moleculeoftheday | August 3, 2007CS2 is kind of a neat molecule - it's the sulfur analogue of carbon dioxide.
It has more in common with other small organic solvent molecules than it does with dry ice (although it will react in some of the same reactions as CO2). Purportedly it doesn't smell at all when pure, or sort of ethereal (one commenter claimed awhile back sp2 sulfur in general didn't smell). However, there's usually some stanky impurities in there.
It's also crazy flammable.
moleculeoftheday | August 2, 2007Aromatic rings have 4n+2 pi electrons, where n is any integer. You don't see odd numbers of carbons in aromatic rings too often because the pattern of alternating double bonds is disrupted - if you have a cation or anion, though, odd-numbered aromatics are possible.
Tropylium cation is one such aromatic ring - same pi electron count as benzene, but one extra carbon. The ion is so stable you can actually isolate tropylium fluoborate (not sure about other counterions). It is also an ubiquitous peak in EI mass spec from alkylbenzenes.
Analogously, complexes of cyclopentadienyl anion are known (…
moleculeoftheday | August 1, 2007I love old bottles of chemicals, and I've spent many a diverting hour perusing the shelves of old university faculty members' labs. Bottles used to come in pounds (or giant "ONE MOLE" sizes). Faded typewritten text, "For medical, pharmaceutical compounding, or research use" labels, yellowed paper - Korean war-era bottles are about as romantic as bottles of chemicals get.
When it's old ether, though, I get away and make a note to warn someone (and not come back anytime soon).
Ethers - chemicals of the general formula R-O-R', can form peroxides (R-O-R'-OOR'') at the carbon adjacent to the…
moleculeoftheday | July 31, 2007Hmmm, people don't like being told not to leave certain comments. Thanks for the snark and corrections of the chemical formula. I am off banned drug-related entries for a long while again, they're just not worth the hassle, and there's plenty of worthy molecules out there. Sorry to anyone who felt snubbed; let's talk about a giant ketone!
Civetone is a macrocyclic ketone expressed by an animal that looks photoshopped: the African Civet. It is used in perfumery.
"Macrocycles" are tricky to make - Nature loves five- and six-sided rings, but larger ones, such as civetone, are nearly as hard to…
moleculeoftheday | July 30, 2007Friday, I alluded to a chemical in the House version of the farm bill. It's calcium nitrate.
Many meth cooks use a modified version of the birch reduction, which involves using an alkali metal (lithium here) in liquid ammonia. Lot of farmers use anhydrous ammonia (which is just barely a gas - put it in a tank much like a propane tank, and it's a liquid) to fertilize their crops. Predictably, this has led to a lot of meth cooks stealing ammonia from farmers.
This is dangerous not only because of the drugs, but because of the ammonia - anhydrous ammonia is an entirely different beast than…
moleculeoftheday | July 27, 2007Like auxins, (see also) alar is a small molecule that modulates plant growth:
Chemists will recognize the N-N moiety as a hydrazine, some nasty stuff (and 1,1-dimethylhydrazine is a hydrolysis product of this stuff). Back in the late '80's, there was a huge cancer scare about this stuff - and farmers were spraying it all over our fruit. It's regarded as many corners as an overblown food scare, but some insist that this was the beginning of a slippery slope towards food libel laws (the basis for Texas ranchers suing Oprah Winfrey for saying she was done with beef during her mad cow episode…
moleculeoftheday | July 26, 2007Cinnabar is an ore containing HgS, or mercury (II) sulfide:
It's a nice red color and pretty easy to get mercury out of - you just cook it, liberating the volatile sulfur and leaving behind mercury metal (volatile too; don't try this at home). It's funny that such a unique metal was isolated so easily.
Back with a real MoTD tomorrow!
moleculeoftheday | July 24, 2007(Simul-blogged with The Lab Lemming - check it out.)
Fluoroacetic acid is plain old acetic acid, plus a fluorine. It is a poison of some potency. Oddly, neither the "fluoro" or "acetic acid" part is associated with any general tox risks - acetic acid, as you'll see, is central to metabolism, and fluorinated compounds aren't inherently bad. It is a "mechanism based" poison.
The overwhelming majority of energy in your food is made useful via the Citric Acid (Krebs) Cycle. Some of it you get directly, and some of it is claimed later, but without Krebs, you're dead.
Fluoroacetic acid will…
moleculeoftheday | July 23, 2007Ammonium thioglycolate is the ammonium salt of thioglycolic acid. Having a thiol (R-SH), thioglycolic acid is a decent reducing agent, particularly of disulfide bonds (R-S-S-R').
Your hair is cross-linked by legion disulfide bonds; determining whether it's curly or straight. Thanks to some chemistry, you can rearrange that frizzy hair. You can reduce it with some thiol (in this case the less-stinky thioglycolate; complain all you want about the stink, but be glad nobody's using beta-mercaptoethanol, which would work just as well, at the cost of all your friends). Style it and oxidize it back…
moleculeoftheday | July 20, 2007When I first heard of sulfur hexafluoride I thought it had to be kind of nasty - it is a sulfur (VI) compound with a bunch of halogens attached (it looks if you added some water, you'd end up with dangerous HF and H2SO4!). However, like so many fluorous compounds, it is surprisingly lackadaisical; the stuff is a nontoxic, inert rock (the related SF5Cl, S2F10, and SF4 are all nasties and will totally throw some sulfrous-fluorous death your way).
What's more important, though, is that it's really dense. Plus - not only is it safe, it's safe enough to breathe! And if you breathe it you sound…
moleculeoftheday | July 19, 2007People did a lot of goofy stuff with regard to chemistry in the gee-whiz days of the 1940s and 1950s. In some ways it's great we've come past that, in a lot of ways it's terrible. The same generation that gave us thalidomide also gave us Chuck Yaeger. I am all for small cell phones and $10 digital cameras, but it's hard to beat the dizzying highs and lows of realizing mass-energy equivalence.
Forty years after its realization as theory by Einstein, it was realized in practice in the form of a bomb, which ended a global war, the end of which started a singularly unique era of tension.…
moleculeoftheday | July 17, 2007Before the benzodiazepines (like Valium) became ubiquitous, chemists discovered that a wide array of molecules could really zonk you out. Chemists found themselves in heady times. They were isolating single molecules that had profound CNS effects - methaqualone (Quaalude), chloral hydrate (which is actually pretty close to hooch, really), ethchlorvynol (Placidyl - Rehnquist took too much of this for too long - at one point, he insisted to a physician the CIA was plotting against him because of the side effects of chronic use), various barbiturates, and meprobamate (Miltown), the subject of…
moleculeoftheday | July 16, 2007Alginic acid is a simple polysaccharide. What makes it neat is that it will form gels in the presence of divalent cations (e.g., calcium and magnesium).
It's useful anywhere a biocompatible and/or edible gel is required - one well-known use is fake cherries. If you drop a solution of sugary, red, cherry-flavored sodium alginate into a calcium-containing solution, the exterior of the droplet will skin over and form a gross little cherry-like thing.
Interestingly, the famous "molecular gastronomy" restaurant El Bulli uses alginate extensively to create caviar-like droplets of various liquids.…
moleculeoftheday | July 13, 2007My Science Project Answers Your Questions. Pretty terrific.
Back Monday.
moleculeoftheday | July 12, 2007It is no secret that I enjoy smelly compounds... a lot. Here's a short list of what I seem to have covered at this blog (hits for "stinky" or "smell"). I'm sure I missed some I've already written up. If I haven't covered your favorite, post a request!
Stinky:
Tosyl Chloride
Triethylammonium Acetate
Ammonium Carbonate
Piperidine
p-Dichlorobenzene
Putrescine
Dimethyl Sulfide
Beta-Mercaptoethanol
Thionyl Chloride
Nice-smelling (or at least inoffensive):
Ethyl Thiolactate
Grapefruit Mercaptan
Hexen-3-al
2-propionyl-1-pyrroline
Muscone
Acetophenone
Isoamyl Acetate
Furfuryl Mercaptan
Ethyl Acetate…
moleculeoftheday | July 11, 2007The drought of chemical drawing software continues - here is the story. Every so often I see how Linux is doing and use it exclusively for a week or two. It is actually a usable desktop environment now, unlike a few years ago, but there isnt anything to draw decent structures. Today I set up XDrawChem, which is the basic idea of ChemDraw or ISIS, but less pretty and functional. I know I could get ChemDraw running on wine, but I can't find the disks. Anyway, onward and upward...tosyl chloride.
I have previously mentioned toluenesulfonic acid on the blog. Its acid chloride, tosyl chloride, can…
moleculeoftheday | July 10, 2007Palladium is really neat stuff. It has an almost absurd affinity for hydrogen - it's one of a few metals we can use as something other than a salt or complex (i.e., just the metal). Pd on C is just carbon dust covered with 5 or 10% Pd metal (you can't see it - it's very expensive copier toner looking stuff).
Pd can transfer H2 to unsaturated functional groups. It can also break down molecules without actually "burning" them - your catalytic converter actually has a good deal of Pd in it. Ford lost a load of money some time back investing in Pd expecting to need to stock up (when cats were…
moleculeoftheday | July 9, 2007Potassium permanganate, or KMnO4, is one of the most well-known oxidizing agents in chemistry. Unfortunately, it's a bit like taking a gun to a knife fight...
One of the big downsides of permanganate is the fact that it's a very polar ion. Crown ethers to the rescue.
Permanganate is a beautiful purple color in solution (almost black as the solid, partly because it's such a rich purple, partly because of MnO2 contamination), which I maintain is responsible for at least part of its popularity. It is a beast, as I alluded to earlier - it will take toluene down to benzoic acid (or even generic…
moleculeoftheday | July 6, 2007Dimethylaminopyridine, or DMAP, finds general use in organic synthesis as a "nucleophilic catalyst." Its strongly donating dimethylamine group affords it substantial nucleophilicity.
The adducts formed by its nucleophilic addition, however, are quite reactive - analogous to an acid chloride - so DMAP can push a reaction along nicely. See the Wikipedia entry for an example mechanism.
moleculeoftheday | July 5, 2007Aziridine, like cyclopropane and oxiranes/epoxides, is one of the simple strained three-membered rings. The strain imparts considerable reactivity.
Aziridine is kind of neat - like many crazy reactive moieties, it's attracted attention for use in cancer drugs. It's also one of my favorite big strong organiker reagents that finds its way into the biology lab. A cysteine residue in a protein (R-CH2-SH) will react with an aziridine to make R-CH2-S-CH2-CH2-NH3+ (Cf. lysine, which it mimics, R-CH2-CH2-CH2-CH2-NH3+). Never done this reaction, but apparently the superlative nucleophilicity of…