Mass spectra, correlation with molecular structure

Fig. 11.3. Electron ionization and methane Cl mass spectra of toluene. The key features of the respective mass spectra are labeled. Spectral interpretation is based on recognition and understanding of these key features and how they correlate with structural elements of the analyte molecule of interest. The signal representing the most abundant ion in a mass spectrum is referred to as the base peak, and may or may not be the molecular ion peak (which carries the molecular mass information). Cl spectra provide confirmation of molecular mass in situations where the El signal for the molecular ion (M+ ) is weak or absent. The Cl mass spectrum provides reliable molecular mass information, but relatively little structural information (low abundance of the fragment ions). Compare with Fig. 11.4.

It is possible to derive structural information from the fragmentation pattern in a spectrum. The appearance of prominent peaks at certain mass numbers is empirically correlated with certain structural features. For example, the mass spectrum of an aromatic compound is usually dominated by a peak at m/z 91, corresponding to the tropylium ion. Structural information can also be obtained from the differences between the masses of two peaks in a spectrum. For instance, a fragment ion occurring 20 mass numbers below the molecular ion strongly suggests a loss of a HF moiety. Thus, a fluorine atom is likely to be present in the substance analyzed. 

The mass spectrum of a molecule is unique and can be stored in a computer. A match of the spectrum with those in the computer library is made in terms of molecular weight and the 10 most abundant peaks and a selection of possibilities will be presented. At this point you need to correlate all the information obtained from the spectroscopic techniques described in Chapters 26, 28, 29 and 30 together with the chemistry of the molecule to attempt to identify the structure of the molecule. 

The spectrum of a compound represents the molecular structure in the form of a complex code. Therefore, a relationship may be expected between spectrum and biological activity. Such a spectra-activity relationship assumes that the mechanism of biological activity is similar to the physical and chemical processes which produce spectra. This similarity is at least doubtful and the direct way of structure-activity relationships seems to be more promising. An attempt to correlate mass spectra with biological activity has led to violent replies in the literature. Controversies on this theme made many chemists very suspicious against applications of pattern recognition. 

Deduce the structure of the compound that gives the following H, and IR spectra (Figs. 9.51-9.53). Assign all aspects of the H, and spectra to the structure you propose. Use letters to correlate protons with signals in the NMR spectrum, and numbers to correlate carbons with signals in the spectrum. The mass spectrum of this compound shows the molecular ion at mlz 96. 

In this example, detection of all three ions as peaks generates what is known as a mass spectrum in which each ion is displayed by its mass for a charge of +1, as in Figure 14.5. Remember that mj is the ion with the heaviest mass and mg has the lightest mass. There are two scales in the mass spectrum. One is the relative abundance of each ion and the other is mJz. If 2 = +1, then each ion is directly correlated with its mass. The initially formed ion is called the molecular ion. The ion with the highest relative abundance (in this case, mj) is called the base ion B) and all other ions are recorded as a ratio of B. On this scale, mg has a relative abmi-dance of about 75% and mg is about 50% of R. The mass spectrometer effectively separates the three ions by their mass and records which ions are more abundant. The higher abundance ions will correlate with bonds in the same molecule that are most easily broken. This fact gives important structural information. 

Like any other problem involving the correlation of spectral data with structure, having a weU-defmed strategy for analyzing mass spectra is the key to success. It is also true that chemical intuition plays an important role as well, and of course there is no substitute for practical experience. Before diving into the mass spectrum itself, take an inventory of what is known about the sample. Is the elemental composition known Has the molecular formula been determined by exact mass analysis What functional groups are present in the compound What is the sample s chemical history For example, how has the sample been handled From what sort of chemical reaction was the compound isolated And the questions can continue. 

Since the reference mass spectra of known compounds have been run previously for a number of years, correlations of SI mass spectra with structure can be made for many of the common classes of organic compounds. Most of these correlations emphasize the spectral pattern or simple decomposition pathways to be expected for a particular molecular structure. This has led to the tabulation of mass spectral correlations to provide empirical and structural formulas of ions that might be found at a particular m/z in a mass spectrum, plus an indication of how each such ion might have arisen. Such a table has been reported elsewhere [10]. 

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