Molecule of the Day

Here’s one of our paper chromatography spots - the yellow dye is the beloved Yellow #5, or tartrazine:

I don’t have a lot to say about it chemically. It is of a class of compounds known as the azo dyes. It’s pretty prone to cause allergies, relatively speaking. It is the dye responsible for Mountain Dew’s color. It doesn’t shrink your testicles, if you were wondering. It is probably more ubiquitous than you realize. Start peeking at labels - FD&C Yellow #5 is one of the most common yellow dyes around in food.

Yesterday, I alluded to the fact that we’d talk about why the chromatograph turned out the way it did. On further thinking, it’s quite hard to explain! The canonical use of chromatography is probably separation of small (<50-100 atoms or so) organic molecules on silica gel. This is not actually a gel at all, but a sort of slurry of solvent and silica - the fine, white, pure sand stuff I’ve talked about before. It is a polymer of SiO₂. The explanation you’d get in sophomore organic chemistry at just about any university is that silica chromatography is a polarity-based phenomenon. Certain polar parts on the surface of silica (Si-OH ends, instead of Si-O-Si, which predominate) interact with polar parts of your compound. Your solvent (or eluent, to use the appropriate nerd parlance) competes for these polar sites, to varying degrees. More polar solvents compete more effectively with the silica, and move compounds down the column. Analagously, more polar compounds will stick more tenaciously to the polar silica. This is a bit sloppy; the forces between all the species in and out of solution here are a bit more complex than this implies. However, it works well enough and predicts how things will turn out OK, most of the time.
A typical solvent mixture is hexane (very, very nonpolar) with ethyl acetate (polar, relatively speaking). A mixture with mostly (or all) ethyl acetate will be more polar, a mixture with mostly hexane (never all, neat hexane will not move anything along silica very well) is not very polar at all. When we use this to purify compounds, we “pack” it in a glass column (that is, pour the slurry in and let it settle in a hopefully homogeneous arrangement) and let solvent percolate through, hopefully moving your compound along at a sufficiently different rate than any impurities, giving you a very pure sample. This technique is absolutely invaluable in organic synthesis, but you will see it in an industrial process once in a blue moon. It’s fine if I’m making a gram or two of something and want to purify it, but if I happen to stumble on the next Gleemonex and we need a few metric tons of it, chromatography isn’t how we’re going to purify it. We’ll have to turn to less expensive (and less labor-intensive) old friends like recrystallization, and other process chemistry techniques of which I remain blissfully unaware.

Enough about what’s normal - let’s talk about what I did Sunday afternoon!

Rather than a somewhat polar stationary phase (silica) and a not-very-polar mobile phase (ethyl acetate/hexane, methylene chloride, etc.), we have a very polar stationary phase (paper - mostly cellulose, a polysaccharide), and an extremely polar mobile phase (isopropanol and water). Paper chromatography is mostly a lost art these days. Even for a quick-and-dirty test separation (before running a silica column, for example), you’d probably use TLC (thin-layer chromatography - chemistry has an abundance of cute acronyms like this). This is an analagous technique to paper chromatography - the mobile phase is the less-polar solvents you’d use on a silica column, and the stationary phase is a glass/plastic/metal plate with silica bound to it in, well, a thin layer. I’m going to speculate and say that our paper chromatograph is a lot like a silica one - the hydroxyl groups on cellulose are polar, and our 70% isopropyl alcohol/30% water (7:3 IPA/Water in chromatography jargon) competes for polar sites on the molecule.

Tartrazine is very polar. Its C-N and C=N bonds (single and double bonds between carbon and nitrogen) are all quite polar, and it is also a trianion - its two sulfates and one carboxylate are all very polar functional groups that will interact with the paper via ion-dipole interactions. These are also, coincidentally, good hydrogen bond acceptors (a hydrogen bond acceptor is typically an electronegative atom that can accept a proton). Sugars have all those OH groups, which are good hydrogen bond donors. All this probably helped it stick to the sugar pretty well, even with the competing interactions with the isopropyl alcohol and water.

You can probably guess tomorrow’s molecule! Night!