Thursday, July 27, 2006

Your hairdryer knows more solid state chemistry than you do

My favorite hairdryer finally kicked it on Wednesday morning, so now I'm in the market for a new one. My old $25 Vidal Sassoon lasted four years, and since then it seems there has been a quantum leap in hairdryer technology. A lot of the high-end and not-so-high-end gadgets feature "Tourmaline Technology". Tourmalines are a family of minerals with a very complex structure that could consist of up to about ten different elements, though all the members have the elements silicon, oxygen, aluminum, and boron in common. I don't know very much about solid state chemistry, but from what I just read, suffice to say that the structure of the mineral endows it with special properties. When heated, charges migrate within the crystals giving you positive charge at one end and negative charge in the other. A hairdryer with tourmaline crystals reduces frizz and static with the help of the charges emitted. Apparently these crystals give off infrared heat, too, but I haven't read anything about that yet. I'm looking forward to the informative pamphlet about the solid state chemistry of tourmalines that I'm certain will be included with my new hairdryer. ;)


Wednesday, July 26, 2006

The tastiest distillation there is

Today I purified my product using the lab's Kugelrohr distillation apparatus. Unlike many of the concepts one comes across in the field of chemical synthesis, Kugelrohr distillation isn't named for anyone. Kugelrohr translates to "ball tube" or "ball pipe" in German. It's my favorite way of purifying solids with low melting points. The idea is that by applying a vacuum to a flask (round bottomed, ie ball-shaped) with the impure, oily solid in it, you lower the boiling temperature. If the boiling points of what you want to separate are different enough, the pure product distills over into a receiver flask (also ball-shaped) chilled with ice water.
There are other setups for distilling things, but the Kugelrohr setup is infinitely easier to handle when dealing with solids, IMHO.
Rotating or swiveling the flask gives you a more even boil, and in the early days of this technology this was accomplished using a windshield wiper motor connected to a tube or pipe.
See this reference:

Graeve, R.; Wahl, G. H. J. Chem. Ed. 1964, 41, 279.

Today you can buy a swanktastic Kugelrohr apparatus from Sigma-Aldrich and other fine retailers. The apparatus comes with a hot air oven to warm the impure sample and get it boiling. Just be careful not to heat your sample too much, or you'll char it.

Random thoughts:
Is there any etymological relationship to the tasty treat we call kugel?
I think one of the coolest-sounding named reactions (lots of organic chem. reactions are named after someone) is the Chichibabin reaction. My opinion changes often on this matter.


Tuesday, July 25, 2006

Lee Silver holds his own

I finally got around to watching that Colbert Report episode with Prof. Lee Silver (thank you, TiVo!).
It's tough to get a word in edgewise with Colbert, but Silver took the offensive early, countering Colbert's bombast by politely asking him to lay out everything he knows about genetic engineering. "I'll ask the questions here," replied a clearly outmatched Colbert.
I think Silver was able to get his message out about balancing "nature" and "technology". My concern is that when the show describes him as believing that "cloning and gene splicing are the way of the future", that viewers will misunderstand the meaning of the words and mentally catalog Silver in the same cubby as the Raelians.
Anyway, the interview's hilarious. Watch it here.


Monday, July 24, 2006

Curb your enthusiasm?

A lot of labs in my field are doubtless interested in a newly-reported compound, platensimycin, which showed potent antibacterial activity in the lab against pathogens that are resistant to multiple antibiotics. The structure is certainly intricate, what with five interlocking rings. Here's the reference:

Wang, J. et al. Nature 2006, 441, 358–361.

Researchers at Merck verified that platensimycin, which was isolated from a simple soil microbe in South Africa, inhibits a key enzyme that bacteria use to make fatty acids. This is cool because it's different from a lot of the antibiotics used in the clinic. Researchers realize that it's important to find new classes of antibiotics in order to stem the tide of resistance that's emerged due to widespread, indiscriminate drug use.

It's also significant that platensimycin is a natural product, that is, a compound crafted by an organism found in nature. Over the last ten or fifteen years, pharma companies had moved away from finding inspiration for new drugs in nature, preferring instead large collections of molecules stored in databases because they were more compatible with emerging high-tech discovery methods. (See this article in C&E News.)

I just thought I'd comment on the spate of articles that tout platensimycin as a potential cure for "the superbugs", as the multiply resistant bacteria have come to be called. (ei: See here and here.) My understanding has always been that if a pharmaceutical company publishes their results this early into the discovery process, it is because there are difficulties that are most likely going to prevent it from being a viable candidate. So while they almost certainly patent the compound, the paper puts the knowledge out there and the total syntheses and other studies can commence outside the company.

I think that the message of the Nature paper isn't really, "Hey everybody, here's platensimycin! It'll be the next magic bullet as soon as we test it in humans!" but rather, "Look, there are still useful ideas to be found by going back to nature and hunting in exotic places, instead of just sticking to libraries of compounds. Let's really dedicate some thought to targeting this fatty acid-making pathway. Nature's probably making compounds like platensimycin for a reason, and plus, it may take bacteria longer to adapt to a new kind of antibiotic." Hmmm.. maybe it doesn't sound as newsworthy that way. I do think that Nature got it right in this article, though.


Thursday, July 20, 2006

Serotonin is a girl's best friend

There's a cute profile in this week's Chemical and Engineering News about Raven Hanna, a Yale-trained molecular biophysicist who quit her postdoc to try science writing and eventually founded a company, Made with Molecules, to market her own line of jewelry. Her designs incorporate molecules like serotonin, acetylcholine, and dopamine, basically neurotransmitters that are known to have affect mood, concentration, etc. Neat concept. I myself am the proud owner of a double helix bracelet that I bought during a daylong conference at Cold Spring Harbor Lab. Some of the "DNA Apparel" on the latter website isn't really my cup of tea, but I suppose I'll run out of Christmas gift ideas sooner or later.


Wednesday, July 19, 2006

You get into Nature your way....

Excuse the shameless self-promotion here. I've been featured in today's issue of Nature as part of their "Survive in Science" series. The article has advice and anecdotes about switching labs during your graduate career. You'll need to be somewhere with a subscription to the journal in order to view the article.
During my second year at Princeton, just after passing the Generals Exam (that's our qualifying exam), I switched from a biochemistry group to a synthetic organic chem lab, and I described the whole process to Kendall Powell, the freelancer who wrote the story. Kendall was a great interviewer; she was very easy to talk to and she even gave me some tips on breaking into the business.


Tuesday, July 18, 2006

Double Your Pleasure, Double Your Fun

Every week, I look up papers about stuff that comes up in group meeting that I’m rusty at or haven’t heard of, and today I stumbled upon these gems while reading about phenol oxidations using hypervalent iodine.

Tet. Lett. 1988, 29, 677-680.
J. Chem. Soc. Perkin Trans. 1993, 1891-6.

They’re published five years apart, and the data tables are exactly the same, except for one new reaction. The person that ran that reaction wasn’t even granted authorship. The Perkin paper expands on the narrative a little, refers you to a few syntheses where the methodology was employed, and has a new scheme with a proposed mechanism, but no data to back up the proposal. At least it cites the Tet. Lett…


Ice-Nine for Proteins

The BBC reports that researchers at Imperial College and the University of Surrey have found a material that can initiate formation of high quality protein crystals. The article emphasizes the finding's potential applicability in drug discovery but cautions that it isn't "one size fits all proteins".

I've really just scratched the surface in terms of my reading list, but it's not often I come upon an orphan news story. Perhaps this is a bit esoteric for the rest of the mainstream media outlets, but I was also curious why the report did not come out in January, which is when the article was published in PNAS. There's nothing the BBC says to suggest there's been any new advance since then.
Chayen, N.E.; Saridakis, E.; Sear, R. P. PNAS 2006, 103, 597-601.

*****Protein X-Ray Crystallography in a Nutshell*****
A protein crystal is a repeated array of a protein molecule, packed together in a regular pattern. Scientists in the field of x-ray crystallography bombard protein crystals with radiation and then determine the protein's 3D atomic structure.
This isn't trivial; proteins contain thousands of atoms. Nowadays, computers do much of the heavy lifting in terms of the math involved, but crystallographers guide the process the whole way through.

(See Dylan's blog for a snippet of a "classic" crystallography paper. It was a lot harder back in the day. That was just ONE AMINO ACID!)X-ray crystal structures of proteins can tell scientists how an enzyme works or how proteins interact with one another. Since these structures reveal the nooks and crannies of these proteins, they allow researchers to sculpt drug candidates that fit the mold.

The BBC tidbit was near and dear to my heart, because when I was an undergraduate, I worked on part of my thesis research in a protein crystallography lab at a nearby pharma company. Though I'll be the first to admit that crystallizing an already-solved enzyme with a point mutant near the active site (a place less likely to perturb crystal packing) isn't the most challenging of projects, at the time I was really proud of having accomplished a little body of work that WORKED and provided some useful information.

My understanding is that crystallization remains the rate-determining step of solving structures. Rock candy this ain't. Any advance that provides a better microscopic picture of nucleation, the starting point for crystal formation, is going to be very helpful in the quest to crystallize "stubborn" proteins. It's known that introducing an external solid into the crystallization "broth" can produce better-ordered crystals. The material Chayen et al. found works because it has a wide distribution of pore sizes and shapes, making it more likely that a given pore will convince protein molecules to stick around and nucleate. If I had more time on my hands, I would check up on the proteins they crystallized using their method and see how diverse they are, or if any were known to be particularly challenging by traditional methods.

PS: The title refers to a material made up for Vonnegut's "Cat's Cradle". Ice-nine was supposed to be a high-melting allotope of water that would act as a "seed crystal" and instantly solidify your afternoon tea, and even (for those with visions of world domination) entire bodies of water.


Monday, July 17, 2006

Lee Silver on tonight's Colbert Report

Tonight's Colbert Report will feature Princeton Molecular Biology's own Professor Lee Silver!
Incidentally, the Colbert Report is one of my favorite shows; I've been following Stephen's career since he was a brash but intrepid correspondent on The Daily Show. He's come so far, and made me so proud (tear).
I haven't read Lee Silver's book, but as the reviews encapsulate it, the book seeks to turn on its head the notion that what is natural necessarily equates to what is good, and explains that roadblocks to scientific advances are being put up from the political left just as much as from the right.
Read this article at The Scientist Magazine for more info.
Anyhow, my TiVo's set; it should be an interesting chat with Colbert about Silver's new book (no doubt he'll be gleeful that the left is getting an earful from Silver). I'll be sure to blog about my thoughts afterward.


Sunday, July 16, 2006

Science Diet

I've been influenced, nay, inspired, by the science-y and oft humorous commentary I read on a near-daily basis. Here's my own small contribution to the blogosphere. Take it for what you will.