Simple Chemistry Conversion


I wanted to know how to deprotonate and/or protonate ionised compounds in Knime using any of the Chemistry kits. I have them all downloaded.

For example, RN2H+ Cl- into RN2 HCl.


I can't see how to do this with any of the available nodes but I am very new to Knime


Does the Hydrogen Manipulator from CDK do what you are looking for?


Nope - doesn't make a difference.

You can do this with the commercial MOE nodes by using the Protonation node.

However, it can be done (with a little more effort) using either RDKit or Indigo. Below is the example using Indigo, but a similar process can be done with RDKit

Convert your structures to Indigo format first.

Then you need to use a Marvin chemical sketcher node, and draw Cl- rxn arrow to HCl, then automap the atoms (so a little 1 appears on both Cl's). Now take this RXN output, connect it to a Query Reaction to Indigo node. Now connect this and your structures in Indigo format to a Molecule Transformation node. That now converts all your Cl-'s to HCl. Now repeat a similar process to convert all PyridineNH+s into Pyridines.

Hope this helps.


Right, thanks.

Will try that. I was hoping that it would be more straigh-forward (i.e. a single node) than this but I will give it a go. Thank you.



The Indigo toolkit has Hydrogen Adder and Hydrogen Remover nodes.

(the other) Simon

No this doesn't work. thanks though

Ahh, no it doesn't either. I thought that I'd used this to neutralize charges once before.