moleculeoftheday

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Coby

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June 12, 2007
Friday's entry on safrole inspired a number of comments on what sort of animal it looked like. One person mentioned a chestnut from a few years back: NanoPutians! NanoPutians are molecules that look kind of like people. James M. Tour at Rice has a grant to use the little nanopeople in chemical…
June 8, 2007
Safrole is a simple organic compound found in sassafras oil: It has a pleasant odor and used to be used to flavor root beer, but sassafras oil has fallen out of favor in the past few years for a few reasons: first, safrole has been deemed carcinogenic and banned as a flavoring agent by the US FDA…
June 7, 2007
Dimethyl sulfide is another one of those small, volatile sulfur compounds: Predictably, it lands on the malodorous side of the fence, but at low concentration, it purportedly smells pleasant. As Derek Lowe notes, it is the "smell of success" when the Swern Oxidation succeeds.
June 6, 2007
Periodically, we get these "Ask a Scienceblogger" questions via email asking for someone to volunteer to answer. Usually I don't feel like I have anything to add, but this one was frivolous enough for me to know something about it... Sorry for the not-a-molecule post, back with the regular content…
June 5, 2007
Trehalose is a simple head-to-head dimer of glucose: Like a lot of sugars, it holds onto water like crazy; some plants use it as a protectant in dry conditions. Molecular biologists also use it in PCR; apparently, it stabilizes the enzyme, while destabilizing the dsDNA produced by the reaction.
June 1, 2007
The phosphoramidite method of oligonucleotide synthesis has been invaluable. WIth a few reagents and an expensive machine, you can make any sequence of DNA or RNA. Purification can be a bit tricky, and it only gets worse as you get longer (once you're up to about 100 bases, you probably have a…
May 30, 2007
Acetaminophen/paracetamol is a great drug. It comes without a lot of the GI irritation problems of aspirin and other typical COX inhibitors. Unlike aspirin, it doesn't increase clotting time. No nagging feeling you're going to give your kid Reye's syndrome. However, it has an unusually low…
May 29, 2007
The atmosphere doesn't just keep you alive and protect you from the sun - it is responsible for the face of life as we know it. One-fifth of the atmosphere is oxygen, happily waiting to accept electrons from whatever's available. Oxidative metabolism turns sugars and the like into CO2, just like…
May 25, 2007
From medicated powder to cigarettes, it's no secret that small molecule ligands can induce a cold sensation. Usually, this means menthol. However, like any protein ligand, non-natural small molecules can stand in. Icilin has an enhanced affinity for receptors to which menthol binds: Icilin induces…
May 23, 2007
You can't measure something unless you can see it. Scientists have loads of instruments to detect things by all kinds of methods, but the most popular and simplest has to be UV-vis spectroscopy. Shine some light over your stuff, see how much gets through, you know something about what's there. UV…
May 22, 2007
Last 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…
May 21, 2007
Whenever 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…
May 18, 2007
About 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,…
May 16, 2007
In 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…
May 15, 2007
Here 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…
May 14, 2007
Ion-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…
May 10, 2007
Galinstan 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…
May 9, 2007
I 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…
May 8, 2007
Yesterday'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…
May 7, 2007
Compounding - 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.…
May 4, 2007
Osmium 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…
May 3, 2007
Brief 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.
May 2, 2007
One 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…
May 1, 2007
Friday'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,…
April 27, 2007
The 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…
April 26, 2007
Back tomorrow.
April 25, 2007
Aqueous 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,…
April 24, 2007
Yesterday'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…
April 23, 2007
The 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…
April 20, 2007
Phosgene 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…