This next section is about the structural analysis of organic compounds using the previously described analytical techniques.
There is no one technique that can be used to elucidate the structure of an organic molecule. The process moves forwards by obtaining small pieces of data that when assembled point towards a logical conclusion.
Syllabus reference S3.2.12Structure 3.2.12 - Data from different techniques are often combined in structural analysis. (HL)
- Interpret a variety of data, including analytical spectra, to determine the structure of a molecule.
Guidance
Tools and links
Relative formula mass
The first step is always to determine the relative mass of the unknown compound. This may be done in several ways, such as using the gas laws on volatile liquids, but the easiest technique is mass spectrometry.
In real life, samples of unknowns appear as components of mixtures and mass spectrometry is often associated with gas chromatographic instruments that separate the components before MS analysis. This is known as GCMS (Gas chromatography mass spectrometry).
To obtain the relative mass from MS data we simply look for the m/z value of the signal with the highest value. Remembering that there is a possibility that isotopes can affect this value.
Isotopes
Organic compounds all contain carbon and most contain hydrogen. Both of these elements have a small percentage of isotopes with higher mass than the common atom. Generally, this does not have much effect on MS signals, but if there is a molecule with large amounts of hydrogen or carbon then there is a mathematical probability of seeing a signal one unit higher than the m/z value of the molecular ion.
For example, butane, C4H10, has a 10% probability of a molecule containing one 2H atom, giving a molecular ion of m/z = 59. This will show as a signal of 10% the intensity of the actual molecular ion with m/z = 58.
It is important to not allow these signals to confuse when determining the molecular ion.
In the case of chlorine, we can actually use the expected pattern to our advantage. In any molecule containing a chlorine atom we would expect a signal to appear with an intensity of 33% at a value of m/z M+ + 2. This can give us an important clue as to the presence of chlorine.
Likewise with bromine, we expect a double signal separated by 2 m/z values at the molecular ion.
MS Fragmentation
Covered in Structure 3.2.8, we can determine from both the m/z values of the signals in the spectrum, and from the differences between signals, possible fragments that have broken off from the molecular ion, M+.
Remember that only the ions can be detected, not the radicals.
Some typical stable ions that give rise to strong signals are shown below.
1H proton NMR
Once we have determined the relative mass from MS, we look to NMR to provide us with more data. The number of signals and the integrals will allow us to determine the number of hydrogen atoms in the molecule. The splitting patterns of the signals and the chemical shift can now be used to start piecing together possible structures.
First, we look at the chemical shift of the signals. The chemistry databook provides you with a list of possible units that match each chemical shift.
Then we look at the relative integral values to get the total number of hydrogen atoms, which must be a multiple of all of the integrals added together. For example, if we have three signals with relative integrals of 1:2:3, then we could have a molecule with 6 hydrogen atoms, or 12 hydrogen atoms, or 18 hydrogen atoms etc..
Now we look at the splitting pattern and try to build the structure, bearing in mind all of the pieces of the jigsaw puzzle previously obtained.
Infrared spectrometry
While, probably the least useful in terms of structural determination, the IR spectrum can give important clues as to units that may appear within a molecule. The most obvious signals are due to -OH, -COOH and C=O. Once again, the databook provided a list of structural units and their typical absorptions in the IR.