Friday, July 16, 2010

Opitmization and Parameterization of IR and GC for Simple Reaction Mixture Analysis in ATRA

ATRA was discovered in 1937 by Karasch, but had low product yields at the time. Later, Minisci discovered metal catalyzed ATRA through his experiments and found this to have a much higher product yield. ATRA is a process by which carbon-carbon bonds are formed by means of a metal catalyst with products of small molecules that are used to create complex organic compounds and pharmaceuticals. The reason that I'm studying this is to achieve a more efficient way to run this mechanism.

In ATRA an alkyl halide reacts with a copper (l) catalyst to form a primary radical and copper (ll). The radical reacts with an alkene forming a secondary radical which abstracts a halogen atom from copper (ll) to regenerate copper(l) and form a monoadduct. Recent advances in this field have found that addition of a reducing agent can be used to dramatically reduce copper concentrations, making this method more attractive to synthetic chemists. Traditionally, analysis has been conducted via 1H NMR spectroscopy, which is inaccessible to smaller research facilities. I'm studying this mechanism with the application of gas chromatography and infrared spectroscopy to analyze these reactions.

My first week here I spent learning what all I would be doing. This included how to calculate the amounts of how much AIBN, internal standard, alkene, alkyl halide and solvent I would put into my test tubes to run. It was all a bunch of stoichiometry problems that were simple enough once I got the hang of it. Then the next few days were spent learning how to use the gas chromatographer (GC) and read the scans that it spit out. The first thing to do is turn on the gas tanks; first nitrogen, then air, then helium and finally to light the machine. The machine should always be purged before using it, to clean out anything that may have been left inside the column. To do this the GC is set to run at 180 degrees Celsius for 20 minutes, or until the scans look clean. Then the parameters are set for the sample; initial temperature, initial time, amount of degrees to ramp per minute (rate), final temperature, and final time. Sometimes this also includes changing the ramp time. Then the parameters on the integrator are set, which is the machine connected to the GC, and prints out the scans. The only parameters that are changed it the attenuation, which is how much the graph is zoomed in or out of the scan, and the stop time, which is how long the integrator should run for. The stop time is calculated by this formula: finial temp - initial temp / rate + initial time + final time = total time. Then .2 micro liters is injected into the column simultaneously while pressing start on both the GC and the integrator. As the machine runs, the sample moves through the column and the substances in the sample will shoot out of the column around their boiling point, as recorded by different sizes peaks on the integrator scan. Sometimes part of a sample will shoot out of the column at a significant time before or after it's boiling point and add and extra unknown peak to the scan. In that case, another scan is run again. At least two scans of every sample is run to confirm that the scan is quantitative. Though, since the machine is old it doesn't always work right and sometimes time is needed to purge again.

The second week I moved to the infrared spectrometer (IR). This machine measures the bonds in samples. First, a background is always collected before using the machine, so that it can tell the difference between what should be recorded, and what shouldn't. Then two drops of the sample is placed between two salt plates and put into the machine. After the IR runs it displays a spectra of the sample, which it obtained by shooting a photon of light through the sample. The light photon causes the connected atoms to vibrate about their bonds and different bonds absorb different amounts of energy, which are displayed in the spectra. The spectras can be checked against the SDBS database for confirmation.

The experiments we did at first were to check if the two machines were quantitative. On the IR we first ran Octene, Methanol, Acetonitrile, CCl4, Styrene, Methyl Acrylate, and Methyl Methacrylate. Then a mystery sample was made of two samples that I had already ran and were mixed together for me to identify what it was. Looking at the scans that I had already done of our materials and comparing the different peaks in the scans did this. If the peaks matched, it meant that the sample did as well. On the GC I ran all of our starting materials a few times, to check that they always came out at the expected time, in the right amounts. This week we've started running our solutions with AIBN, internal standard, alkene, alkyl halide and solvent through the GC. AIBN is our reducing agent and the reason this is used is because it gives a higher product yield than the other reducing agent, ascorbic acid, even though it's more environmentally friendly. We've ran four different scans all with differing ingredients and all but the first one came out okay, but we've yet to figure out why.

Next week the other IR head might be back, the one that's more quantitative, since the one we have now isn't and I might run some samples on that if it does.

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