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 will admit to more than a casual fascination with smell. I am forever wafting vials of compounds for a whiff - which I get more and more flak for, as people get more and more cautious. I figure a few femtograms of small molecules here and there are the last thing that will do me in.

Perfumers (and biologists) still are looking for structure-odor rules, which prove to be continuously elusive. As I’ve mentioned before, one problem here is language; describing odor is hard! Read the rest of this entry »

But I’m just getting home. See you tomorrow.

Many of you have this in your homes. If you have those slow-dissolving tablets that leave a bleachy smell in your water, there’s a good chance you have N-chloro-N-bromo-dimethylhydantoin in one of those giant tablets in your toilet tank.

Read the rest of this entry »

The vast majority of molecules you will ever see here don’t contain a metal ion. And so it goes for many chemists - myriad possibilities exist with just carbon, hydrogen, nitrogen, and oxygen - add in sulfur and the halogens and you have lifetimes of work for armies upon armies of chemists. The chemistry of metal compounds merits its own subfield, inorganic chemistry, which encompasses essentially the rest of the periodic table (plus the aforementioned atoms).

The number of possible molecules, as you can imagine, goes up sharply as you start putting other atoms in there, so many inorganic compounds are only known to inorganic chemists and those who work routinely with them. There are a few inorganic all-stars that every chemist will recognize, though. In synthesis, Grignard reagents are amazing compounds that are generated by the addition of magnesium (metal - you actually use bits of metal!) to alkyl halides. These are workhorses in organic chemistry, as are Grubbs’ Catalysts, a series of ruthenium complexes which won Grubbs the 2005 Nobel.

In biochemistry (and laundry science - more on that in a minute), the inorganic-complex forming hero is EDTA, or ethylenediaminetetraacetic acid: Read the rest of this entry »

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.

Hydrogen peroxide seems boring at first blush- after all, you can get it in those little brown bottles at the drugstore, and they don’t do much but fizz - and then, only when

you pour it on a cut (more on that later). H₂O₂ has a structure a lot like water - H-O-O-H instead of H-O-H. That O-O bond is the peroxide bond, and it’s what’s responsible for H₂O₂’s oxidizing power.

The drugstore H₂O₂, you’ve probably noticed, is only a 3% solution (and it can still burn your skin a little bit). Even in a lab, the highest concentration I can easily get is 30%. These bottles are vented, since peroxide tends to decompose to water plus oxygen. This is the bubbling reaction you obersrve when you pour it on a cut. This is due to the action of the enzyme catalase, which exists to do just this. Like many enzymes, catalase is present at an unusually high concentration in liver. Chop some liver up finely and pour some peroxide on it (3% from the store will do) and you’ll see what I mean. Certain other metal compounds will work, notably silver and manganese dioxide.

The 30% peroxide we get in the lab comes with dire warnings not to spill it on paper or anything combustible (because it would ostensibly start a fire). I believe it, but it’s never happened to me. Peroxide actually gets dangerous in the 70%+ range. It will happily propel a rocket. It’s really amazing how a 25-fold or so increase in concentration can make something act like a completely different substance.

(hopefully, this week is a bit much)

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 »