Sitting in Organic Chemistry 2, the first time I saw the mass spectral data from mass spectrometry and the NMR spectrum from a nuclear magnetic resonance I was daunted. But, my organic chemistry professor quickly eased my stress by whipping out his awesome notes! I am certain that he should write a textbook one day. He hasn’t posted his notes online for Organic Chemistry 2, yet, because he hasn’t written all of them. I’ll try my best to break down mass spectrometry with the knowledge I gained from him, Kaplan, and the trusty Internet! This is a handy guide which will hopefully supplement your MCAT studying. This isn’t designed for your Organic Chemistry class because your class will be more in-depth than the MCAT.
What’s Going On:
A chemical is bombarded by an intense amount of high energy electrons. These electrons break apart covalent and valence electrons and result in charged ions and free radicals. These charged fragments show up in the mass spectrum. You can visualize this process here and choose different substances to send through the mass spectrometer. (Requires Java)
What to Know:
Only charged fragments show up on your mass spectrum.
M+ stands for the molecular ion peak. The molecular ion peak represents the original molecule that passed through the spectrometer, but in radical form (without one electron.)
Base peak is the tallest peak and is the most abundant fragment; sometimes it can be the same as the molecular peak and sometimes not.
What You Do:
You use the mass spectrum to figure out what the fragments of our molecule are. This is basically a big guessing game. In the example above you know that the mass of your molecular ion is 44 g/mol because the molecular ion peak is at 44. There are essentially equivalent even though your molecular ion is missing an electron–remember that the mass of an electron is tiny!
Now that you know the mass of your mystery molecule you have to figure out what it is. This is more or less through trial and error and quick mental math. Most important you need to know the molecular mass of basic compounds: carbon, oxygen, and hydrogen.
I like to start with carbon and determine the maximum number of carbons that could fit into the molecule.
Trial 1 — Our molecule’s weight is 44 g/mol, so I determine the maximum number of times that 12 (carbon) can go into 44 is 3.
12 times 3, however is only 36, meaning that there are other substances making up the compound.
44 minus 36 is 8, which isn’t on our target list and there is no naturally occurring element whose mass is 8 g.
Trial 2– Very unlikely that our compound is composed of 44 hydrogen, so let’s move on to oxygen. Our molecule’s weight is 44 g/mol; the maximum number of times that 16 (oxygen) can go into 44 is 2.
44 minus 32 is 12. Conveniently this is the mass of a naturally occurring element: carbon.
Prediction: The mystery molecule is CO2!
Mass spectrometry likely was more difficult in your college classroom, but to my knowledge this should be sufficient for the MCAT.
What’s Going On:
A chemical is irradiated with infrared light and vibrates; the vibrations are recorded on a spectrum that allow you to identify the functional groups of the molecule.
What to Know:
To read IR spectrums you need to decode them using this table.
|Alkynes (C≡C)||2100 (sharp)|
|Terminal Alkynes (≡C-H)||3300 (sharp)||if internal alkyne, no band at all|
|Nitrile (C≡N)||2250 (sharp)||longer than alkyne|
|*Alcohol (-OH)||3000-3700 (broad)|
|Terminal Aldehyde (O=C-H))||2700-2900|
|Internal Aldehyde||1725-1750||similar to ketone|
|*Ketone (C=O)||1700-1750||more sharp than aldehyde|
|Carboxylic Acid (C=O-OH)||2800-3500 (broad)
|shows both peaks because it’s like an alcohol and ketone together|
|Amine (N-H)||3200-4600 (sharp)
two peaks if primary amine
one peak if secondary amine
no peak if tertiary amine
|shorter than alcohol|
|less broad than alcohol; like an amine and ketone together|
If you are short on time just memorize the asterisked ones–alcohol and ketone, and remember that the alkane/alkene/alkynes are somewhat sharp and on the right side. That will be good enough to get you to the answer!
What You Do:
The whole point of looking at an IR spectrum on the MCAT is to determine what the molecule is. Fortunately the MCAT is multiple choice, so through process of elimination (based on the functional groups) you can figure out which molecule you are being shown. In the spectrum above, the most obvious stretch is the alcohol stretch, occurring around 3300 as indicated on our chart. Note that this is broad, unlike the C-H stretch which would be considered more sharp and at around 2900. Going back to the table you can determine that this C-H stretch is certainly an alkane. Do some practice problems to feel comfortable with this and comment below if you have any questions. Here is a practice IR spectroscopy problem.
What’s Going On:
A chemical with an odd atomic number is placed in a magnetic field and its nucleus acts as a spinning charge aligning with or against the field. The nucleus is then flipped by exposing it to radiation; when this energy is absorbed, the detector records resonance signal which shows up as a peak. There are two types of NMR: H1-NMR and C13-NMR.
What You Need to Know:
Different elements have different absorption ranges. This means that -CH3 and -CH2 will appear in different places on your spectrum. The more electrons surrounding the protons (hydrogen) that are being radiated, the more shielded the hydrogen is. Remember that the electron density around your hydrogen depends on the electronegativity of its neighboring atom. The more shielded the hydrogen is, the further right (upfield) it will appear on the spectrum, and thus a lower chemical shift is occurring. The scale for H1-NMR is 0 to 10.
In the image above note that the proton in CHO is less shielded because oxygen is quite electronegative while CH3 is more shielded because carbon is less electronegative than oxygen.
Things get more interesting when there is more than one proton nearby the proton at hand. When this occurs, your peak will split, also known as coupling. If there is one hydrogen near your proton, then your peak (which you thought would be a single peak–or a singlet) will split into two (a doublet); if there are two hydrogen near your proton, then your peak will be a triplet. This is known as the n+1 rule where n is equal the to number of proton neighbors within 3 bonds of your proton, and “n+1″ is equal to the number of splits in your peak.
Note above that the peaks for hydrogen A and hydrogen B both became doublets although they appear in different places on the spectrum because of shielding.
- isopropyl group pattern: large doublet and a small heptet (ratio: 6:1)
- ethyl group pattern: triplet and quartet (ratio: 3:2)
- aromatic pattern: a ton of little tiny peaks all together
Note that the isopropyl group pattern is shown above at (a) and (b).
Here is a quick table of the chemical shift range at which different functional groups should occur, although you can certainly memorize a more detailed chart which I can add here, at request.
|Carboxylic Acid||10-12 ppm|
If you guessed that carbon-13 NMR deals with carbon-13 instead of hydrogen, you are right! In a C13-NMR spectrum we are concerned with the chemical shift for carbon instead of hydrogen. Here, peaks will occur on your spectrum because carbon-13 is absorbing the radiation. This occurs on a much larger scale than H1-NMR, being about 0-200.
In C13-NMR there is also splitting of your peaks (aka coupling), but unlike H1-NMR where the splitting occurred because a proton (hydrogen) was near your hydrogen, a split occurs in C13-NMR because there is a hydrogen near your carbon-13. Usually there aren’t any other carbon-13s neighboring the carbon-13 you are considering, so thus carbon-proton splitting occurs in C13-NMR. The n+1 rule can be used here, too, where n is still the number of neighboring protons, but the number of neighboring protons to your carbon.
C13-NMR spectra will be presented as proton-coupled or proton-decoupled. Proton-coupled means you will have splitting, but in C13-NMR this is too hard to read sometimes because there are so many peaks they all overlap with each other. In proton-decoupled C13-NMR there are only singlets; none of the peaks will split. However, scientists prefer to use off-resonance decoupling; this is the same as your proton-coupled NMR because peaks are allowed to occur, but they are weakened. These muted peaks are much easier to read!
Note that in the NMR above, the scale is much larger than the H1-NMR. The 4 peaks in this field represent each of the carbons in the structure. The peak marked CDCl3 simply indicates the solution used.
What To Do:
The MCAT will likely ask you conceptual questions about NMR, requiring you to understand how it works. I didn’t concern myself with re-learning how to read the NMR spectra we studied in my organic chemistry class. However, I don’t design the MCAT. Do what you feel comfortable with and go as in-depth on NMR as you have time to do. It’s always better to be prepared. I think the most important thing here is to understand coupling.
I hope this helps you! Let me know if there are any corrections I should make or if there is more to add.