Molecular structure mass spectra

Typical MS/MS configuration. Ions produced from a source (e.g., dynamic FAB) are analyzed by MS(1). Molecular ions (M or [M + H]+ or [M - H]", etc.) are selected in MS(1) and passed through a collision cell (CC), where they are activated by collision with a neutral gas. The activation causes some of the molecular ions to break up, and the resulting fragment ions provide evidence of the original molecular structure. The spectrum of fragment ions is mass analyzed in the second mass spectrometer, MS(2). 

Time-of-flight mass spectrometers have been used as detectors in a wider variety of experiments tlian any other mass spectrometer. This is especially true of spectroscopic applications, many of which are discussed in this encyclopedia. Unlike the other instruments described in this chapter, the TOP mass spectrometer is usually used for one purpose, to acquire the mass spectrum of a compound. They caimot generally be used for the kinds of ion-molecule chemistry discussed in this chapter, or structural characterization experiments such as collision-induced dissociation. Plowever, they are easily used as detectors for spectroscopic applications such as multi-photoionization (for the spectroscopy of molecular excited states) [38], zero kinetic energy electron spectroscopy [39] (ZEKE, for the precise measurement of ionization energies) and comcidence measurements (such as photoelectron-photoion coincidence spectroscopy [40] for the measurement of ion fragmentation breakdown diagrams). 

Multivariate data analysis usually starts with generating a set of spectra and the corresponding chemical structures as a result of a spectrum similarity search in a spectrum database. The peak data are transformed into a set of spectral features and the chemical structures are encoded into molecular descriptors [80]. A spectral feature is a property that can be automatically computed from a mass spectrum. Typical spectral features are the peak intensity at a particular mass/charge value, or logarithmic intensity ratios. The goal of transformation of peak data into spectral features is to obtain descriptors of spectral properties that are more suitable than the original peak list data. 

As we have just seen interpreting the fragmentation patterns m a mass spectrum m terms of a molecule s structural units makes mass spectrometry much more than just a tool for determining molecular weights Nevertheless even the molecular weight can provide more information than you might think... 

DDT resistant insects have the ability to convert DDT to a less toxic substance called DDE The mass spectrum of DDE shows a cluster of peaks for the molecular ion at m/z 316 318 320 322 and 324 Suggest a reasonable structure for DDE... 

A single instrument — a hybrid of a quadrupole and a TOF analyzer — can measure a full mass spectrum of ions produced in an ion source. If these are molecular ions, their relative molecular mass is obtained. Alternatively, precursor ions can be selected for MS/MS to give a fragment-ion spectrum characteristic of the precursor ions chosen, which gives structural information about the original molecule. 

The steps (reactions) by which normal ions fragment are important pieces of information that are lacking in a normal mass spectrum. These fragmentation reactions can be deduced by observations on metastable ions to obtain important data on molecular structure, the complexities of mixtures, and the presence of trace impurities. 

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). 

A diagrammatic illustration of the effect of an isotope pattern on a mass spectrum. The two naturally occurring isotopes of chlorine combine with a methyl group to give methyl chloride. Statistically, because their abundance ratio is 3 1, three Cl isotope atoms combine for each Cl atom. Thus, the ratio of the molecular ion peaks at m/z 50, 52 found for methyl chloride in its mass spectrum will also be in the ratio of 3 1. If nothing had been known about the structure of this compound, the appearance in its mass spectrum of two peaks at m/z 50, 52 (two mass units apart) in a ratio of 3 1 would immediately identify the compound as containing chlorine. 

By measuring a mass spectrum of normal ions and then finding the links between ions from the metastable ions, it becomes easier to deduce the molecular structure of the substance that was ionized originally. 

Oxetane, 2-(o -chlorobenzyl)-2-phenyl-X-ray crystal structure, 7, 366 Oxetane, 3-chloromethyl-3-ethyl-ring strain, 7, 370-371 Oxetane, 2-(o-chlorophenyl)- H NMR, 7, 367 Oxetane, 2-cyano-synthesis, 7, 391-392 Oxetane, 2-cyano-3,3-dimethyl-2-phenyl-thermolysis, 7, 372 Oxetane, 2,2-dialkoxy-synthesis, 7, 396 Oxetane, 2,2-dialkyl-isomerization, 7, 377 Oxetane, 3,3-dialkyl-alkylative cleavage, 7, 381 polymers, 7, 382 Oxetane, 2-diethylamino-synthesis, 7, 390 Oxetane, 3,3-difluoro-molecular dimensions, 7, 365 Oxetane, 2,2-dimethyl-mass spectra, 7, 368-369 photolysis, 7, 373 synthesis, 7, 393 Oxetane, 2,3-dimethyl- H NMR, 7, 366 thermolysis, 7, 372 Oxetane, 2,4-dimethyl-mass spectrum, 7, 369... 

Fullerenes are described in detail in Chapter 2 and therefore only a brief outline of their structure is presented here to provide a comparison with the other forms of carbon. The C o molecule, Buckminsterfullerene, was discovered in the mass spectrum of laser-ablated graphite in 1985 [37] and crystals of C o were fust isolated from soot formed from graphite arc electrodes in 1990 [38]. Although these events are relatively recent, the C o molecule has become one of the most widely-recognised molecular structures in science and in 1996 the codiscoverers Curl, Kroto and Smalley were awarded the Nobel prize for chemistry. Part of the appeal of this molecule lies in its beautiful icosahedral symmetry - a truncated icosahedron, or a molecular soccer ball, Fig. 4A. 

There is another oxygen-stabilized cation of mIz 87 capable of being formed by fragmentation of the molecular ion in the mass spectrum of sec-butyl ethyl ether. Suggest a reasonable structure for this ion. 

Figure 12.3 Mass spectrum of 2,2-dimethylpropane (C5Hi2 MW = 72). No molecular ion is observed when electron-impact ionization is used. (What do you think is the structure of the M+ peak at m/z = 57 )...

Because mass-spectral fragmentation patterns are usually complex, it s often difficult to assign structures to fragment ions. Most hydrocarbons fragment in many ways, as the mass spectrum of hexane shown in Figure 12.4 demonstrates. The hexane spectrum shows a moderately abundant molecular ion at m/z = 86... 

Structure of Oxy-F Compound F is extremely unstable and is difficult to obtain at a level of purity suitable for NMR studies. However, an oxidation product, Oxy-F, formed when F is left standing at — 20° C, is considerably more stable than F and can be purified to a sufficiently high level of purity. Oxy-F is nonfluorescent and shows absorption maxima at 237 nm and 275 nm (shoulder). The high-resolution FAB mass spectrum indicated the molecular formula of Oxy-F to be C33H3809N4Na2 [m/z 703.2363 (M + Na)+ and 681.2483 (M + H)"1"]. The H and 13C NMR data allowed the assignment of structure 7 to oxy-F (Fig. 3.2.6 Nakamura et al., 1988). 

GC/MS was used to distinguish between the two structures. The mass spectrum showed a molecular ion at m/z 260. The fragment ions occurred at m/z 245, 241, 231, and 205. This is a good example of nitrogen atom-influenced fragmentation therefore, structure I was highly favored. 

The mass spectrum of 2-methylbenzaldehyde suggests an aromatic compound because of the intensity of the molecular ion and peaks at m/z 39, 51, and 65 (see Figure 6.2). The loss of hydrogen atoms and loss of 29 Daltons from the molecular ion indicate that this is an aromatic aldehyde. Looking up m/z 91 in Part III suggests the following structure ... 

The identification of a molecular structure from a mass spectrum requires good chemical detective work. Let s see how that is done by trying to identify a simple compound,... 

MS-MS is a term that covers a number of techniques in which two stages of mass spectrometry are used to investigate the relationship between ions found in a mass spectrum. In particular, the product-ion scan is used to derive structural information from a molecular ion generated by a soft ionization technique such as electrospray and, as such, is an alternative to CVF. The advantage of the product-ion scan over CVF is that it allows a specific ion to be selected and its fragmentation to be studied in isolation, while CVF bring about the fragmentation of all species in the ion source and this may hinder interpretation of the data obtained. 

The MS-MS spectrum of the (M + H)+ ion from the parent drug contains an ion at m/z 465, the structure of which is indicated in Figure 5.40. The mass spectrum of metabolite 1 indicates that it has a molecular weight of 482 Da, while the MS-MS spectrum from its MH+ ion contains both an ion at m/z 466 and aXm/z 364, also present in that from the MH+ of the parent drug. It is not unreasonable, although not necessarily always correct, to assume that the ion of... 

The use of cone-voltage fragmentation (CVF) to obtain structural information was discussed earlier in Section 4.7.4 and the comment was made there that because this has the potential to bring about fragmentation of aU ions in the source of the mass spectrometer the spectra were often difficult to interpret. When the analyte under consideration is of a low molecular weight, its spectrum is likely to consist only of a few ions and CVF is of more practical value. 

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