This is click chemistry.

I’m pretty sure this isn’t, though.

[1] But that isn’t stopping Larock and friends from calling it click chemistry, right in the title, no less. Before I start ranting, let’s go over some of those criteria K. Barry Sharpless wrote in stone and brought down from Mt. Nobel:

• Really fucking efficient.
• Atom economical. All parts of the reactants should be part of the product. (Catalysts and byproducts that are benign are okay.)
• Inert to solvent, and neat is nice. You should be able to do them in water. If the word “ionic liquid” hits your lips, Barry will smite you.
• The reaction should be (one of my favorite words) bioorthogonal. This word also describes CBC- orthogonal to biology.
• Thermodynamically downhill like whoa. Sharpless calls them “spring-loaded reactions.” One might also call them “bam,” particularly if one is Emeril Lagasse.

Okay, then. So the “click reaction,” the copper-catalyzed Huisgen [3+2] cyclization, is the clickiest reaction around. All you need is some copper, some vitamin C, an azide and an alkyne. And they just come and stick together like white on rice. And it almost always works, hooray. You can imagine how nice an idea this is for materials- if all you want to do is stick two things together covalently, starting from simple precursors, then there’s a protocol that’ll work more often than not. Lots of materials chemists have used them for a variety of purposes, and biologists have done some insanely cool things with it, too. There’s a reason it’s rather hyped- it’s cause non-organic chemists are making this reaction useful at a rate previously unheard of. It’s clicktastic.

But Larock’s example, while cool, is bit of a stretch on the clicky dogma. Now the cycloaddition between benzyne and an azide is clicky- of course, it’s thermodynamically downhill, and it doesn’t even need a catalyst to go, owing to the ridiculous reactivity of benzyne.

But it’s the MAKING of benzyne that makes it not very clicky. Okay, first, you start with o-(trimethylsilyl)phenyl triflate. So how do you make that? You’ll likely need some butyllithium and some triflic anhydride. So it’s not terribly clicky to make the precursor. The formation of benzyne itself is a really, really cool reaction: take your precursor and treat it with fluoride at room temperature. Then add your azide, wait, and whee! A benzotriazole you get, in good yield.

But is it clicky? I don’t think so, mostly cause you have to make that benzyne using chemistry that isn’t very clicky. On the other hand, how do you make azides and alkynes for the copper catalyzed click chemistry? With non-click chemistry. Sodium azide? Nasty shit. Alkynes? Probably not going to be clickable much in the making, either.

I mean, don’t get me wrong, it’s the idea that’s important, and a worthwhile goal to achieve. And the chemistry is still very much in its infancy. Regardless, even though those one (or two) click reactions have been utilized in many different ways, we shouldn’t be limiting ourselves to them necessarily- unless, of course, it gets you funding. Then I would recommend you take your science and click the shit out of it.

[1] I wish all graphical abstracts were as awesome as these. Floating Head Barry should make more appearances in the literature.

Shi, F., Waldo, J.P., Chen, Y., Larock, R.C. (2008). Benzyne Click Chemistry: Synthesis of Benzotriazoles from Benzynes and Azides. Organic Letters DOI: 10.1021/ol800675u

Since we are stuck in the basement of an old and drafty building, we occasionally see insects running around.[1]  Don’t ask me how they survive in some of the labs, or what they eat…they’re not a constant plague so much as an occasional annoyance, though, so no big deal.  We still don’t really like them, though.  I’ve been known to step on anything with six to eight legs that happens to startle me.

But at least that’s a quick and relatively painless death, right?[2]  Nothing like what the crazies in my lab did recently.  As it turns out, conc sulfuric is an insecticide:

And pretty effective, at that.

[1] Seriously, there’s about an inch or two of gap under one of the doors.  Anyone want to think about how much the university might save in heating and cooling if they did something about that?  Or at least ensured that our hoods were adequate.  Fume hoods are a huge energy suck.

[2] When I was working in an entomology lab, our group used malaise traps to catch braconids.  Also seems like it would be a pretty bad way to go.  I’m glad I’m not an insect…

Rule #1: No more than four bonds to carbon.

It’s the first important rule you learn in sophomore organic chemistry. When you write an exam [1], putting five bonds to carbon (the infamous “Texas carbon”) is akin to going to the Vatican and telling everyone Jesus was black. People are going to yell at you and tell you you’re wrong, they instruct you to go to the Sistine Chapel and look up, and you might even get excommunicated, but you still know better. Well, this is one of those “Jesus is black” papers. [2] It’s a step up from the texas carbon (which have already been characterized)- it’s a Canada carbon. [3]

Well, kind of. Yamamoto et al. describe a molecule with a “hexacoordinate” carbon in it, though it’s not six covalent bonds like the kind sophomore orgo drills you on- they’re more like dative bonds, more akin to inorganic chemistry. The molecule is a weird bis-anthracene with an allene bridge, which looks not unlike Feringa’s molecular motors. The methylated version, shown below, requires highly unreactive carborane counterions for x-ray analysis. The carbon in the middle of the allene bridge, they claim, is hexacoordinate, as the four peripheral oxygens donate a lone pair into the carbon’s HOMOs.

Using x-ray crystallography, they found that the allene carbon-oxygen bond lengths (around 2.6 Å) are longer than a covalent C-O bond but shorter than the sum of the van der Waals radii, implying that they might be bonding. High-resolution x-ray anaylsis (using a synchotron!) showed that there were bond paths between the carbon and oxygen, although the interactions were pretty weak. DFT shows that the oxygen is likely donating electron density into the π* orbital of the carbon, not unlike a charge transfer complex.

So… not exactly a Canada carbon, but a pretty interesting complex, nonetheless. It’s always fun to read papers that, had you seen them when you were in sophomore orgo, would have made your head asplode.

[1] Americans say “take exams” but I like “write exams” more.
[2] Politically correct? moi?
[3] Everything might be bigger in Texas, but in Canada everything’s so big you have to drink to forget about it.

Yamaguchi, T., Yamamoto, Y., Kinoshita, D., Akiba, K., Zhang, Y., Reed, C.A., Hashizume, D., Iwasaki, F. (2008). Synthesis and Structure of a Hexacoordinate Carbon Compound. Journal of the American Chemical Society DOI: 10.1021/ja710423d

We’ve been super-busy lately, which is pretty much always our excuse for a lull in posting.[1] And it looks like we’re going to stay that way, too. So this is a good time to open up a discussion, yes?

Topic of choice: environmental chemistry.[2] Fluorescent sensors for heavy metals in aqueous solutions: practical or not? Argue at length.  I’ll reserve my $0.02 until things get…interesting.

If you cooperate, I’ll post a video of the discrete working its magic. 

[1] But it’s true! By the way, those who missed out on seeing Dimmu Borgir Saturday (I’m guessing all of you are in that category)…sucks for you! They were awesome.

[2] I don’t post much about work in that lab, though it’s where I spend most of my time awake. Then again, there is a much better blog out there for those so inclined…and I highly recommend you check it out.

This deserves a moment of silence.

Confession: I am attracted to shiny graphical abstracts. Even if your research has nothing to do with my interests, even if I’ve never heard of your group, you have my immediate and undivided attention if you include some pretty pictures. Bright colors and glowing things will usually persuade me to at least flip through your paper, and if you’re (un?)lucky, I might like it enough to post it. Behold:

Shiny, yes? Better yet, they’re single crystalline nanowires (2,4,5-triphenylimidazole, in case you were wondering). Some of you may be scratching your heads: “That doesn’t look like a laser…” But what’s at the heart of laserdom is stimulated emission.[1] I don’t really want to go into more detail on how they work.[2] But the extremely short version is that you have a gain medium (in this case, the nanowires) that gets pumped (optically, in this case). The pumping leads to population inversion, which is what makes stimulated emission possible. These guys found that the dimensions of the nanowires influenced the lasery behaviour. Cool paper, yes? I thought so.

And here’s one that’s arguably even cooler, but without an awesome graphical abstract…the authors used a laser to photopolymerise some resin with a little (yay, organic!) dye. This created a Fabry-Perot cavity with a waveguide inside. They make it sound very quick-and-easy and propose that it could be useful in the development of integrated optical circuits. Now, this isn’t my field, so I don’t actually know all that much about it…but that sounds pretty badass.

Since this post is on lasers, I’m totally obligated to post the following video.

[1] For some reason, that phrase always sounds so dirty to me.

[2] Bear with me, OK? I’ve never actually had the chance to play with lasers in the lab (damnit! but Sam is around to correct me where I’m wrong). But I took a spectroscopy class that …I’m just too sick to get up and search for the ginormous binder right now. Besides which, discussing Einstein coefficients involves scary math, and this is (presumably) an organic chemistry blog. We count to four and draw hexagons.[3]

[3] Well, ALL organic chemists do that…but seriously, not all of us are afraid of physics.

Those of you who find it a struggle to read anything out of a journal might be intrigued by this excerpt:

“sexual freedom (including an unusual recognition…of female sexuality)”

Oh, and see also: “repeated fornication”

I had a feeling that would get your attention! Only Roald Hoffmann could get away with publishing it in Angewandte Chemie. (Rock on, man.)

[0] Time for another hard-hitting post that asks the important questions: what’s pretty and has pretty colors?

This is perylene. It’s yet another polycyclic aromatic hydrocarbon (PAH), and probably the one of the largest pure PAH that is soluble in most organic solvents. It’s unbelievably fluorescent. So fluorescent, in fact, that ambient light is enough to see its blue fluorescence in solution. [1]

This is a pretty dilute solution of perylene in acetone under ambient light. The blue twinge is from its fluorescence. Shallow solutions of the stuff appear green as a result, like when I was filtering a solution with some perylene in it. [2]

I just thought this next pic was pretty.

And when you put a blacklight (365 nm) up to a solution of the stuff:

It just GLOWS.

[0] Yeah, you liked that pun. Admit it.
[1] You can derivatize perylenes too- the most popular being the perylene diimides (PDI), which are brilliantly colored and can fluoresce anywhere from the yellow to near-IR region, depending on the substitutents. viz:

[2] That mess in the back of the hood was there when I moved there. I don’t want to know what it is.

STM (scanning tunneling microscopy) constantly fascinates me. Above the fundamental basis of why it works (which all the but the most basic ideas of quantum tunneling constantly elude my understanding), STM gives us the ability to do something that should really be impossible: the ability to look at atoms.

Well, kind of. I mean, obviously you can’t “see” an atom- it’s a wee bit difficult to visualize features and objects that are smaller than the wavelengths of light that our eyes can process. So, we have to improvise. Instead of looking at optical features, STM gives us an electronic picture: If we’re trying to visualize an atom, what we’re actually seeing is electron density (or, more precisely, the density of states as measured by the electron tunneling current). The jist- STM is pretty sweet. Bask in my figure:

Fear not, organikers: you can look at organic molecules too, but it’s trickier, since you have to put it on something conductive. Gold works due to pi-d orbital interactions. If the molecule you want to see is flat and aromatic, then you can use highly-ordered pyrolitic graphite (HOPG), which will force the pi-face of the molecule parallel to the surface, due to pi-stacking interactions. So a flat, aromatic molecule like pentacene will do just that:



Which is good, cause that means all the fun pi-clouds are ready for the analyzin’. You can use STM, then, to look at two-dimensional network solids, and see how they interact. Colin Nuckolls did that with his cruciform pi-systems, which make nice little X shapes on HOPG and happen to be chiral in two dimensions.


Yeah, so that’s what molecules look like. Neat!

Florio, G., Klare, J., Pasamba, M., Werblowsky, T., Hyers, M., Berne, B., Hybertsen, M., Nuckolls, C., Flynn, G. (2006). . Langmuir, 22(24), 10003-10008. DOI: 10.1021/la0617199

hie thee to the library and read this awesome book.[1]  It was written with chemists in mind (yay!), and bases many explanations on MO theory.  I’m only about 40 pages in, but the squiggly little lines already make sense.  Seriously, pick up a copy of this!  NOW!  (Even if band theory doesn’t do anything for you, it’s an excuse to read something by Hoffmann, whose writing is AMAZING.)  There’s a chance I might do a quickie post on the subject in the future, for those who are allergic to books, but that involves having free time.

While we’re on the subject of reading things, good news for people who have limited journal access–lots of RSC articles are FREE! this month.  Free is always good, right?[2]

Also, the best cure for a solid-state-physics-induced headache is a kitty.  Here are two of mine for you to awwwww over.

[1] Infinite thanks to everyone who recommended I read this.

[2] Especially as it pertains to beer.