Coby
moleculeoftheday
Posts by this author
April 19, 2007
Carbon, with its four valence electrons, is in a unique position; its valence shells are exactly half filled. Compounds of elements with three valence electrons (such as boron) and elements with five valence electrons (such as nitrogen) can act very much like their carbon analogues. Boron nitride…
April 18, 2007
Inulin is polymeric fructose:
Unlike cellulose (another sugar polymer, which comprises such indigestibles as wood), inulin is quite soluble. To you, it's almost entirely undigestible, and so is one of the "soluble fibers" in your diet.
You can find inulin in various plants, such as jicama, onions…
April 17, 2007
Sorry for the short updates this week! Chloranil is an oxidizing agent. Part of its usefulness comes from its solubility in organic solvent, which you don't see with things like permanganate or H2O2.
The idea with chloranil is that it's a stronger p-quinone. It is a pain to use. It's not very…
April 16, 2007
Meta-chloroperbenzoic acid is a common organic oxidant used in synthesis. It is popular in part because it is very easy to handle; another common peracid, peracetic acid, is a liquid.
Like many peroxides, it's somewhat shock sensitive. The mixture sold as MCPBA is actually only about 70-75% MCPBA…
April 13, 2007
Propylene carbonate is a very polar aprotic organic solvent. Usually, this makes synthetic chemists think of DMSO, then DMF, then maybe acetonitrile or HMPA. Not many people will get down far enough on their list to get to name propylene carbonate.
It is the cyclic ester of propylene glycol and…
April 12, 2007
Benzophenone is a colorless solid, tetrahydrofuran is a colorless liquid, and sodium metal is unremarkable stuff. When pure, it's silvery and bright, but it tarnishes easily in the presence of oxygen or water, leaving it looking like any other metal - kinda greyish silver. If you mix the three…
April 11, 2007
Yesterday, I covered the intense odorant found in popcorn. Today's molecule is another intense odorant, cis-hexen-3-al.
This molecule has an odor threshold in the high ppt-low ppb neighborhood. It's responsible for the smell of cut grass. Take a look at the Molecule of the Month entry for more…
April 10, 2007
I have a love-hate relationship with microwave popcorn. It can be tasty from time to time. It can be absolutely nauseating, however, at 10am on a Wednesday when someone at work decided to make it for some reason, leaving the office smelling like a movie theater all day. Let's not even talk about…
April 9, 2007
Lithium aluminum hydride is one of the most prodigous reducing agents you find in organic synthesis. In organic chemistry, reduction almost always means the addition of hydrogens - the "hydride" part is the business end of LAH. It will reduce just about anything but an olefin or an aromatic ring.…
April 5, 2007
The pet food recall scare continues unabated; a couple weeks ago, people were pointing at aminopterin, a folic acid analogue, which was covered here. Now, people are pointing fingers at melamine as a potential contaminant.
Melamine is a pretty simple compound, with a number of uses. Here, it's…
April 4, 2007
Nitromethane has some odd properties, due to the singular weirdness of the nitro group.
The electron-withdrawing nature of the group makes it a decent acid; in neutral (i.e., pH 7) water, about 1 in 1000 molecules of nitromethane will have a formal negative charge on the carbon and exist as CH2NO2…
April 3, 2007
Retinal is a pigment in your eyes that is necessary for vision. This is why vitamin A is so essential for vision - retinal is just one oxidation state up from retinol or one down from retinoic acid.
Upon absorbing a packet of light, retinal assumes the trans conformation you see above. Normally,…
March 29, 2007
Via Fark: a blog last week remarked about McDonald's chicken products, quoting The Omnivore's Dilemma::
But perhaps the most alarming ingredient in a Chicken McNugget is tertiary butylhydroquinone, or TBHQ, an antioxidant derived from petroleum that is either sprayed directly on the nugget or the…
March 28, 2007
The American Chemical Society is having its Spring meeting as we speak. One neat thing about a meeting that tries to take on as broad a field as "chemistry" is that there's all kinds of stuff there. Some of it trickles out to the mainstream media - usually picked up by a science reporter (or maybe…
March 27, 2007
Chloral hydrate was in the news yesterday because it showed up in the autopsy report for Anna Nicole Smith.
Chloral hydrate is what individuals of a certain age (or just aficionados of dated slang) refer to when they mention "slipping someone a Mickey." It is a very simple drug, discovered by von…
March 26, 2007
Friday's entry was on juvenile hormone, an epoxide-containing species (as in epoxy, see here and here). Today, I'll show you an example of how we've used it to battle bugs.
Methoprene doesn't contain an epoxide (many of the juvenile hormones don't), but it's a good mimic for JH. In its presence,…
March 24, 2007
Special Saturday edition of MoTD: aminopterin.
People have (quite understandably) been a little frantic about the putative taint found in pet food in recent days. Friday, ABC News reported that aminopterin was the contaminant, calling it "rat poison." I can't speak to the accuracy of the claim,…
March 23, 2007
Epoxides aren't just found in glue and disinfectants (see here and here. They also occur occasionally in nature (not too often, since they're very strained, high-energy structures - this is why they're so reactive and useful). One such example is in JHB3, a "juvenile hormone" found in insects.…
March 22, 2007
Yesterday's entry on epichlorohydrin got us halfway to an epoxy resin, with the aid of good old bisphenol A. In that other tube, you'll often find some sort of amine, which, when mixed with a prepolymer like that formed with epichlorohydrin-bisphenol A, heats up and hardens.
This triamino-phenol…
March 21, 2007
Yesterday's entry on epoxides may have brought to mind epoxies. The similarity isn't a coincidence. Chloromethylepoxide, or "epichlorohydrin," is the basis for many epoxy adhexives.
One tube contains some epoxide, such as epichlorohydrin, along with some bisphenol A - the very same stuff you find…
March 20, 2007
Ethylene oxide is the simplest possible epoxide, or three-membered cyclic ether:
It is a superior disinfectant, but it's a gas, and quite toxic, so you'll probably never use it. Even in biology labs, an autoclave is used to disinfect (essentially a pressure cooker - water is heated 12C/21.6F…
March 16, 2007
Edit: Looks like I might be off on this.
If you're in Chicago, the river will be green this weekend. For that, you can thank fluorescein:
Fluorescein is strongly fluorescent - if it absorbs a photon, 97 times out of 100, it will be re-emitted as light (see yesterday's entry on fluorene for more…
March 15, 2007
Fluorene is a very simple aromatic hydrocarbon. It's often used in physical chemistry classes to teach an important lesson about fluorescence: rigidity matters:
Fluorene is essentially a rigidified biphenyl:
When a molecule absorbs a photon of light, it carries around an extra packet of energy;…
March 14, 2007
Lunesta shares its mechanism of action with the benzodiazepenes - Valium, Rohypnol, Xanax, etc. It doesn't actually belong to the benzodiazepene class of drugs, but they all work on the same system - GABA. Not coincidentally, the much-maligned GHB works by virtue of the fact that it is metabolized…
March 13, 2007
Seroquel antagonizes serotonin, dopamine, and histamine, but it doesn't look a whole lot like any of these:
The benzothiazepene (benzene fused to the seven-membered ring containing nitrogen and sulfur) ring system bears a little resemblance to the benzodiazepines, the class to which Valium belongs…
March 9, 2007
Like ethidium, proflavine is a nucleic-acid binding dye that intercalates, or inserts itself between base pairs.
Proflavine found some use as an antiseptic at one point (as far as I know, that day has passed). It is one of the earliest known intercalators. Unlike ethidium, its fluorescence…
March 8, 2007
I've been thinking about chromophores a lot lately; expect the entries to reflect this.
POPOP is a laser dye and has an exceptional amount of resolvable fine structure for a relatively large molecule. See the spectrum here, from the Oregon Medical Laser Center's excellent collection of spectra and…
March 7, 2007
See also: yesterday's entry on folate.
Methotrexate is a mimic of folic acid. Shortly after we discovered what folate was, we started looking into what else we could do with it.
During the 1940's, George Hitchings and Gertrude Elion started work on a number of nucleic acid-related compounds that…
March 6, 2007
Folate is a cofactor, or a small molecule that is involved in the function of an enzyme. It's involved in a number of enzymatic reactions; perhaps the most important relate to the biosynthesis of DNA.
It's amazing to think about the fact that we've only known about its existence for seventy-odd…
March 5, 2007
For quantum mechanical reasons; triply bonded carbon tend strongly to be linear. Benzene-like compounds derive their special stability by virtue, in part, of being in a planar ring. Surprisingly, certain substituted benzenes can form "benzynes," which have an additional degree of unsaturation. Less…