanics > Reaction Network > Swap Fragments
  3. In the Reference Structures section of the panel, next to Import reference structures from selected entries, click Import
    • All of the reference structure information is populated from our previous effort

Figure 6-2. Including and importing the novel structure.

  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. the structure of the L2ZrMe2 complex, L2Zr_precursor
  2. In the Novel Structure section of the panel, click Import from Workspace
    • The Name changes to the name in the entry list: L2Zr_precursor

 

Figure 6-3. Specifying the atoms for replacement and superposition.

  1. For Specify a collection of atom indices to be replaced, input 1,46,47,48,49,50,51,52,53
    • These indices are the ZrMe2 atoms which we are going to replace
    • Caution: If you built the complex yourself, be sure that these are the atom numbers for the ZrMe2 atoms. If not, use the numbers that match your structure
  2. For Specify novel atom indices for superposition, input 6,1,14 (in that order)
    • These indices are the atoms in the new ligand that align with our reference atom indices for superposition in the template structure
    • Caution: If you built the complex yourself, be sure that these are the atom numbers for the Cp bridgehead carbon, Zr and N, respectively. If not, use the numbers that match your structure
    • When input, the Reference Structures section of the panel will update accordingly

The Color button at the top colors the atoms according to their kept/replace properties. This can be useful in visualizing which atoms are being kept and replaced.

Figure 6-4. Running the job.

  1. Click Run
    • If there are any close contacts, a warning message may appear. Click Continue if so to proceed with the job
  2. Close the Swap Fragments panel

Figure 6-5. Output of the job after renaming. The reactant is shown in the workspace.

This job should finish almost instantly. A new rxnwf_input_L1_reference (3) group 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 the first group entry, L2Zr_precursor_Et-Ethene, 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..

Feel free to visualize the three structures. We have successfully swapped our new ligand onto our reference structures with the key substituents in place.

  1. Change the entry group name to rxnwf_input_L2_reference

7. Running and Analyzing Reaction Network Profiler

At last, the structures for the novel reaction can be used as input for the Reaction Network Profiler panel to calculate the energy profile of the new system. This panel will run the calculations that will allow us to analyze the performance of our novel (L2) catalyst.

Figure 7-1. Reaction Network Profiler panel.

  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 group, rxnwf_input_L2_reference (3) from Section 6
  2. Go to Tasks > Materials > Quantum Mechanics > Reaction Network > Reaction Network Profiler Calculations
  3. Click Import
    • (3 structures imported) appears to indicate the input has been loaded into the panel

Let’s learn a bit more about the Reaction Network Profiler panel:

  • Begin by importing a reaction network profiler input, which should be prepared either with the Create Reaction Network Profiler Input Structures or Swap Fragments panel
  • The Conformational Search section allows you to specify parameters for the conformational search to be performed before any quantum mechanical calculations.
    • Any restraints that were predefined will be maintained
    • The conformational search used is a Monte Carlo Multiple Minimum (MCMM) search (see Li and Scheraga 1987, linked in the For Further Reading section) with 100 steps and the requested minimum or maximum number of structures using the specified force field
  • In the Jaguar section of the panel, specify the Jaguar settings for the optimization, transition state search and thermochemistry
    • If interested in energy values for various temperatures or pressures, a range can be defined
  • Use the Anharmonic Workflow to introduce anharmonicity for low-energy modes to improve rate constant calculations

Read more in the detailed help documentation

Figure 7-2. Additional Jaguar settings.

  1. Click Jaguar Options
  2. Change the Theory to B3LYP-D3 and the Basis set to LACVP*
    • The DFT-D3 method is more accurate due to the inclusion of van der Waals information
    • LACVP* basis set includes only polarization on the non-hydrogen atoms, unlike the default of LACVP**
    • This choice allows for a smaller basis set while still maintaining the properties that are important to the calculation as the hydrogens are not important for the chemistry being studied
  3. Change Maximum iterations to 300
  4. Click OK

Note: An option for a machine learning force field (MLFF) is available as an alternative in the Jaguar Options. Additional information regarding MLFF can be found in the help documentation, on our website, or the Reaction Network Profiler panel documentation.

Figure 7-3. Final settings, naming and running the job.

  1. Check Deduplicate structures using this RMSD: 0.25 Å
  2. Check Return Jaguar job files
  3. Change the Job name to reaction_profiler_L2Zr
  4. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 8 hours with 8 CPUs per jobs across 10 parallelized jobs
  5. If you would like to run the job yourself, click Run. Otherwise, to proceed with pre-generated files, go to File > Import Structures, navigate to where you downloaded the tutorial files and import: Section_07 > reaction_profiler_L2Zr > reaction_profiler_L2Zr-out_rxnwf.mae

Figure 7-4. Output after importing or running the job. One of the nBu conformers is shown in the workspace.

When the job finishes or after importing, a new entry group titled reaction_profiler_L2Zr (10) 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 ten entries associated with various conformers of the reactant, transition state and product. The entries are grouped accordingly.

Feel free to visualize any of the complexes in the workspace. Notice that for the nBu product, five conformers were found. This is not surprising given the many degrees of freedom associated with a butyl chain.

To confirm that the Et-Ethene and nBu outputs are minima, and that the Et-Ethene-TS outputs are a transition state, view the vibrations as we did in Section 3.

Figure 7-5. Viewing energy data in the Project Table.

To view energy data, go to the Project Table ()

Use the Property Tree () to add additional data points to the table. For example, under Jaguar > Secondary, add Free Energy (kcal/mol) 298.15K 1.00E+00atm to see the Free Energy values corresponding with each species.

Figure 7-6. Reaction Profile for the lowest energy states.

Feel free to generate a Reaction Profile, as we did in Section 3 using the lowest energy conformer of the reactant, transition state and product, respectively. (The lowest energy conformer can be determined by analyzing the Free Energy values displayed in the previous Figure. You can also add these values to the entry list to easily select the lowest energy conformers, see the Locating Transition States: Part 2 tutorial).

Analysis of the reaction profile indicates that switching the L1 ligand to L2 results in a higher barrier (∆GTS), indicating that this reaction, as compared to the reference reaction, is less kinetically favorable.

Figure 7-7. Reaction Profile using Boltzmann weighting.

Because we have calculated energies for various conformers, we can also look at a more precise energy diagram in which we use Boltzmann weighting to average the Free Energy. This is provided in the directory output from the Reaction Network Profiler job. Outside of MS Maestro, navigate to the provided reaction_profiler_L2Zr directory and open the reaction_profiler_L2Zr_e_diagrams.pdf to see various energy profiles

The Boltzmann weighted total Free Energy plot is shown in the Figure.

Note: The output directory has many other useful files, for example, a keq.csv file with kinetic data.

8. Conclusion and References

In this tutorial, we learned how to use the Reaction Network tools to efficiently calculate a reaction pathway for a novel catalyst using a known reaction pathway as a reference.

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. 

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

For further reading:

9. 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.

Reaction pathway - a path on the potential energy surface that connects the reactant minimum-energy structure to the transition state and then to the product or intermediate minimum-energy structure.

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.