CHM 2211 Honors Written Report

Kimberly Rogers

CHM 2211 Honors Written Report

April 30, 2004

Chemical Structure Determination:

Gas Chromatograph, Mass Spectrometry, and Nuclear Magnetic Resonance Experiments

For our honors presentation for the spring semester, Lydia Johnson and I were given a substance the two of us had obtained from a previous organic chemistry lab involving the Grignard Reaction. After three weeks of laboratories involving heating, separating, and hydrolyzing mixtures, the two of us finally obtained the substance we intended to prepare: 2-Methyl-2-Hexanol. The chemical structure of 2-Methyl-2-Hexanol appears below.

Because Grignard reactions are complicated and comprehensive reactions, we needed to verify that the structure that we obtained was indeed 2-Methyl-2-Hexanol. On recommendation from Dr. Breivogel, we took our substance to the University of West Florida’s chemistry laboratory, where two professors, Dr. Michael Huggins (a Chipola graduate) and Dr. Jerome Gurst, helped us perform several experiments to confirm that our structure was definitely 2-Methyl-2-Hexanol.

The first experiment we performed on our obtained substance was gas chromatography. In gas chromatography, organic compounds are separated due to differences in their portioning behavior between the mobile gas phase and the stationary phase in the column. The following is a picture of the University of West Florida’s combined Gas Chromatograph/Mass Spectrometer (which I will discuss later).

The right portion of the machine is specifically for gas chromatography. You will notice the control panel on the far right; this is mainly used to put in the amount of time for the substance to run its course through the machine. As one might imagine, it takes longer periods of time for more complicated substances (i.e. benzene rings, carbonyl compounds) to run through the gas chromatograph, but since our substance was relatively simple, it only took about five minutes to truly determine our structure; however, for verification purposes, we ran our substance for fifteen minutes. The following is a scanned copy of our mass spectrometry results.

The first thing that one would notice is the large peak at 2.6 minutes; this represents the amount of time that this substance would take to transition from the liquid to the gaseous state. By checking with the University of West Florida’s computerized database of gas chromatographies of substances (they have thousands of reports), we confirmed that the high peak at 2.6 minutes is representative of 2-methyl-2-hexanol.

Another peak is evident at 7.37 minutes, but this represents an impurity. However, the impurity did not come from our substance; it was from the university’s gas chromatograph. This peak represents decamethylcyclopentasiloxane, a very complicated cyclic compound.

Since the gas chromatograph and the mass spectrometer are present in the same machine, we next ran our substance through this device. Mass spectrometry is a technique for measuring the mass, and therefore the molecular weight, of ions. Of course, once one determines the molecular weight of a substance, it is much easier to figure out the exact structure of the molecule. The following is a scanned copy of our mass spectrometry reading.

The arrow on the copy represents 116g/mol, which is the molecular weight of 2-methyl-2-hexanol (chemical formula C7H15OH). This peak (it is more evident from the larger scanned copy) is known as the parent peak. The most obvious and largest peak at 59 represents what is called the base peak. If one takes the original molecular mass of the compound (116g/mol) and subtracts 59 from this amount, one would get 57 g/mol, which coincidentally, is the weight of a butyl group (CH3CH2CH2CH2). This means that a butyl group is lost. Looking back at the chemical structure of the molecule, it can be seen that this is very likely, since the butyl group is “open” in the molecule with no substituents and can “leave” the rest of the molecule rather easily. I also circled two other key peaks on the mass spectrometry reading: the peak at 98 (which represents dehydration, the loss of a water group, H20, which is 18g/mol), and the peak at 101 (which corresponds to the loss of a methyl group, CH3, which is 15 g/mol). We used these key peaks and predominately the base peak at 59 to again verify that our substance we obtained in the experiment was indeed 2-methyl-2-hexanol.

In addition to gas chromatography and mass spectrometry, we used the University of West Florida’s Nuclear Magnetic Resonance (NMR) machine. NMR is a spectroscopic technique that provides detailed and comprehensive information regarding the carbon-hydrogen framework of a molecule. Basically, NMR works when a molecule is placed in a strong magnetic field (and this was a very powerful magnetic field; we had to remove our drivers licenses before stepping close to the machine in fear that they would become demagnetized!) and irradiated with radiofrequency waves. Below is a picture of the NMR at the University of West Florida’s chemistry department.

There are two main types of NMR: Carbon-13 NMR (13C NMR), and the proton NMR (1H NMR). We first obtained the 13C NMR, and a scanned copy is below.

Although it is hard to see at times, every peak on the 13C NMR represents a different carbon atom. Disregard the three peaks to the left of the graph, as they represent deterochloroform, which is added to the compound so the NMR could be run more effectively. Now, seven main peaks remain, and coincidentally, there are 7 carbons present in 2-methyl-2-hexanol. The carbon peak furthest to the left does represent the alcohol, since that is the area of the NMR graph that corresponds to C-O bonds. The other peaks represent CH2’s and CH3’s (we have no CH’s in our substance), and are very closely related.

In addition to running the 13C NMR, we also were able to obtain the 13C APT for our substance. Personally, I very much enjoyed the APT, since you were able to see the different carbon bonds easily in one main graph. The following is a scanned copy of the APT for our substance.

Although there are certainly more than seven peaks in the APT, one should only really consider the larger variety; the little lines in other areas represent mirror images because they are closely related to each other. The alcohol is on the bottom because it is not represented by the others; it has no hydrogens on it.

In addition to running the 13C NMR, we also ran the 1H NMR, which represents more of the hydrogen framework of the molecule. On the next page, you will find a scanned copy of our 1H NMR.

We know that the farthest peak on the 1H NMR is the alcohol, because of the large chemical shift of the oxygen. Additionally, we know that the tallest peak is the methyl group (CH3), because it has an equivalent (our molecule has three total CH3 groups).

After we ran both the 13C NMR and the 1H NMR, we were ready to compare the two. The University of West Florida had a very convenient way of accomplishing this task, and the following is a scanned copy of how we achieved this act.

I found this technique extremely useful in “matching up” each carbon with it’s corresponding hydrogen (a notable exception to this graph is the absence of the “blue” line for our alcohol C-O bond; this is because there are no hydrogens attached to that bond, and thus, no comparison to make between a carbon and a hydrogen.) The black dots you see are a little off, but we added them so you could see where each carbon corresponded to each hydrogen. We found the carbons from the APT I wrote of earlier, and we placed them onto the comparison, as well. From this, we knew by process of elimination that the furthest peak to the right responds to the number six carbon-hydrogen bond in our molecule, we also concluded that the furthest CH2 to the left is the number three carbon-hydrogen bond, primarily because of the chemical shift of the oxygen. The other two CH2’s are extremely close in character and distance on the chart, but if we had to assume, we would say that the CH2 farthest to the left is the number four carbon-hydrogen bond (again, dealing with the chemical shift of the oxygen, although in this case, it is minimal).

After taking the time to visit the University of West Florida’s chemistry department and analyzing our structure, I learned two main things: 1) that I wished the Chipola Chemistry department had machines this comprehensive (things would be so much easier to understand at times!), and 2) after long analysis, we concluded that our substance we obtained months ago during the Grignard reaction laboratory was indeed 2-methyl-2-hexanol.