moleculeoftheday | February 16, 2007Cinnamaldehyde is a straightforward-looking molecule:
It's the principal odorant in cinnamon. If you're in the Seattle area, your cinnemaldehyde use is being monitored. Drug precursor? Guess again...
Cinnamaldehyde is oxidized in vivo to cinnamic acid, which you excrete in your urine:
Rick Keil at UW has been collecting treated sewage destined for Puget Sound and analyzing it for cinnamic acid (along with other flavoring agents, food signatures, and their metabolites). Apparently Christmas cookies make an appreciable spike in vanilla consumption as measured via Seattleites' urine.
I just…
moleculeoftheday | February 15, 2007Busy couple days. You get some odorants.
For historical reasons, some fragrance contains ingredients inspired by the odor of (or originally found) in a gland in a certain species of false deer. The deer and fragrance are called musk. One substantial contributor to the natural fragrance is muscone:
The deer are endangered, so the overwhelming majority of putative musk you smell is synthetic muscone (or another musk-smelling odorant).
Synthesizing big cyclic molecules is hard ("macrocycles") - closing a long chain of carbons into a ring often results in just making polymers and oligomers ("…
moleculeoftheday | February 14, 2007Reichardt's dye is pleasing in structure and function:
It is related to yesterday's molecule, betaine. It is technically a "betaine," but in a much broader sense, since it is an ammonium zwitterion (has a positive and negative charge). It posesses the property of solvatochromism - that is, it actually changes color depending how polar a solvent you use.
You can get it to turn essentially any color in the visible, just by varying the solvent you use. It has found a lot of use in characterizing how polar certain microenvironments are (such as cell membranes and similar micelle-type structures…
moleculeoftheday | February 13, 2007Betaine is a simple little molecule:
It finds use in medicine in treating elevated homocysteine levels - a molecule that deserves its own entry. It also can act as a denaturant - things like urea, formamide, and guanidinium are useful for this in biology. Betaine, at the right concentration, can help to unfold DNA a little bit, while leaving certain DNA polymerases untouched. For this reason, some people use it in DNA amplification by PCR.
moleculeoftheday | February 9, 2007As discussed in the entry on telomestatin, drugs that bind to guanine quadruplexes are of a lot of interest. One model compound is TMPyP (tetrakis(N-methylpyridyl)porphyrin)). The idea is that the big aromatic porphyrin surface stacks on the guanines, and the positive pyridinium moieties are near the negative DNA phosphates for a favorable Coulombic interaction. It's probably the most studied quadruplex ligand.
There isn't a lot I can say about quadruplexes, telomeres, and why they're important that I didn't cover in the telomestatin entry.
moleculeoftheday | February 8, 2007Buffers are a bit tricky. In biology, a buffer contains at least one ingredient: something to set the pH. This means having something that ionizes (takes on or loses a proton) at about the pH you want. You can set the pH within about one unit of this value (the pKa). This constraint exists because of thermodynamics: anything ionizable will absorb protons or hydroxide equivalents around its pKa, without changing pH much. In the strict, correct sense, this is a buffer.
Really, though, what most biologists call a "buffer" is all the supporting players in a solution - the buffering agent,…
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 6, 2007Chromated copper arsenate is an interesting one. It is a mixture of the copper salts of chromic acid and arsenic acid.
CCA provides robust protection against the sun, fungus, and bacteria. Unfortunately, chromium (VI) and arsenic are quite toxic, and can leach from the wood.
One problem with wood is that it's essentially tree meat - once it's separated from its host, loads of protection against microbial action and sunlight are absent. CCA provides this, and quite well. You've seen lots of CCA wood - most lumber with a greenish tint is CCA-treated. During wood's regular life, CCA doesn't…
moleculeoftheday | February 5, 2007
Jasmone is an odorant constituent, of, unsurprisingly, jasmine flowers. It's somewhat unique by virtue of its biosynthetic pathway.
Back with a full entry tomorrow.
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 29, 2007I don't have much to say about acetophenone chemically - It is a useful (and very common) synthetic precursor. It's one of a relatively few chemicals that aren't used as a solvent that many labs keep around in liter bottles. The main reason I like it, though, is that it smells wonderful.
Predictably, it is used in perfumery. Like many single chemicals, its smell is puzzlingly hard to pin down (smells, such as coffee, where you definitively say "that's it," are very often mixtures). I'd describe it as something like orange blossom with a bit of artificial cherry/almond.
Acetophenone also is…
moleculeoftheday | January 26, 2007Piperidine is a useful little heterocycle - Walter Gilbert won a Nobel Prize, due in part to his development of a method of sequencing DNA (which uses piperidine as a base). It also has some use in peptide synthesis. Piperidine is also a very useful thing to hang off a drug, because it adds some lipophilic bits (the ring is mostly paraffinic carbon, after all), as well as an amine. These are often two very useful things to have in a drug molecule.
There are also some less-savory uses of piperidine.
Piperidine derivatives are found in fire ant venom. It is also a precursor to PCP and has been…
moleculeoftheday | January 25, 2007Benzoylecgonine is the primary metabolite of cocaine - it's actually just cocaine minus a methyl group. It's not really used as an intoxicant, but it does have one interesting use: figuring out just how much cocaine people are using.
One study in 2005 in Germany examined the total amount of benzoylecgonine in wastewater (a good chunk of cocaine-derived benzoylecgonine is excreted in urine). Their result suggested the proportion of cocaine users was substantially larger than the 8 per 1,000 previously thought.
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 23, 2007Brodifacoum is warfarin's mean sibling: it is another vitamin K analogue. It's so potent and has such a long half-life (on the order of months!) that it's more of a poison than an anticoagulant. It's used for the expected things; as a rat poison, etc. Interestingly, despite its lavish toxicity, all warfarin-type compounds, including brodifacoum, have an antidote: vitamin K (in controlled doses).
moleculeoftheday | January 22, 2007Warfarin belongs to a previously-covered class of molecules known as the coumarins. Coumarins see use both as anticoagulants (in people) and poisons (in certain small animals).
Warfarin works by inhibiting a crucial step in vitamin K metabolism. Its structure isn't so far off:
Vitamin K is named for the German koagulation. We get a lot of our chemical vocabulary from German - it wasn't that long ago that American chemistry undergrads had to take German as part of their degree. This is no longer the case, and it probably leads to a lot of frustration the first time people are looking over a…
moleculeoftheday | January 18, 2007Nickel tetracarbonyl, like a lot of metal carbonyls, is an odd duck. Many complexes of metals and carbon monoxide don't act much like metal at all, and Ni(CO)4 isn't an exception. Nickel carbonyl is a liquid, but only just - it boils at 43C, or just above blood temperature. It's subject to lots of reactions, and just passing CO over impure nickel is a viable method of purifying nickel from a mixture (it will leave as the liquid or gas, depending on the temperature).
Unfortunately, it will give up that CO readily, including, as pointed out here, to certain vital enzymes, such as your…
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).