In electron ionization (EI) mass spectrometry, a small sample of a chemical compound is vaporized, bombarded with high energy electrons to ionize the sample, and the ions produced are detected based on the mass to charge (m/z) ratio of the ions. The electron ionization (EI) mass spectrum of an organic compound can provide valuable information regarding the molecular mass of the compound in question determined from the molecular ion (M+) signal (usually the most intense high molecular weight signal in the spectrum), and the presence (or absence) of a given functional group or groups plus structural details from an analysis of the major fragment ions revealed in the spectrum.
For many classes of organic compounds, however, the molecular ion is quite unstable and decomposes before it can reach the detector. As a result, molecular ions for these types of compounds are absent from the spectrum, and valuable information is lost. To overcome this potential problem, another type of mass spectrometry can be used. In chemical ionization (CI) mass spectrometry, the sample is vaporized along with a reagent gas, usually methane. The ionization chamber ionizes the methane and not the sample. Ion-molecule collisions result in the formation of CH5+, a strong Lewis acid. This acid can protonate the sample yielding an ion that is one mass unit heavier than the molecule itself. This new ion can be detected, resulting in an M+1 signal (which is the molecular weight of the sample plus one).
This tutorial is a summary of the common fragmentation pathways, induced by EI, of the more familiar organic functional groups. Understanding and applying the principles outlined below will provide an introduction to structural determination of organic compounds through mass spectrometry. It should be noted that the mechanisms described below are not exhaustively vetted. However, all are based on the application of sound chemical principles. While some may take issue with the proposed mechanisms, no one would argue that they are wholly without merit. Several mechanisms avoid the question of the location of a radical entirely (especially those mechanisms concerning the fragmentation of saturated hydrocarbons). These are less instructive, albeit safe, descriptions of fragmentation. In some cases, the exact nature of the radical cations produced from EI mass spectral analysis is not agreed upon. In these cases, proposed mechanisms are given in the spirit of providing complete and generally satisfying descriptions of molecular fragmentation.
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