Mass Spectrometry
Mass Spectrometry
Mass spectrometry (mass spec is a method to measure the molecular weights of molecules and parts of molecules. This is a wonderful marvel of technology. If we want to identify a compound, perhaps a new molecule we made in the lab, mass spectrometry is a great first step in identifying that compound. Mass spectrometry can give us the molecular weight of a molecule. Mass spectrometry also breaks molecules into pieces and measures the molecular weights of those pieces. Mass spectrometry can also quickly tell us whether a molecule contains nitrogen, sulfur, or halogen atoms. These are all very useful in helping us identify and learn more about a molecule.
How it works
There are several methods by which mass spectrometry can be done. Electron impact (EI) is one of the simplest.
Generic Mass Spectrometer
A beam of high-energy electrons strikes a sample. This beam of electrons breaks the molecule apart. The molecule and its fragments are ionized. The molecular weights of the ionized molecule and its fragments are measured and graphed. This graph is called the mass spectrum.
Let’s look at propane. An electron beam slams into propane and knocks an electron away making what is called the molecular ion (M+), a radical cation. It is a radical because it has an unpaired electron and it is a cation because it has a positive charge. The mass spectrometer measures the molecular weights of ions only. The ions enter into a vacuum tube and flies towards the detector. A magnetic field bends the ion. Heavy ions have too much inertia and are not bent enough to reach the detector. They hit the wall. Light ions have too little inertia and are bent too much by the magnet to reach the detector. They hit the wall. Ions that have a certain mass for that magnetic field are bent in just the right way to reach the detector. Once an ion hits the detector, it records that is has been hit.
The magnetic field strength can be varied. If it is increased, it allows the heavier ions to bend more and hit the detector. If it is lessened, it allows the lighter ions to hit the detector. Before a mass spectrum is obtained, the instrument is calibrated with molecules of different masses. The magnetic field strength for the various molecular weights is carefully measured. Then, when an unknown sample is run, the magnetic field strength is varied. When the detector records a hit, knowing the magnetic field strength for that detector hit gives the molecular weight of that ion.
What is reported on the mass spectrum is actually a mass-to-charge ratio (m/z), the mass (m) divided by the charge (z). Usually, the charge, z, is +1, so what is recorded on the mass spectrum is the molecular weight of the ion. If an ion happens to have +2 charge, the magnet would bend it twice as much resulting in a peak on the mass spectrum at ½ the molecular weight of the ion.
Fragments
Not only is the M+ molecular weight measured, but the molecules also break into ion fragments whose weights can be measured. The mass spectrum graphs how many of each ion of different m/z hits the detector. Don’t worry about identifying every peak in a mass spectrum. Some strange reactions occur in the mass spectrometer. For our purposes, it is best to just look at the simpler ions made. Remember that a carbon atom has an atomic mass of 12 and a hydrogen atom has an atomic mass of 1.
Mass Spec Fragmentation of Propane
The Mass Spectrum
The molecular ion peak of a mass spectrum is the peak that represents the molecular weight of the entire molecule being studied. It is usually the peak farthest to the right in the mass spectrum, the heaviest peak. The weights of the fragments also appear. In propane’s mass spectrum, ion fragments that weigh 29 are the most abundant. More of those fragments hit the detector than any other. The base peak is the largest, tallest peak in the mass spectrum. For propane, the base peak is at 29 m/z.
Mass Spectrum of Propane
Isotopes
It is possible to easily see if a compound contains a special atom, a bromine, chlorine, or sulfur atom. We look to the right side of the spectrum and at the area for the molecular ion peak (M+). An M+2 peak is a peak that is two amu higher than the M+ peak. If the molecule being studied contains one of these special atoms, there will be a larger than usual M+2 peak. These M+2 peaks exist because these special atoms have two major isotopes that are two amu apart from each other.
Bromine
The periodic table says that the atomic mass of bromine is 79.9amu. No bromine atom weighs 79.9. Bromine atoms either weigh 79 or 81. We call these various forms of an atom with different weights, isotopes. They differ by the number of neutrons in their nucleus. In nature, there is about an equal mixture of the two (with just a little more of the 79 isotope). We average those weights of the isotopes found in nature to come up with the atomic mass found on the periodic table of 79.9.
Since bromine atoms weigh either 79 or 81, what would we expect for the molecular weight we would see in a mass spectrum for bromomethane, CH3Br? There are two forms of CH3Br. One bromine isotope weighs 79 and one weighs 81. Since carbon weighs 12 and hydrogen weighs 1, CH3 weighs 15. Therefore, the molecular mass of CH3Br when Br weight 79 is 94 while the molecular mass of CH3Br when Br weight 81 is 96. Since the two isotopes of bromine are found in nearly equal amounts, we see these two peaks in the mass spectrum in nearly equal amounts. The peak at 94 is the M+ and the peak at 96 is the M+2.
Mass Spectrum of bromomethane
We often look at the M+ peak in a mass spectrum to see if there is an M+2 peak. If we see an M+ and an M+2 peak with equal heights, it indicates a bromine atom is present. This is a fingerprint for bromine.
You might wonder about being confused and calling the peak farthest to the right the M+ peak and thinking that there is another fragment peak two amu less (an M-2 peak). It would be quite strange to lose something that weighs two amu off of a molecule. So, we know that we are nearly always dealing with an M+ and an M+2 isotope peak
Bromine pattern
Chlorine
Chlorine’s atomic weight on the periodic table is 35.5 amu. Chlorine has two isotopes, 35Cl and 37Cl. 75% of all chlorine naturally found is 35Cl while the other 25% is 37Cl.
Therefore, the M+2 peak for a compound that contains chlorine is about 1/3 the height of the M+ peak.
Chlorine pattern
Mass Spectrum of Chloromethane
Iodine
Iodine only has one isotope. All iodine atoms are iodine-127. So, in a mass spectrum for a compound that contains iodine, we often see a peak at 127. This is the molecular weight for iodine. A peak of M+-127 (loss of an iodine atom) is also seen.
Mass Spectrum of Iodomethane
Sulfur
Sulfur has two main isotopes, sulfur-32 and sulfur-34. The natural abundance for sulfur-34 is 4.2% of sulfur-32. So, in a mass spectrum, the M+2 peak is usually about 4% of the M+ peak. Usually, if there is no special isotope, the M+2 peak is non-existent. Look for an M+2 peak that is larger than usual to indicate the presence of sulfur.
Sulfur pattern
Mass spectrum of dimethyl sulfide
Nitrogen
Nitrogen atoms do not have M+2 isotope peaks to help us identify them. But, they do give a clue when they are present. All of the M+ peaks you have seen so far have something in common; they all have an even number m/z. This is remarkable. But, nitrogen compounds are different. If a molecule has an odd number of nitrogen atoms in it, it has an odd molecular mass. So, a typical nitrogen-containing compound with one nitrogen atom will be odd, but if there are two nitrogen atoms present, it is even. Below is the mass spectrum for methylamine, CH3NH2.
Mass spectrum of methylamine
1. Identify the atom the following mass spectrum data indicates.
a) The M+2 peak is 1/3 the height of the M+ peak.
b) The M+ peak is an odd number.
c) The M+2 peak is nearly equal the height of the M+ peak.
d) There is a large peak at 127 and M+ - 127 is also prominent.
e) The M+2 peak is slightly larger than usual, about 4% of the M+ peak.
M+1 peaks
The special isotope peaks are all at M+2. There is usually a very small peak at M+1. This peak mostly arises because even though most carbon is carbon-12, about 1% of carbon is carbon-13. Don’t let this very small peak at M+1 confuse you. It is not sulfur! Usually, the M+2 peak is missing for compounds that contain only C, H, and O atoms. If the M+2 peak is suspiciously large, look for the presence of a special atom in the molecule.
Typical M+1 pattern with only C, H, and O atoms in molecule
Degrees of Unsaturation
A compound’s molecular formula gives some insight into its structure. For a hydrocarbon, every extra -bond or ring formed decreased the molecular formula by two hydrogen atoms. Each of these -bonds or rings is called a degree of unsaturation or an element of unsaturation.
Examples for Number of Degrees of Unsaturation
So, if we know a compound has the formula C4H8, we could know that the compound has one degree of unsaturation, either a π-bond or a ring. We can determine the degrees of unsaturation from a molecular formula by using the following formula. Take a couple of minutes and memorize this formula now.
Formula to calculate degrees of unsaturation
A compound normally has 2C+2 hydrogen atoms. So, our formula is taking the normal number of hydrogen atoms that should be present in a saturated compound and subtracts the number of hydrogen atoms that are actually there. Two hydrogen atoms are removed for each unsaturation. That is why we divide by two. Oxygen atoms do not count in the formula. Nitrogen atoms count as ½ a carbon atom. Halogens count as one H atom. This is because halogen atoms and hydrogen atoms both usually only have one bond. The number of degrees of unsaturation should always be a whole number. If you ever get 0.5 of an unsaturation, you did something wrong.
2. How many degrees of unsaturation are in the compounds with the following formulas?
C6H6O =
C2H4ONCl =
C3H7OBr =
C7H8 =
3. Is propene the only compound with the formula C3H6?
Answers
1. Identify the atom the following mass spectrum data indicates.
a) The M+2 peak is 1/3 the height of the M+ peak. (Cl)
b) The M+ peak is an odd number. (N)
c) The M+2 peak is nearly equal the height of the M+ peak. (Br)
d) There is a large peak at 127 and M+ - 127 is also prominent. (I)
e) The M+2 peak is slightly larger than usual, about 4% of the M+ peak. (S)
2. Identify the atom the following mass spectrum data indicates.
C6H6O = (4)
C2H4ONCl = (1)
C3H7OBr = (0)
C7H8 = (4)
3. Is propene the only compound with the formula C3H6?
No. Both propene and cyclopropane have one degree of unsaturation with the formula C3H6.
