moleculeoftheday | May 22, 2007Last November I mentioned the Dess-Martin reagent. Hypervalent iodine reagents are mild oxidants that tend to be more soluble in organic solvent than many of the alternatives. Dess-Martin has largely supplanted another iodine oxidant - IBX acid.
Dess-Martin is more soluble, and, as I understand, a little less inclined to get lively under pressure or impact. Too bad IBX acid is a much cooler name.
moleculeoftheday | May 21, 2007Whenever I mention artificial sweeteners, it seems to rouse a fight about what's safe, what's not, saccharin this, Stevia that. Around the time saccharin was discovered, another sweetener came on the market: dulcin.
I'm not sure how dangerous it is relative to saccharin - it was banned due to putative carcinogenicity, which the warning label touts as one of saccharin's dangers as well. If you take a look at refused FDA imports from China, you can see that some food imports are rejected because of their dulcin content!
I am told the fact that every shipment in that link containing dulcin was…
moleculeoftheday | May 18, 2007About a year ago, I covered aspartame, the sometimes-maligned intense artificial sweetener. There is still a camp of substantial size insisting aspartame is deadly. Of course, it's widely sold, and still FDA-approved, etc. There is one group of people for whom aspartame is undisputedly dangerous, however: phenylketonurics.
Aspartame is metabolized via esterases and peptidases - esterases remove the methyl ester as methanol (tiny, tiny quantities, but this is a big part of why some people insist this is a dangerous sweetener). This yields a dipeptide of aspartic acid and phenylalanine.…
moleculeoftheday | May 16, 2007In the most common form of silica chromatography, more polar molecules stick to the stationary phase. Silica is just sand, and the polar silanol groups (-Si-OH) interact with the polar parts of the molecule. You can "reverse" the properties of silica by converting the silanols into something nonpolar.
ODS-Cl was the first reagent commonly used to do this - it converts the -Si-OH into -Si-O-Si-O-(CH2)15CH3. This means that polar molecules are effectively indifferent to this modified silica and will flow right past, while greasy things will stick like crazy. This is often a useful thing, and "…
moleculeoftheday | May 15, 2007Here is a quickie: sodium triacetoxyborohydride.
Most people use sodium cyanoborohydride as their mild reducing agent in reductive aminations. Triacetoxyborohydride works just fine and has the added advantages of not stinking and not being quite so poisonous. Sodium triacetoxyborohydride: now without cyanide!
moleculeoftheday | May 14, 2007Ion-exchange resins are surprisingly simple things - here's the idea: just about everything that has a charge has to have an opposite charge around somewhere. Ususally, charged things float around willy-nilly in solution (your Na+ and Cl- in your salt, for example). If you have something insoluble, like a plastic, that will carry a charge, it will always have some intimately associated neighbors of opposite charge. This can slowly (or rapidly) exchange its charged neighbors with its environment, depending on solution conditions. Enter amberlite IRP64.
Say you're addicted to some form of…
moleculeoftheday | May 10, 2007Galinstan is an alloy of gallium, indium, and tin (the Latin is stannum). It's (relatively) nontoxic and liquid at room temperature. For this reason, it's used as a mercury replacement in some applications (you can find galinstan thermometers, for example).
Unfortunately, galinstan isn't quite as cool as mercury - mercury tends to bead, while galinstan "wets" things (coats them). This makes it a mess to handle and not useful to many of the applications mercury is best at.
moleculeoftheday | May 9, 2007I just love this. Ever wonder how a rewritable CD works?
AgInSbTe is just an alloy of the four metals. When you heat it with rapid bursts of intense laser light, you get amorphous AgInSbTe (not very reflective). When you heat it with long pulses of low-intensity laser light, you get crystalline AgInSbTe (reflective). Get the intensity, beam size, and pulse length just so, and you can make discrete areas that reflect laser light (of a much lower intensity) to a much different extent. There's your ones and zeroes, there's your CD.
When you're done with it and want to rewrite, just blank…
moleculeoftheday | May 8, 2007Yesterday's entry on diethylene glycol reminded me of another public safety incident that occured pre-FDA: Jake leg.
Jamaican ginger extract, or "jake," was just like the extracts you buy at the grocery store today - full of alcohol. During prohibition, a lot of people realized it made a decent substitute for real booze. As far as I know, extracts can't use denatured alcohol - they're intended for consumption.
Soon, the treasury department wised up to this and declared that ginger extract had to have a certain amount of dissolved solids. Solomonic - if you wanted ginger extract, you were…
moleculeoftheday | May 7, 2007Compounding - that is, mixing up pharmaceuticals in the appropriate form for dosing - used to be something that happened at the pharmacy. You can still find "compounding pharmacies" willing to do this - they'll mix up your stuff into a kid-friendly elixir, or prepare ointments, and the like. However, increasingly complex and fragile molecules in drugs (not to mention an increased level of caution) mean that the vast, vast majority of compounding is done at the pharmaceutical company level. This often means single-dose vials and the like, and we're probably safer for this, with the trade-off…
moleculeoftheday | May 4, 2007Osmium is a rare metal, but its oxide is so useful it finds its way into chemistry in all sorts of places.
Its widest use is probably the addition of two vicinal hydroxyl groups where a double bond used to be. Barry Sharpless pioneered its use in the presence of a chiral amine to make hydroxylation selective and faster. And not too long ago, we realized that any amine would speed it up - if you want a racemate, just use an achiral amine.
OsO4 is also very useful as a stain, because it'll leave behind a heavy metal (and very dark area) - useful for a contrast agent in both optical and…
moleculeoftheday | May 3, 2007Brief entry today, watching more debates...
Diacetone alcohol is a common solvent industrially - it is responsible for a substantial portion of the ineffable aroma of Sharpies.
moleculeoftheday | May 2, 2007One use of nitrous acid, or HONO, is the transformation of amines (i.e., R-NH2) into diazonium salts (i.e., R-N2+).
You learn about this transformation in organic chemistry as an undergrad. It finds its way into a number of reactions, but the most famous is no doubt the Sandmeyer, which sounds absolutely wonderful until you try it and realize it produces an absolute mess. If anyone has any luck with these, I want to hear it.
Its conjugate base is "nitrite," which is an important part of the nitrogen cycle in fish tanks - fish excrete ammonia, which bacteria oxidize to nitrite, which another…
moleculeoftheday | May 1, 2007Friday's mention of chromatography got me thinking about HPLC. HPLC, or high-performance (alternately high-pressure) liquid chromatography, is a way of separating mixtures. It can be a pain to do, but there are times when absolutely nothing else will do. You can purify just about anything with it, from small molecules (drugs) to biomolecules.
The most common HPLC is "reversed phase", with a greasy solid phase and a mix of something polar and less polar (typically water and a polar organic solvent, like methanol or acetonitrile). Just the solvents work fine for a lot of small molecules -…
moleculeoftheday | April 27, 2007The word chromatography, reveals its origins - in the beginning of the 20th century, Mikhail Tsvet - color compounds. The modern stable of robust, tunable separation techniques (i.e., chromatography) is probably one of the most important things chemistry has given us - and it's only a hundred years old. Today, chromatography is used mostly to separate compounds without any visible color at all!
It's hard, however, to understate the importance of dyes in the development of modern chemistry. We take colored fabrics completely for granted today, but dyes used to be a luxury. Dyes, too, also…
moleculeoftheday | April 25, 2007Aqueous bio-compatible reducing agents are legion, but people end up using the same ones over and over. Probably the least used is TCEP (which doesn't stink at all), next is dithiothreitol (and the related but slightly less effective dithioerythritol), which stinks, but not too badly. Perversely, biologists usually seem to end up using beta-mercaptoethanol, which is the stinkiest of the lot.
BME stinks, but not too badly - the burnt rubber smell has a pleasant organic alcohol note in the background, making it not such a miserable smell. Uninitiated coworkers might disagree.
Certain synthetic…
moleculeoftheday | April 24, 2007Yesterday's entry on Dithiothreitol garnered one lone comment. Remarking on the smell. True enough; it's a thiol - where there's sulfur, there's often stink. There is a biologically compatible reducing agent that doesn't stink at all: tris(carboxyethyl)phosphine, or TCEP.
It's usually sold as the hydrochloride salt. Interestingly, phosphines almost always stink too, but TCEP is nonvolatile, since it's charged. It's oxidized to the phosphine oxide (which are often quite insoluble, but the charges save you again here):
I've never actually used TCEP, but I've had a bottle of it in the fridge…
moleculeoftheday | April 23, 2007The environment within a cell is actually rather reducing, this is evidenced by the free cysteine found in some proteins. Many proteins require a free cysteine to operate properly, and once they're outside the cell, they can easily become oxidized. Enzymologists have had to deal with this for some time since we started taking oxidizable stuff out of cells. Just over 40 years ago, Cleland realized that dithiothreitol would probably work pretty well for this.
Using thiols for a reducing agent is a common strategy; the idea is you dissolve much more reducing agent than protein (often in 1,000-…
moleculeoftheday | April 20, 2007Phosgene is a very useful molecule, but it's often not the best for the situation, and it has the unfortunate side effect of being a gas. A war gas.
Carbonyl diimidazole isn't exactly a pussycat; by nature, it has to be very reactive. At least it's not a gas. It's a useful phosgene alternative that acts very much like an acyl chloride. It finds some use in peptide synthesis, along with various other spheres of organic chemistry.