6.1 Introduction
Before discussing fragmentation and interpretation, it is important to understand the many ways in which mass spectra can be utilized. For the analytical chemist, a mass spectrum is useful for two applications. The first is the relatively simple case when the analyst is looking for a particular compound in a sample and has a reference material to compare spectra. The second occurs when an analyst observes the presence of an unknown compound and wishes to identify it. The mass spectrum allows an experienced analyst to identify the compound, or at a minimum, narrow the possibilities down to a few compounds from millions of potential chemicals. Then, a reference standard can be more easily selected from this knowledge to confirm the identity of this unknown compound. A synthetic chemist encounters the same situation when synthesizing a previously analyzed product or when developing the synthesis of a new compound.
All four problems center on the same difficult task, identifying the structure of a compound under various conditions. There are three main instruments that perform this task for organic compounds, infrared spectroscopy, mass spectroscopy, and nuclear magnetic resonance (NMR). Often these three techniques are utilized in combination to identify a particular unknown; however each technique requires valuable time and resources. As a result, it is important that both synthetic and analytical chemists are able to select a tool that will identify their unknown in a quick and inexpensive fashion. The mass spectrometer has a few advantages over the other analytical methods. Mass spectrometry, when coupled with either gas or high pressure liquid chromatography, can analyze a complex mixture where NMR or IR spectroscopy fails. In addition, MS is the only tool that can determine the molecular mass of a compound. The most significant advantage for analytical chemists is that mass spectroscopy can elucidate structural information from an extremely small sample concentration (part per million quantities).
A distinctive advantage of MS over IR spectroscopy is that more structural information can be determined, though the information contained in a mass spectrum is more difficult to interpret. The MS can also acquire information more rapidly than the NMR. However, mass spectroscopy has a distinct disadvantage when analyzing compounds with multiple functional groups. For these types of compounds and when the analyst has milligram quantities of a relatively pure compound, NMR is usually the preferred analytical tool.
Based on these advantages and disadvantages, mass spectrometry is normally used to perform three tasks. The first is quantitative analysis when there is a small concentration of analyte. The second is identifying compounds that contain few functional groups, for example in bulk industrial synthesis. The third is confirming steps in a complex synthesis of a new product to determine the molecular mass and some structural information. In the third case, identification of newly developed compounds is always confirmed by NMR analysis.
When mass spectroscopy is selected as the appropriate analytical technique, the analysis must also select between gas and high pressure liquid chromatography. Gas chromatography has better resolution than high pressure liquid chromatography and is the preferred method of analysis for volatile and thermally stable compounds (up to 300 °C). Liquid chromatography is then utilized for all other compounds, notably thermally unstable and high molecular weight molecules. With the advent of capillary column HPLC, resolution in liquid chromatography has improved significantly. As a result, this chapter will focus upon interpreting structural information from the types of compounds commonly analyzed with GC-MS.
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