Protonation

pK_a Plugin

Most molecules contain some specific functional groups likely to lose or gain proton under specific circumstances. Each ionization equilibrium between the protonated and deprotonated forms of the molecule can be described with a constant value called pK_a. The pK_a plugin calculates the pK_a values of all proton gaining or losing atoms on the basis of the partial charge distribution.
Learn more about how the plugin calculates pK_a.

We introduced the trainable pK_a calculation from version 5.2! You can define a file with experimental data, and use its values for the correction of calculations.

The pK_a options panel offers different parameters to set:

• Mode: micro, macro: micro and macro acidic dissociation constants. Read details.
• Acid/base prefix:
  • static: submitted ionic forms are converted to their neutral forms (adding or removing protons) and their pK_a is calculated.
  • dynamic: the pK_a of ionic forms are calculated, not their conjugated acids or bases.
• Min basic pK_a: widens the calculation range because weak bases will have lower pK_a values than the default -10.
• Max acidic pK_a: widens the calculation range because weak acids will have higher pK_a values than the default 20.
• Temperature: setting the temperature in Kelvin.
• Correction library
  • Use correction library: check this box to use a file with experimental data for the calculation. See the detailed guide for training data setup.
• Consider tautomerization: checking this option, the most feasible tautomer and resonance structures are considered as subject of the pKa calculation.
• Show distribution chart: checking this box, you will have microspecies/macrospecies distribution as function of pH calculated and displayed. Go to Display Options tab for further settings of the distribution chart. Unchecking this box, only the pK_a of the drawn molecule will be calculated.

• Decimal places: setting the number of decimal places with which the result value is given.
• Distribution chart: you can set the range of displaying the microspecies distribution diagram.
  • pH lower limit
  • pH upper limit
  • pH step size
• Show log[%] - pH distribution: checking this box, the common logarithm of microspecies/macrospecies distribution is calculated and displayed as function of pH.
  • log[%] - pH distribution lower limit: you can set the lower value of the Y axis ranging from -35 to zero.

Results are shown in a separate window. When checking the Show microspecies distribution box, this window appears (for the explanation about the red&blue color representation of the pK_a values next to the protonable groups read this document):

The chart shows the microspecies distribution, or the common logarithm of microspecies distribution curves vs. pH. The microspecies images are shown in the legend. When clicking on an image, the corresponding microspecies molecule is displayed in the upper-left viewer. (The viewer can be detached from the chart panel by double clicking in it, or else by selecting Open Viewer from the View menu.) The original molecule with the pK_a values is shown when clicking on the chart outside of the legend image areas, or else when selecting pKa Values from the View menu.

Note: If there are 8 or less ionizable atoms in the molecule, then microspecies distribution is displayed on the chart, otherwise macrospecies distribution is shown. Images of microspecies are displayed only on the microspecies distribution chart; on macrospecies distribution chart the formal charges of the macrospecies are shown.

The contents of the text field can be copied to the clipboard by Ctrl+C, the structure field offers a context menu from MarvinView.

When moving the mouse over one of the microspecies images, the corresponding (pH : % of the microspecies) coordinates appear on the curves.

Calculation with the option 'Take major tautomeric form' gives same values for different tautomers.

Major Microspecies Plugin

Determines the major protonation form at a specified pH.

The pH can be set in the Major Microspecies Options panel, the default pH is 7.4.

• Take major tautomeric form: if tautomeric forms are more likely to occur, tha major tautomer is used to calculate the major microspecies.

The result is shown in a separate window, indicated the pH value and the structure in a MarvinView field.

The contents of the text field can be copied to the clipboard by Ctrl+C, the structure field offers a context menu from MarvinView.

Isoelectric Point Plugin

Net charge of an ionizable molecule is zero at a certain pH. This pH is called the isoelectric point, also referred to as pI. Isoelectric point plugin calculates gross charge distribution of a molecule as function of pH.

The Isoelectric Point Options panel contains the pH, and the option to switch off the charge distribution chart of the charge of the molecule vs. pH:

The result is shown in a separate window, containing the molecule structure at the pI and the value of pI. If the Show charge distribution checkbox was checked, the charge vs. pH curve is displayed. When moving the mouse over the dots in the curve, the coordinates (pH : charge) appear.

The contents of the text field can be copied to the clipboard by Ctrl+C, the structure field offers a context menu from MarvinView.