One component or transformation from boron to Iodine or other

Hi Everyone,

I’m trying to do a diversity selection of a set of various boron coupling reagents. I have a mix… Boronic acids, boronates, fluoroboronates, etc. I wanted to transform them to all the same atom. For example iodine or carbon. Looking at the examples, the ones I found are all scaffold enumeration types. I am trying to replace the boron species of any compound to that same compound with a standard atom.

I was able to tackle this another way using smiles to filter and create atom lists and then use a rooted fingerprint not including the searched smiles but I figured I need to also learn how to do it this way.

I’ve attached a draft of the workflow example.

Thanks in advance for looking!
Boron transformation.knwf (114.3 KB)

I am trying to replace the boron species of any compound to that same compound with a standard atom.

It’s unclear to me what you’re trying to accomplish. I don’t really understand your workflow - the reaction you drew has the same molecule on both sides of the arrow.

Can you provide some more details about your expected results?

Hi @elsamuel yes my bad with the copy paste error. Here is a replacement. What I’d like to do is for every molecule replace the boronic acid, boronate, trifluroboronate with some standard atom such as iodine or carbon.

Here is an updated workflow,
Boron transformation.knwf (40.1 KB)

I can’t run the latest workflow you updated. You didn’t package the sd file with the workflow, and the molecule sketcher doesn’t have a reaction in it when I open the node configuration.

In any case, I would just create SMARTS strings for all the transformations I want to do:

  1. for boronates/boronic acids: [#6:1][B:2](O)O>>[#6:1]I
  2. for trifluoroboronates: F[B-:2](F)([#6:1])F>>[C:1]I

If you’re interested in a single string for all the reactions, then [#6:1][B:2]>>[#6:1]I might work

If you’re unfamiliar with SMARTS you can visualize them by pasting the string into ChemDraw, or at Examples and theory are here: Daylight Theory: SMARTS - A Language for Describing Molecular Patterns.

Here’s the workflow in action:




Thanks @elsamuel I was looking at that daylight reference and wasn’t grasping it very quickly but now I see what is going on and how that works. Too bad you can’t sketch the reaction in chemdraw and copy special like you can smiles…

I’ll also try sketching into the KNIME molecule sketcher and see if I can get the same result.

Thanks again so much!

You can, in fact, sketch a reaction in Chemdraw and copy it as a SMILES/SMARTS string. However you’ll need to be careful to properly assign the atom mapping beforehand. You’ll also need to modify the string afterwards to include any special queries if you haven’t included them in the Chemdraw drawing.

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Hi @elsamuel

Yes, I noticed that playing around. For example the same reaction with mapping out of chemdraw came out like this:
[CH3:1]B([*])[*]>>[CH3:1]I which I converted to [#6:1]B([*])[*]>>[#6:1]I

I also was able to get the same transformation working with ketcher after playing around with chemdraw. To help others who might come across this I’ve uploaded an updated workflow not reset so the data and reactions should be intact.

Boron to iodide transformation.knwf (370.4 KB)

Thanks so much again!

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