moleculeoftheday

The urea entry ended up with a discussion in the comments I encourage you to read about early organic chemists, one of whom was Kolbe, who first prepared acetic acid (an indisputably organic and biologically relevant molecule) from inorganic compounds. He worked with Wohler (mentioned in the urea…

Normally, iodine just makes one bond, as you'd expect from a halogen. Some compounds, though, force it into lively higher oxidation states (hopefully without the tendency to explode, as some highly oxidized iodine reagents worryingly exhibit). There is a whole field of "hypervalent iodine"…

Urea gets a bad name. By the name, you'd expect it to stink. It doesn't. It finds use in biology as a denaturant, in farming as a fertilizer, in polymer science, and the odd cameo in cosmetic products. It also was among the very first organic molecules to be prepared from inorganic starting…

Para-dichlorobenzene is the principal molecule found in mothballs. We used to use naphthalene, but these days, we've switched. I suspect neither may be particularly healthy, and I suspect that you wouldn't have much luck getting such a product on the market these days, but mothballs have been…

I know a lot of people don't have access to these journals, so I try and avoid links to walled content, but there's a review article on fenestranes and planar carbon in Chemical Reviews some might enjoy. Check out "Carbon Flatland: Planar Tetracoordinate Carbon and Fenestranes." Check out the…

Saccharin, like so many sweeteners, was discovered by accident. From the Wikipedia article: Saccharin's sweetness was accidentally discovered by Ira Remsen, a professor at Johns Hopkins University, and Constantin Fahlberg, a research fellow working in Remsen's lab. In 1879, while working with coal…

Another drug that can claim diphenhydramine as an ancestor is fexofenadine, sold as Allegra: Diphenhydramine for comparison: Fexofenadine is a member of a later generation of antihistamines. Diphenhydramine worked fine as an antihistamine (still does - you can still get the stuff OTC as Benadryl…

Last night I mentioned that diphenhydramine is a somewhat promiscuous molecule, binding to a number of disparate receptors. One of its effects is some inhibition of serotonin reuptake. As you've probably read in countless pop science articles by now, this is one mechanism of action for…

Diphenhydramine is one of the earliest antihistamines: Being a first generation antihistamine, it has all the associated problems such as drowsiness and dry mouth. These are some of the least specific small molecule therapeutics you could hope for, which gives rise to many of the side effects.…

Fundamental to learning how energy is moved around in biology is understanding ATP equivalents. You've probably heard about how ATP is "the energy currency of life" - and rightly so; every mole of ATP hydrolyzed is equivalent to about 10 kcals. Bioenergetics isn't really a direct food-to-ATP…

Potassium iodide isn't much of a structure: It's a source of iodide. Thyroid hormones contain iodine; the source of this is dietary iodide. The human dietary requirement for iodine is vanishingly small; on the order of 100 micrograms per day. Trace iodine is present in seawater and many soils, so…

Iodine week continues with IPBC, or 3-iodo-2-propynyl-N-butylcarbamate, a fungicide: IPBC has been around for ages, but you see it more and more in cosmetic products. That "iodopropynyl" part, where the iodine is bound to the triply-bonded carbon, is a very reactive functional group. IPBC has been…

Methyl iodide is another simple organoiodide: Probably the most common lab use is tacking a methyl group onto something; MeI is a great substrate for the SN2 reaction. Despite its ubiquity, methyl iodide isn't nearly the best alkylating agent. It's cheap and simple, so it sees a lot of use, but…

Another theme week: Iodine. Iodoform is, as the name suggests, the iodine analogue to chloroform. Iodoform, as the Wikipedia entry mentions, isn't the best antiseptic in the world, but they're mistaken in saying it's not used anymore: iodoform impregnated gauze is still found in hospitals. Another…

L-methamphetamine is a fine example of how molecules that vary only in their chirality can have very different biological effects. Chiral molecules have non-superimposable mirror images. L-methamphetamine, at left, below, is found in Vicks Vapor Inhalers. (Notice how they obfuscate the name a…

Kavain is a member of a class of compounds known as the kavalactones. (A lactone is a cyclic ester; click here for examples). Kavain is a species found in the kava plant, which is used by the aboriginal residents of some Pacific islands and has psychoactive activity. It's attracted use as a…

Arecoline is a compound that occurs in the seed of the betel palm. It's taken by chewing the nut. Arecoline, like nicotine, binds to certain receptors for acetylcholine. I've grouped them together so you can note the structural similarities. Remember all that talk about protonated amines…

It's weird drugs for the rest of the week! Salvia probably means one of two things, if anything, to most people: a houseplant (for which purpose it is ubiquitous) or a recreational drug that you can still get your hands on legally (for which purpose it is ubiquitous). It is funny to flip back and…

This might not apply to a lot of the readers, but I think a decent subset might find it important. As you know, it's not so easy to search for chemical information. With most search engines, you're limited to the tags associated with the document or (more often) the text within the document.…

Pyridines and thiols are two of the stinkiest kinds of compounds you can come across in chemistry. You'd think if you put them together in a molecule, you'd have something nasty. Oddly, you don't: Bafflingly, thiopyridine is apparently odorless. You'll notice I've drawn two structures here - this…

For a better idea of how the bond angles look, here is an energy-minimized structure of windowpane (4.4.4.4). Notice how it's (nearly) planar. That central carbon atom (middle gray dot, blues are hydrogens) is the one to watch. Here is 5.5.5.6 windowpane: And here is an unstrained compound,…

Like cubane, windowpane (also named "[4.4.4.4]fenestrane" for the Latin for window) is another of those compounds people like because it looks like something anthropomorphic, with clean right angles (in contrast to the bulk of molecules, which assume their bond angles with little regard for what…

PET is an ubiquitous plastic. You've heard it referred to as "dacron", "mylar," or just "polyester." It it produced by (among other methods) the condensation of terephthalic acid and ethylene glycol: PET is all over, from soft drink bottles to fabrics. Perhaps the neatest use is as mylar; an…

Here is another molecule that's gone out of favor in recent decades: carbon tetrachloride: Chlorinated solvents are great solvents. Something about the polarizability, medium polarity, (relative) lack of reactivity, just makes them the only thing that will work in a lot of applications. The three…

Have a great weekend.

Ethidium is a dye that's used in molecular biology to allow DNA to be visualized. Regular DNA isn't colored; it absorbs ultraviolet but not visible light, so you need to use tricks like making the DNA radioactive (which makes it pretty easy to spot), or using dyes that selectively bind to DNA.…

Sorry, but you're hearing about another odorant today: 2E,6Z-nonadienal is an aldehyde responsible for a good chunk of the ineffable aroma of fresh cucumber. Being an aldehyde, it's a bit of a fragile molecule, and doesn't last long in the pickling process, as this blurb explains.

Isoamyl acetate is a nice, fruity smelling ester - like a lot of the low-molecular weight esters. For this reason, it's used in the flavor and fragrance industry. You won't find it in perfume, though, for two reasons. The first is that esters aren't so hot for perfumery in general. They tend to…