99 problems, and crosslinking is definitely one

Hold on to your goggles, we’re about to do some polymer chemistry!

While I wait for the final edits to come back on the paper I’ve been writing, I have been buttoning up the trusty lab coat to tackle some data for another project.  Unfortunately (but par for the research course), science isn’t doing what I want it to.

It’s based on a typical coupling polymerization, like this:

To simplify things, I’ve just got a small molecule with reactive ends A and B.  Stick a bunch of them in a pot, stir it up, and you get a polymer chain.  Tada!  Coupling polymerizations are a good friend of mine, and generally we get along famously.

What I’m really interested in doing is putting some functionality on the “block” of the small molecule, so I can use the resulting polymer chain for even more chemistry later.  It actually ends up more like this, where the extra functionality is marked C (for “criminey that’s awesome!” – what, you think I’m beholden to some bourgeois alphabetical labeling?).

That C could be anything to make the final product useful.  It could be a chemical group that emits light in the presence of a deadly toxin.  It could be a binding site for a protein you want to interact with in a medical application.  It can be a miniature Tony Stark who sits around being snarky to all the other non-awesome molecules.  Anything.  There are thousands of polymers out there with everyone’s pet side group attached to it for doing awesome physics/chemistry/biology.

And that’s the nice thing about coupling reactions.  Joining A and B is usually accomplished using a catalyst that’s been finely tuned to be highly efficient.  The catalysts work well, and bear more than a passing resemblance to Justice Scalia in that they are extremely selective for joining A-to-B with non of that unnatural horrific A-to-A homocoupling.  So generally putting that extra functional group in there doesn’t hurt too much.

Until this unexpectedly happens:

Suddenly that new handy chemical group wants in on the coupling fun!  And you end up with a giant gelatinous cross-linked mess in the bottom of your test tube.

The weird thing, and what’s happening for me, is when there’s no clear chemical route for C to start linking in with A and B.  It’s definitely happening – there’s really no other way to make grade A chemical goop.  So somehow C is getting by the Scalia-like laser vision of the catalyst, and it’s back to the drawing board for me (but not before pinning the data to the wall to maybe check out as a side project for looking into on some rainy day).

Behold the joys of research!

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