Chemistry 101

Well today I thought I'd talk a little about what I do, I'm not going to go into too much detail, but I thought, what the heck. I mean how many people know what an organic chemist does?

Anyway, in the movies all chemistry labs involve the bubling of colored liquids and these strange set ups of aparatus. This is not the case, really a more acurate representation is that depicted in CSI. I have a fume hood, and a lab bench, plus lots of glassware, most of it not very funky.

You see most reactions are set up in a round bottom flask or vial, and the reaction is stirred using a magnetic stir bar (which is basically a small magnet coated in teflon). So you add your reagents to the flask, add solvent, and stir. Occasionally you'll have to heat or cool the solution depending on the reactivity of your reagents. The more reactive your reagents the cooler you have to go down to usually -78 degrees celcius, if your reagents are fairly unreactive you may have to heat them up. Now there is a little more to this, but basically this is all it takes to run a reaction.

But you see after the reaction is completed, not only do you usually have your product, but you usually have starting materials, other side products as well as polymerisation products all floating around in the solution. But for the purposes of new pharmaceutical agents you need to have pure product. So, the real difficult part of the chemistry process actually begins.

Purification, is the most important step and probably what I spend a majority of my time doing and is the reason I've decided to write this today. See today I had thought I had purified a reaction, but in reality it is still a mixture of very similar products and now I have to try and develop a new method to purify it.

There are several ways to purify an organic compound.

1) Extraction: You can take your organic solvent with your mixture (chloroform, dichloromethane, hexane, ether, ethyl acetate, and many more) and you can add water to this, which will form two layers, and then shake them up so that they mix and let them settle. What will happen is compounds that are hydrophillic (ie preference for water), will be extracted into the water layer where as the more hydrophobic (ie dislike water) comopunds will stay in the organic solvent. Extraction is a good way to get rid of water soluable compounds, but I try to avoid it like the plague because usually it's not the water soluable compounds that are a problem, plus most the compounds I'm trying to make right now are fairly water soluable and trying to get rid of water is a nightmare.

2) Crystalization: This is a very nice technique and can lead to very pure compounds, the problem is that the more impure your starting sample the more difficult it is to recrystalize out a single material. This technique is usually only used to purify out material that is fairly pure to start with.

3) Chromatography: This is the method of choice for most organic chemists. You see chromatography takes into account the polarity of your molecules. Poor mans chromatography involves using a glass column filled with ultra pure sand, these sand molecules are very fine and very pure Si02. You place your compound at the top of the silica, and then you run organic solvents through it. What happens is that your compounds get absorbed and deabsorbed onto the silica, which translate into them moving down the column at different rates depending on their polarity. You see silica is fairly polar, so the more polar your molecule the longer it will stay absorbed to the silica.

The opposite to this is reverse phase chromatography, in this case you have a very non-polar solid material, usually some sort of long chain carbon containing group and you use polar solvents such as water and methanol or ethanol or acetonitrile. In this case the more polar your molecule is, the faster it travels through the column.

Anyway, right now I have a very polar molecule that I've tried to purify using both methods, and in both cases I can't seem to seperate out the mixture. Right now it's a mixture of two very similar products and now I have to design some sore of normal or reverse phase chromatography method to give them enough seperation so that I can purify them and submit them for testing.

Anyway, I'm sorry for boring you all. If you made it this far that is.