Owing to the poor vacuums available prior to the contributions of Gaede and Langmuir (see above), this subject was forced on the attention of early experimenters. They observed masses of 3 and 19, which could not have been produced by simple ionization and which arise from the following reactions, respectively:
These “problems” disappeared with improved vacuum. Ion-molecule reactions are important in understanding the chemistry of flames, of electrical discharges, of the upper atmosphere, and of samples subject to radiation. The mass spectrometer is the instrument of choice for such investigations.
Mass spectrometry has a critical role in organic chemistry. Its utility in chemical analysis was discussed earlier when describing appropriate experimental techniques. The same techniques can be used in determining the structure of complicated molecules, but perhaps of even greater value for such work are high-resolution measurements.
With a high-resolution mass spectrometer it is possible to carry out mass measurements on the molecular ion (or any other ion in the spectrum) to an accuracy of approximately one part in one million. This mass provides the best index for determining ionic formulas. The accurate masses of the ions C6H12+ and C4H4O2+ are, for example, 84.0939 and 84.0211, respectively, and these ions can easily be distinguished solely on the basis of their masses. Once the molecular formula is known it is possible to deduce the total of rings and double bonds making up the molecular structure and to begin to speculate on possible structural formulas. In order to deduce structural formulas from molecular formulas, it is essential to study the fragment ions in the mass spectrum. It is still not possible to predict definitively the fragmentation patterns for organic molecules, but many semi-empirical rules of fragmentation are known, and it is usually possible to pick out peaks in the spectrum that are characteristic of particular chemical groups. The technique is valuable in that it is generally not necessary to know any details of the composition of the unknown compound in order to deduce a complete or partial structure. Only a small quantity of compound, a hundred micrograms or less, is necessary for an analysis.
Using a computer coupled to a high-resolution mass spectrometer, about 1,000 mass peaks per minute can be plotted at a resolving power of up to 20,000, accurate measurements can be made on each peak, and peak heights and ion compositions can be printed out in the form of an “element map” to aid in the interpretation of the spectrum. It is also possible for the computer to carry out many of the logical steps in reducing the data that lead to structural elucidation.
Continuous sampling of the materials contained in a reaction vessel, followed by analysis with a mass spectrometer, has been used to identify and measure the quantity of intermediate species formed during a reaction as a function of time. This kind of analysis is important, both in suggesting the mechanism by which the overall reaction takes place and in enabling the detailed kinetics of reactions to be resolved.
Isotopic labeling is widely used in such studies. It can indicate which particular atoms are involved in the reaction; in rearrangement reactions it can show whether an intramolecular or intermolecular process is involved; in exchange reactions it can show that particular atoms of, for example, hydrogen are exchanging between the reacting species. Labeling is also widely used in mass-spectrometric research to give information about the fragmentation reactions occurring in the mass spectrometer.
Fields of investigation that employ mass spectrometry include studies of protein structure, drug metabolism, flavour and smell, petroleum and petrochemicals, organic fossils, inherited metabolic diseases, atmospheres and respiratory gases, and many other highly specialized subjects.