Rigid and Relaxed Coordinate Scans

Tutorial Created with Software Release: 2024-4
Topics: Catalysis & Reactivity, Organic Electronics, Polymeric Materials, Thin Film Processing
Methodology: Molecular Quantum Mechanics
Products Used: Jaguar, Jaguar, MS Maestro, Maestro

Tutorial files

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

 

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

In this tutorial, we will learn how to use rigid and relaxed coordinate scans for exploring potential energy surfaces and bond cleavages.

Tutorial Content

  1. Introduction to Coordinate Scans

  1. Creating Projects and Importing Structures

  1. Running Rigid Scans

  1. Running Relaxed Scans

  2. Locating Transition States via Coordinate Scans

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to Coordinate Scans

Exploration of the potential energy surface (PES) is a very common task in molecular modeling. A typical exercise is to calculate the change of energy along a particular molecular coordinate (i.e. a distance, angle or dihedral), while at the same time keeping the rest of the coordinates frozen or letting them relax (rigid and relaxed coordinate scans, respectively). Schrödinger’s quantum mechanics engine, Jaguar, automates this procedure for both rigid and relaxed coordinate scans. In a scan, you specify the values of the coordinates, and Jaguar performs single point energy or geometry optimization calculations on the molecule at those coordinate values.

 

Figure 1: Relaxed coordinate scan for a dihedral in ethylene glycol.

With Jaguar, there are three methods that can be used for coordinate scans. The chart below outlines these methods: rigid, relaxed and consecutive relaxed.

Rigid Scan

Relaxed Scan

Consecutive Relaxed Scan
  • Change the scan coordinate and do not relax the other coordinates     (do not perform a geometry optimization at each step)
  • Scan points are all generated at once
  • Calculations (single point energy) run very quickly with initial geometries frozen
  • Can lead to non-equilibrium geometries
  • Change the scan coordinate and relax the other coordinates (perform geometry optimizations at each step)
  • Scan points are all generated at once
  • Calculations (geometry optimizations) take slightly longer
  • More reasonable geometries
  • Set the first scan coordinate and relax the other coordinates then adjust the next scan coordinate using the previously optimized geometry and relax and so on
  • Scan points are generated point after point
  • Calculations (geometry optimizations) take much longer
  • Most realistic geometries

Rigid coordinate scans are most useful in scenarios where a quick estimate of energetics can provide valuable information such as investigating the impact of multiple coordinates (i.e. changing multiple bonds/angles) on the energy of a system. After identifying the coordinates of interest, we can use relaxed coordinate scans to further refine the initial rigid scan. Relaxed scans are efficient and provide reasonable data which is why they are used in most scenarios when exploring a PES. Consecutive relaxed scans take more time, as the calculations have to be done sequentially, but as mentioned in the above table, they typically provide the best geometries and are recommended when having accurate geometries is necessary. For more examples of relaxed coordinate scans, with fixed and dynamic constraints, see the Dynamic Relaxed Coordinate Scans tutorial. For a basic review on geometry optimizations, see the Introduction to Geometry Optimizations, Functionals and Basis Sets tutorial.

Coordinate scans can contribute to our understanding of different molecular processes, for example, we can see what the energy landscape looks like for a particular parameter (e.g. is this bond very rigid? does this dihedral have a high degree of freedom?) and through that we can understand features such as rotational barriers and conformational landscapes. By understanding bond breaking or bond forming processes, we can generate initial guesses for transition states as is discussed later on in this tutorial. To learn more about other methods for finding transition states, visit the Locating Transition States: Part 1 tutorial. Additionally, optimal bond lengths, bond angles and dihedrals identified from coordinate scans can be used to parameterize a force field.

In this tutorial, we will calculate the molecular energy of ethylene glycol as a function of the O-C-C-O dihedral using rigid, relaxed, and consecutive relaxed coordinate scans. We will plot and compare the relative energies as a function of the coordinate for the different scan types.

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.

OR

  1. Double-click the Maestro or Materials Science icon

Note: This Jaguar workflow can be performed in Maestro or Materials Science Maestro. Use whichever interface you are comfortable with or typically use for your projects.

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/qm_coordinate_scans.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 coordinate_scans, click Save
    • The project is now named coordinate_scans.prj

Figure 2-3. Importing ethylene glycol.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the tutorial files (presumably in your working directory), and choose input_molecules.mae. Click Open
    • A new entry group titled input_molecules (3) appears in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
    • This input contains the lowest energy conformation of ethylene glycol which has been geometry optimized at the B3LYP-D3 level of theory and 6-31G** basis set
    • The NH3_ and TiCl4_optimized structures have been optimized using the B3LYP-D3 functional and LACVP** basis set

If you are interested in building and optimizing the structure yourself, feel free to do so. For a refresher on using the 2D Sketcher or importing structures, see the Introduction to Materials Science Maestro tutorial. For how to perform the geometry optimization, see the Introduction to Geometry Optimizations, Functionals and Basis Sets tutorial.

3. Running Rigid Scans

In this section, we will use the Jaguar - Rigid Coordinate Scan panel to perform a rigid coordinate scan on the O-C-C-O dihedral in ethylene glycol. Note that the input molecule should be geometry optimized, as in this example. The Rigid Coordinate Scan panel will automatically generate the initial structures for all scan points along the specified coordinate and submit single point energy calculations for each.

Figure 3-1. Opening the Rigid Coordinate Scan 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 ethylene_glycol in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  2. Go to Tasks > Browse All > Jaguar > Rigid Coordinate Scan
    • The Jaguar - Rigid Coordinate Scan panel opens
    • The level of theory and basis set shown in the Input tab are set to the defaults which match those of the original geometry optimization

Figure 3-2. Viewing the Scan tab.

Rigid coordinate scans involve running single point energy calculations at each point along the scan. These single point energy calculations will be run in the gas-phase. If you are interested in coordinate scans for a solvated system, please use the Solvation tab to select a solvation model. The default settings in the remaining tabs are sufficient for this example. We can now indicate the coordinate we are interested in studying, rotation about the O-C-C-O dihedral, in the Scan tab:

  1. Go to the Scan tab
    • Here we can specify the parameters for our coordinate scan

Let’s understand the settings and capabilities of the Scan tab in the Jaguar - Rigid Coordinate Scan panel a bit more:

  • With respect to the coordinates
    • The Type gives you the choice between scanning about Distances, Angles, Dihedrals, and Coordinates
    • You can Pick the coordinate of interest interactively in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed by selecting either Atoms or Bonds
    • You can choose up to five coordinates of interest
  • The Selected coordinate section allows you to ​​set the range of the scan and the spacing of the points along the scan coordinate for the coordinate that is selected in the table
  • Visit the help documentation for a complete summary of the parameters

Figure 3-3. Adding the coordinate of interest.

  1. From the Type drop-down menu under Add new coordinate, ensure Dihedral is selected
  2. Check Pick and ensure Atoms is selected from the menu
    • We will indicate the atoms that make up the dihedral of interest in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
  3. Arrange the panel and (MS) Maestro window in a way that you can see the structure in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and the panel simultaneously
  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 following atoms in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed as shown in the Figure: O, C, C and O
    • The dihedral angle we wish to rotate about is shown in the workspace with a blue arrow

Figure 3-4. Setting the scan parameters.

  1. For the Selected coordinate, enter -90 for the Starting value
  2. For the Final value, enter 90
    • The starting and final value here allow us to rotate 180 degrees about the dihedral
  3. For the Increment, enter 10
    • The scan points will be 10 degrees apart
    • The Total number of structures to be calculated updates to 19

Figure 3-5. Running the rigid coordinate scan.

  1. Change the Job name to jag_ethylene_glycol_rigid_scan
  2. Adjust the job settings () as needed. This job requires a CPU host. This job can be parallelized across resources as there are 19 short, independent jobs to be run. The job can be completed in 5 minutes on 10 CPUs
  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 03 > jag_ethylene_glycol_rigid_scan > jag_ethylene_glycol_rigid_scan_scan > jag_ethylene_glycol_rigid_scan.01.mae
  4. Close the Jaguar - Rigid Coordinate Scan panel

Figure 3-6. Visualizing the output.

  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 first entry from the jag_ethylene_glycol_rigid_scan.01 (19) 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
    • We can analyze the coordinate scan by visualizing the different entries in this group

Figure 3-7. Opening the Plot Coordinate Scan Results panel.

Now, let’s analyze our coordinate scan more quantitatively. We will use the Plot Coordinate Scan Results panel to look at the relative energies for each step of our coordinate scan:

 

  1. Use the WAM button () to open the Plot Energy Across Scan Coordinates panel

Figure 3-8. Plotting the results.

If you used the WAM button, feel free to skip steps 17 and 18 as the results of your rigid scan will be loaded into the panel automatically.

  1. If you opened the panel from the tasks menu, click Load Results
  2. Navigate to the jag_ethylene_glycol_rigid_scan.grd file in the output directory and click Open
    • The relative energy (kcal/mol) for each unoptimized structure is plotted as a function of the coordinate
    • The energy units can be adjusted using the Energy Options menu

Let’s combine the qualitative and quantitative information about the rigid coordinate scan for the O-C-C-O dihedral angle to learn more about ethylene glycol:

The highest energy is seen near 0 degrees due to a clash between two hydrogen atoms of the hydroxyl groups as shown in the image below. It is also important to note that the relative energy scale here for the rigid scan reaches a maximum of 13.7 kcal/mol for this structure. We will compare this value to that of the relaxed scans at the end of Section 4.

As seen in the GIF above, all atoms not directly involved in the coordinate scan are kept frozen in the rigid scan. This allows us to solely study the impact of the coordinate of interest on the energy of the molecule. The starting conformation of the molecule plays a large role in the rigid coordinate scan because all scan points are generated from it and do not optimize their shape. Certain starting conformations might miss favorable energetic effects (like formation of a hydrogen bond), whereas other conformations might bring about a clash between atoms (as seen here). The ability to optimize the geometry at each scan point would increase the chances of finding favorable interactions and avoiding clashes. Consequently, we find that our geometry optimized initial configuration has the lowest energy compared to all unoptimized structures derived from it.

4. Running Relaxed Scans

In this section, we will use the Jaguar - Relaxed Coordinate Scan panel to perform a relaxed coordinate scan on the O-C-C-O dihedral in ethylene glycol. Note that the input molecule should be geometry optimized, as is in this example. The Relaxed Coordinate Scan panel will automatically generate the initial structure for one or all scan points along the specified coordinate and submit geometry optimization calculations for each. For a basic review on geometry optimizations, see the Introduction to Geometry Optimizations, Functionals and Basis Sets tutorial. Here, we will run two types of coordinate scans as described in the Introduction, a relaxed scan and a consecutive relaxed scan.

Figure 4-1. Opening the relaxed coordinate scan.

  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 input molecule, ethylene_glycol, in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  2. Go to Tasks > Browse All > Jaguar > Relaxed Coordinate Scan
    • The Jaguar - Relaxed Coordinate Scan panel opens
    • The level of theory and basis set shown in the Input tab are set to the defaults which match those of the original geometry optimization

Figure 4-2. Viewing the Scan tab.

  1. Go to the Scan tab
    • The Relaxed Coordinate Scan panel is almost identical to the Rigid Coordinate Scan panel with one key difference, the Generate starting geometries from section

 

The Generate starting geometries from section dictates whether the coordinate scan will be a relaxed scan (initial geometry without optimization) or a consecutive relaxed scan (previous optimized geometry)

Figure 4-3. Setting the scan parameters.

We will proceed with the same settings used for the Rigid Coordinate Scan in Section 3 with the addition of a Generate starting geometries from selection:

 

  1. From the Type drop-down menu under Add new coordinate, ensure Dihedral is selected
  2. Check Pick and ensure Atoms is selected from the menu
  3. Arrange the panel and (MS) Maestro window in a way that you can see the structure in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed and the panel simultaneously
  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 following atoms in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed as shown in the Figure: O, C, C and O
    • The dihedral angle we wish to rotate about is shown in the workspace with a blue arrow
  5. For the Selected coordinate, enter -90 for the Starting value
  6. For the Final value, enter 90
  7. For the Increment, enter 10
  8. For generate starting geometries from, select initial geometry without relaxation
    • We will refer to this as the relaxed coordinate scan. The geometry for each point along the coordinate scan, 19 points, will be generated from the input molecule, similar to what was done for the rigid scan. Each structure will be independently geometry optimized during the relaxed scans with the scan coordinate frozen

Figure 4-4. Running the relaxed coordinate scan.

  1. Change the Job name to jag_ethylene_glycol_relaxed_scan
  2. Adjust the job settings () as needed This job requires a CPU host. This job can be parallelized across resources as there are 19 short, independent jobs to be run. The job can be completed in 15 minutes on 10 CPUs
  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 > jag_ethylene_glycol_relaxed_scan > jag_ethylene_glycol_relaxed_scan_scan > jag_ethylene_glycol_relaxed_scan.01.mae
  4. Close the Jaguar - Relaxed Coordinate Scan panel

Figure 4-5. Viewing the output.

  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 first entry from the jag_ethylene_glycol_relaxed_scan.01 (19) 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
    • We can analyze the coordinate scan by visualizing the different entries in this group

Figure 4-6. Plotting the results.

Now, let’s analyze our coordinate scan more quantitatively. We will use the Plot Coordinate Scan Results panel to look at the relative energies for each step of our coordinate scan:

 

  1. Use the WAM button () to open the Plot Energy Across Scan Coordinates panel
    • The Plot Coordinate Scan Results panel opens
    • The relative energy (kcal/mol) for each unoptimized structure is plotted as a function of the coordinate
    • The energy units can be adjusted using the Energy Options menu

 

We will look at these results further and compare to the consecutive relaxed scan in the next few steps

Figure 4-7. Setting up the consecutive relaxed scan.

Repeat all of the steps in this section for a consecutive relaxed scan. Ensure you make the following changes in your procedure:

  • For generate starting geometries from, select previous optimized geometry
    • We will refer to this as the consecutive relaxed coordinate scan. The geometry for the first point along the coordinate scan will be generated from the input molecule. Each subsequent structure along the coordinate will be generated from the geometry optimized scan point preceding it
  • Change the Job name to jag_ethylene_glycol_consecutive_relaxed_scan
  • Adjust the job settings () as needed. This job requires a CPU host. This job cannot be parallelized across resources as each of the 19 steps depends on the previous one. The job can be completed in 45 minutes

Let’s combine the qualitative and quantitative information about the relaxed and consecutive relaxed coordinate scans for the O-C-C-O dihedral angle to learn more:

relaxed coordinate scan

 

consecutive relaxed coordinate scan

Similar to the rigid coordinate scan, for both relaxed scans here we see the highest energy is seen near 0 degrees. The relative energy value of this maxima is only ~4 kcal/mol which is much smaller than the 13.6 kcal/mol seen in the rigid scan. The optimized structure at the high energy point shows the two hydrogen atoms no longer clash, rather they no longer directly face one another, making the structure more energetically favorable. The relaxed scans are less dependent upon the initial conformation of the molecule because the structure at each point is able to change its shape. Relaxed scans also tend to have lower energies than rigid scans across the coordinate as seen here.

As discussed in the Introduction, the relaxed and consecutive relaxed coordinate scans have different advantages and disadvantages to them. The initial geometry without relaxation option, or relaxed scan, can lead to bad initial geometries containing atom collisions. These clashes may or may not be resolved in the subsequent geometry optimizations. These optimizations run quickly because they are highly parallelizable. The previous optimized geometry option, or consecutive relaxed scan, is more likely to produce smoother scan plots, less prone to energy artifacts. The geometries at each point will be the most reasonable, but the optimizations will take a long time because they are dependent upon one another and must be run in sequence. Additionally, the results could be dependent on the scan direction because the previous geometry is influencing the next. When using consecutive relaxed coordinate scans, it is important to also scan in the opposite direction to avoid making conclusions that are artifacts of the scan directionality.

5. Locating Transition States via Coordinate Scans

For another example of the usefulness of coordinate scans, we will look at how the Jaguar - Relaxed Coordinate Scan panel can be used to find a good starting geometry for a transition state. By performing a coordinate scan for one, or several, of the bonds involved in the transition state search we can create a better starting geometry that can then be optimized via the Transition State Search or QM Multistage Workflow panels. For more details about transition states, see the Locating Transition States: Part 1 tutorial.

In this example we will study a generic organometallic reaction in which TiCl4 reacts with an amine (ammonia, NH3) to generate a titanium amido complex, Ti(NH2)Cl3 with HCl as the byproduct. The reaction studied herein can be expressed as follows, with a 2D sketch of a proposed transition state included:

Reaction with sketched transition state.

Figure 5-1. Merging, moving and renaming the scan starting point.

The NH3_ and TiCl4_optimized structures that were imported at the start of the tutorial have been optimized using the B3LYP-D3 functional and LACVP** basis set. To begin looking at the transition state of the reaction that occurs between these two molecules, we will merge them into one entry:

  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 both NH3_optimized and TiCl4_optimized
  2. With both entries 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, right-click and select Merge
    • A new entry titled TiCl4_optimized NH3_optimized is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  3. Click, hold and drag this new entry to the bottom of the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  4. Rename the entry scan_starting_point by double-clicking on the entry name in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  5. 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 entry in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • A structure appears in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed in which the ammonia and TiCl4 molecules are overlapping

Figure 5-2. Selecting one molecule to move.

For this method, we simply wish to place the two reactants side-by-side in preparation for the scan

  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 five atoms composing the TiCl4 molecule
  2. Right-click on any of the selected atoms and select Move Atoms

Figure 5-3. Moving the titanium complex.

  1. Click and hold the center mouse button (the scroll wheel or trackball) in order to translate the TiCl4 in space. Slide the molecule just to the side of the ammonia molecule, then click OK

Figure 5-4. Reactants prepared for a scan.

  1. Make any additional adjustments, as before, until your structure resembles that which is shown in Figure 5-4. The distances and angles do not need to match exactly, we just need a ‘reasonable’ starting input
    • If you are having trouble, feel free to import scan_starting_point.mae from the provided tutorial files

Figure 5-5. Opening the Jaguar - Relaxed Coordinate Scan panel.

  1. With the scan_starting_point entry 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 and includedthe entry is represented in the Workspace, the circle in the In column is blue, go to Tasks > Materials > Quantum Mechanics > Molecular Quantum Mechanics > Relaxed Coordinate Scan

Figure 5-6. Selecting the distance to scan.

  1. Go to the Scan tab

In order to find a reasonable transition state guess, we are going to pick one of our breaking bonds, and perform a series of geometry optimizations in which we elongate that bond systematically. In this case, we will stretch the Ti-Cl bond. Doing so should allow us to extract a crude energy surface in which the point of highest energy might resemble the transition state structure reasonably well.

  1. For Add new coordinate change Type to Distance
    • Pick is automatically checked
  2. In the workspacethe 3D display area in the center of the main window, where molecular structures are displayed, select the titanium atom as well as the chlorine atom (be sure to select the chlorine atom that is aligned with the N-H breaking bond)
    • The Defined coordinates table is populated with the Ti Cl distance
    • You can leave Fixed Value checked

Figure 5-7. Parameterizing the scan.

For the Selected coordinate we can define the scanning parameters. In this case we know that the ground state Ti-Cl bond is ~2.2 Å, and that the final Ti-Cl distance will be that of the separated molecules. We might crudely guess that the transition state Ti-Cl distance is somewhere around 3 Å and wish to scan a range including that distance:

  1. Set the Starting value to 2.7, the Final value to 3.6 and the Increment to 0.05
    • The number of structures to be calculated updates to 19
    • This will geometry optimize all of the structures with a fixed Ti-Cl bond distance along that scan
  2. Select Generate starting geometries from previous optimized geometry
    • As stated in the introduction to this tutorial, this will give the most realistic geometry out of the three scan methods shown

Note: More or fewer scans (changing the increment) over a smaller or larger range (changing the starting or final value) can also work. There is no fixed methodology for choosing the right scanning parameters.

Note: Additional coordinates can be scanned simultaneously (maximum of 5)

Figure 5-8. Changing the Basis set and running the job.

  1. Go to the Input tab
  2. Keep the Theory set to B3LYP-D3 and change the Basis set to LACVP**
  3. Change the Job name to TS_consecutive_relaxed_scan
  4. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 10 minutes on a 12 CPU host
  5. If you would like to run the job yourself, click Run. Otherwise, import the pregenerated Section_06 > TS_consecutive_relaxed_scan > TS_consecutive_relaxed_scan.out file
  6. Close the Jaguar - Relaxed Coordinate Scan panel

Note: Sometimes coordinate scans are performed at a cheaper level of theory than the level of theory used for the final energies. Here the jobs are relatively fast even with B3LYP-D3 // LACVP**

Figure 5-9. The scan output.

When the job is complete (or after importing) a new entry group is incorporated titled TS_consecutive_relaxed_scan.01 (19) containing all nineteen geometries from the scan

  1. To follow the scan, includethe entry is represented in the Workspace, the circle in the In column is blue each entry one at a time from top to bottom.
    • The Ti-Cl bond elongates and coincidingly, the other three relevant distances change as expected
    • We can visually notice the largest change between Step 15 and Step 16

Figure 5-10. Adding a property to the entry list.

Our objective is to pick the geometry from the scan that we believe most closely resembles the transition state. We can use this geometry as an input for the transition state calculation. Rather than trying to deduce visually, we can analyze the energies. This can be done in the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data, or in this instance, it is preferable to view the energies directly in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion:

  1. Right-click on the Title header in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  2. Select Show Property

Figure 5-11. Choosing the property.

  1. Click Choose and from the dropdown menu select Gas Phase Energy
  2. Click OK

Figure 5-12. The updated entry list.

The gas phase energies corresponding with the various entries are now displayed in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion (you may need to adjust your window by clicking and dragging on the side bars). We can confirm that the 15th step is the highest energy step, and therefore is most likely to resemble the transition state. We could then take this structure, and following the procedure outlined in the Locating Transition States: Part 1, optimize this transition state structure.

Figure 5-13. Energy graph associated with the scan.

As in the previous sections, you can also use the WAM button () to open the Plot Energy Across Scan Coordinates panel to look at how the energy of the optimized structures varies as the Ti-Cl distance changes.

 

6. Conclusion and References

In this tutorial, we learned how to calculate and analyze the results of rigid and relaxed coordinate scans using Jaguar.

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.

If you are interested in running Jaguar calculations from the command line, please visit the documentation for example files and guidance.

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

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

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