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Chapter: Organic Chemistry: Organic spectroscopy and analysis

Mass spectroscopy

A mass spectrum is obtained by ionizing a molecule to give a molecular ion.


Key Notes


A mass spectrum is obtained by ionizing a molecule to give a molecular ion. This is then accelerated through a magnetic field and the ion is deviated according to its mass and charge. Routinely, ionization is carried out by electron ionization, but chemical ionization and fast atom bombardment are milder methods. Detecting the molecular ion allows identification of the molecular weight. If this is an odd number it indicates that an odd number of nitrogen atoms are present.

Isotopic ratios

The pattern of peaks present for a molecular ion can reveal the presence of chlorine or bromine since there are two naturally occurring isotopes for these elements. Carbon also has two naturally occurring isotopes (12C and 13C) and so a small peak is often observed one mass unit higher than the molecular ion.

Fragmentation patterns and daughter ions

The molecular ion is unstable and fragments, producing daughter ions. The fragmentation patterns that take place are indicative of functional groups in the molecule. Daughter ions vary in stability and the more stable ones give stronger peaks. The most intense peak in the spectrum is called the base peak.

Analysis of a mass spectrum

The molecular ion and base peak are identified first. Daughter ions are then identified and fragmentation patterns determined.

High-resolution mass spectroscopy

High-resolution mass spectroscopy is used to measure the mass of a molecular ion to four decimal places. This allows the determination of the molecular formula002E



Mass spectroscopy is useful in the analysis of an organic compound since it can provide information about the molecular weight, the presence of specific elements (e.g. nitrogen, chlorine or bromine) and the presence of specific functional groups. Put at its simplest, a mass spectrum measures the mass of ions, but to be more precise, it is a measure of the mass/charge ratio (m/e). However, the vast majority of ions detected are singly charged (e=1). In order to obtain a mass spectrum, the molecules of the test compound have to be ionized under reduced pressure. Thereare several ways in which this can be carried out, but the most common method is known as electron ionization (EI)

Electron ionization involves bombarding the test molecule with high-energy electrons such that the molecule loses an electron and ionizes to give a radical cation called a molecular ion (also called the parent ion). This molecular ion is then accelerated through a magnetic field towards a detector. The magnetic field causes the ion to deviate from a straight path and the extent of deviation is related to mass and charge (i.e. the lighter the ion the greater the deviation). Assuming a charge of 1, the deviation will then be a measure of the mass. The mass can then be measured to give the molecular weight.

The mass of a molecular ion must be even unless the molecule contains an odd number of nitrogen atoms. This is because nitrogen is the only ‘organic’ element with an even mass number and an odd valency. Therefore, an odd numbered mass for a molecular ion is an indication of the presence of at least one nitrogen atom.

Sometimes, the molecular ion is not observed in the spectrum. This is because electron ionization requires compounds to be vaporized at high temperature and the molecular ion may fragment before it can be detected. In cases like this, it is necessary to carry out the ionization under milder conditions such that the mole-cular ion is less likely to fragment (i.e. by chemical ionization or by fast atombombardment). You may ask why these milder conditions are not used routinely.The reason is that fragmentation can give useful information about the structure of the molecule (see below).

The molecular ion peak is usually strong for aromatic amines, nitriles, fluorides and chlorides. Aromatic and heteroaromatic hydrocarbons will also give intense peaks if there are no alkyl side chains present greater than a methyl group. How-ever, the peaks for molecular ions can be absent for long chain hydrocarbons, highly branched molecules, and alcohols.

Isotopic ratios     

The pattern of peaks observed for a molecular ion often indicates the presence ofparticular halogens such as chlorine or bromine. This is because each of these elements has a significant proportion of two naturally occurring isotopes. Since the position of the peaks in the mass spectrum depends on the mass of each individual molecular ion, molecules containing different isotopes will appear at different positions on the spectrum. Chlorine occurs naturally as two isotopes (35Cl and 37Cl ) in the ratio 3 : 1. This means that the spectrum of a compound containing a chlorine atom will have two peaks for the molecular ion. The two peaks will be two mass units apart with a ratio of 3 : 1. For example ethyl chloride

will have two peaks for C2H535Cl and C2H537Cl at m/e 64 and 66 in a ratio of 3 : 1. The naturally abundant isotope for carbon is 12C. However, the 13C isotope is also present at a level of 1.1%. This can result in a peak one mass unit above the molecular ion. For methane, the relative ratios of the peaks due to 12CH4 and 13CH4 is 98.9 : 1.1, and so the peak for 13CH4 is very small. However, as the number of car-bon atoms increase in a molecule, there is a greater chance of a molecule contain-ing a 13C isotope. For example, the mass spectrum for morphine shows a peak at m/e 308 and a smaller peak at m/e 309 which is about a fifth as intense. The peak at m/e 308 is due to morphine containing carbon atoms of isotope 12. The peak at 309 is due to morphine where one of the carbon atoms is 13C (i.e. 13C12C16H18NO3). The intensity of the peak can be rationalized as follows. The natural abundance of 13C is 1.1%. In morphine there are 17 carbon atoms and so this increases the chances of a 13C isotope being present by a factor of 17. Hence, the peak at 309 isapproximately 18% the intensity of the molecular ion at 308.

Fragmentation patterns and daughter ions

The molecular ion is not the only ion detected in a mass spectrum. The molecularion is a high-energy species, which fragments to give daughter ions that are alsodetected in the spectrum. At first sight, fragmentation may seem to be a random process,but fragmentation patterns are often characteristic of certain functional groups and demonstrate the presence of those groups.

Due to fragmentation, a mass spectrum contains a large number of peaks of varying intensities. The most intense of these peaks is known as the base peak and is usually due to a relatively stable fragmentation ion rather than the molecular ion. Examples of stable ions are the tertiary carbonium (R3C+), allylic (=C-CR2+), benzylic (Ar-CR2+), aromatic (Ar+), oxonium (R2O+) and immonium (R3N+) ions.

It is not possible to explain every peak observed in a mass spectrum and only the more intense ones or those of high mass should be analyzed. These will be due to relatively stable daughter ions. Alternatively, a fragmentation may result in a stable radical. The radical being neutral is not observed, but the other half of the fragmentation will result in a cation which is observed.

Many fragmentations give a series of daughter ions that are indicative of a particular functional group. In other words, the molecular ion fragments to a daughter ion, which in turn fragments to another daughter ion and so on.

The intensity of a peak may sometimes indicate a favored fragmentation route. However, care has to be taken since intense peaks can arise due to different frag-mentation routes leading to the same ion, or be due to different fragmentation ions of the same m/e value.

Analysis of amass spectrum

To illustrate the analysis of a mass spectrum, we shall look at the simple alkanenonane (Fig. 1).

Nonane has a molecular formula of C9H20  and a molecular weight of 128. Theparent ion is the molecular ion at 128. There is a small peak at m/e 129, which is due to a molecule of nonane containing one 13C isotope (i.e. 12C813CH20). The nat-ural abundance of 13C is 1.1%. Therefore the chances of a 13C isotope being present in nonane are 9 × 1.1% = 9.9%.

The base peak is at m/e 43. This is most likely a propyl ion [C3H7]+. There are peaks at m/e 29, 43, 57, 71, 85 and 99. These peaks are all 14 mass units apart which corresponds to a CH2 group. The presence of a straight chain alkane is often indicated by peaks which are 14 mass units apart (Fig. 2).

The characteristic peaks for a straight chain alkane are 14 mass units apart, but this does not mean that the chain is being ‘pruned’ one methylene unit at a time. Decomposition of carbocations occurs with the loss of neutral molecules such as methane, ethene and propene, and not by the loss of individual methylene units. For example, the daughter ion at m/e 99 can fragment with loss of propene to give the ion at m/e 57. The daughter ion at m/e 85 can fragment with loss of ethene or propene to give the ions at m/e 57 and m/e 43 respectively. The daughter ion at m/e 71 can fragment with loss of ethene to give the ion at m/e 43.

There are significant peaks at m/e 27 and m/e 41. These peaks result from dehydrogenation of the ions at m/e 29 and m/e 43 respectively. The peak at m/e 41 can also arise from the ion at m/e 57 by loss of methane.

The most intense peaks in the mass spectrum are at m/e 43 and m/e 57. The ions responsible for these peaks [C3H7]+ and [C4H9]+ can arise from primary frag-mentations of the molecular ion itself, as well as from secondary fragmentations of daughter ions (m/e 99 to m/e 57; m/e 85 to m/e 43; m/e 71 to m/e 43).

In mass spectroscopy, the ions responsible for particular peaks are enclosed in square brackets. This is because it is not really possible to specify the exact struc-ture of an ion or the exact location of the charge. The ionization conditions used in mass spectroscopy are such that fragmentation ions can easily rearrange to form structures more capable of stabilizing the positive charge. For example, the frag-mentation ion at m/e 57 arising from primary fragmentation is a primary carbo-cation, but this can rearrange to the more stable tertiary carbocation (Fig. 3).

High-resolution mass spectroscopy

The molecular weight is measured by mass spectroscopy and is usually measuredas a whole number with no decimal places. However, it is possible to measure themolecular weight more accurately (high resolution mass spectroscopy) to four decimal places and establish the molecular formula. Consider the molecules CO, N2, CH2N and C2H4

All of these molecules have the same molecular weight of 28 and in a normal mass spectrum would produce a molecular ion of that value. In a high-resolution mass spectrum, the molecular ion is measured to four decimal places and so we have to consider the accurate atomic masses of the component atoms. The accurate mass values for the ions are as follows:

If the measured mass of the molecular ion is 28.0076, this would be in line with the theoretical accurate mass for nitrogen (i.e. 28.0062). Note that the peak being measured in the mass spectrum is for the molecular ion. This ion contains the most abundant isotope of all the elements present. For example, the molecular ion for carbon monoxide is made up of 12C and 16O only. There are no molecules pre-sent containing 13C or 17O since these would occur at a higher position in the mass spectrum. Therefore, the theoretical values for the molecular weight are calculated using the atomic weights for specific isotopes and not the accurate atomic weights of the elements as they occur in nature. The latter (relative atomic weights) take the relative abundances of the different isotopes into account and will be different in value. For example, the accurate atomic weight of the carbon isotope 12C is 12.0000 and this is the value used for calculating the accurate mass of a molecular ion. The accurate relative atomic weight of carbon is higher at 12.011 due to the presence of the isotope 13C.


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