Molecule mass spectrum

Collision-induced dissociation mass spectrum of tire proton-bound dimer of isopropanol [(CH2)2CHOH]2H. The mJz 121 ions were first isolated in the trap, followed by resonant excitation of their trajectories to produce CID. Fragment ions include water loss mJz 103), loss of isopropanol mJz 61) and loss of 42 anui mJz 79). (b) Ion-molecule reactions in an ion trap. In this example the mJz 103 ion was first isolated and then resonantly excited in the trap. Endothennic reaction with water inside the trap produces the proton-bound cluster at mJz 121, while CID produces the fragment with mJz 61. 

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). 

It is well known that the electron-impact ionization mass spectrum contains both the parent and fragment ions. The observed fragmentation pattern can be usefiil in identifying the parent molecule. This ion fragmentation also occurs with mass spectrometric detection of reaction products and can cause problems with identification of the products. This problem can be exacerbated in the mass spectrometric detection of reaction products because diese internally excited molecules can have very different fragmentation patterns than themial molecules. The parent molecules associated with the various fragment ions can usually be sorted out by comparison of the angular distributions of the detected ions [8]. 

In contrast to IR and NMR spectroscopy, the principle of mass spectrometry (MS) is based on decomposition and reactions of organic molecules on theii way from the ion source to the detector. Consequently, structure-MS correlation is basically a matter of relating reactions to the signals in a mass spectrum. The chemical structure information contained in mass spectra is difficult to extract because of the complicated relationships between MS data and chemical structures. The aim of spectra evaluation can be either the identification of a compound or the interpretation of spectral data in order to elucidate the chemical structure [78-80],... 

There is a small peak one mass unit higher than M m the mass spectrum of ben zene What is the origin of this peak d What we see m Figure 13 40 as a single mass spectrum is actually a superposition of the spectra of three isotopically distinct benzenes Most of the benzene molecules contain only and H and have a molecular mass of 78 Smaller proportions of benzene molecules contain m place of one of the atoms or m place of one of the protons Both these species have a molecular mass of 79... 

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... 

The mass spectrum is a fingerprint for each compound because no two molecules are fragmented and ionized in exactly the same manner on electron-impact ionization. In reporting mass spectra the data are normalized by assigning the most intense peak (denoted as base peak) a value of 100. Other peaks are reported as percentages of the base peak. 

In GC-MS effluent from the column is introduced directly into the mass spectrometer s ionization chamber in a manner that eliminates the majority of the carrier gas. In the ionization chamber all molecules (remaining carrier gas, solvent, and solutes) are ionized, and the ions are separated by their mass-to-charge ratio. Because each solute undergoes a characteristic fragmentation into smaller ions, its mass spectrum of ion intensity as a function of mass-to-charge ratio provides qualitative information that can be used to identify the solute. 

If the substrate (M) is more basic than NHj, then proton transfer occurs, but if it is less basic, then addition of NH4 occurs. Sometimes the basicity of M is such that both reactions occur, and the mass spectrum contains ions corresponding to both [M + H]+ and [M + NH4]. Sometimes the reagent gas ions can form quasi-molecular ions in which a proton has been removed from, rather than added to, the molecule (M), as shown in Figure 1.5c. In these cases, the quasi-molecular ions have one mass unit less than the true molecular mass. 

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. 

Electron ionization occurs when an electron beam crosses an ion source (box) and interacts with sample molecules that have been vaporized into the source. Where the electrons and sample molecules interact, ions are formed, representing intact sample molecular ions and also fragments produced from them. These molecular and fragment ions compose the mass spectrum, which is a correlation of ion mass and its abundance. El spectra of tens of thousands of substances have been recorded and form the basis of spectral libraries, available either in book form or stored in computer memory banks. 

Molecules interact with electrons to give molecular and fragment ions, which are mass analyzed. A mass spectrum relates the masses of these ions and their abundances. 

An example of enhanced ion production. The chemical equilibrium exists in a solution of an amine (RNH2). With little or no acid present, the equilibrium lies well to the left, and there are few preformed protonated amine molecules (ions, RNH3+) the FAB mass spectrum (a) is typical. With more or stronger acid, the equilibrium shifts to the right, producing more protonated amine molecules. Thus, addition of acid to a solution of an amine subjected to FAB usually causes a large increase in the number of protonated amine species recorded (spectrum b). 

Schematic diagram of an orthogonal Q/TOF instrument. In this example, an ion beam is produced by electrospray ionization. The solution can be an effluent from a liquid chromatography column or simply a solution of an analyte. The sampling cone and the skimmer help to separate analyte ions from solvent, The RF hexapoles cannot separate ions according to m/z values and are instead used to help confine the ions into a narrow beam. The quadrupole can be made to operate in two modes. In one (wide band-pass mode), all of the ion beam passes through. In the other (narrow band-pass mode), only ions selected according to m/z value are allowed through. In narrow band-pass mode, the gas pressure in the middle hexapole is increased so that ions selected in the quadrupole are caused to fragment following collisions with gas molecules. In both modes, the TOF analyzer is used to produce the final mass spectrum.

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. 

In a mass spectrum, removal of an electron from a molecule (M) gives a molecular ion (Equation 38.1). The mass of an electron is very small compared with the mass of even the lightest element, and for all practical purposes, the mass of M +is the same as that of M. Therefore, mass measurement of a molecular ion gives the original relative molecular mass of the molecule. 

The interaction of electrons with molecules gives molecular ions, some of which can break down to give smaller fragment ions. The collection of molecular and fragment ions is separated by a mass analyzer to give a chart relating ion mass and abundance (a mass spectrum). 

Eventually, not only neutral solvent molecules but also ions start to desorb from the surface of each droplet, Ions, residual droplets, and vapor formed by electrospray are extracted through a small hole into two evaporation chambers (evacuated) via a nozzle and a skimmer, passing from there into the analyzer of the mass spectrometer, where a mass spectrum of the original sample is obtained. 

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. 

The size distribution of the clusters produced in the cluster source is quite smooth, containing no information about the clusters except their composition. To obtain information about, for example, the relative stability of clusters, it is often useful to heat the clusters. Hot clusters will evaporate atoms and molecules, preferably until a more stable cluster composition is reached that resists further evaporation. This causes an increase in abundance of the particularly stable species (i.e., enhancing the corresponding peak in the mass spectrum, then commonly termed fragmentation spectrum ). Using sufficiently high laser fluences (=50 /iJ/mm ), the clusters can be heated and ionized simultaneously with one laser pulse. 

Some classes of compounds aie so prone to fragmentation that the moleculai ion peak is very weak. The base peak in 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 conespond to cleavage of each possible cai bon-cai bon bond in the molecule. This pattern is evident in the mass spectrum of decane, depicted in Figure 13.42. The points of cleavage aie indicated in the following diagran ... 

Understanding how molecules fragment upon electron impact pennits a mass spectrum to be analyzed in sufficient detail to deduce the structure of an unknown compound. Thousands of compounds of known structure have been examined by mass spectrometry, and the fragmentation patterns that characterize different classes are well documented. As various groups are covered in subsequent chapters, aspects of their fragmentation behavior under conditions of electron impact will be described. 

FIGURE 5.23 Electrospmy mass spectrum of the protein, aerolysin K. The attachment of many protons per protein molecule (from less than 30 to more than 50 here) leads to a series of m/z peaks for this single protein. The inset shows a computer analysis of the data from this series of peaks that generates a single peak at the correct molecular mass of the protein. (Adapted from Figure 2 in Mann, M., and Wilm, M., 1995. Trends in Biochemical Sciences 20 219-224.)... 

The shift of m/e 88 in Figure 2 to m/e 90 in the mass spectrum (not shown) of the D20-exchanged analog 5a indicates that this fragment has the part of the original molecule shown in structure 12 rather than the part in structure 13, both of which add to 88. This assignment is... 

The 5-deoxy isomer, methyl 5-deoxy-/ -D-xt/Zo-furanoside (6), gives a mass spectrum (Figure 3) which contains no molecular-ion peak, but does contain peaks at m/e 117 [119] and m/e 116 [117] for the losses of the C-l methoxyl group and a molecule of methanol, respectively. 

Problem 12.4 1 List the masses of the parent ion and of several fragments you might expect to find in the mass spectrum of the following molecule ... 

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... 

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