moleculeoftheday

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Coby

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October 2, 2007
Nitinol is an alloy of nickel and titanium. It can do some neat stuff: Nitinol exhibits "shape memory" - which is an advertising-type name, really. This just means it's not permanently deformable below a critical temperature, above which it will "remember" its shape, upon cooling. For this reason,…
October 1, 2007
Tin is a nice enough metal, strong and nontoxic enough that for some time we made food-grade cans and foil using it in part. It has a darker side, however: tin pest. Below a relatively high temperature (ca 13C/55F), "white tin" can convert to a different, more brittle phase, "grey tin." This is…
September 28, 2007
As I noted in a recent entry on strychnine, NMR is important. Sometimes reference compounds like yesterday's molecule, TMS, will help you out. This is all well and good for most organic chemists - TMS will go into just about any organic solvent. It won't work so well in water, however, so there's a…
September 27, 2007
As I alluded to in a recent entry, NMR has been vital to science in recent decades - it's used in characterizing chemicals, cells, people, textiles - just about anything people have managed to figure out how to get into a strong enough field. Like many organosilicon compounds, tetramethylsilane…
September 24, 2007
Pyridine is simply benzene with a nitrogen substituted for one of the CHs: Such a simple change has myriad effects. The addition of the electronegative nitrogen makes pyridine a good base (it's commonly used in reactions that generate protons to mop up the acid as you go). The same change makes it…
September 21, 2007
Benzophenone is something you probably encounter most often in sunscreen: It looks like it should be a profoundly fluorescent molecule to the semi-initiated, but for quantum-mechanical reasons, it is instead a phosphorescent molecule and won't emit much at all at room temperature.. If you cool it…
September 20, 2007
The previous entry on cyclohexadiene reminded me of another important piece in some hydrogenations - Raney nickel. If you have an alloy of nickel and aluminum, and put a chunk of it into a sodium hydroxide solution, you'll end up dissolving the aluminum selectively (generating some hydrogen gas…
September 18, 2007
Integral to organic chemistry is hydrogenation - sometimes you need to make a functional group something a little less oxidized. For example, an azide or a nitrile can become an amine. Often, we just use hydrogen for this! Metals like palladium can work some real magic doing the heavy lifting here…
September 17, 2007
While taking organic chemistry, most people end up learning about octane ratings. If gasoline burns too fast, engine knock occurs. A number of factors influence this, the easiest of which to appreciate is branching. By definition, so-called "isooctane" (the structure of which I didn't even realize…
September 13, 2007
Strychnine is a well-known poison and detective novel trope with a moderately low LD50 (ca 10mg). You find it more often in NMRs these days. NMR jocks love strychnine for some reason. It is a pretty good example of a molecule with a hard-to-solve structure that NMR quickly dispatches - see this…
September 12, 2007
Electrons are reactive guys when they're on their own, and tricky to isolate. If you take a bit of fur and rub it on some amber, you end up with a surplus of electrons, but they won't hang around long (the reason I mention amber is because this is what the Greeks used - the word electron comes from…
September 11, 2007
Tiron is a metal ligand and can be used in colorimetric metal assays. Transition metal complexes tend to have the happy property of having their frontier orbitals separated by energy characteristic of photons of visible light - that is, they end up having pretty colors. I've never actually used it…
September 10, 2007
Let's see if I can do better this week. Tazarotene is a retinoid, or vitamin A analogue: It's unusual because of its diarylacetylene moiety. Like most retinoids, it modulates some aspects of skin turnover and metabolism and finds use in dermatology.
September 5, 2007
See, you're ahead of the curve when you MoTD. A story about popcorn lung came out today, and just last week, ConAgra announced they were removing diacetyl from their buttered popcorn. I could swear some sharp reader had pointed out the popcorn lung angle, but my entry mostly focuses on the…
September 4, 2007
Chorismate lies along a biosynthetic pathway in plants that leads to the aromatic amino acids. A bit further up the pathway is shikimate, which is present in many organisms but especially abundant in star anise, and a precursor to Tamiflu (see also)
August 30, 2007
Mellitic anhydride is unusual - as mentioned in the argument over urea, it seems like it should be organic - it's a benzene derivative - but there's no hydrogen. This causes it to fail some peoples' tests for whether something's organic. More bafflingly, mellitic acid's aluminum salt is a mineral…
August 28, 2007
Formaldehyde's funny stuff. It's naturally a gas. If you put too much of it in solution, it will polymerize and form a polyacetal, "paraformaldehyde," which is just -O-CH2- repeating over and over. Because of this tendency towards polymerization, formaldehyde of commerce is sold with a little…
August 27, 2007
Ellman reagent can be used to quantitate the amount of free thiol present in a protein or other molecule: It reacts with the free thiol and releases a nitrocarboxythiophenolate, which is bright yellow. You can then quantitate it with a UV-vis.
August 24, 2007
Previously, I covered ethyl thiolactate, which is one of those oddly sweet smelling thiols (like grapefruit mercaptan). Ethyl lactate also smells nice. Ethyl lactate is the ester of ethanol and lactic acid - Wikipedia claims it's biocompatible, because, after all, you have ethanol and lactate in…
August 23, 2007
Hydrazine, H2N-NH2 is the nitrogen analogue of hydrogen peroxide: It's useful in the Gabriel synthesis of amines via phthalimide (or saccharin, oddly, but I'm not sure if hydrazinolysis works as well here). In contrast to peroxide, hydrazine is a potent reducing agent and finds use in rocket fuel!…
August 22, 2007
This reagent is one of my favorite ones for replacing an alcohol with an iodine. Eric Kool's lab has made good use of it to iodinate the 5'-OH after automated synthesis of a DNA strand.
August 20, 2007
I have alluded multiple times (see here and here) to the ubiquity of benzodiazepines in modern medicine. Xanax is one very popular one: Xanax is just another benzodiazepine, but it's mostly used in antianxiety roles. Its triazole ring is unique; it's a heterocycle you don't see too often. More…
August 17, 2007
AM404 is an active metabolite of acetaminophen: Acetaminophen is an unusual painkiller - it isn't quite like ibuprofen or other NSAIDs. AM404 is its arachidonic acid conjugate, which has some cannabinoid activity (as well as COX activity). Anyone who knows anything interesting about cannabinoids…
August 16, 2007
Carfentanil is an absurdly strong opiate - ca 10^4 times stronger than morphine. It's so strong a ug will have effects on you, and it's really only good for tranquilizing lions and Jurassic Park dinosaurs. I spent one summer in a medchem lab synthesizing potential opiates and often wondered what…
August 15, 2007
Chloroauric acid is obtained by the oxidation of gold in the presence of chloride, as in aqua regia. Chloroauric acid is central to one of the sweetest stories in science, ever: hiding Nobel prizes from the Nazis. From the old blog: My very favorite story about aqua regia is this: during World War…
August 14, 2007
Clenbuterol is a phenethylamine, like adrenaline, tyramine, ecstasy, sudafed, wellbutrin, and methamphetamine. Don't let anyone ever tell you all these drugs are the same again. Clenbuterol is a potent beta-adrenergic agonist with a long half-life. It's very long-lived and has found some use as an…
August 10, 2007
Nitrobenzene is a simple enough molecule. It smells just like benzaldehyde - it's really strikingly similar if you've smelled both. If you haven't, it's the artificial almond-cherry flavoring smell. Nitrobenzene, like many nitroaromatics, is a bit toxic (although not as bad as plain benzene,…
August 9, 2007
4-ethylphenol is a simple substituted phenol. It smells like band-aids. You can find it in some wines or beers - rarely, this is intentional, and provides an interesting flavor at high dilution. Usually, though, it's because someone was homebrewing and contaminated the wort or must with…
August 8, 2007
Methyl salicylate, much like aspirin (ASS to the Germans) is an analgesic drug. It's structurally quite similar to aspirin, but less polar and doesn't ionize in water. This affords it some vapor pressure (it smells of wintergreen, and is actually used as a flavoring agent in low concentration!).…
August 7, 2007
5-nitro-2-propoxyaniline is a potent artificial sweetener: It's banned in the States. Nitroaromatics tend to be tox liabilities. One toxic nitroaromatic with a very specific mechanism of action is 2,4-dinitrophenol.