Mass Spectrometry The substance being analyzed (solid or liquid) is injected into the mass spectrometer and vaporized at elevated temperature and reduced pressure. The gaseous molecules are bombarded with high-energy electrons, which convert some of the molecules into positively charged ions. Magnetic and electric fields in the spectrometer separate the ions according to their mass/charge ratios (m/z). The vast majority of the ions generated carry only a single positive charge, i.e. z = 1, so m/Z represents the molecular mass of the ions detected. The spectrometer displays a spectrum of peak intensity (y-axis) versus m/z (x-axis). The peak intensity is shown as a % (relative to the abundance of the most abundant peak (the base peak, which is set as 100%).

Diagram of a Simple Mass Spectrometer, Showing the Separation of Neon Isotopes

Interpretation of Mass Spectra. The most important information obtained is the integral molecular weight of the compound. i.e. the mass in the largest fragment. The integral molecular weight is obtained from the molecular ion peak of the compound, designated as m +. This will appear at the high end (to the right hand side) of the m/z scale. Two molecular ion peaks may be found when the parent compound contains an element having two abundant isotopes (e.g. Cl and Br). In some instances a molecule will not show a molecular ion peak (because it has decomposed into smaller fragments) or its intensity will be too low to be recorded.

Determination of Molecular Structure from Fragmentation Pattern. The molecular structure can often be deduced from the masses of the fragments obtained from the breakdown of the compound into smaller fragments, i.e. from the fragmentation pattern. Higher mass fragments are usually more important than smaller ones for structure determination. Each major peak identifies a particular mass fragment. Intense peaks correspond to high probability fragments. Rearrangements of ionized fragments, to structures not obviously related to the parent compound, can sometimes complicate the analysis. The fragmentation pattern obtained depends on the activation energy for bond cleavage (  bond energy) and on the stability of the resulting positive ion. The stability of the positive ion is generally of greatest importance. It will depend on the effectiveness with which the positive ion fragment can delocalize its charge.

Intensity (% of Base Peak) m / z CH 2 OH + M - (H 2 O and CH 2 =CH 2) M - (H 2 O and CH 3 ) M - H 2 O M Molecular Ion Peak Base Peak

Isotope Peak Rules When the parent compound contains an element that has more than one stable abundant isotope, more than one peak will be found for each fragment containing this element. Although nearly all elements occur naturally as a mixture of isotopes, for the lighter elements of interest in organic chemistry (H, C, N, O), one isotope, the lighter one, predominates. Since the abundances of 79 Br and 81 Br are 50.5% and 49.5%, two peaks of nearly equal intensity, separated by two mass units, will occur for all bromine-containing fragments. e.g. in the spectrum of CH 3 Br, two peaks of nearly equal intensity will occur at m/e values of 94 and 96, corresponding to (CH 3 79 Br) + and (CH 3 81 Br) +. Since the abundances of 37 Cl and 35 Cl are 24.6% and 75.4%, two peaks with an intensity ratio of 1:3, separated by two mass units will occur in a mass spectrum of a compound containing a single Cl atom.

The Nitrogen Rule The integral molecular weight of the majority of organic compounds (containing the lighter elements H, C, N, O, P, S, Cl, Br, I) will be an even number, except for those containing an odd number of N atoms. The appearance of an odd number for the integral molecular weight of the molecular ion indicates that the compound contains an odd number of N atoms.