Characterization Techniques for Organic Compounds. When we run a reaction in the laboratory or when we isolate a compound from nature, one of our first tasks is to identify the compound that we have obtained. There are a number of different analytical techniques that can be used to do this. We can compare its physical properties (melting point, boiling point, optical rotation, physical appearance, odor and taste) to a known compound to see if they are identical. This method is not terribly reliable. We can burn the compound, measure the amount of CO2, H2O, and other compounds that are produced, and use the proportions of the combustion products to determine an empirical formula. This method, elemental analysis, is the oldest method of organic structure determination. Elemental analysis is still used today, but it is a relatively crude method, used more to determine the purity of a compound whose structure is already known than to identify an unknown compound. The most widely used methods of organic compound identification today are those that measure the interactions of compounds with electromagnetic radiation of different wavelengths. Mass Spectroscopy. Mass spectrometry (MS) provides a means of measuring the molecular weight and determining the molecular formula of a compound. The MS experiment works as follows: a compound is vaporized and ionized, usually by bombardment with a beam of high-energy electrons, under vacuum. These electrons collide with the compound, knocking one or more electrons out of an orbital. A radical cation, a compound with one unpaired electron and a positive charge, is left behind. The radical cation is accelerated in an electric field and then passes into a magnetic field. The magnetic field causes the path of the positively charged compound to curve. The extent of curvature is determined by the mass to charge ratio, which is written as m/z. The detector, at the other end of the magnetic field, measures m/z by finding where the fragments emerge from the magnetic field. Usually z= 1, so the method provides a measure of the mass of the particle. The quantity of fragments emerging at a particular m/z ratio, the intensity, is also measured (see Fig 13.1). Electrons in the highest energy occupied molecular orbital (HOMO) are most likely to be ejected. Since they already have more energy than other electrons in the compound, it takes less energy to eject them. The HOMO is usually a lone pair or s bond, but it can be a p bond if there’s no other choice (note the order of decreasing energy). Electrons from O, N, S, and the halogens are usually ejected most readily. Note that the incomingelectron does not become part of the compound; one electron goes in but two electrons come out. After the radical cation is formed and before it travels through the detector, it may fragment, that is, break up into smaller pieces. Fragmentation is a characteristic reaction of radicals. Fragmentation occurs to give a neutral radical and an even-electron cation, and it usually occurs to give the stabler cation. When this happens, the cation is deflected through the magnetic field and detected while the neutral fragment is lost. Each compound has a characteristic fragmentation pattern. These are predictable, but we’re not going to worry about that. The m/z ratios and intensities of the fragments that are detected are usually presented as a bar graph with intensity on the y-axis and the m/z ratio on the x-axis. As I said, usually only one electron is ejected from each molecule, so the x-axis is usually thought of as the mass of the fragments. The most intense peak is called the base peak. The intensities of other peaks are measured as a percentage of the base peak. The heaviest peak that is observed is usually the molecular ion, M+·, which is the unfragmented compound. If M+· is very unstable or can fragment into very stable species, it may not be observed at all. On the other hand, if M+· can’t fragment into more stable species, it might be the base peak. The simplest piece of information that the mass spectrum can give us is the molecular weight and hence formula of a compound. This can easily be distinguished to a single atomic mass unit (amu). For example, M+· for propane MeCH2Me weighs 44 amu, while that for dimethyl ether Me2O weighs 46 amu. If we have a sample that is one or the other of these, we can easily identify it. Similarly, if a compound has a M+· of 110 amu, its molecular formula must either be C8H14, C7H10O, C6H6O2, or C6H10N2. (There are tables available that tabulate the possible formulas for a given molecular ion.) The molecular weight also gives a clue as to whether N atoms may be present. The nitrogen rule is the following: A compound has an odd molecular weight if and only if there are an odd number of nitrogen atomsin its formula. The nitrogen rule holds only for compounds containing H, C, N, O, Si, P, S, or any of the halogens, i.e. for any compounds we would see in this class. Every C-containing ion has a small peak accompanying it that weighs one mass unit more. The ratio of the intensities of the (M+) and (M+1) peaks is directly proportional to the number of C atoms in the ion. The peak is due to small amounts of naturally occurring 13C, which has 1.1% natural abundance. The intensity of the (M+1) peak allows one to determine exactly of how many C atoms a particular ion consists. For example, a C6 ion has a 6.6% probability of having one 13C atom in it, so its (M+1) peak is 6.6% of the intensity of the M+· peak. Other isotopes that are used to identify peaks include Cl (75% 35Cl, 25% 37Cl) and Br (50% 79Br, 50% 81Br). Natural H, N, O, F, and I consist almost exclusively of a single isotope (deuterium and tritium have very low natural abundance), so, among elements the most commonly encountered in organic compounds, we need only to worry about isotope peaks from C, Cl, and Br. The molecular ion is unfortunately not always observed. But we can also gain information from the fragmentation pattern. The fragmentation pattern constitutes a kind of "fingerprint" for a compound. Different structural isomers and even stereoisomers give different fragmentation patterns, so the fragmentation pattern can be used to distinguish different compounds that have the same molecular formula. The fragmentation pattern also provides evidence for and against certain structural elements in the unidentified compound. If the major fragments can be identified,