At the end of the previous week we were trying to figure out the content of a product that was not what we expected. To further characterize the compound, in addition to LC-MS, the post-doc Brian took me down to the nuclear magnetic resonance (NMR) machine. Apparently the magnetic field around the machine is so strong that if you had a credit card in your pocket it would be deactivated. Brian tried to explain to me how the NMR works in simple terms because the actual theory requires chemistry and physics knowledge that are well beyond my level. So basically the NMR creates a magnetic field that can change the direction an electron spins (it can only spin in two possible directions), and the machine can measure the amount of energy required to make that change. The energy required is presented on the resulting graph as a chemical shift, which is essentially the position of a peak on the graph. In a proton NMR, the integration of each peak shows the number of protons at that location; in a carbon NMR, each peak represents one carbon atom. Because the energy required to make the change in spin direction is related to the chemical environment that the atom is in (which simply means the other atoms around it in the chemical structure), each proton or carbon in a specific location will have a specific range of chemical shift. So if you know that a carbon atom in a carbonyl group will always show up on the left end of the graph, a peak on the left end will indicate that you have a carbonyl carbon. The NMR essentially gives us more information on the structure of the compound that we have made.
The NMR result certainly did not represent the compound we wanted, so while Dr. Ballatore and Brian were trying to figure out what was going on with the NMR (I can't interpret a NMR graph), he had me set up another reaction to deprotect the compound. The isobutane that was attached in the first step of the reaction was a "protection" of the reactive carbonyl oxygen. Once deprotected, we ran another LC-MS to see what was in the compound. As expected, the largest peak showed the same molecular weight as before minus an isobutane. After some guessing around, Dr. Ballatore figured it out. What happened was that the reaction produced a large amount of dimers, compounds that had two cyclopentanediones. It was pretty amazing how he just guessed the right one.
While all this was happening, we had set up a separate reaction which was a lot simpler than the one we were working on, it only had one step and didn't require reflux or deprotection. The reaction sill uses cyclopentanedione, and it basically adds the benzyl ring on the other side of the structure. Changing the location of the benzyl group can affect the compound's acidity and ability to penetrate membranes.
After figuring out what went wrong, we redid the reaction and this time modified the run-time to minimize dimerization.
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