Goodnight Moon, Goodnight Sun, Goodnight Calix[6]arene

If you're into molecular machines (and who isn't?) then you might get a kick out of this recent JACS paper. The rest of you who could care less will at least like their graphical abstract:


Cuuuute! Look at that happy sun! And that content moon! And... what the hell is that red thing? And blue thing with the blue tail? And it's... going.. in... what? Now vigilant CBC readers are probably thinking "oh god, not this shit again. He's probably gonna call it a nanotampon or something, isn't he?" Well, that's where you're wrong. I'm not going to stoop to your pedestrian humor, cause I'm a classy guy. Perish the thought that I would ever sink so low as to use bodily humor to illustrate the diverse and fascinating chemistry of rotaxanes, which is exactly what this system is, and is activated in the presence of light by a photoacid.


Anyway, the nanotampon (...dammit) is a simple monoalkylated 4,4'-bipyridinium, with one basic site. The, um, nano...ah, fuck it. It's a calix[6]arene.[1] Now as it turns out, the protonated bipyridinium forms a nice pseudorotaxane with the calixarene. So the authors decided to use a merocyanine photoacid to turn the rotaxane assembly and disassembly into a process that can be switched on and off with light. Photoacids are simply molecules that, when exposed to light, release a proton. This merocyanine-spiropyran system is a photoacid:


So, upon release of that proton in the presence of light, the bipyridinium is protonated, and the pseudorotaxane is formed. Put it in the dark, and the system slowly (~7 days for full conversion) disassembles. And unlike real tampons, the process is completely reversible.[2]

One can debate the usefulness of molecular machines- I frankly don't see any real use for this thing. But c'mon, cuuuuuuuute graphical abstract, and I think photoacids are awesome. I wish more papers had happy suns.

[1] God I am SO GLAD the authors used the default ChemDraw template for calixarenes here. Seriously.
[2] I deeply apologize for that gross remark.

Because Organic Chemistry Doesn't Smell Bad Enough

Someone published an Org. Lett. paper on analyzing rotting fish guts. Yeah.

So let's say you're a hungry shark. You want some fish, and you want to make sure it's delicious and fresh and whatnot. How does a hungry shark go about quantifying the following analysis?


I mean, to a shark, it's all good, probably. Dead and rotting? Dory? A hungry shark will eat them all. But those rotting fishies can have some nasty toxic amines in them like putrescine or histamine that can accumulate before you can smell them. So what's a shark to do?

Basically, nothing. The shark's totally fucked in this case.* ** But lucky for us humans, a new technique for detecting nasty amines has been developed using some functionalized polythiophenes. Using a polythiophene that has been functionalized with a carboxylic acid, the Lavigne group has shown in the latest Org. Lett. ASAP that the UV/Vis absorbance profiles of poly(thiophene)s changes when amines form aggregrates with them.

Since every amine is a little different either in size, binding character, or both, the poly(thiophene) aggregates that form will vary from amine to amine. In other words, one amine will aggregate poly(thiophene) such that the polymer molecules are closer to one another, while another amine will space them out more. This "multidimensional response," as the authors call it, changes the solution absorbance profile of the polymer, which can be qualified for each amine. After testing the profiles of different amines, they did a blind test with 97% accuracy, regardless of the complexity of the matrix.


But the best part of the paper was the "proof of concept," or, as I like to call it, "the PI suckered some poor grad student to blend rotting fish guts with trichloroacetic acid." Seriously. They took "fish matrix," which was canned tuna doped with a known amount of histamine (a common biogenic amine found in rotten tuna). They blended it in trichloroacetic acid, centrifuged and added the polymer, then measured the absorbance. Then they repeated it, over and over again. (And you thought you had to do shitty work for your PhD.) Turns out their little polymer makes for a pretty handy amine detector, able to quantify the amount of histamine in your rotten tuna.

It's not without its limitations (what if you have more than one amine? you're screwed; it'd be nice if you could just make a freshness sticker like they do with other meats), but still a neat idea that utilizes familiar chemistry in a really freaking stinky way. Someone give that fish guts guy/gal a medal.

*EDIT: Or not.

**Okay, more relevant example that'll appeal to the retro gaming crowd. Let's say you're playing Final Fantasy III (VI in Japan or if you're a prick) and the world just ended. And you're Celes, and you just woke up a year later on an island with Cid, who's basically your adopted father. And he's really sick after taking care of you for so long. You have to get fish for him to eat, but if he eats bad fish, he gets worse and dies and Celes attempts suicide (depressing!). What do you do? WHAT DO YOU DO? (The real answer is just catch the fast fish, but what if you couldn't tell?)

solid-state synthesis: sans solvent?

Stuart at The Sceptical Chymist recently did a quick interview with Mike Zaworotko, so I'll continue what he started and point you in the direction of a recent paper in Crystal Growth & Design.[1]

The idea behind it is C³S³, which is a much faster way of saying co-crystal controlled solid state synthesis. Naphthalenetetracarboxylic dianhydride (NTCDA) and an amine were ground together with maybe a drop or two of solvent thrown in. Heating gave a co-crystal of the two. The co-crystal was then heated like crazy to give the corresponding diimide.

I'm guessing that the product was not so soluble, which might explain why they recrystallized using DMSO or DMF. I'm pretty sure the corresponding perylene diimide would be brickdust. Still, greasy amines (with looong alkyl attachments) would probably be too volatile for this.

In any case, it's an interesting little paper that caught my eye, and I needed to post something, so here it is. You might expect to see more crystal engineering-related lit on CBC in the next month or so, by the way, since I've been staring down a few of those papers lately.

[1] It has to be pure coincidence that everyone covered in Sceptical Chymist's Reactions so far is doing something I find interesting. I will attribute this to Stuart's fantastic taste in subjects rather than mind-reading.

Quick post on cool idea from people we like

What? Someone who isn't Excimer is posting? Every now and then I have to take a break from staring at equations or my eyes will cross. Spring break isn't far off, though, so if Excimer is lucky, I will pick up the slack then.[1]

Confession: Both of us behind CBC have a raging chemical celebrity crush on Bob Grubbs and Sir Fraser Stoddart.[2] With that in mind, I've been meaning to mention this, but it got buried on the flash drive...better late than never, right?

In short, the gray three-armed piece is the template, and the ring-looking piece is a crown ether with two little arms terminated by alkenes. The crown ether threads itself onto the template, then ADMET occurs to assemble the trimer. In the absence of the template, there is no trimer, although a bit of dimer is formed.

Granted, this definitely isn't the beginning of such work. There are more papers out there than I want to link to, but here is something along the same lines from Org Lett in 2006.

[1] An upcoming exam has me confronting the irony inherent in being Ψ*Ψ. If it didn't sound so cool, growing p-chem antipathy would force me to change it.
[2] Especially since the latter was knighted. You have to admit that's pretty cool.