Mass spectra, unknown, molecular

The importance of linked scanning of metastable ions or of ions formed by induced decomposition is discussed in this chapter and in Chapter 34. Briefly, linked scanning provides information on which ions give which others in a normal mass spectrum. With this sort of information, it becomes possible to examine a complex mixture of substances without prior separation of its components. It is possible to look highly specifically for trace components in mixtures under circumstances in which other techniques could not succeed. Finally, it is possible to gain information on the molecular structures of unknown compounds, as in peptide and protein sequencing (see Chapter 40). 

The nitrogen rule of mass spectrometry says that a compound with an odd number of nitrogen atoms has an odd-numbered molecular weight. Thus, the presence of nitrogen in a molecule is detected simply by observing its mass spectrum. An odd-numbered molecular ion usually means that the unknown... 

In summary, if the unknown mass spectrum has an intense peak at m/z 59 and an abundant m/z 72 with an odd molecular ion, this suggests a primary amide. 

The mass spectrum of the unknown compound showed a molecular ion at m/z 246 with an isotope pattern indicating that one chlorine atom and possibly a sulfur atom are present. The fragment ion at m/z 218 also showed the presence of chlorine and sulfur. The accurate mass measurement showed the molecular formula to be C]3FI7OSCl R + DB = 10. 

The molecular ions are detectable for all isomers except the 2,3-isomer, with the 3,4- and 3,5-isomers being the most abundant and the 2,6-isomer being the least abundant (2%). Because in the 2,3- and 2,6-isomers nitro groups are ortho to the methyl group, OH is readily lost at the expense of the molecular ion. If the molecular ion (m/z 182) is intense, the unknown mass spectrum is either the 3,4- or the 3,5-isomer. If the m/z 165 peak is very abundant then the mass spectrum represents the 2,3-, 2,4-, 2,5-, or a 2,6-isomer. 

Unknown 5. Can the ion of the highest mass be the molecular ion if the following series of fragment ions is detected in the high m/z region of the spectrum ... 

Unknown 17. Calculate mass spectrum in the region of the molecular ion for the sample of 4,7-difluoronaphthylmethylketone containing 10% of unlabeled, 20% di, 30% d2 and 40% d3 labeled molecules. 

The general procedure is to use reconstructed ion chromatograms at appropriate m/z values in an attempt to locate compounds of interest and then look at the mass spectrum of the unknown to determine its molecular weight. MS-MS can then be employed to obtain spectra from this and related compounds to find ions that are common to both and which may therefore contain common structural features. Having the same m/z value does not necessarily mean the ions are identical and further MS-MS data or the elemental composition may be required. If these data do not allow unequivocal structure identification, then further MS" information may be required. 

For example, to determine the empirical formula of di-n-octylphthalate, the daughter spectrum of the containing molecular ion (392) was obtained (Figure 7). The relative peak areas of adjacent peak pairs at m/z 149 and 150 is 2 1. This indicates that the M+1 ion is twice as likely to lose a atom as retain it. Thus the ratio of the number of carbon atoms lost to those retained is 2 1. Since the identified phthalate substructure contains 8 carbons, the unknown compound (di-n-octylphthalate) must contain 24 carbon atoms. These data, along with the molecular weight of 390 as determined from the conventional Cl mass spectrum of the unknown was fed into the empirical formula generator and the output was one empirical formula C24H38O4. 

In many cases, the results of the IR and mass spectrum interpretation are sufficient to allow a complete molecular structure to be deduced. In preliminary tests on 12 unknown compounds of molecular weight 100-200, the author, using the results reported by the program but without access to the original spectra, was able to correctly identify 9 of the unknowns. 

Searches through the MSSS data base can be carried out in a number of ways. With the mass spectrum of an unknown in hand, the search can be conducted interactively, as is shown in Figure 5. In this search the user finds that 24 data base spectra have a base peak (minimum intensity 100% maximum intensity 100%) and an m/e value of 344. When this subset is examined for spectra containing a peak at m/e 326 with intensity of less than 10%, only 2 spectra are found. If necessary, the search can be continued in this way until a manageable number of spectra are retrieved as fulfilling all the criteria that the user cited. These answers can then be listed as is shown. Alternatively, the data base can be examined for all occurrences of a specific molecular weight or a partial or complete molecular formula. Combinations of these properties can also be used in searches. Thus all compounds containing for example, five chlorines and whose mass spectra have a base peak at a particular m/e value can be identified. 

Some aspects of the chemistry of helicenes require still more attention. Since the interpretation of the mass spectrum of hexahelicene by Dougherty 159) no further systematic work has been done on the mass spectroscopy of helicenes, to verify the concept of an intramolecular Diels-Alder reaction in the molecular ion. Though the optical rotation of a number of helicenes is known and the regular increase of the optical rotation with increasing number of benzene rings has been shown, the dependence of the rotation on the helicity is still unknown. The asymmetric induction in the synthesis of helicenes by chiral solvents, or in liquid crystals, though small, deserves still more attention because application to other organic compounds will be promoted when the explanation of observed effects is more improved. 

Each mass spectrum has a story to tell. The molecular ion, M+ , tells us the molecular mass of an unknown. Unfortunately, with electron ionization, some compounds do not exhibit a molecular ion, because M+ breaks apart so efficiently. However, the fragments provide the most valuable clues to the structure of an unknown. To find the molecular mass, we can obtain a chemical ionization mass spectrum, which usually has a strong peak for MHH. 

In addition to forming molecular ions, organic molecules decompose into fragment ions in a mass spectrometer. As a result, a host of ions form that have a m/z less than that of the molecular ion. These ions give rise to the characteristic mass spectrum of the molecule. The fragmentation pattern of a molecule is characteristic of the molecule, and an unknown compound may be identified by comparison with a catalog of standard spectra. 

If the protein molecular weight is unknown, then the charge states are also not known. The process of determining the molecular weight for an unknown protein from such a mass spectrum is known as deconvolution and is based on simple algebra. If MW is the... 

In summary, the Py-FI mass spectrum shows a great diversity in the molecular rhizodeposit composition which could not be explained by previous chromatographic analyses of root exudates (e.g., Gransee and Wittenmayer, 2000). These focused mainly at the identification and quantification of a priori expected compounds (Fan et al., 2001). Therefore, Py-FIMS may contribute to the detection of previously unknown rhizodeposits and high-molecular-weight products of rhizodeposit interaction with genuine SOM compounds. 

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