Synthesis
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…
moleculeoftheday | June 13, 2007Polyphosphoric acid is a mixture of phosphoric acids and its anhydrides:
I like it as an acid catalyst in organic synthesis - a lot of people hate it because it's so thick and hard to handle. The stuff is absolutely gooey mess; when you heat it up, it gets down to about the consistency of honey. The neat thing is that lots of stuff will go into it (it is a strong acid goo, after all), but once you quench your reaction with water, your stuff will often crash out.
During a blissful few months, I cranked out a series of Fischer indoles with the stuff. Everything seemed to work!
moleculeoftheday | May 23, 2007You can't measure something unless you can see it. Scientists have loads of instruments to detect things by all kinds of methods, but the most popular and simplest has to be UV-vis spectroscopy. Shine some light over your stuff, see how much gets through, you know something about what's there. UV light is particularly popular - anyone who's ever done DNA work has used 260nm light for this purpose.
One problem, though, is that just about everything absorbs some UV light - 260nm is pretty well-behaved, but not without its difficulties. Colored things, however, are a bit rarer. If you can…
moleculeoftheday | May 15, 2007Here is a quickie: sodium triacetoxyborohydride.
Most people use sodium cyanoborohydride as their mild reducing agent in reductive aminations. Triacetoxyborohydride works just fine and has the added advantages of not stinking and not being quite so poisonous. Sodium triacetoxyborohydride: now without cyanide!
moleculeoftheday | May 4, 2007Osmium is a rare metal, but its oxide is so useful it finds its way into chemistry in all sorts of places.
Its widest use is probably the addition of two vicinal hydroxyl groups where a double bond used to be. Barry Sharpless pioneered its use in the presence of a chiral amine to make hydroxylation selective and faster. And not too long ago, we realized that any amine would speed it up - if you want a racemate, just use an achiral amine.
OsO4 is also very useful as a stain, because it'll leave behind a heavy metal (and very dark area) - useful for a contrast agent in both optical and…
moleculeoftheday | May 2, 2007One use of nitrous acid, or HONO, is the transformation of amines (i.e., R-NH2) into diazonium salts (i.e., R-N2+).
You learn about this transformation in organic chemistry as an undergrad. It finds its way into a number of reactions, but the most famous is no doubt the Sandmeyer, which sounds absolutely wonderful until you try it and realize it produces an absolute mess. If anyone has any luck with these, I want to hear it.
Its conjugate base is "nitrite," which is an important part of the nitrogen cycle in fish tanks - fish excrete ammonia, which bacteria oxidize to nitrite, which another…
moleculeoftheday | April 20, 2007Phosgene is a very useful molecule, but it's often not the best for the situation, and it has the unfortunate side effect of being a gas. A war gas.
Carbonyl diimidazole isn't exactly a pussycat; by nature, it has to be very reactive. At least it's not a gas. It's a useful phosgene alternative that acts very much like an acyl chloride. It finds some use in peptide synthesis, along with various other spheres of organic chemistry.
moleculeoftheday | April 17, 2007Sorry 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 soluble, and I've never had very much luck with it.. On the other hand, it has a beautiful yellow color.
moleculeoftheday | April 16, 2007Meta-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. The balance is MCBA - meta-chlorobenzoic acid, and water. This serves to desensitize the mixture to shock somewhat.
moleculeoftheday | April 13, 2007Propylene 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 carbonic acid. It's surprisingly robust - if propylene carbonate hydrolyzed appreciably, the container would hiss a bit when you opened it (due to CO2 release). I've actually held some propylene carbonate and 6M HCl in a sealed container for a week accidentally; no hiss.
moleculeoftheday | April 9, 2007Lithium 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.
LAH will go absolutely nuts in the presence of water, evolving a great deal of hydrogen and heat. Sodium does the same thing, and you may have seen people blow it up by throwing chunks of it into water. LAH is a powder, and that huge surface area means a very, very, quick reaction. "Quenching" a LAH…
moleculeoftheday | April 4, 2007Nitromethane 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-. There aren't many of these "carbon acids," and their properties make them useful in organic synthesis.
The "nitro" part of nitromethane doesn't disappoint if you associate the prefix/word with nitrous oxide and TNT, either; nitromethane is a very energetic compound and can be explosive (it was…
moleculeoftheday | March 5, 2007For 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 surprisingly, they're very reactive species; these tend to be something observed by virtue of what products they produce. It's not something you get in a bottle.
moleculeoftheday | February 7, 2007You know a compound has a story when nobody calls it by a chemically descriptive name (or the inventor's name). Proton sponge, or 1,8-bis(dimethylamino)naphthalene, is one such compound.
Proton sponge was discovered in Roger Alder's lab in 1968. It is a non-nucleophilic base (like DBU), which, as mentioned before, is something that's often useful in synthesis (take, for example, the use of Hunig's base when using phosphoramidite chloride in preparing monomers for automated DNA synthesis). It is unusual, however, for at least one other reason. Aromatic amines are normally terrible bases;…
moleculeoftheday | February 2, 2007I swore I posted this yesterday, but there's no sign of it. Thanks to Hillary for prodding me...
Titanium isopropoxide is a Lewis acid and useful in organic synthesis for this reason. It's also useful for synthesis of various titanium compounds.
Another neat thing about Ti(OIPr)4 is that it hydrolyzes into a voluminous precipitate of titanium (IV) oxide (titanium dioxide).
Titanium (IV) isopropoxide's propensity to hydrolyze makes it useful for a number of things - its hydrolysis tends to generate nanoparticulate suspensions.
The fact that it reacts with water so avidly means that it can…
moleculeoftheday | January 31, 2007Thionyl chloride is one of the classics of organic synthesis - it is a robust reagent for converting carboxylic acids into acid chlorides.
I think it smells unpleasantly like buttered popcorn (mutiple people have told me I'm crazy for thinking this, but I insist it's there). There is a definite sulfur note, of course. It's a bit like tosyl chloride (see also Derek Lowe).
One hard thing to explain to someone who hasn't ever smelled sulfur compounds in any real quantity is the hangtime they have - you can get whiffs of it hours after leaving the lab. Additionally, they can pervert your sense…
moleculeoftheday | January 30, 2007The automated chemistry for making DNA uses special monomers called phosphoramidites. To make this, you have a nucleoside (a DNA base + a DMT-protected sugar - everything but the phosphate) - and couple it to a phosphoramidite chloride. Once you've made (and purified) this, it's ready to go into a DNA synthesizer.
The final product of coupling the nucleoside to the phosphoramidite chloride is what we usually call a "phosphoramidite" - sometimes just an "amidite." The reaction produces HCl as it moves along, so it's usually done in the presence of a little Hünig's base (N,N-…
moleculeoftheday | January 24, 2007Basicity and nucleophilicity are two related concepts, but they don't always correlate. This is part of what makes teaching and learning chemistry so tricky, especially at first, when it seems like you're just learning a collection of facts (rather than the holistic wonder that is chemistry!). A base, by one pretty good definition, is something that is good at donating its electrons, allowing it to accept H+ - a proton. A nucleophile is a bit trickier to explain - it is good at donating its electrons, allowing it to react with certain species called electrophiles, forming a bond. The groups…
moleculeoftheday | January 17, 2007
Sodium bisulfite is a decent reducing agent, but lots of synthetic chemists know it as a convenient (and positively ancient) reagent for forming derivatives of aldehydes, which are useful preparatively. When you treat an aldehyde with NaSO3H, an insoluble adduct often precipitates, leaving behind most of the non-aldehyde junk (assuming it was water-soluble in the first place). I like it because it's clean and old-timey. You don't see it used as often as you'd hope. It also has some utility in deaminating aromatic amines (and reaminating aromatic alcohols, given its reversibility).