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Determination of structure
Determination of structure (discovering the structure of a molecule) is a very important part of organic chemistry. The problem is that the molecules cannot be 'seen' as such and indirect evidence for the structure must be gleaned by a variety of methods. The final 'proof' is often the synthesis of the molecule from simpler units, producing a compound with identical characteristics to the unknown substance.
The mass spectrometer
Mass spectrometry
The first stage to find out is the relative molecular mass of the substance in question. Nowadays, this may be done accurately using a mass spectrometer. In the past it was necessary to find the percentage composition of each component element to find the empirical formula and then to find the molecular mass by one of several physical techniques.
Once the relative molecular mass and chemical formula are known, structural
information may be obtained by both electronic and 'wet' chemical means.
The molecular ion
The highest m/e peak in the mass spectrum always consists of the molecular ion; i.e. the ion that has been formed by dislodging one electron from the molecule under investigation.
Mass spectrometry m/e values can be read to many decimal places. As all atomic isotopes have slightly different masses, this allows the molecular formula to be obtained directly from the m/e value of the molecular ion.
Mass calculator from formula: http://www.bmrb.wisc.edu/metabolomics/mol_mass.php
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Example: The two compounds ethenol and propane both have the same relative masses:
However, using accurate values for the relative masses of the atoms we get:
Clearly, these two values are not the same and can be differentiated in the mass spectrometer. |
Fragmentation
Once the molecular ion has been formed in the high energy beam of electrons, it is likely that this ion wlll break apart into fragments. Each fragment is either an ion itself, or a neutral species. The ions formed by fragmentation can also be detected in the mass spectrometer trace, but neutral fragments are neither accelerated, deflected nor detected.
The likelihood of a specific ion forming depends on the bond energy of the bond that must be broken and the stability of the fragment formed.
Typically, alkyl groups, acyl groups and allyl groups are most easily formed and often appear in mass spectra.
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Alkyl fragments
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Acyl fragments
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Allyl fragments
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[CH3]+
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[CH3CO]+
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[CH2=CH2]+
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| [C2H5]+ | [C2H5CO]+ | [CH3CH=CH2]+ |
| [C3H7]+ | [C3H7CO]+ |
As each of these fragments has a specific m/e value, an experienced analyst recognises the fragments as they are formed and uses this information to help build a structure of the fragmenting molecule. It's like being given pieces of a jigsaw puzzle and fitting them together to get the final picture.
The spectrum, showing several different peaks due to fragmentation, gives rise to a fragmentation pattern, which is the suggested way that a specific molecule has broken apart.
The molecular ion
As the previous section shows, the molecules that enter the mass spectrometer get ionised by a stream of high energy electrons. These electrons dislodge one (or more) electrons from the molecule, which then gets accelerated into the deflecting magnetic field.
Electrons have very little mass in comparison to the mass of atoms or molecules. Hence the mass of the ion formed by dislodging one electron is virtually the same as that of the molecule (or atom) itself.
This ion is called the molecular ion; it is the particle that appears at the highest mass/charge ratio on the mass spectrum.
This makes determination of the relative mass of a sample very easy indeed. You look for the peak that appears at the highest mass/charge value and that is it.
Isotopes
The presence of isotopes in the sample may cause confusion as regards the molecular ion. For example, a compound containing a chlorine atom will show two peaks due to the presence of 35Cl and 37Cl.
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The intensity (height) of the peaks containing isotopes is always in the ratio of the natural abundance of the isotopes. In the example above, chlorine occurs in nature in the ratio 75% of the 35-Cl isotope to 25% of the 37-Cl isotope. This is a ratio of 3:1.
The heights of the peaks due to C3H735Cl and C3H737Cl, i.e. the C3H735Cl peak is three times higher than the C3H737Cl, peak.
Deducing the molecular formula
The highest m/e peak in the mass spectrum always consists of the molecular ion; i.e. the ion that has been formed by dislodging one electron from the molecule under investigation.
Mass spectrometry m/e values can be read to many decimal places. As all atomic isotopes have slightly different masses, this allows the molecular formula to be obtained directly from the m/e value of the molecular ion.
Mass calculator from formula: http://www.bmrb.wisc.edu/metabolomics/mol_mass.php
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Example: The two compounds ethenol and propane both have the same relative masses:
However, using accurate values for the relative masses of the atoms we get:
Clearly, these two values are not the same and can be differentiated in the mass spectrometer. |
Fragmentation
Once the molecular ion has been formed in the high energy beam of electrons, it is likely that this ion wlll break apart into fragments. Each fragment is either an ion itself, or a neutral species. The ions formed by fragmentation can also be detected in the mass spectrometer trace.
The likelihood of a specific ion forming depends on the bond energy of the bond that must be broken and the stability of the fragment formed.
Typically, alkyl groups, acyl groups and allyl groups are most easily formed and often appear in mass spectra.
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Alkyl fragments
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Acyl fragments
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Allyl fragments
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|---|---|---|
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[CH3]+
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[CH3CO]+
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[CH2=CH2]+
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| [C2H5]+ | [C2H5CO]+ | [CH3CH=CH2]+ |
| [C3H7]+ | [C3H7CO]+ |
As each of these fragments has a specific m/e value, an experienced analyst recognises the fragments as they are formed and uses this information to help build a structure of the fragmenting molecule.
The spectrum showing several different peaks due to fragmentation, gives rise to a fragmentation pattern, which is the suggested way that a specific molecule has broken apart.
Fragmentation patterns
There are two approaches to fragmentation.
Start from the molecular ion and calculate the mass of the particles that have been subtracted from the m/e value of the molecular ion to give the peaks seen.
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Example if the molecular ion appears at m/e = 58, and the next lowest peak appears at m/e = 43, then a fragment has been lost that corresponds to 58 - 43 = 15 mass units. This corresponds to a methyl ion fragment, [CH3]+. |
The second approach involves looking at the fragments at the low m/e end of the spectrum.
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Example If a fragment appears at m/e = 29, then this could be due to a ethyl ion fragment, [C2H5]+. |
Rearrangement
One complication that arises during molecule fragmentation is that the bonds don't simply break giving fragments, but they can also reform and fragments themselves can rearrange to give more stable structures.
Full treatment of this is beyond the course, but it should be noted, as fragments often appear that cannot be explained by simply breaking bonds.
