Recognizing the Molecular Ion

The recognition of a molecular ion in the mass spectrum is the most critical step to identifying an organic compound. This information provides the molecular mass and the elemental composition of the compound, in the absence of which it may be a losing battle to identify an unknown. At times, however, it is not easy to identify the molecular ion correctly because of the interference of background ions and due to the fact that many labile molecules with respect to ionization fail to yield the molecular ion at 70-eV ionization. The correct molecular ion must meet the following criteria  

It must be the most abundant ion in the high-mass cluster. In most cases this statement is true, but there are a few exceptions, especially when the compound contains more than two Cl atoms or one Br atom. For example, in the spectrum of CH2Br2, the most abundant ion in the molecular ion region is at m/z 174, although its molecular mass is 172 u. Also, for a few compounds, the (M — 1)+ ion is more abundant than the M+ ion. 

It must be an OE ion that is, it must be at an even miz value, except when the compound contains an odd number of nitrogens (see Section 6.4.3). 

According to common wisdom, if the molecular ion is in doubt, a Cl or ESI spectrum should be obtained. These techniques produce abundant EE or protonated molecule ions (MH+), from which the molecular ion can readily be discerned. 

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If some of the molecular ions remain intact long enough to reach the detector, we see a molecular ion peak. It is important to recognize the molecular ion peak because this gives the molecular weight of the... 

Example In the electron ionization mass spectmm of a hydrocarbon, the molecular ion peak and the base peak of the spectrum correspond to the same ionic species at m/z 16 (Fig. 1.2). The fragment ion peaks at m/z 12-15 are spaced at 1 u distance. Obviously, the molecular ion, M" , fragments by loss of H which is the only possibility to explain the peak at m/z 15 by loss of a neutral of 1 u mass. Accordingly, the peaks at lower m/z might arise from loss of a H2 molecule (2 u) and so forth. It does not take an expert to recognize that this spectrum belongs to methane, CH4, showing its molecular ion peak at m/z 16 because the atomic mass... 

The El mass spectra of thiols and thioethers also show a series of onium ions generated by a-cleavage of the molecular ion (Table 6.9). Sulfonium ions can easily be recognized from the isotopic pattern of sulfur (Fig. 6.9). The fragmentation patterns of thioethers will be discussed in greater detail later (Chap. 6.5.2 and 6.12.4). 

Note Phthalates, especially di-2-ethylhexyl phthalate (also known as dioctyl phthalate, DOP), are commonly used plasticizers in synthetic polymers. Unfortunately, they are extracted from the polymer upon exposure to solvents such as dichloromethane, chloroform or toluene, e.g., from syringes, tubing, vials etc. Therefore, they are often detected as impurities. They are easily recognized from their peaks at m/z 149 (often base peak), m/z 167, and [M-(R-2H)] m/z 279 in case of DOP). The molecular ion is often absent in their El spectra. 

Nitroarenes are recognized from their characteristic neutral losses due to the NO2 substituent. Normally, all theoretically possible fragment ions, the plausible [M-N02] and [M-O] ions as well as the unexpected [M-NO] ion, are observed. It is worth noting that molecular ions are 1,2-distonic by definition, because nitroarene molecules are best represented as zwitterion (Chap. 6.3). The molecular ion may either dissociate directly by loss of an oxygen atom or a NO2 molecule or it may rearrange prior to loss of NO. For the latter process, two reaction pathways have been uncovered, one of them involving intermediate formation of a nitrite, and the other proceeding via a three-membered cyclic intermediate. [208]... 

Mass analysis is a relatively simple technique, with the number of ions detected being directly proportional to the number of ions introduced into the mass spectrometer from the ion source. In atomic mass spectrometry the ion source produces atomic ions (rather than the molecular ions formed for qualitative organic analysis) which are proportional to the concentration of the element in the original sample. It was Gray who first recognized that the inductively coupled plasma would make an ideal ion source for atomic mass spectrometry and, in parallel with Fassel and Honk, and Douglas and French developed the ion sampling interface necessary to couple an atmospheric pressure plasma with a mass spectrometer under vacuum. 

You have little difficulty in recognizing the molecular formula as by convention listing the number of carbon atoms as the subscript to the initial C, then followed by the number of hydrogen and then other atoms in alphabetical order. The final suffix indicates the charge on the system and reconciles with the use of the term ion, and you will notice that the suffix reveals the presence of an unpaired electron. 

Electron ionization leads to fragmentation of the molecular ion, which sometimes prevents its detection. Chemical ionization (Cl) is a technique that produces ions with little excess energy. Thus this technique presents the advantage of yielding a spectrum with less fragmentation in which the molecular species is easily recognized. Consequently, chemical ionization is complementary to electron ionization. 

Mass spectra of most of these compounds are not reported and therefore their identification by Py-GC/MS analysis is difficult. Only a small number of them were recognized in Curie point pyrolysates of peptides. A study on glycyl dipeptides [11a] showed that a common electron impact ionization shows the molecular ion of dipeptides, and also the ion m/z =113 generated by the loss of substituents that takes place prior to ring fragmentation (except for Ala-Gly). 

The addition of a mass-signature element that contains a 1 1 ratio of one or more stable isotopes ( C, N. or H) splits the molecular ion into two equal peaks (similar to bromine). All compounds that contain the peak-splitting component are easily recognized in the spectrum as goalpost-like peaks separated by the mass difference between the natural and isotopically labeled components. The peak-splitting element provides a valuable means for recognition of the compounds synthesized on the solid phase. 

This theorem is recognized as an approximation as, apart from the inaccuracies inherent in the S.C.F. method (such as neglect of electron correlation and relativistic effects), it assumes that the molecular orbitals are the same for the molecule and the molecular ion. Many ASCF calculations have shown (see for example 14 16)) that if an electron is removed from a metal localized orbital, considerable charge migration towards the metal occurs this is termed relaxation. These relaxation effects give ionization energies smaller values than those expected on the basis of Koopmans theorem. For ionization from ligand based orbitals, relaxation effects are smaller and more constant. 

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