The molecular ion

The molecular ion represents the molecular mass of the compound. Specifically, the molecular mass is the sum of the masses of the most abundant isotope of each element present. You can derive an approximate formula for a compound based on its molecular mass, especially if only some or all of the following elements are present C, H, N, 0, F, or I. 

If the compound contains or may contain nitrogen, the nitrogen rule is applicable. According to this rule, any molecule with an odd number of nitrogen atoms has an odd mass. For example, in the compound N(CH3)3 the mass is 59 g/mole. 

In some cases the (M + 1) ion is important. The primary source of this ion is the presence of carbon-13. This isotope is about 1.1 percent of all the carbon atoms present. The relative intensities of the (M + 1) to the M ions indicates the number of carbon atoms present in the molecule. To determine the number of carbon atoms, you have to calculate the relative intensities of the (M + 1) peak, which you do by multiplying the intensity of the (M + 1) peak by (100/(intensity of the M peak)). Dividing the relative intensity of the (M + 1) peak by 1.1 gives the number of carbon atoms present in the formula. 

The presence of a chlorine or bromine atom results in an intense (M + 2) peak due to the presence of either two chlorine isotopes (chlorine-35 and chlorine-37) or two bromine isotopes (bromine-79 and bromine-81). In the case of chlorine, the (M + 2) peak is about one-third the intensity of the M  

Sulfur has a less obvious (M + 2) peak because the abundance of sulfur-34 is only 4.4 percent of sulfur-32. (A little sulfur-33 is also present, which contributes to the [M + 1] peak.) 

The molecular ion,, provides the most valuable information in the mass spectrum its mass and elemental composition show the molecular boundaries into which the structural fragments indicated in the mass spectrum must be fitted. Unfortunately, for some types of compounds the molecular ion is not sufliciently stable to be found in appreciable abundance in the El spectrum. An increasingly large proportion of mass-spectrometry facilities also have a soft ionization technique such as chemical ionization or fast-atom bombardment (Cl or FAB, Chapter 6) available. Such data should be used for molecular-weight assignment wherever possible. However, even with evidence from soft ionization, the unknown spectrum should still be examined as described in this chapter, since this should lead to useful structure information as well as verification of the M assignment. 

By convention, mass spectrometrists calculate the molecular weight (m/z of the molecular-ion peak) in terms of the mass of the most-abundant isotope of each of the elements present. For benzene (CgHg), which has substantial mjz 79 and m/z 80 peaks, the molecular ion is considered to be at mass 78 (C = 12, H = 1). for the molecule Brj is considered to be 158, twice the mass of the most-abundant isotope, Br, although in the mass spectrum of Br2 the most-abundant ion is at mjz 160 (Section 2.2). Within these constraints, in the El mass spectrum of a pure compound the molecular ion, if present, must be found at the highest value of m/z in the spectrum. There are further tests which must be used to ascertain if this peak does not represent the molecular ion, although these tests cannot demonstrate the converse. 

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When subjected to an electron bombardment whose energy level is much higher than that of hydrocarbon covalent bonds (about 10 eV), a molecule of mass A/loses an electron and forms the molecular ion, the bonds break and produce an entirely new series of ions or fragments . Taken together, the fragments relative intensities constitute a constant for the molecule and can serve to identify it this is the basis of qualitative analysis. 

SIMS is, strictly speaking, a destructive teclmique, but not necessarily a damaging one. In the dynamic mode, used for making concentration depth profiles, several tens of monolayers are removed per minute. In static SIMS, however, the rate of removal corresponds to one monolayer per several hours, implying that the surface structure does not change during the measurement (between seconds and minutes). In this case one can be sure that the molecular ion fragments are truly indicative of the chemical structure on the surface. 

If the molecules could be detected with 100% efficiency, the fluxes quoted above would lead to impressive detected signal levels. The first generation of reactive scattering experiments concentrated on reactions of alkali atoms, since surface ionization on a hot-wire detector is extremely efficient. Such detectors have been superseded by the universal mass spectrometer detector. For electron-bombardment ionization, the rate of fonnation of the molecular ions can be written as... 

While helium normally has a 0 valence, it seems to have a weak tendency to combine with certain other elements. Means of preparing helium difluoride have been studied, and species such as HeNe and the molecular ions He+ and He++ have been investigated. 

The main features are the molecular ions as the base peak and the M-t-1 ions arising from another species. For 2-aminothiazole the m/e 73 ion (M-HCN) is shifted to m/e 75 in the spectrum of the dideuteroamino derivative and, therefore, largely arises via rupture of 2-3 and 4-5 bonds (Scheme 18). This fragmentation process could involve the kind of intermediates postulated in photochemical rearrangements (see Chapter III, Section IX.3.B). The other fragments fit well the general pattern of fragmentation proposed by Clarke (136). 

During the course of biochemical studies (138). the mass spectrum of 2-acetamidothiazole was recorded its main peaks are the molecular ion (m/e= 142, relative intensity = 26%) and fragments 100 (100), 58 (2. 5), and 43 (39). For 2-acetamido-5-bromothiazole the main peak results again from the loss of C2H2O by the molecular ion. 2-AcetyIacet-amido-4-methylthiazole (2S) exhibits significant loss of from the... 

The 4-Hydroxy-thiazoles are characterized by infrared absorption near 1610 cm (KBr) (3) or 1620 to 16.S0cm (CCI4) (8), indicating a strongly polarized carbonyl group. H-5 resonates near 5.6 ppm in the NMR spectrum like similar protons in other mesoionic compounds (3). Two fragmentations of the molecular ion are observed in the mass spectra. The first involves rupture of the 1,2 and 3,4 bonds with loss of C2R 0S . In the second, the 1,5 and 3,4 bonds are cleaved with elimination of C2R 0. ... 

The mass spectra of more substituted thiazoles, or those with larger alkyl groups are more complex and involve other fragmentation patterns (117, 118, 374). The molecular ion is still abundant but decreases with increasing substitution past the ethyl group. 

For 4,5-dialkylthiazoles, the molecular ion decomposes by two competitive pathways, either loss of HCN followed by elimination of the radical R in the position /3 to the double bond of the resulting substituted thiirene, or by p cleavage followed by elimination of HCN (119). 

The spectra of alkylarylthiazoles generally possess fragmentation patterns similar to those previously mentioned for alkyl- and arylthiazoles. In this case, scission of the S-Cj and C3-C4 bonds of the thiazole ring can occur in ion fragments as well as in the molecular ion (124). 

We say the molecule AB has been ionized by electron impact The species that results called the molecular ion, is positively charged and has an odd number of electrons—it IS a cation radical The molecular ion has the same mass (less the negligible mass of a single electron) as the molecule from which it is formed... 

The mass spectrum of benzene is relatively simple and illustrates some of the mfor matron that mass spectrometry provides The most intense peak m the mass spectrum is called the base peak and is assigned a relative intensity of 100 Ion abundances are pro portional to peak intensities and are reported as intensities relative to the base peak The base peak m the mass spectrum of benzene corresponds to the molecular ion (M" ) at miz = 78... 

Benzene does not undergo extensive fragmentation none of the fragment ions m its mass spectrum are as abundant as the molecular ion... 

Not only the molecular ion peak but all the peaks m the mass spectrum of benzene are accompanied by a smaller peak one mass unit higher Indeed because all organic com pounds contain carbon and most contain hydrogen similar isotopic clusters will appear m the mass spectra of all organic compounds... 

Knowing what to look for with respect to isotopic clusters can aid in interpreting mass spectra How many peaks would you expect to see for the molecular ion in each of the following compounds At what m/z values would these peaks appear (Disregard the small peaks due to and )... 

Unlike the case of benzene in which ionization involves loss of a tt electron from the ring electron impact induced ionization of chlorobenzene involves loss of an elec tron from an unshared pair of chlorine The molecular ion then fragments by carbon-chlorine bond cleavage... 

Some classes of compounds are so prone to fragmentation that the molecular ion peak IS very weak The base peak m most unbranched alkanes for example is m/z 43 which IS followed by peaks of decreasing intensity at m/z values of 57 71 85 and so on These peaks correspond to cleavage of each possible carbon-carbon bond m the mol ecule This pattern is evident m the mass spectrum of decane depicted m Figure 13 42 The points of cleavage are indicated m the following diagram... 

FIGURE 13 42 The mass spectrum of decane The peak for the molecular ion is extremely small The most prominent peaks arise by fragmentation... 

Although GGMS is the most widely used ana lytical method that combines a chromatographic sep aration with the identification power of mass spectrometry it is not the only one Chemists have coupled mass spectrometers to most of the mstru ments that are used to separate mixtures Perhaps the ultimate is mass spectrometry/mass spectrome try (MS/MS) m which one mass spectrometer gener ates and separates the molecular ions of the components of a mixture and a second mass spec trometer examines their fragmentation patterns ... 

Mass Spectrometry The molecular ion peak is usually quite small m the mass spec trum of an alcohol A peak corresponding to loss of water is often evident Alcohols also fragment readily by a pathway m which the molecular ion loses an alkyl group from the... 

Mass Spectrometry Ethers like alcohols lose an alkyl radical from their molecular ion to give an oxygen stabilized cation Thus m/z 73 and m/z 87 are both more abun dant than the molecular ion m the mass spectrum of sec butyl ethyl ether... 

Mass Spectrometry Aldehydes and ketones typically give a prominent molecular ion peak m their mass spectra Aldehydes also exhibit an M— 1 peak A major fragmentation pathway for both aldehydes and ketones leads to formation of acyl cations (acylium ions) by cleavage of an alkyl group from the carbonyl The most intense peak m the mass spectrum of diethyl ketone for example is m z 57 corresponding to loss of ethyl radi cal from the molecular ion... 

Mass Spectrometry Aside from a peak for the molecular ion which is normally easy to pick out aliphatic carboxylic acids undergo a variety of fragmentation processes The dominant fragmentation m aromatic acids corresponds to loss of OH then loss of CO... 

First the peak for the molecular ion M for all compounds that contain only car bon hydrogen and oxygen has an m z value that is an even number The presence of a nitrogen atom m the molecule requires that the m z value for the molecular ion be odd An odd number of nitrogens corresponds to an odd value of the molecular weight an even number of nitrogens corresponds to an even molecular weight... 

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... 

Mass Spectrometry A peak for the molecular ion is usually quite prominent m the mass spectra of phenols It is for example the most intense peak m phenol... 

The peak at rn/z 70 corresponds to loss of water from the molecular ion The peaks at m/z 59 and 73 correspond to the cleavages indicated... 

Fragmentation pattern (Section 13 22) In mass spectrometry the ions produced by dissociation of the molecular ion... 

Molecular Identification. In the identification of a compound, the most important information is the molecular weight. The mass spectrometer is able to provide this information, often to four decimal places. One assumes that no ions heavier than the molecular ion form when using electron-impact ionization. The chemical ionization spectrum will often show a cluster around the nominal molecular weight. 

Characteristic Low-Mass Neutral Fragments from the Molecular Ion... 

Decomposition (fragmentation) of a proportion of the molecular ions (M +) to form fragment ions (A B+, etc.) occurs mostly in the ion source, and the assembly of ions (M +, A+, etc.) is injected into the mass analyzer. For chemical ionization (Cl), the Initial ionization step is the same as in El, but the subsequent steps are different (Figure 1.1). For Cl, the gas pressure in the ion source is typically increased to 10 mbar (and sometimes even up to atmospheric pressure) by injecting a reagent gas (R in Figure 1.1). 

The formation of a simple El mass spectrum from a number (p) of molecules (M) interacting with electrons (ep. Peak 1 represents M , the molecular ion, the ion of greatest mass (abundance q). Peaks 2, 3 represent A+, B. two fragment ions (abundances r, s). Peak 2 is also the largest and, therefore, the base peak. 

Simple fragmentation of the molecular ion of iodobenzene gives a fragment ion, CjH,. The difference in measured masses between the molecular and fragment ions gives the mass of the ejected neutral iodine atom. 

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