Chemistry 101 con't

Back by popular demand (meaning nobody actually reads or comments), here is another installment of Chem 101. I should probably rename the course to Organic Chem 101, because that's what I'll be talking about.

So today in the lab, I set up a Mitsunobu reaction, which is named after, yes you guessed it, a chemist named Mitsunobu. Here is a link to what the reaction actually does, showing actual structures. Isn't that exciting. I can't actually show you what I'm doing exactly because that information is confidential but I'll go over the basics of it.

Mitsunobu reaction

So basically what a Mitsunobu reaction does is convert an alcohol into an amine and also inverting the stereochemistry. Sounds complicated right? Stereochemistry what the hell is that? Well I'm going to try and explain it as best as I can.

You see, Carbon, likes to bond to four things, like Methane or CH4. There is only one way that these atoms can be combined and they can only form one product. However, when Carbon bonds to four different atoms it can actually bond to them in two differnt ways. Therefore this Carbon atom has what we call chirality. Show below are the two different ways of drawing CHFBrCl.



As you can see from the picture, the two molecules are mirror images of each other. This pair of molecules are known as Enatiomers. What this means physically, is that they basically have all the same physical properties, such as melting points, boiling points, etc. BUT they each react differently to plane polarized light. Trying to isolate one from the other is incredibly difficult because they are so similiar, I won't go into details of how one can accomplish that. Anyway, this is what is known as stereochemistry. As chemists we refer to them as having either R or S stereochemistry.

We arive at the R or S, by looking at the above molecule on the left and assigning priority to the different groups. An atom with the largest molecular weight bonded to the chiral carbon is labled with a 1, and then so on. In the case of the molecule on the left bromine has top priority and we label that with a 1, Chlorine is next, Fluorine is next and finally hydrogen. Now with the lowest priority group facing into the page (which is drawn for the molecule on the left) you draw an arrow connecting 1 to 2 then to 3, if this arrow is clockwise, then we assign the molecule as R (it's a german term for clockwise I believe) and if it's Counterclockwise you assign it S. Now for cases where the drawn molecule doesn't have the lowest priority group in the back, you can do the same thing, but if your drawing gives you R you just have to reverse it, therefore it would be S.

In the case of the above drawing, the molecule on the right is R and the molecule on the left is S. Fun? A 50/50 mixture of enantiomers is known as a racemic mixture.

Okay, now the reason that chirality is important in my line of work is because our bodies are made up of amino acids and they all exist in one single chiral form. What this means and it has been shown in the past by some drugs. Is that usually only one enantiomer works on a specific target, but sometimes the other enantiomer acts on a different target causing very sevre and often fatal side effects. Drugs now a days are not allowed to be a mixture of enantiomers just for this reason. So, it's very important in my job to make sure that things are enantiomerically pure. Sounds complicated doesn't it?

Well I hope you enjoyed this little stereochemistry lesson, if you have any questions please feel free to ask, and please just comment away anyway