A catenane is a topologically locked two-ring system. Put more plainly, it is a molecular chain (with interlocking links). I used to doodle molecules like this before I knew they existed. As I was going through organic chemistry in undergrad, I always figured they were impossible to make. Read the rest of this entry »

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.

I’ll admit it - sometimes, when I have no idea what molecule to write up, I’ll look at the American Chemical Society’s Molecule of the Week Page. And sometimes I pick the one with a name that makes me smirk. Enter zingerone:

The name is easily dissected. Zingerone is a natural product from ginger. “Zinger” is ostensibly from the ineffable zest associated with ginger. “-one” is the suffix associated with the functional group known as a ketone.

As the ACS page notes, zingerone shares some common structural characteristics with capsaicin and vanillin:

Thinking like enters into it when a chemist looks at the structure and metabolic pathways leading to chemicals that plants make. The really weird stuff always seems to come from plants. There is a whole subfield of chemistry known as natural products chemistry devoted to studying this stuff. Plants, you see, are distinctly lacking in legs, fangs, claws, and guns, and they have had to make do with some (often strikingly toxic) chemical defenses. You see it in sea life, too, as in the case of fugu’s tetrodotoxin.

Vanillin (and I’d guess the other “vanillinoids”, but I’m not sure), are synthesized from two closely related amino acids, phenylalanine and tyrosine. As naturally occuring amino acids, they are ubiquitous, and find their way into all sorts of structures (since they’re relatively “cheap” to use).

Have a good weekend.

Cubane, unsurprisingly, is a cube-like structure with formula C₈H₈:

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In the comments, yesterday, we started talking about other retinoids a bit. We were talking about naturally occuring ones and close pharmaceutical analogues. I was racking my brain today trying to come up with one that didn’t follow the terpenoid/long chain of alternating double bonds pattern. I know of one that a friend targets for his research, but I can never remember the structure. Then I remembered another: adapalene!

Not very like retinoic acid (a vitamin A-related compound):

It is a topical acne drug. Many of the acne drugs, such as Accutane (isotretinoin) and Retin-A (tretinoin, just retinoic acid, above) target Vitamin A (really retinoic acid) receptors.

My favorite part about adapalene is that it has an adamantyl group:

Adamantane is named from Latin, from Greek, from adamas (”diamond,” or “invincible” depending whom you ask). This is because the 3-d structure of that ugly thing is actually very much like diamond. This has led into a bunch of research on diamondoids and molecular diamonds, which are kind of neat. Here, it is just a bulky alkyl group.

I think it’s 4-day weekend time. See you later.

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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Here’s a quacky one for you. If you lived through the 70’s, you remember this as Laetrile. Amygdalin is a cyanide compound found in almond, peach pits, and some other stone fruits. Fun fact: “amygdala,” like in your brain, comes from the same Greek root as amygdalin. Here, it describes the source of the compound, in “amygdala,” it describes the shape of the structure. Sort of like naming the pituitary “Mr. Peanut,” then translating it into a dead tongue for some added class.

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Have you ever wondered whether you would swim faster in syrup or water? I hadn’t, either, until I found out someone had actually brought a swimming pool up to to Mrs. Butterworth’s-level viscosity and had people swim in it. Then I became intensely curious.

Proell admits he was slightly taken aback when he first heard Cussler’s proposal to dump 700 pounds of guar gum, a thickening agent, into one of the University’s pools. Fortunately, though, he recognized the proposal’s educational merits.

“Cussler is persuasive, but we didn’t need much persuading. We all agreed that we had an opportunity here to be part of the University’s educational mission. [The experiment] involved movement through water. [I]n aquatics, that’s our business. It intrigued us.”

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