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!

Turn down that noise!

After thinking about yesterday’s Success of the Day post, I’ve decided it’d be good to make it a regular (though probably not daily) thing. It’s too easy to get caught up in why a particular experiment isn’t working. Daily successes are pretty good optimism boosts, even if it’s just a successful pot of tea.

Success of the Day: Polymer LED and its emission spectrum.

It’s a pretty terrible spectrum…I’m surprised I can see anything above the noisiness of it. BUT, it’s the the first spectrum from our new spectrometer, so huzzah! Optimization will clearly be needed.

Let’s not die, shall we?

Frightening dilemma of the day: how to get lithium fluoride inside my glove box?

I spend a lot of time working in a glove box, where the idea is to keep oxygen and moisture out. You fill the box with your favorite inert gas (we’ve got nitrogen in the one I use), and that let’s you do all sorts of fun science that would normally get messed up by oxygen or water. As a benign example: magnesium oxidizes like crazy in air. Nothing dangerous, sort of like the equivalent of rust. So if you need non-rusty magnesium, get yourself a glove box (there are far easier and cheaper ways to make sure magnesium doesn’t oxidize, but it’s a good example). There are more dangerous situations where you want a glove box becasue, say, things explode in water, but you get the idea.

So. First rule of glove box: don’t put oxygen/water inside. Seems simple but is sometimes a bit less intuitive than not sticking your cup of coffee inside. Jars of chemicals can go in fairly frequently, for example. If you close a chemical jar outside the glove box, you’ve now got oxygen inside the jar. If you then put it in your box and open it, you’ve just broken glove box rule #1 (guilty!). So generally you open your jar, pull out the air with a vacuum pump, then put it in your box. Easy!

Well, today I got some lithium fluoride that needed to go in my glove box. It arrived with an enormous skull and cross-bones poison label on the UPS box. It’s nasty stuff (even by chemist standards), and you don’t want to breathe it. Really. Unless you like, and I quote, “immediate defecation, writhing, … liver edema and necrosis, respiratory and cardiac failure.” (To be fair, that’s just for “large doses”, whatever that means.) I was thrilled. The problem then became how best to open it up so I could vacuum out the oxygen (so I could put it in the glove box) without killing myself. Welcome to the exciting life of chemistry grad students.

Long story short, the stuff is in the box. I am not dead.

No, we do not have an extra electron microscope just lying around

Our lab has had a problem recently with people from other parts of the building “borrowing” equipment. The term here is used loosely, since we’re rarely told when they take stuff, or even asked for that matter.

I worked in retail for a very short bit during my undergrad career, and for some reason I’m a bit surprised at how similar the situation is in research academia. Given the whole building is one big department, we’ve definitely got that community vibe going strong. It’s not too surprising then when you realize there’s something you need on the next floor down, and hey, we’re all in this together right? It happened a lot at my retail gig; the price gun would spontaneously teleport across the store (mind you, this was a large department store), your extra roll of receipt paper would be gone, that sorta thing. So it happens here too. The difference of course being that a loose coat hangar isn’t really equivalent to a $8000 dual channel source meter, if only for the fact that I can’t hang my lab coat on it.

"Gaseous Metal" sounds like a musical sub-genre

Task of the Day: Learning to do things like a mad scientist. As a specific example: How do I get some of this Big-Chunk-O-Metal to stick onto a flat sample surface?, I asked myself. Well, you just heat the bejeezus out of it. And I do mean the bejeezus. Skin-blisteringly hot isn’t nearly good enough. You heat it up until the metal evaporates (yes, you can get something like iron to evaporate; yes, seeing metal boil is as awesome as it sounds), stick your sample somewhere close, and voila! The gaseous metal atoms stick to your surface and resolidify since it’s cold.

Unfortunate side effect: everything else in the immediate vicinity gets coated in a fine film of, say, aluminum.

And just for kicks: boiling steel

2004 was really that long ago?

Task of the day: trying to order a new canister of compressed gas to replace the one that the group last ordered…6 years ago. Apparently in that time span the friendly local gas company the group used to use got bought out by Bigger Badder Gas Company (see, it doesn’t just happen to grocery stores), so they had no idea what we needed.

It also didn’t help that the gas was a little non-standard. Argon or nitrogen or something would have been easy enough to order whether we had the product number or not. Forming gas made from a 5% mixture of hydrogen in nitrogen? Not so much. They had a 10% mixture instead, which would have been great if we wanted to blow the converter box off the side of the machine we were using. Suffice it to say, doing so is not Standard Lab Procedure.