This is a bizzare molecule. As I was discussing yesterday, structure-odor relationships are tricky. One very reliable predictor, though, is that the compounds of the later chalcogens (that is, compounds containing a sulfur, selenium, or tellurium atom) stink. Sulfur being the second most common member of this group after oxygen, this usually means thiols.

Thiols have a prodigous appetite for metal, especially mercury. This led to a second name for them: mercaptans (describing their ability to capture mercury).

All this leads up to a truly unusual thiol: grapefruit mercaptan. You’ll notice it looks like another terpene, like carvone and damascone. Grapefruit mercaptan is such a singular compound because it is a nice-smelling thiol. It’s another one I haven’t smelled, but I’m told it’s very complex and grapefruity. It’s also unique because not many things synthesize thiols on purpose (thiols being reactive and stinky - skunks are a notable exception here).

The Wikipedia article notes that this is a bit of a thorn in the flavor industry’s side - almost ALL thiols stink, and this is a notable exception. Thiols have a nasty habit of oxidizing to form dimers in the presence of oxygen (R-SH -> R-S-S-R), and even if grapefruit mercaptan doesn’t stink, its decomposition products probably do. All these leads to a not-so-hot flavoring agent.

Here’s the structure:

See you Monday.

Esters are a continuing source of fascination for me. Chemically, they’re unremarkable. If you heat an alcohol and carboxylic acid together under conditions that allow it to eliminate water (say, by doing the reaction in the alcohol or acid under concern, if one’s liquid), they will form a compound called an ester. Usually you add a trace of additional acid as a catalyst - a drop of hydrochloric acid solution is common.

What’s remarkable, though, is the smell. Pentanol (amyl alcohol, in old-school chemspeak, rarely used, but I learned this ester as “amyl butyrate”) is unremarkable, and it smells like most low-molecular weight alcohols - a bit like ethanol, a bit like lighter fluid. Butyric acid, however, is Satan’s own carboxylic acid - it is a sort of B.O./vomit/Sex Panther odor. Read the rest of this entry »

This is one of those boring-seeming ones: cysteine. However, biochemistry really wouldn’t work without it. Cysteine is the sulfur analogue of the amino acid serine. I say “sulfur analogue” because oxygen and sulfur are in the same group (column) of the periodic table. They are in group 6B, also known as the “chalcogens”, from the greek for “ore formers.” (Oxygen and sulfur, as well as, to a lesser extent, selenium and tellurium being ubiquitous in ores of metals). Many oxygen compounds have a sulfur analogue. In many ways members of the same group are very similar to each other, because their electrons are configured in analagous ways.

Oxygen can form a structure called a peroxide. R-OH (R representing something else attached to the oxygen) is an alcohol that has a peroxide brother in R-O-O-R. Peroxides are potent oxidizers (witness hydrogen peroxide and benzoyl peroxide’s use as disinfectants in low concentrations). At very high concentrations, they can be initiators for explosives (or explosives themselves!).

The sulfur analogue of a peroxide is a disulfide. This is a dimer of R-SH (a “thiol”), or R-S-S-R. This is an oxidized compound as well, but R-S-S-R is a much milder oxidant than R-O-O-H. Mild is the name of the game in biochemistry, since you only have cells, enzymes, blood, etc. to hold these things in. Peroxides are a bit much outside of our glass and plastic vessels. So it’s fortunate we have something mild and easily reversed, like disulfide bonds. Cysteine is what forms just about every disulfide bond in your body. The disulfide oxidized cysteine dimer is called cystine:

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One thing they touch on in biology class but never really get into is the fact that DNA is wound up into a tight little structure in the nucleus of eukaryotic cells, as well as sperm. Just how the cell gets the DNA to cooperate isn’t really explained. DNA is a polyanion - that is, it has a repeating negative charge.

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Everyone has heard of superglue. If it weren’t so entrenched in everyone’s mind as something that existed, you’d be absolutely amazed. Whenever I am at Wal-Mart, a drug store, a dollar store, or anywhere that has the six two-gram tubes of superglue for a dollar, I compulsively grab at least one, usually shaking my bemused shopping mate or getting one on the phone (”Guess what I just found at Wal-Mart?!” “The six tubes of superglue again, huh?” “Don’t patronize me, it’s AMAZING!”). I have tolerant friends.

Superglue is a trade name (probably a generic name, by now, I guess, considering my vast superglue collection is definitely not all marketed by the same company) for a class of adhesives called “cyanoacrylates.” The superglue you buy at the store is typically either methyl or ethyl cyanoacrylate. Another cyanoacrylate adhesive, 2-octyl cyanoacrylate, is available to seal wounds. I’ve heard it’s commercially available as “dermabond,” but I’ve never seen it, even in the suture cabinet back when I volunteered in a hospital for a few years. You can be sure I will own some someday.

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The other day we talked chirality. Here’s the example they give in every organic chemistry class when they’re teaching chirality. Carvone!

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How smell works is one of those things we’re chipping away at, but we just don’t have it worked out yet. There is a prevailing theory. There are also some less popular but still intriguing newcomers being put forth by…intriguing newcomers. A predictive theory of smell eludes us - given a structure, we can make some guesses as to how it’s going to smell, but they’re pretty crude: sulfur stinks. Gee, thanks. It’s not quite that bad, but close.
Olfaction is also unique because a Nobel was issued for working out how every other sense works, long before that for smell. Richard Axel and Linda Buck’s smell Nobel was for working out the genes encoding odor receptors. A predictive theory of the relationship between chemical structure and odor remains elusive. Until we get it figured out, we will have plenty of weirdoes in the odorant world. After we get it figured out, well, they’ll still be weirdoes, but at least we’ll understand them and be able to relate to their stinky plight. One such rascal is indole.
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Here is a molecule you’ve probably used, especially if you happen to be of that type of person who never does laundry. Cyclodextrin is what’s known as an cyclic oligomer of glucose molecules. The cyclic part means that it forms a ring, and “oligomer” means a repeating series of the same molecule. It’s different from a polymer in that it’s smaller. The difference between “oligomer” and “polymer” is not well-defined, but a good general rule is: if you can count the number of monomers (glucose subunits), it’s probably better termed “oligomer.” This is the structure of glucose:

The important thing to note here is that there are a number of hydroxyl groups (-OH) bound to carbon. The bond between carbon and oxygen is quite polar, as is that between oxygen and hydrogen. This means that it will tend to dissolve in polar liquids — water! So, this isn’t that much of a surprise: sugar dissolves in water.

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