moleculeoftheday | November 7, 2008Cyprodenate is an old antidote for benzodiazepene overdose:
It is a relatively rare drug that doesn't have a single aromatic ring - steroids are the broad class of exceptions that come to mind. It looks like this is some sort of cholinergic compound, but that's just an educated guess. Doesn't look like anyone uses it anymore, except some of the "smart drugs" crowd. Anyone know anything about it?
moleculeoftheday | November 3, 2008Limonene is a monoterpene that occurs in citrus peel, and it has a strong generic citrus smell. Many terpenes are smelly, like carvone (spearmint or caraway). Interestingly, limonene is cheap and abundant enough to use as a semi-green degreaser or solvent.
Green or not, limonene isn't totally safe. You can actually get sensitized to it - essentially developing an allergy - and then you're in the unpleasant position of being allergic to citrus peels. Careful lab technique and a certain amount of luck have allowed me to avoid sensitization to any lab chemicals. And that's a great thing -…
moleculeoftheday | October 30, 2008Atropine can:
Dilate pupils
Speed the heart
Inhibit sweat and salivation
Serve as an "antidote" to "nerve gas"
Sounds like powerful medicine, and it is, indeed. On the other hand, it is named for Atropos, the Greek goddess responsible for deciding how people die, for a reason. This is a molecule best used by doctors, and only then with a surfeit of caution. Unfortunately, it seems to pop up everywhere!
The somewhat disparate effects of the compound come from its ability to block a particular neurotransmitter receptor. It has a lot of medical uses, due to the above effects.
However, as…
moleculeoftheday | October 27, 2008Geosmin smells of earth:
You can smell vanishingly small amounts of it, too - mere nanograms of the stuff! It smells this way for a reason - countless soil bacteria busily produce it in your backyard as you read this.
The first thing I thought of when I started this entry was Demeter's Dirt fragrance. I imagine this has to have some of the stuff in it - I've only ever smelled it briefly in Whole Foods, though.
I love smell because I never fail to marvel at the fact that a pure single molecule can exhibit such complex aromas. My favorite example is acetophenone.
moleculeoftheday | October 9, 2008Takin' off that TBDMS? TBAF isn't your only choice:
TEA.(HF)3 is another source of the fluoride ion. Neat TEA-HF3 is a liquid, so it's about 10 M vs typical 1 M TBAF. A little nastier than TBAF, since it's able to liberate HF.
moleculeoftheday | October 8, 2008Stick that TBDMS on Monday and helplessly flailing around, looking for a way to get your alcohol back? Have a little TBAF:
TBAF is one of the most common sources of fluoride ion for silyl deprotection. You usually get a 1M solution in THF with a little water, too. It can be a pain to get rid of when you're not working with big, greasy, drug-like molecules and you're working with water-soluble molecules like RNA.
moleculeoftheday | October 6, 2008Just like boc protects amines, TBDMS protects alcohols.
TBDMS chloride will protect alcohols. The silicon-oxygen bond is pretty strong, and the silicon-fluorine bond is even better. This provides a protecting group that's pretty robust - fluoride reagents are typically used for removing the silyl ether. More on that shortly...
moleculeoftheday | September 30, 2008Last year, we were fretting about melamine contamination in foods from China. Again, this week, it's happening - melamine was put into milk by some unscrupulous vendors. The idea here is that melamine is high in nitrogen and cheap. An easy way to get an idea of how much protein is in something is to assay for nitrogen - by cutting milk with water and adding melamine, the unscrupulous can pass off watered down milk as full-strength.
It's become enough of a concern that it's hit US shores again and WHO is working on a test kit.
There's a very good chance it will involve cyanuric acid, which…
moleculeoftheday | September 24, 2008Yesterday, I discussed ammonium nitrate, an industrial fertilizer. One problem with it is its lavish reactivity. On its own, and particularly in combination with hydrocarbons, it makes a potent explosive - it was used in the attack on Oklahoma City in the 1990's.
Apparently, adding a different counterion makes a world of difference. This week, Honeywell reported a new fertilizer, Sulf-N26, which is just a mix of ammonium nitrate and ammonium sulfate. Apparently, it doesn't support the explosive combustion of fuel oil like pure ammonium nitrate does.
moleculeoftheday | September 23, 2008Plants need nitrogen. You're soaking in it - the air is 78% N2 Trouble is, the kind of nitrogen plants need is reduced (i.e., has more electrons) relative to dinitrogen in the air. In the past, this meant rotating crops - peanuts, for example, promote nitrogen-reducing, or "nitrogen-fixing" bacteria.
We learned some time ago, though, that we could fix our own nitrogen. The Haber-Bosch process can take dinitrogen and dihydrogen and produce significant amounts of ammonia - "fixed" or reduced nitrogen. You can use ammonia as a fertilizer - if you keep it in big tanks like you use for BBQ propane…
moleculeoftheday | September 15, 2008The camping series continues. Previously: octenol, the related octenone, and DEET. Today we move away from insects for the time being, turning our attention to water purification.Sodium hypochlorite, or NaOCl, is sold as an aqueous solution - laundry bleach. It is also a great disinfectant, and dilute bleach solutions are used by hospitals and IV drug users alike as a disinfectant.
A little bleach will disinfect water, too, but laundry bleach decomposes fairly rapidly (over periods of time as short as months). A shelf-stable source of hypochlorite is Ca(OCl)2 powder, which can be found in…
moleculeoftheday | September 12, 2008I've been following this hurricane season unusually closely, because I know more people in affected regions than ever. My favorite place to stay caught up is Jeff Masters' blog. You can find lists of survivors and donate to hurricane relief at the Red Cross.
moleculeoftheday | September 10, 2008The ubiquitous active ingredient in insect repellent, DEET, is a great solvent. Anyone who's spent much time outdoors has discovered this empirically, as he's inevitably seen it fog polycarbonate glasses, dissolve a gear sack, or destroy $500 raingear.
DEET-based insect repellents come in a variety of strengths, from 10-25% creams, to bottles of pure DEET. It's probably the only organic solvent that comes in a bottle designed for intentional skin application:
For quite awhile, the presumed mechanism of action for DEET was blocking the receptor for things like octenol. Just last month in…
moleculeoftheday | September 9, 2008Yesterday, I discussed octenol, a lipid degradation product that's all over your skin. Ever wonder why a cut on your hand smells "like metal," or your hands smell "like metal" after handling some?
Metal ions are great at shuttling electrons around, and that's just what they're doing here. The iron ions in blood (or metal oxides on the metal surface) catalyze the oxidation of the same lipids that degrade to octenol to something a little more oxidized (that is, octenone) - the oxidizing equivalents just come from the air. Octenone is where that metal smell comes from!
Of course, you need skin…
moleculeoftheday | September 8, 2008The other day, I was trying to hunt down a tool for the lab. The closest store with any decent complement of tools is one of those big-box stores, so off I went. Unfortunately, I tend to get distracted in the presence of more than a few choices. Somehow, I found myself in the camping aisle, picking up stuff off the rack to read what chemical was in it, and setting it back. A few minutes into doing this, I always wonder: do I look like a shoplifter, someone shopping for ingredients to whip up a fresh batch of drugs, or just a careful shopper? Then, I pulled out the camera phone to take some…
moleculeoftheday | September 3, 2008Oxymetazoline is yet another arylethylamine:
The broad class tickles adrenergic receptors in some way. This one finds use in nasal sprays and eyedrops, making you less dribbly and look less terrible in the morning, respectively.
moleculeoftheday | August 27, 2008Potassium chlorate, KClO3, is quite oxygen-dense and a potent oxidant. It is used in what we called "whippersnappers" and the suppliers called "Pop-Pops" as kids, along with silver fulminate. There is a singular irony in that the wimpiest firework, the one we could buy even in my solidly blue no-fireworks mommy state, contains two components of some dangerous explosives. But we're talking micro- to milligrams, so don't get any ideas.
Oh, who am I kidding, you just want to see it destroy a gummi bear:
moleculeoftheday | August 25, 2008Sarin is an organophosphate that irreversibly inhibits cholinesterase. it's a neurotoxin, and a potent one. It'd be absolutely terrifying as a weapon, if it weren't so unstable. Even if a rogue state had gobs of Sarin last year, it's all pretty much a dud by now. The instability of acid halides (carbonyls there, but all of them in general) pretty much ensures this. So the civilized world has that going for it, which is nice.
How do you test for sarin leaks? With a rabbit.
moleculeoftheday | August 21, 2008Short alkanoic acids stink. Apparently hexanoic acid smells of goats:
Hexanoic acid, as Dylan Stiles (L:tender P:button) memorably mentioned, smells of goats. Goats! Alkanoic acids smell of vinegar, cheese, vomit, poo, and, apparently, goats.
moleculeoftheday | August 19, 2008Sodium borohydride is intermediate to the jackhammer that is LAH and the pussycat that is cyanoborohydride.
Borohydride is just on the cusp of reducing protons to hydrogen. In acidic solution, it'll bubble off hydrogen, in basic solution, it's stable enough that Aldrich sells the stuff.