The Future is Here

Hey Coroneneketeers,

That didn't have a very good ring to it, did it? Oh well. We're moving to our own domain! Check out the new CBC here!

The Blogger blog will stay here as an archive for all these old posts, but we're going to start posting over at the new site from now on... unless we decide to move all the posts over there (read: fat chance).

Enjoy! Feedback is encouraged!


orange!! (the most exciting thing i've seen in a while)

You've seen a lot of the perylene diimides I've made. (In case you missed them, here they are.) To this point, they've all looked the same--red to violet in the solid state. This one is different. It's so tangerine it hurts a little. Also, it isn't a fibrous pancake--all the others give me long, flexible needles, if they crystallize at all (perylenes are infamous for gellating). This one actually behaves like a normal crystalline solid! And it's sparkly! See?

Why orange, though? This is neatly explained by quantum interference effects in a super-cool but somewhat ancient paper by Roald Hoffmann and friends. (Do not fear the theoreticalness, undergrads and synthetikers. It's an easy read--very clearly written. I'd kill to see more like this in the literature.)

I'll say first that the black PDIs they report sound really exotic and I kinda wish mine were that color.[1] One of the more interesting conclusions of the paper is that the dyes with the most substantial band-broadening in the solid state are the ones with the highest photosensitivities. Cool, eh? I won't say too much more about crystallochromy, since the paper discusses it so much more nicely than I could if I tried, so...just read it?[2]

Since--as Kazmaier and Hoffmann state--the color of these compounds depends on their crystal packing, and this derivative is a markedly different color than anything else I've made, I'd KILL to see a structure of it. Of course, crystal growing takes time, so I'll be patient.

Also, keep an eye on CBC. We're planning something REALLY COOL! We just can't tell you what it is yet. ;)

[1] Black is a super awesome color if you're trying to make solar cells. Black with significant near-IR absorption is even better. Black leather with spikes is good for BDSM and death metal.

[2] For another, more recent, nifty paper on dye aggregates, check this out. Someone covered it already. I tried to find their post, but...I read a lot, and I've forgotten who pointed it out. Care to correct my memory?


google brings you to the strangest places...

Well, these have been collecting for a while, and tonight happens to be excellent for a fluff post, so instead of chemistry you get...weird Google searches that ended up at CBC. Chemistry can wait for tomorrow, yes?

  • We have a few people who apparently don't think much of us authors:
    dumb people in grad school
    grad school for undergrad fuck ups
    the internet is full of assholes
    The third search was probably looking for Uncle Al. I wouldn't call Excimer dumb (EDIT: Excimer does)--far from it (EDIT: all the time)--but I am most definitely a fuckup, so that one's right on target. (EDIT: the last time Excimer argued with her and said she wasn't a fuckup, he got pwnz043d pretty hard. So there you go.)

  • It's pretty clear what this person was looking for:
    I wanted a shark that's big enough to eat you, and in a large enough amount of liquid so that you could imagine you were in there with it.
    I really don't know why, though.

  • A few people appeared to be legitimately seeking information, but I don't know why Google thought they might find it here:
    % of men who act on gay curiosities
    pics of what mole poo looks
    what happens when you see medusa's gaze
    how to edit a picture to look like an acid trip
    I guess I should take that last one as a compliment? The colorful things in the lab never make me wonder whether I'm tripping acid, though.

  • This person has apparently been reading too much Palahniuk:
    can you live without a cerebral cortex

  • whereas this one has a grooming issue:
    removing nasal hair

  • and this one probably cut himself after finding nothing emo except for an emergency button on CBC:
    something emo to read

  • The last few are just WEIRD, and there's no sane way to categorize them, so here they are:
    condoms clothesline weird
    tennis ball machine gun
    wanting to break hot water heater
    I wonder why these wackos never comment. Or maybe they do...

EDIT: The past hour has seen all sorts of searches, presumably from people who already
read CBC. My favorites are carbon-based condoms and is my nasal hair large enough.


Friday Potpourri

Just a few things to sate your appetite for the ol' CBC this weekend:

  • James Watson, as it turns out, is a complete prick. Shocking. Given his treatment of Rosalind Franklin in The Double Helix, frankly nothing that comes out of this man's mouth surprises me- he's always had a lack of tact. The concept of "race" is a purely socioeconomic one, which has a long, sordid, awful history in this country. No amount of science is going to fix that. If Watson has his way, such science would only make things worse.

  • I think this is a point worth repeating. There are some things that science can't fix. Race discrimination is undoubtedly one of those things.

  • Roger Kornberg does chemistry! Who knew? *epic lulz* In an incredible paper that came out in Science this week, the Kornberg group isolated and got a crystal structure of a gold nanoparticle with 102 Au atoms capped by 58 mercaptobenzoic acid ligands. Given the difficulty of generating sufficiently monodisperse nanoparticles to even make crysals, this is quite an achievement. A great read! (thanks to anonymous for the tip, whoever you are.)

  • Another cool paper from Advanced Materials, aka that one journal with the awesome research and no supporting information: the Japanese have succeeded in fabricating a gel that walks. On its own. Using metal redox chemistry and no biologicals. I, for one, submit to our walking jelly overlords, which I suspect will take over Japan, and soon the world, in the next twenty years.

  • In the "yet another paper on carbon nanotubes" department, a Nano Letters paper from the Burke group at UCI, where they made a carbon nanotube radio. The nanotube acts as the AM demodulator of the radio source, and they even made a video demonstrating how it works with those newfangled iPods all the kids have nowadays. The music choice is pretty dumb (it was like muzak or something- why not some real music?), but the concept is cool.

  • EDIT: The video is on YouTube! woot

  • And finally, in the self-congatulatory deparment, an article in this week's Science about this year's Nobel Prize in Chemistry going to Gerhard Ertl has the following quip:

    "In an earlier phone interview with Science, Ertl was quick to offer credit to fellow researchers. His field, he says, was propelled by the parallel development of many surface characterization techniques. And, he adds, many scientists were adept at applying them--including Gabor Somorjai of the University of California, Berkeley, with whom he shared the 1998 Wolf Prize in Chemistry for their work in surface science. "I was a little bit disappointed he didn't share [the Nobel Prize] with me," Ertl says. Last week, several chemistry bloggers went further, arguing that Somorjai deserved recognition for his vital role in laying the foundations of surface science."

    So basically 1. Gerhard Ertl is a nice guy; 2. Ertl also thinks Somorjai should have won; 3. Apparently the chemblagosphere whined loud enough about this that Science took notice and felt it necessary to add that last part in. I feel partly responsible. Yay me!

There, that should keep you occupied for the weekend. See you Monday!


change of plans? (no-content post)

I was planning to post some beautiful red crystals that finished growing after two weeks of resisting the temptation to look at them every five minutes. You would have liked them--they were fibrous and tangled and somewhat reminiscent of hair. Some are shorter and more blocky, and look like they will diffract very well. Unfortunately, I don't have them anymore, and unless some nice people at NIST want to take a shot of them once they arrive, you'll never see them. Sorry!


A Mighty Inorganic Kablooie

You couldn't pay me enough money to work with polyazides- that's pretty much the bottom line for me. For some reason, though, these potential molecular bombs have attracted a lot of interest lately. The total synthesis of tetraazidomethane* was finally completed earlier this year, and the synthesis of the complex Ti[N3]4, among other metal-polyazides, was completed a few years back.

Fresh off the heels of their previous successes with metal-azide complexes, those crazy sons of bitches at the Christe group have published the synthesis of more bombs, this time with selenium: the (lame) Se[N3]4, the much more awesome Se[N3]5- and the Chuck Norris special Se[N3]62-. That's right, kids. SIX azide groups on one atom. Six.

Six. That's a lotta firepower in one molecule. (Actually, as it turns out, the pentaazido and hexazido compounds, which are anionic, are more stable than the neutral tetrazido species... but they're still not THAT stable.) Surprisingly, they were able to obtain a crystal structure for the hexaazide- badass. And as one would expect, these nanobombs decompose readily at room temperature via the following pathway:

[Ph4P]2[Se(N3)6] --> 2 [Ph4P]N3 + Se + N2 + A GIANT FUCKING EXPLOSION**

While I'm sure there is always great interest in the inorganic community to study the structure and reactivity of new inorganic complexes, I draw the line at ten feet- where the compound, even in small quantities, has enough force to kill me from ten feet with shrapnel or whatnot. This leads me to propose the following transformation:

This work will (not) be continued and I wish to reserve the field for myself.

*Yes, it's a total synthesis. Suck it.
**Explosion only subtlely reported. Read between the lines. Or just read the "Safety Precautions" section which takes up a sizable chunk of the experimental section.


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.


glowy byproduct

This is discarded junk from a successful reaction.  One of the postdocs was looking over my shoulder while I worked it up, and asked why it looked a little green--the product, after all, is red as a solid and orange in solution.  I grabbed the TLC lamp to check for fluorescence, and...BAM!  Aqua.  Cool!


it takes some serious talent to screw this up

I will never really understand why people bother to buy tetrakis(triphenylphosphine) palladium(0). On any given day, it's definitely the easiest reaction I do, and it always works. On a bad day, the bright yellow crystals are enough to make me feel a little better. (Also, palladium catalysis is MAGIC.) Apparently, it doesn't ship well and might show up in funny colors (unless maybe you get it from Strem). It only takes about half an hour.

Excimer asked me a long time ago to post the procedure I use to make this, and I'm finally getting around to it. One of my labmates googled this a while back, and it's never failed us. It also has the advantage of being free. Usually I work on about a hundredth of their scale, which still works well enough--I'll maybe never have an excuse to make over 100 grams of the stuff.

Store under nitrogen and in the dark--it's ready for whatever coupling reaction you want to throw it into. (This batch is going toward a Sonogashira and a Stille.)


Nobody Cares Who I Think Should Get A Nobel

EDIT: Gerhard Ertl won the Prize for Chemsitry this year. Well-deserved on his part, and I'm glad surface chemistry is being recognized this year, but the fact that Somorjai and Whitesides didn't win is, in my professional opinion, 'tarded. Oh well. Like Kyle said, the Nobel is a silly thing anyway.

First off, suck it Bush. Suck it long and suck it hard. I say that a lot, but why this time? Because pioneering work in embryonic stem cell research and its impact on gene therapy was awarded with a Nobel Prize in Medicine today. Bush's veto of the embryonic stem-cell research bill last year and today's Nobel announcement further illustrates the divide between scientific progress and the Bush Administration's policies. While the Nobel was for research on mice, and the ban on human stem cells, the announcement still shows the importance of stem cells in gene research.

Anyway. They're announcing the Nobel Prize in Chemistry on Wednesday, which means it's time for speculation- one can debate the usefulness of such speculation (ok whatever it's a worthless waste of time), but it sure is fun. I'm not banking on a prize in materials chemistry or organic chemistry, based on the chemistry selection committee, a hodgepodge of p-chemists and biologists with umlauts in their names. However, most of the work I do, and the work of many people who do work on novel materials, is centered around the truly pioneering work of three chemists who, in my opinion (and, after five minutes of discusion with Ψ*Ψ, her opinion as well) are highly deserving of the Nobel Prize. This is meant on no way to predict who the winner will be on Wednesday. I am neither Swedish nor broadly knowledgeable in all areas of chemistry (especially the molecular biology aspects), but go here if you wanna place your bets.

George Whitesides and Ralph Nuzzo. I call Whitesides the world's smartest chromedome. He might object to that, but I have yet to find evidence to the contrary. If they do get the Nobel, it will be for their research on self-assembled monolayers. (That paper, according to Web of Science, has been cited over 2,100 times.) However, Whitesides has been a pioneer in nearly everything he's had his hand in, from his early work on C-H activation in metals to soft lithography to, more recently, multi-ligand interactions in enzymes (well, I thought it was neat). But his work on self-assembled monolayers is Nobel-worthy. It's had a large impact on the miniaturization of electronic devices as well as simply being a simple method for creating ordered monolayers on conductive substrates. Another pioneer in surface chemistry has been Gabor Somorjai, whose work on studying surface metal-metal interactions and metal-organic interactions on the atomic level has also had a huge impact on surface chemistry.

Richard Heck. Heck's work needs no introduction to organic chemists. Most noted for the reaction that bears his name, Heck's work on palladium catalysis preceded pretty much everyone else's at the time. The Suzuki reaction? Heck's work set the stage for that. The Sonogashira reaction? Heck did it first (without the copper). Seeing as both academia and industry have benefitted from palladium-catalyzed organic reactions, Heck certainly deserves a Nobel for this early work that led to some of the most important reactions of the late 20th century. (Metathesis was honored two years ago, which, while important, hasn't had half the impact palladium has.) Plus, Heck's getting up there in age, so they need to get it to him quickly.

So that's what I think. In my professional (?) opinion, neither of them will win the Nobel, and it'll be given to people whose research I don't really care about (I has an idea lets give it to another biologists lol).