MolDraw Docs

pKa and Microspecies plugin

Short answer: Install pKa and Microspecies from the + menu next to the Structure tab, draw a molecule, then set the pH.

Last updated · By the MolDraw team at LabCanvas

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MolDraw pKa and Microspecies plugin showing cetirizine with its species chart and the Sites table
Cetirizine at pH 7.4. The chart shows each charged form from pH 0 to 14 and the Sites table lets you type in a measured pKa.
  1. Chart of every microspecies from pH 0 to 14.
  2. pH controls with a slider and presets.
  3. Summary: major species, net charge, isoelectric point and pKa values.
  4. Sites table with the estimate and a box for your own value.

What it does#

MolDraw finds each acidic or basic group, starts from a measured value for that type of group, and adjusts it for nearby groups using the Hammett and Taft equations. Groups that sit close together affect each other. Every protonation state is then weighted at your pH to give the percentages. No server and no AI model are used.

All values are estimates. On about 2,000 test molecules the tool never saw during tuning, the average error is 0.92 pKa units and 71% of values are within 1 unit. For common drugs the average error is about 0.45. Acids, amines and phenols do well. Some ring systems, tautomers, amidines, enols and C-H acids can be off by 2 units or more.

The test data comes from the SAMPL6, SAMPL7 and SAMPL8 challenges (MIT licence), the AvLiLuMoVe, DataWarrior and Novartis sets shared by Baltruschat and Czodrowski (CC BY 4.0), and literature drug values. Full credits are in the MolDraw source under plugins/pka/bench/SOURCES.md.

Who it is for#

Students learning acids and bases, medicinal chemists checking charge at blood pH, and anyone who needs protonation states for docking or a figure.

How to use it#

  1. Open the MolDraw editor and sign in. Click Settings, then Plugins, then Install next to pKa and Microspecies.
  2. Draw a molecule, or select one if the canvas has several.
  3. Click + next to the Structure tab and install pKa and Microspecies. You can also right-click a molecule and choose pKa and microspecies.
  4. Set the pH with the slider or a preset (callout 2).
  5. Read the major species and the percentages (callouts 1 and 3).
  6. To use a measured value, open Sites and type it in (callout 4).
  7. Press Insert major species or Replace drawing to put the charged form on the canvas.

Tips#

  • Leave a Your pKa box empty to keep the estimate.
  • Click the chart to jump to that pH.
  • Switch to Major at pH to see the charged structure.

Questions and answers

How accurate is it?

It is an estimate. The average error on held-out test molecules is about 0.9 pKa units, and about 0.5 for common drugs.

Does it send my molecule anywhere?

No. Everything runs in your browser.

Is it free?

Yes, with a free MolDraw account.