pKa Predictions with Jaguar pKa

Tutorial Created with Software Release: 2023-2
Topics: Quantum Mechanics, Small Molecule Drug Discovery
Methodology: Molecular Quantum Mechanics
Products Used: Jaguar, Jaguar, MS Maestro, Maestro
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 displayedthe 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:

 

This tutorial demonstrates the use of Jaguar pKa for prediction of pKa values of organic molecules. As you run through each computation, you may find that the exact output numbers/ cpu time may not be identical to those proposed here. For some types of calculations, the exact numbers are dependent on the starting geometry and operating system and while the qualitative conclusions should be the same, the exact numbers may differ slightly.

 

Tutorial Content

  1. Creating Projects and Importing Structures

  1. pKa of a Molecule with Two Symmetry-Equivalent Functional Groups

  1. pKa of a Molecule with More than One Functional Group

  1. Conclusion and References

  1. Glossary of Terms

1. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location that files are saved in Maestro to make file navigation easier. Each session in 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 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 created, the project is automatically saved each time a change is made.

Structures can be imported from the PDB directly, or from your Working Directorythe location that files are saved using File > Import Structures..., 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 icon to start Maestro

Figure 1-1. Change Working Directory option.

At the start of the session, change directory to your chosen Working Directorythe location that files are saved. This makes file navigation easier.

 

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose

Figure 1-2. The Save Project Panel.

  1. Go to File > Save Project As
  2. Change the File Name box to Jaguar_pKa_prediction, click Save

2. pKa of a Molecule with Two Symmetry-Equivalent Functional Groups

Jaguar pKa predicts micro-pKa values, which are the pKa values of single protonation/deprotonation processes involving one functional group. If the molecule contains multiple functional groups, several of them might contribute to the single, experimentally observed pKa transition. In the first part of this tutorial, we will consider a molecule that has only one functional group, or one symmetrically equivalent functional group. Jaguar pKa is not designed to predict tautomeric forms existing in solution. Jaguar pKa is also not going to predict the relevant protonation form (singly protonated, doubly protonated etc). So before using Jaguar pKa, if necessary, you should generate and analyze the tautomeric and protonation forms with Epik, at pH relevant to the pKa transition of interest. For the pKa prediction with Jaguar pKa, select the form (in either its protonated or deprotonated form) that you believe is the dominant species responsible for the experimentally observed pKa that you are trying to model. For a tutorial introducing the prediction of macro-pKa constants with Macro pKa, see pKa Predictions with Macro pKa.

We will predict the first pKa transition of 1,4-dihydroxybenzene (also known as hydroquinone). From basic chemical intuition, we know that this molecule possesses only one tautomeric form. The first pKa transition is caused by the dissociation of one hydroxy group. Either of the two hydroxy groups can dissociate, and because the groups are symmetric, they contribute to the observed pKa to the same degree. Therefore, we will be modeling the following dissociation process:

The second pKa transition is caused by the dissociation of the second hydroxy group, after the first one has already dissociated. Even though both pKa transitions can be modeled with Jaguar pKa, it is only the first one that will be of interest to us in this exercise.

It is always advisable to perform a conformational search as part of Jaguar pKa predictions. For a simple and a relatively inflexible molecule like ours, conformational search and its particular settings are not likely to matter much, and you might get away with generating a reasonable pKa value for this molecule without performing any conformational search. However, for accurate pKa predictions of larger and flexible molecules conformational search is necessary. In this section, we will set the conformational options that should be a good choice for most molecules.

Since Jaguar pKa launches quantum chemical calculations (at the DFT level), they are computationally expensive. For a small molecule like ours, the pKa prediction can take a few minutes. However, it can take numerous hours for large and flexible molecules depending on the size of the molecule, the computational power of your machine and the number of CPUs used.

2.1     Build the structure

Figure 2-1. The 2D Sketcher panel with 1,4-dihydroxybenzene drawn in it.

Build 1,4-dihydroxybenzene using the 2D Sketcher

  1. Open the 2D Sketcher panel: Edit > 2D Sketcher…
  2. Draw 1,4-dihydroxybenzene
  3. Click Save as New
  4. Type 1-4-dihydroxybenzene in the Entry Title dialog that appears
  • The 3D structure appears in the Maestro Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and the corresponding entry is available in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion on the left

 

You can draw a 3D structure directly using tools from Edit > 3D Builder…

Examine the 3D structure and make sure that the automatically generated conformation is approximately as desired. The molecule in this exercise is very simple, and we would not expect it to have multiple conformations. It is recommended, though, that you visually inspect more complicated molecules. If the 2D > 3D conversion does not generate a desired conformation, modify the 3D structure using structure modification tools in Maestro to produce an appropriate 3D structure.

2.2 Select pKa atom

Figure 2-2. Locate pKa in the Tasks menu.

Open the Jaguar pKa panel

  1. Go to Tasks and type pka
  2. Select pKa
    • The Jaguar - pKa panel opens and the 1-4-dihydroxybenzene entry is automatically includedthe entry is represented in the Workspace, the circle in the In column is blue in the panel

Figure 2-3. The Jaguar pKa panel with 1,4-dihydroxybenzene shown in its mini table and in Workspace.

  1. Double-click on the pKa Atom cell

Figure 2-4. 1,4-dihydroxybenzene with atom H13 picked as the pKa atom.

  1. Click on the hydrogen atom from one of the hydroxyl groups in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and click anywhere in the panel for the selection to take effect
  • The hydrogen atom is now marked with an orange asterisk in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and is also listed in the pKa Atom cell (H14)

Depending on how you built the structure, your actual atom number might vary. The marked hydrogen atom is the atom that is going to dissociate in the process you are modeling.

Figure 2-5.  Various ways of finding pKa atoms in the Jaguar pKa panel.

Note : In addition to specifying the pKa atoms manually, they can also be found in the molecule by checking the box for Find pKa atoms and selecting any of the two options from the dropdown. The Automatic search option automatically identifies the pKa atoms in the molecules and runs a pKa calculation for each. The SMARTS option, on the other hand, is used to specify one or more SMARTS patterns to identify pKa atoms.

2.3 Set conformational options

Figure 2-6. The Jaguar pKa panel with the recommended conformational settings for accurate pKa prediction.

  1. In the Input tab, ensure that the box is checked for Perform conformational searches on input structures (requires MacroModel license)
  2. Ensure that Accuracy is set to Thorough
  3. Ensure the Max number of conformers to use for each species is set to 5
  4. Check the box for Allow use of zwitterion functional groups

The lowest-energy conformer is used for each species by default in a microscopic pKa calculation, but you can set an energy window and a maximum number for selection of multiple conformers for macroscopic pKa calculations, which we have done here.

Figure 2-7. The Solvent tab of the Jaguar pKa panel with the recommended conformational settings for accurate pKa prediction.

  1. Click the Solvent tab
  2. Check the box for Use solvation for geometry optimization step  

The remaining settings in the panel are left at their defaults

 

  1. Change Job name to jag_1-4-dihydroxybenzene_pka

2.4 Set host and CPU options

Figure 2-8. The Job Settings panel.

  1. Click the Job Settings button (cog symbol)
    • The Jaguar - pKa - Job Settings dialog box opens
  2. Select an appropriate host and set the number of processors to use in this calculation
  3. Click Run
  • The pKa prediction calculation job starts, and will take a few minutes

2.5 Examine the results

Figure 2-9. The result of the pKa prediction of 1,4-dihydroxybenzene, displayed in the Workspace.

On job completion, the resulting annotated structure appears in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed, with the pKa indicated next to the pKa atom.

 

Note: You need to toggle on labels, and include the lowest energy protonated or deprotonated conformer entry if this structure does not appear. For more information about this calculation please see the Jaguar pKa Calculations page in the documentation.

Figure 2-10. Property tree from the Project Table with all Jaguar properties (Primary and Secondary) selected.

The predicted pKa is also shown 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.

  1. Press Ctrl+T or choose  Window > Project Table
    • 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 opens
  1. If the Property Tree is not open, click the Tree icon 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 toolbar. Alternatively, you can choose Property > Tree
    • The Property Tree opens alongside 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. Under Jaguar, check Primary and Secondary properties

Figure 2-11. Project Table listing the result of the pKa prediction in the pKa water column.

  1. Scroll 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 the right until you find the column called pKa water which, in the appropriate cell, should show 8.85

Figure 2-12. A fragment of the Monitor panel showing the output file of the finished  jag_1-4-dihydroxybenzene_pka job.

More detailed information about the pKa prediction can be obtained from the pKa output file.

  1. To view the file, choose Window > Job Monitor or select the Jobs icon
  2. Select jag_1-4-dihydroxybenzene_pka (the job name when launching the pKa calculation) to find a list of files associated with this job

Figure 2-13. The contents of the output file showing different pKa’s predicted by different pKa models. The first (topmost) model is usually more accurate and the one that should be preferred.

  1. Double click on  jag_1-4-dihydroxybenzene_pka.out which is the output file for our calculation
    • The contents of the output file will be shown

In our case, the output file lists three different models with which the pKa of 1,4-dihydroxybenzene was predicted. The first column (#) indicates the model index, the second column (Shell) indicates the model name, the third column (pKa) shows the pKa, and the fourth column (RMSD) shows the RMSD of the linear fit on the training set corresponding to the fitting of the model. The models and their predictions are sorted by RMSD. The model that has the smallest RMSD is usually the most specific and the most accurate, and therefore should be preferred. In our case, the most accurate model (shell) is called phenol excluding o-nitro and o-nitrosophenols and it yields pKa equal to 9.11. This value has already been automatically corrected for symmetry. Jaguar pKa automatically recognized that the second hydroxyl group in the molecule is symmetrically equivalent to the one whose pKa we computed, and adjusted the final pKa so that it corresponds to the macro-pKa resulting from the contribution of both functional groups.  The experimental pKa of 1,4-dihydroxybenzene in water is 9.85, according to H. Baxendale, Transactions of the Faraday Society, 1953, 49, 1140-1143.

3. pKa of a Molecule with More than One Functional Group

We will now continue to predict the first pKa transition of a more complex structure, 1,4-dihydroxy-2-methylbenzene. It is obvious that this molecule possesses only one tautomeric form. However, the first observable pKa transition is caused by the dissociation of 1- and 4-hydroxy groups, and since the groups are no longer symmetric (one is closer to the methyl group and the other is further away), the two hydroxy groups are going to contribute differently to the observed pKa. The difference of the chemical environment of these two groups is fairly small, so the micro-pKa values of each group are expected to be close to one another, and below the resolution power of a typical pKa measurement. This means we need to compute two micro-pKa values, one for each functional group:

This calculation will take longer than the previous one for two reasons: 1) there are now two micro-pKa values (one for each non-equivalent hydroxy group) to compute and 2) the molecule is a little larger than the previous one.

3.1 Build a structure

Figure 3-1. The 2D Sketcher panel with 1,4-dihydroxy-2-methylbenzene drawn.

Build 1,4-dihydroxy-2-methyl-benzene, using the 2D Sketcher

 

  1. Choose Edit > 2D Sketcher
  2. Draw the structure of 1,4-dihydroxy-2-methylbenzene
  3. Click Save as New… and give the molecule the name 1-4-dihydroxy-2-methylbenzene

3.2 Select pKa atoms

Figure 3-2. The Jaguar pKa panel with 1,4-dihydroxy-2-methylbenzene shown in its mini-table and in the Workspace, with the conformational search options used from the previous calculation.

Open the Jaguar pKa panel

  1. Go to Tasks > Browse > Quantum Mechanics > pKa
  • The 1-4-dihydroxy-2-methylbenzene entry is automatically shown in the panel because the default setting is to show the included (Workspace) entry

 

Note: The recommended conformational search options are remembered from the previous pKa prediction and are automatically applied

 

Figure 3-3. The Jaguar pKa panel with 1,4-dihydroxy-2-methylbenzene shown in its mini table and in the Workspace, with atoms H13 and H14 picked as the pKa atoms.

  1. Double-click on the pKa Atom cell
  2. Click on the hydrogen atoms from both hydroxy groups in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and click back anywhere in the panel for the selection to take effect
  • The hydrogen atoms are now marked with orange asterisks in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and are also listed in the pKa Atom cell (H14, H13)

 

Note: The actual atom number might vary. The marked hydrogen atoms are the atoms that are going to dissociate in independent dissociation processes, starting from the molecule shown in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

  1. Set the Job name as jag_1-4-dihydroxy-2-methylbenzene_pka
  2. Click Run
    • This job will take approximately 30 minutes. Please see section 3.3 to save time and view the results.

To model a sequential dissociation (pKa2) you would have to start with a singly dissociated molecule in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

Since the conformational options were already set and the host and CPU options were also remembered from the previous calculation, we were able to run the job without altering the computational resources to be used.

3.3 Examine the results

Figure 3-4. The result of the pKa prediction of 1,4-dehydroxy-2-methylbenzene in the Workspace.

When the calculation finishes, the resulting annotated structure appears in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

The micro-pKa results of the lowest energy protonated conformers are shown next to each of the hydroxy-groups in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and can also be viewed 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 in the Jaguar pKa output file, as explained in the first part of this tutorial for 1,4-dihydroxybenzene

 

  1. Observe the pKa values
    • The micro-pKa values of the two groups are nearly the same in this case. The 1-OH group turns out to be a slightly weaker acid than the 4-OH group

3.4 Convert the micro-pKa’s into the macro-pKa

The dissociation of the two hydroxy groups in different chemical environments contributes to pKa1, the first observable pKa transition in the experiment.

In the current version of the program, Jaguar pKa does not convert micro- into macro-pKa values, so we need to do this manually or via the Calculator function - an embedded icon in your 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. This manual exercise will, however, demonstrate how the micro- and macro-pKa values are related.

The macro-Ka is connected with the micro-Ka values by the formula

Ka (macro) = Ka (micro, first group) + Ka (micro, second group)

Note: We need to take the sum of the Ka, not pKa values. The analogous sum applies in case of three or more groups contributing to the macro-Ka.

Since the micro-pKa of the first group is 9.34 and that of the second group is 9.40, we have Ka of the first group = 10-9.34 and that of the second group = 10-9.40:

Ka = 10-9.34 + 10-9.40,

pKa = -log (Ka) = -log (10-9.34 + 10-9.40) = 9.07

The experimental pKa of 1,4-dihydroxy-2-methylbenzene in water is 10.14, according to M. P. Youngblood, Journal of American Chemical Society, 111, 1989, 1843-1849.

4. Conclusion and References

This tutorial demonstrated the use of the Jaguar pKa panel for typically simple pKa predictions involving one or more functional groups. It also taught us how to convert micro-pKa’s of several functional groups into the macro-pKa that can be compared with the experimental pKa measurement. For calculations involving molecules that might possess several tautomers it is best to use Epik in order to predict the tautomeric and protonation forms before attempting a Jaguar pKa calculation.

5. 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

incorporated - once a job is finished, output files from the working directory are added to the project and shown in the Entry List and Project Table

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 that files are saved

Workspace - the 3D display area in the center of the main window, where molecular structures are displayed