Bond and Ligand Dissociation Energy

Tutorial Created with Software Release: 2024-2
Topics: Catalysis & Reactivity, Consumer Packaged Goods, Energy Capture & Storage, Organic Electronics, Pharmaceutical Formulations, Polymeric Materials, Thin Film Processing
Methodology: Molecular Quantum Mechanics
Products Used: Jaguar, MS Maestro, MacroModel

Tutorial files

14.2 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 the Bond and Ligand Dissociation panel to calculate the energy associated with the fragmentation of a parent molecule at various dissociation sites.

 

Tutorial Content

  1. Introduction to Bond and Ligand Dissociation Energy

  1. Creating and Saving Projects

  1. Drawing Vanillin and Performing a Conformational Search

  1. Calculating Bond Dissociation Energy for Vanillin

  1. Analyzing the BDE Results for Vanillin

  1. Calculating H-BDE for Ibuprofen

  1. Calculating BDE for a Metal Complex

  1. Conclusion and References

  1. Glossary of Terms                

1. Introduction to Bond and Ligand Dissociation Energy

Formally, bond dissociation energythe standard enthalpy change associated with homolytic bond scission at zero K (BDE) is a measure of the standard enthalpy change associated with homolytically cleaving an R1-R2 bond into R1⦁ and R2⦁ radical fragments. Bond and ligand dissociation energies can be studied as general measures of molecular stability with a range of applications, including but not limited to: organic electronic design, probing chemical reactivity, drug stability towards chemical degradation, and precursor design for thin film processing.

The Bond and Ligand Dissociation panel allows the user to both target specific R1-R2 bonds, and also to define the initial reactant state (ground state, excited state, ion), allowing bond strength to be selectively probed as a proxy for molecular stability (e.g. thermal, UV, among others). Moreover, the panel intelligently considers duplication to optimize the screening of all relevant bond cleavages.

Analyzing BDE is a useful tool with respect to both organic and organometallic systems for a variety of materials science applications, some of which are outlined here:

Organic Applications

Organometallic Applications
  • Optoelectronics (e.g. OLED hosts or emitters)
  • Active pharmaceutical ingredients (APIs, measuring H-BDE)
  • Design of photoinitiator molecules (measuring BDE from the S1 state)
  • Polymer chemistry (e.g. the UV stability of a monomeric unit)
  • Optoelectronics (e.g. OLED emitters)
  • Precursors for atomic layer deposition (ALD)
  • Precursors for catalysis (computing the energetics of ligand dissociation)

In this tutorial, we will use the Bond and Ligand Dissociation panel to analyze the stability of vanillin by calculating the BDE of all of the single, acyclic, non-hydrogen-containing bonds in the molecule considering various initial reactant states. Then, we will study H-BDE of ibuprofen: the energy associated with breaking the unique R-H bonds in the molecule. Finally, we will use the BDE tools to predict the energy of metal-ligand bond cleavage, in particular, the energy associated with the dissociation of a triphenylphosphine ligand from Pd(PPh3)4.

This workflow automates the design and performance of individual Jaguar DFT calculations, which are covered in the Introduction to Geometry Optimizations, Functionals and Basis Sets tutorial. Also note that other decomposition pathways can be studied in an automated fashion, including Beta Elimination Reactions. For manually calculating reaction energies, see the Calculating Reaction Energetics for Molecular Systems tutorial.

2. Creating and Saving Projects

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

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

  1. Double-click the Materials Science icon

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. Pre-generated input and results files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/bond_ligand_dissociation_energy.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 BDE_tutorial, click Save
    • The project is now named BDE_tutorial.prj

3. Drawing Vanillin and Performing a Conformational Search

We will first draw the vanillin molecule in 2D form, convert it to 3D form and then perform a Conformational Search to find a reasonable starting point for the BDE calculations.

Figure 3-1. Sketching vanillin.

  1. From the main menu, go to Edit > 2D Sketcher
    • The 2D Sketcher opens
  2. Sketch a vanillin molecule (as shown in the Figure)

 

 

 

Note: If unfamiliar with sketching organic molecules for 2D to 3D conversion, see the Introduction to Materials Science Maestro tutorial and the 2D Sketcher Panel documentation.

Figure 3-2. Saving and naming a 2D Sketch.

  1. Click Save as New
  2. Name the entry vanillin
  3. Click OK
  4. Close the 2D Sketcher

Figure 3-3. Applying ball-and-stick. representation.

The 3D vanillin molecule will be both 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 and selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

  1. Change to a ball-and-stick representation by clicking Style > Apply ball-and-stick representation

Figure 3-4. Performing a Conformational Search.

While the structure generated in the 2D > 3D conversion is a reasonable starting point, we can improve our input molecule by sampling the conformational space with a computationally inexpensive force-field based Conformational Search:

  1. Go to Tasks > Browse All > MacroModel > Conformational Search
  2. For Use structures from, maintain Workspace (included entries)
  3. Click the Mini tab
  4. Set Maximum iterations to 100
    • This is the number of iterations the calculation is allowed to do before stopping if the minimization procedure does not complete
    • If the calculation is unable to find a minimum you can try increasing the number of iterations
  5. Change Job name to mmod_csearch_vanillin
  6. Click Run
    • This job takes ~1 minute on a CPU localhost
  7. Close the Conformational Search panel

Figure 3-5. The lowest energy conformer included in the workspace and selected in the entry list.

When the job is complete, a new group titled mmod_csearch_vanillin-out1 is added to the entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

  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 first vanillin entry in the output group
    • This entry is the lowest energy conformation (based on the force field)

Note: The number of conformers output may vary depending on your software version or any of your previous settings in the Conformational Search panel.

Figure 3-6. Analyzing relative energies.

  1. Open 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 ()
  2. Analyze the Potential Energy and Relative Potential Energy columns
    • The entries are automatically sorted by potential energy. The top entry is the lowest energy conformer
  3. Close 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

4. Calculating Bond Dissociation Energies for Vanillin

With a reasonable starting geometry in hand, we will now proceed to run and interpret the Bond and Ligand Dissociation calculation.

Figure 4-1. Selecting and including the entry and opening the panel.

  1. Ensure that the lowest energy vanillin conformer 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 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
  2. Go to Tasks > Materials > Quantum Mechanics > Workflows > Bond and Ligand Dissociation
  3. For Use structures from, ensure Project Table (1 selected entry) is chosen

Figure 4-2. Choosing structures and calculating dissociation sites. 

  1. Keep Single, acyclic bonds checked and click Recalculate
    • (4) appears next to Single, acyclic bonds, indicating the number of dissociation sites (see below for further description)
    • (0) appears next to Ligands complexes to metals, indicating that there are no metal-ligand bonds here, as expected

Note: The panel is not restricted to one structure as input. If multiple structures are specified, the BDE calculation on each input will follow the subsequent specifications.

Figure 4-3. Setting up the Bond and Ligand Dissociation panel and running the job.

  1. For Initial reactant states, click on all five options, and for Excited State via TD-DFT, maintain the Singlet option
  2. Change the Job name to bde_vanillin
  3. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about an hour on a CPU host with 12 processors
  4. If you would like to run the job, click Run. Otherwise, instructions for importing pre-generated files are provided in Section 5
  5. Close the Bond and Ligand Dissociation panel

The input is interpreted as follows, which is outlined in the schematic below:

  • The dissociation sites are selected as single, acyclic bonds, excluding bonds to hydrogen, which in this case specifies four bonds (see schematic inset upper left). Clicking Recalculate will allow you to compute the number of dissociation sites based on your selections.
  • By selecting several initial reactant states, we are performing the BDE calculation on five different starting states of vanillin: the singlet ground state, the lowest triplet state via SCF, radical anion (reduced), radical cation (oxidized) and an excited state via TD-DFT. See the help documentation for complete detail on the various initial states.
  • For each initial state, the BDE calculation on all four of the specified bonds is performed.
  • For the ground state and excited states, the four bonds are broken homolytically to generate two ground state radical fragments, resulting in four reactions in each case.
  • In the case of the radical ions, the bonds are broken homolytically to generate a radical and a closed shell fragment, which can happen in two ways, generating 8 possible reactions.
  • In all, 28 unique BDEs from 5 reactants and 24 unique fragments are specified from this input.

Within the Jaguar section of the panel, several additional specifications are also possible. You may choose to:

  • Compute Free energies at SATP which will compute vibrational frequencies and therefore thermal corrections.
  • Freeze products at reactant geometry which will specify that the product geometries are not relaxed.
  • Use solvation.
  • Select a different functional or basis set (for anion calculations, it may be advisable to add diffuse functions to the basis set).
  • Use Machine Learning Force Fields (MLFF). Additional information regarding MLFFs can be found in the help documentation or on our website.
  • Specify other SCF or optimization parameters, such as restricting spin states.
  • See the help documentation for complete detail on the various Jaguar settings.

5. Analyzing the BDE Results for Vanillin

In this section, we will analyze the results of the calculation.

Figure 5-1. Import the output files.

If you ran the job, 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 entry group from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion: bde_vanillin (57) and proceed to Step 4.

  1. If you did not run the job, from the main menu, go to File > Import Structures
  2. Navigate to where you downloaded the tutorial files and choose the provided Section_05 > bde_vanillin > bde_vanillin-bde.maegz file found in the bde_vanillin directory
  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. 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 entry group: bde_vanillin (57)

Figure 5-2. Analyzing the output in the Project Table.

One place to analyze the data is 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.

  1. Open 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
  2. View the Bond Dissociation Energy (kcal/mol) column for each bond dissociation reaction, labeled Rxn (N)
    • For example, vanillin Rxn 4 has a BDE of 58.65 kcal/mol

To interpret the data, here are some notes:

  • (N) designates a number linking to a particular bond dissociation reaction in the table
  • Within each initial reactant state, the BDE values are sorted from lowest to highest
  • There are property columns for BDE Reactant, BDE Product A, and BDE Product B for each Rxn (N), which can be cross referenced in the output entry groups titled Reactants (N) and Fragments (N) or visualized in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 5-3. Analyzing the output in the workspace.

Another way to visualize the data is in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed. To visualize all of the bond dissociation energies associated with one Initial reactant state, close 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, and includethe entry is represented in the Workspace, the circle in the In column is blue the reactant of choice:

  1. Include the reactant titled vanillin under the Reactants (5) entry group to see the BDE values for all four cleavages of vanillin from the ground state

Figure 5-4. Visualizing a fragmentation reaction.

Individual reactions can also be visualized by including the reaction of choice

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the reaction titled Vanillin Rxn 4 under the Reactions (28) entry group to see the BDE value and the fragmentation for the C-O bond cleavage to generate the methyl radical

Figure 5-5. Visualizing a single fragment.

Individual fragments can be visualized by including the fragment of choice. Refer back to 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 to confirm which fragment is associated with which reaction, considering that one fragment may be a product in several reactions.

  1. Include the fragment titled fragment 1 bde_vanillin under the Fragments (24) entry group to see the corresponding fragment

Figure 5-6. Viewing Spin multiplicity in the workspace.

Given the various spin states associated with the reactants and products, particularly when analyzing several initial reactant states, it may be useful to include the Spin Multiplicity and the Title in the upper-left corner of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

  1. In the main menu, go to Window > Workspace Properties and make sure this options is checked
    • The Title: appears in the upper left-hand corner
  2. Right-click on Title in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and select Edit Workspace Properties
    • The Workspace Properties window opens
  3. Click Add, select Spin multiplicity and click Close
    • The Spin multiplicity should now be included in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed under the Title
    • fragment 1 bde_vanillin is a radical with a multiplicity of 2

Feel free to analyze additional reactions and fragments 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 and/or Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

6. Calculating H-BDE for Ibuprofen

In this section, we will calculate BDE for all unique bonds to hydrogen (H-BDE) in ibuprofen, a simple example of an active pharmaceutical ingredient (or API molecule). This calculation is a useful approach for determining the susceptibility of a compound to undergo autoxidation.

Figure 6-1. The 2D structure of Ibuprofen.

  1. For the next example, either a) follow Steps 2-4 to import a starting structure, or b) repeat the above steps to sketch and perform a conformational search for Ibuprofen (shown in Figure 6-1) and then proceed to Step 5

Figure 6-2. The imported ibuprofen molecule.

  1. From the main menu, go to File > Import Structures
  2. Navigate to where you downloaded the tutorial files and choose the Section_06 > ibuprofen.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. The entry is automatically 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
    • This is the lowest energy conformation from a conformational search

Figure 6-3. Bond and Ligand Dissociation panel.

  1. Ensure that the ibuprofen entry 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
  2. Go to Tasks > Materials > Quantum Mechanics > Workflows > Bond and Ligand Dissociation
  3. For Use structures from, ensure Project Table (1 selected entry) is chosen
  4. From the dropdown menu, select Include only bonds to hydrogen
  5. Click Recalculate
    • Confirm that the panel shows Single, acyclic bonds (10) and Ligands complexed to metals (0)

Figure 6-4. Running the job.

  1. For Initial reactant states, select only Singlet ground state
  2. Change the Job name to bde_ibuprofen
  3. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 3 hours on a CPU host with 12 processors
  4. If you would like to run the job, click Run. Otherwise, instructions for importing pregenerated files are provided in the next steps
  5. Close the Bond and Ligand Dissociation panel  

Figure 6-5. Import the output files.

If you ran the job, 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 entry group from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion: bde_ibuprofen (20) and proceed to Step 18. Otherwise:

  1. From the main menu, go to File > Import Structures
  2. Navigate to where you downloaded the tutorial file and choose the bde_ibuprofen-bde.maegz 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

Figure 6-6. Visualizing the H-BDE analysis.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue the reactant titled ibuprofen under the Reactants (1) entry group to see the BDE values for all of the unique R-H cleavages of ibuprofen from the ground state in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed
    • All of the unique H-BDE values appear as labels  

Note: The algorithm reduces computational cost by considering only one representative in a group of symmetrically equivalent R-H bonds Indeed, there are 18 hydrogen atoms in ibuprofen, but only 9 fragmentations are required to capture all of the H-BDE values.

It is empirically established that with the computational parameters used in this tutorial that an H-BDE < 90 kcal/mol indicates potential liability to autoxidation (see references 3-5). In cases of instability, it may be useful to include antioxidant compounds in the formulation. For ibuprofen, the hydrogen in the carboxylic acid group appears most susceptible to undergo cleavage (H-BDE of 78.5 kcal/mol).

For additional practice with studying API molecules with Materials Science Maestro, visit the Molecular Dynamics for API Miscibility and Glass Transition Temperatures of APIs tutorials.

7. Calculating BDE for a Metal Complex

In this section, we will calculate BDE for a metal-ligand bond. Specifically, we will calculate the Pd-P bond dissociation energythe standard enthalpy change associated with homolytic bond scission at zero K for a prototypical complex, particularly in homogeneous catalysis, Pd(PPh3)4, for which ligand dissociation is key in many mechanisms.

Figure 7-1. Pd(Ph3)4 molecule in the workspace.

  1. From the main menu, go to File > Import Structures
  2. Navigate to where you downloaded the tutorial files and choose the PdP4.mae file
  3. Click Open
    • A new entry entry is added to the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  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 and includethe entry is represented in the Workspace, the circle in the In column is blue the Pd(PPh3)4 entry

 

Note: To learn how to build and enumerate organometallic structures, visit the Organometallic Complexes tutorial.

Figure 7-2. Recalculate bond types.

  1. Go to Tasks > Materials > Quantum Mechanics > Workflows > Bond and Ligand Dissociation
  2. For Use structures from, ensure Project Table (1 selected entry) is chosen
  3. Uncheck Single, acyclic bonds
  4. Ensure Include only bonds to hydrogen is selected in the option menu
  5. Next to Ligands complexed to metals, click Recalculate
    • Confirm that the panel shows Single, acyclic bonds (0) and Ligands complexed to metals (1), as shown in the Figure

Figure 7-3. Choose reactant states and Jaguar Options.

  1. For Initial reactant states, maintain only Singlet ground state
  2. Click Jaguar Options
    • The Jaguar Options dropdown appears

Figure 7-4. Setting the Jaguar options.

  1. For Theory, choose M06-L
  2. For Basis set, choose LACVP**
  3. Increase Maximum iterations to 200 and Maximum steps to 200
  4. Click OK

Figure 7-5. Naming and running the job.

  1. Change the Job name to bde_PdP4
  2. Adjust the job settings () as needed
    • This job requires a CPU host. The job can be completed in about 24 hours on a CPU host with 12 processors
  3. If you would like to run the job, click Run. Otherwise, instructions for importing pregenerated files are provided in the next steps
  4. Close the Bond and Ligand Dissociation panel

Figure 7-6. Import the output files.

If you ran the job, 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 entry group from the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion: bde_PdP4 (4) and proceed to visualize the results. Otherwise:

  1. From the main menu, go to File > Import Structures
  2. Navigate to where you downloaded the tutorial file and choose the bde_PdP4-bde.maegz 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

Figure 7-7. Viewing the reaction in the workspace.

As before, feel free to visualize the results in the workspacethe 3D display area in the center of the main window, where molecular structures are displayed or 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.

The predicted BDE associated with the reaction of Pd(PPh3)4 → Pd(PPh3)3 + PPh3 is +31.2 kcal/mol, which agrees well with previous literature reports [Organometallic reactivity: the role of metal-ligand bond energies from a computational perspective. DOI:10.1039/c1dt10909j]

8. Conclusion and References

In this tutorial, we learned how to use the Bond and Ligand Dissociation panel to calculate the energy associated with the fragmentation of a reactant molecule at various dissociation sites. Specifying dissociation sites and initial reactant states allows for probing of molecular stability. This tool has widespread applicability in both organics and organometallics.

For further learning:

For introductory content, focused on navigating the Schrödinger Materials Science interface, an Introduction to Materials Science Maestro tutorial is available. Please visit the materials science training website for access to 70+ tutorials. For scientific inquiries or technical troubleshooting, submit a ticket to our Technical Support Scientists at help@schrodinger.com.

For self-paced, asynchronous, online courses in Materials Science modeling, including access to Schrödinger software, please visit the Schrödinger Online Learning portal on our website.

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

For further reading:

9. Glossary of Terms

Bond Dissociation Energy - the standard enthalpy change associated with homolytic bond scission at zero K

Entry List - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Homolysis - a covalent bond dissociation where each of the fragments retains one of the originally bonded electrons

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

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