Mass-spectrometry

Mass-spectral fragmentation of cholesterol and its analogues with A -unsaturation pathways to account for (M —85) and (M 111) ions 

Mass-spectral fragmentation of 5 -steroidal 1-enes, including a quasi-thermal retro-Diels-Alder cleavage 

Mass spectra of the classical and nonclassical thienothiophenes as well as thieno[3,4-c]pyrrole derivatives were discussed in the first edition 84CHEC-i(4)i037 . Other A,B-diheteropentalenes were not mentioned. 

Mass spectral studies of organophosphorus compounds, published up to 1973, have been reviewed, as have the problems involved in the use of mass spectral data for the detection of phosphinidenes. However, peaks corresponding to the phosphini-dene (183) were the most intense peaks in the spectra of the phenylenediamine compounds (184) and their sulphides. A considerable amount of work has been carried 

Field desorption mass spectrometry has been successfully applied to mono- and bis-alkyl- and -alkenyl-triphenylphosphonium salts (187). The phosphonium cation gave rise to the base peaks.  

There has been keen interest in ion-molecule reactions. Cyclotron resonance spectroscopy showed that methylphosphines, the fluorides (188 =1 or 2),  

Koketsu, K. Ohashi, and Y. Ishii, Chubu Kogyo Daigaku Kiyo, 1975, llA, 85. 

The pJ a values of phosphine oxides have been measured. Their deviation from Hammett base behaviour, their Ho dependencies, and their sites of protonation have been studied. The acidifying effects of phosphoryl, phosphinyl, and thiophosphinyl groups have been studied. Ionization constants have been used to examine substituent effects in alkanephosphonic acids and phosphinyl-carboxylic acids, structural correlations in various phosphorus acids, and solvent effects on the properties of thiophosphorus acids. The linear free-energy relationships, which are based mainly on p a data, have been analysed and reviewed.  

Mass spectrometric methods are routinely used to characterise a wide variety of biopolymers, such as proteins, polysaccharides, and nucleic acids. Nevertheless, despite its advantages, MS has been under utilised in the past for studying synthetic polymer systems. It is fair to say that, until recently, polymer scientists have been rather unfamiliar with the advances made in the field of MS. 

However, MS in recent years has rapidly become an indispensable tool in polymer analysis, and modern MS today complements in many ways the structural data provided by NMR and IR methods. Contemporary MS of polymers is capable of changing the 

Some of the most significant applications of modern MS to synthetic polymers are (a) chemical structure and end-group analysis, (b) direct measurement of molar mass and molar mass distribution, (c) copolymer composition and sequence distribution, and (d) detection and identification of impurities and additives in polymeric materials. 

In order to analyse any material by MS, the sample must first be vapourised (or desorbed) and ionised into the instrument s vacuum system. Since polymers are generally nonvolatile, many mass spectral methods have involved degradation of the polymeric material before analysis of the more volatile fragments. 

Two traditional methods to examine polymers have been flash-pyrolysis GC-MS and direct pyrolysis in the ion source of the instrument. 

The mass spectra of compounds described in this chapter usually show the molecular ion in traditional techniques. For instance, 10 shows the molecular ion peak 237 (MH+) by FAB. Other mass spectroscopy techniques have been successfully used for compounds in this class, such as electrospray ionization (ESI) (MNa+) 2006T9043 or El (M+) 2000BMC557 . Nowadays mass spectroscopy has become a common tool in organic chemistry and mass spectral data are presented for most structures described in this chapter. 

The mass spectrum (70 eV E.I.) of phosgene has been recorded (Table 7.5), and is totally unremarkable [lb,934a,1071]. 

The mass spectra of methoxydimethylphosphine (182 X = O) and the corresponding sulphur compound (182 X = S) show base peaks corresponding to PO+ and MePS+ respectively. Whereas the methoxyphosphine also shows a fragmentation path commencing with loss of a methoxy-group, the positive ions from the sulphur derivative show a strong tendency to 

Lumbroso, C. Pigenet, A. Arcoria, and G. Scarlata, Bull. Soc. chim. France, 1971, 3838. 

The appearance potentials of a series of phosphine oxides (186 R = propyl, propenyl, or propynyl) are all similar to that of acetone, which supports the postulate that the predominant ionization is loss of an electron from oxygen. The fragmentation patterns were examined to see if there is a relationship with alkaline cleavage. The ion at m/e 92 is the base peak in the spectrum of (186 R = propyl) and is attributed to the 

The mass spectra are also reported for the thiophosphates (192), derivatives of dimethylphosphinic acid (193), and the phosphadiazoles 

Mass spectra have been used to identify the position of 0 labels in phosphinic acid derivatives and to estimate the content of inorganic phosphate after silylation. The molecular distance between silylated phosphate groups and/or silylated hydroxy-groups has been estimated from the abundance of the rearrangement ions (195) and (196).  

In a mass spectrometer, ions are produced from a sample and separated according to their mass-to-charge ratio (m/z) and then recorded in terms of 

Mass spectrometry (MS) is probably a famhiar tool to chemistry and biology students as a technique commonly used to measure the molecular mass of a sample. Often, MS is used in tandem with other techniques for chromatic separation of the sample before mass measurement. Some common hyphenated techniques include HPLC-MS, high-pressure liquid chromatography coupled to MS GC-MS, gas chromatography coupled to MS or CE-MS, capillary electrophoresis coupled to MS. 

Mass spectrometry studies on proteins can determine the purity of the sample, verify amino acid substitutions in mutants, detect post-translational modihcations, or calculate the number of disulfide bridges. Amino acid 

Usually the number of charges on an ion will not be known, but it can be calculated using a formula based on two different ions appearing in the spectrum. Actually, the molecular mass of a sample can be calculated automatically, or semiautomatically, by the processing software associated with the mass spectrometer. Experimentally, the automatic calculation of molecular mass is very helpful because a complex peptide or protein mixture will display an m/z spectrum with several overlapping series of multiply charged ions. 

Peptide and protein sequencing and its importance in the proteomics field were discussed in Section 2.2.3. The following gives a brief description of the mass spectrometry methods used to achieve sequencing. First, to produce protein or oligonucleotide structural/sequence information by mass spectro-metric techniques, one needs to use tandem mass spectrometry (MS-MS). In this technique, a sample is first fragmented and analyzed in one mass spec- 

A protein identification study might proceed in the following manner. Pirst, the protein is analyzed by mass spectrometry to determine its molecular mass to within 0.01%. Second, the protein is digested with an enzyme, commonly trypsin. The enzyme trypsin cleaves polypeptide chains at points following lysine and arginine residues. Using this proteolytic enzyme ensures that each 

Mass spectrometry provides a more direct and precise technique to study histone modifications. As with the other methods discussed above, mass spectrometry also has several pitfalls that should be taken into account when analyzing histone modifications. First of all histones and especially the core histones H3 and H4 are rich in lysine residues. Consequently, trypsin as an enzyme that is routinely used for the identification of proteins via peptide mass fingerprints cannot be used for regular in gel digestion of histones. Other enzymes that have a different specificity (such as Asp-N or Arg-C) are more frequently used in the analysis of histones [25]. A drawback 

The use of different approaches to study complex histone modification patterns ranging from the bottom up approach that allows a detailed and quantitative measurement of particular histone modifications to the top down methods that help the dissection of interdependencies between different modifications will greatly facilitate the analysis of complex modification patterns and provide a deeper insight into the biological role of these patterns. 

1 Walsh, C.T. (2005) Posttranslational Modfcations of Proteins, Roberts Company Publishers, p. 576. 

2 Mann, M. and Jensen, O.N. (2003) Proteomic analysis of post-translational 

Williams, K.L. and Hochstrasser, D.F. (1999) High-throughput mass spectrometric discovery of protein post-translational modifications. Journal of Molecular Biology, 289, 645-657. 

Mass spectrometry is used to measure the molecular mass of a compound and provides a method to obtain the molecular formula. It differs from the other instrumental techniques presented thus far because it does not involve the interaction of electromagnetic radiation with the compound. Instead, molecules of the compound being studied are bombarded with a high-energy beam of electrons in the vapor phase. When an electron from the beam impacts on a molecule of the sample, it knocks an electron out of the molecule. The product, called the molecular ion (represented as A/f), has the same mass as the original molecule but has one less electron. It has both an odd number of 

CHAPTER I 5 ULTRAVIOLET-VISIBLE SPECTROSCOPY AND MASS SPECTROMETRY 

Because the electron beam is highly eneigetic, many of the molecular ions are formed with considerable excess energy. Fragmentation of the molecular ions with excess energy produces a number of other cations and radicals. 

The mass spectrum is a report of the relative numbers or abundances of ions of each mlz that are detected, and it is often presented in the form of a bar graph. The most abundant ion, the base ion, is assigned a value of 100, and the amounts of the other ions are expressed as percentages of this. A mass spectrum for benzene is shown in 

Mass spectrometry is a technique used for measuring the molecular weight and determining the molecular formula of an organic molecule. 

The term spectroscopy is usually used for techniques that use electromagnetic radiation as an energy source. Because the energy source in MS is a beam of electrons, the term mass spectrometry Is used instead. 

The species formed is a radical cation, symbolized M . It is a radical because it has an unpaired electron, and it is a cation because it has one fewer electron than it started with. 

A mass spectrometer analyzes the masses of individual molecules, not the weighted average mass of a group of molecules, so the whole-number masses of the most common Individual isotopes must be used to calculate the mass of the molecular ion. Thus, the mass of the molecular ion for CH4 should be 16. As a result, the mass spectrum of CH4 shows a line for the molecular ion—the parent peak or M peak—at miz =16. 

The tallest peak in a mass spectrum is called the base peak. For CH4, the base peak is also the M peak, although this may not always be the case for all organic compounds. 

Mass spectrometry (MS) involves the bombardment of molecules, in the gas phase, with electrons. An electron is lost from the molecule to give a cation, the molecular ion (M ), which then breaks down in characteristic ways to give smaller fragments, which are cations, neutral molecules and uncharged radicals (Fig. 30.1). 

The mixture of molecular ion and fragments is accelerated to specific velocities using an electric field and then separated on the basis of their different masses by deflection in a magnetic or electrostatic field. Only the cations are detected and a mass spectrum is a plot of mass-to-charge ratio (w/z) on the x-axis against the number of ions (relative abundance, RA, %) on the y-axis. A schematic of the components of a mass spectrometer is shown in Fig. 30.2 and an example of a line-graph-type mass spectrum in Fig. 30.3. 

There are many types of mass spectrometer, from high-resolution double-focusing instruments, which can distinguish molecular and fragment masses to six decimal places, to bench-top machines with a quadrupole mass detector which can resolve masses up to about m/z = 500, but only in whole-number differences. Routinely you are most likely to encounter data from bench-top instruments and therefore only this typie of spectrum will be considered. 

The standard low-resolution mass spectrum (Fig. 30.3) is computer generated, which allows easy comparison with known spectra in a computer database for identification. The peak at the highest mass number is the molecular ion (M ), the mass of the molecule minus an electron. The peak at RA = 100%, the base peak, is the most abundant fragment in the spectrum and the computer automatically scales the spectrum to give the most abundant ion as 100%. The mass spectrum of a compound gives the following information about its chemical structure  

The mjz value of the molecular ion is the summation of all the atomic masses in the molecule, including the naturally occurring isotopes. For organic molecules you will find a small peak M + 1) above the apparent molecular ion mass (M ) value due to the presence of C. The importance of isotope peaks is the detection of chlorine and bromine in molecules since these two elements have large natural abundances of isotopes, e.g. Cli Cl = 3 1 and Br Br = 1 1. The mass spectra produced by molecules containing these atoms are very distinctive with peaks at M + 2 and even M + 4 and M + 6 depending on how many chlorine or bromine atoms are present. The identification of the number and type of halogen atoms is illustrated in Box 30.1. 

Mass spectrometry (MS) is a widely used detection technique that provides quantitative and qualitative information about the components in a mixture. In qualitative analysis it is very important to determine the molecular weight 

An MS detector consists of three main parts the ionization source (interface) where the ions are generated, the mass analyzer (separation), which separates the ions according to their mass-to-charge ration (m/z), and the electron multiplier (detector). There are several types of ion sources, which utilize different ionization techniques for creating charged species. 

Illustration of the electrospray process in positive ion mode. The picture was kindly provided by Andreas Pettersson, Depertment of Analytical Chemistry, Uppsala University. 

In ESI the formation of ions from the liquid to the gas-phase is achieved by applying an electric field over the liquid phase to create charged droplets. The solvent evaporation decreases the size of the droplets while the charge remains constant, thus the charge to volume ratio increases, and will eventually form gas-phase ions [73], The formation of gas-phase ions from the very small droplets is still not definitely clear [74, 75], but the gas formation has little if any influence on the use of ESI with LC-MS. 

When a method has been developed it is important to validate it to confirm that it is suitable for its intended purpose. The validation tells how good the methods are, specifically whether it is good enough for the intended application. The method validation is today an essential concern in the activity of analytical chemistry laboratories. It is already well implemented in pharmaceutical industry. However, in other fields like food, petrol chemistry or in the biotechnological field, regulations have not reached such a level of requirement. The US Food and Drug Administration (FDA) have edited draft 

Mass spectrometry has been applied in electrochemical investigations predominantly as an ex situ method because of the obvious incompatibility of the high vacuum needed for all types of mass spectrometry and the presence of a liquid electrolyte solution. Because of the amount of information provided in a mass spectrum, there have been various attempts to couple mass spectrometers with electrochemical cells as described below. 

The terms mass spectrometry and mass spectroscopy are used synonymously because of the usage in another major field of application, the mass spectrometers used in the applications reviewed here are sometimes called residual gas analysers (RGA). 

Wolter and Heitbaum shortened the delay time significantly. In addition, they applied a different and more effective method of evacuation [811, 812]. The porous electrode and the inlet system connecting the electrochemical cell and the mass spectrometer are shown schematically in Fig. 5.135. 

As a result, Wolter and Heitbaum obtained a mass signal proportional to the rate of the electrochemical reaction, i.e. to the current flowing through the porous electrode. Because of the applied pumping technique and because of the proportionality between electrochemical current (i.e. derivative of consumed charge) and mass signal, the method was called differential electrochemical mass spectrometry (DEMS).  

Instrumentation. The experimental setup includes a mass spectrometer (initially this was a standard type using magnetic mass separation in subsequent versions and 

Mass spectrometry is the study of the mass, or molecular weight, of ions created via ionization or fragmentation and determined electrically in the gas phase. In the study of polymers, mass spectrometry has two broad applications  

To characterize functionality. Unknown polymers, residual volatile chemicals, and additives can be identified. This application depends on the fragmentation or degradation of the polymer chain or chemicals during the ionization see Chapter 2. 

To provide a new basis for the determination of absolute molecular weights. Novel techniques, developed below, now allow for the determination of absolute molecular weights and molecular weight distributions for polymers. In some cases individual molecular species can be 

The mass spectrum obtained is a plot of the ion abundance against mass-to-charge ratio, m/z, where m represents the mass and z the charge (95). The most important peak is the molecular ion, M.  

The main problem with mass spectrometry involves the low volatility of polymers. The classical Unfit was about 10,000 g/mol without encountering significant degradation. The need, of course, is for stable, charged macromolecules in the vapor phase. 

Mass spectrometry is another useful tool for the identification and structural elucidation of lichen substances. Tlje principles of the method are given in a review by Lehmann and Schulten (1976). The mass spectra (MS) of numerous depsides, depsidones, depsones, dibenzofuranes and diphenylbutadienes have been discussed by Huneck et al. (1968a). In the same year, Letcher (1968) published the MS of some pulvinic acid derivatives. Martinez and Mestres (1972) recorded the MS of depsidones derived from norstictic acid, and Holland and 

Wilkins (1979) studied the MS of di- and tri-oxygenated stictane triterpenoids and their trimethylsUyl derivatives. A paper by Grigsby et al. (1974) deals with the MS of derivatives of polyporic acid, and Krause (1976) investigated the MS fragmentation of depsides, depsidones, usnic acid, terpenoids, fatty acids, di- and triglycerides and carbohydrates from lichens. Some papers deal with the MS of usnic acid and derivatives Kutney et al. (1974), Huneck and Schmidt (1980), and Schmidt et al. (1981). Ruef (1990) reported on the MS of numerous lichen xanthones. 

Holzmann and Leuckert (1990) applied the methods of negative Fast Atom Bombardment 

Another technique for thermically labile substances is the field-desorption method. 

Santesson (1969b) developed a special technique, the so-called lichen mass spectrometry, where small fragments of lichens are introduced 

Mass spectrometry [75-83] involves four steps (1) isolation of the component of interest, (2) ionization, (3) separation of the ions in a combination of electric and magnetic fields according to their mass/charge (m/z) ratio, and (4) detection. The molecular ions and ionic fragments ai e detected by an electrometer and their relative abundances are recorded in the mass spectra. The sensitivity of detection can be increased with an electron multiplier. 

The thermospray technique [84—87] uses a heated vaporizer from which the HPLC eluent containing the dissolved electrolyte is sprayed as a jet into a heated chamber. A sampling orifice is positioned normal to the axis of the vaporizer probe. The ions and molecules are pumped through the sampling orifice into the mass spectrometer. Electron impact or collision-activated ionization, although optional, provides structural information. 

Schroder [88,89] analyzed fluorinated surfactants in water and wastewater using HPLC coupled by a thermospray interface to a tandem mass spectrometer (MS/MS). Alternatively, the chromatographic column was bypassed and the analyte was injected into the mass spectrometer (FIA, flow injection analysis). 

Supercritical fluid chromatography using COo as the mobile phase eliminates the problems associated with the evaporation of a liquid eluent and is, therefore, more compatible than liquid chromatography with MS. 

Modem soft ionization techniques have overcome the sample volatility requirement by combining the first two steps in mass spectrometry sampling and ionization. The soft ionization techniques used for the analysis of surfactants include fast atom bombardment (FAB), field desorption (FD), desorption chemical ionization (DCI, also called direct chemical ionization), secondary-ion mass spectrometry (SIMS), and laser desorption methods. 

Mass spectrometry can do more than simply determine the molecular weight of a compound. A high-resolution instrument can determine it to three or more decimal places, and this allows the formula of the molecule to be determined (extensive tables exist). Although we often think 

In all of these spectra, we have seen peaks for parts or fragments of the molecules. This is because the molecular ion is generated with a lot of excess energy—enough to break bonds within the molecule. However, the fragmentation is not random but generally takes place to give 

FIGURE 5.24 Stabilization of carbocations by lone pair donation. 

The molecular ions for polyhalogenated compounds are complicated. Taking the natural abundance of iBr and Br as 50 % each and the abundance of Cl and Cl as 75 % and 25 %, respectively, calculate the masses of the molecular ions of compounds of the following formulae. What are the relative amounts of each ion  

FIGURE 5.29 Schematic of an isotope ratio mass spectrometer. 

3 Mass Spectrometry. - A review on the use of mass spectrometry for identifying flavonoid glycosides has been published.  

3 Mass Spectrometry If a mass spectrometer is available, a mass spectrum will probably have been run at an early stage to determine the exact molecular weight and the molecular formula as described above. An attempt may also be made to gain further structural information from the cracking pattern in the spectrum (Fig. 3-1). Since the energy available when 

In recent years mass spectrometers have become increasingly robust, compact and less expensive, at least on a gathered information/price basis. Bench-top instruments are available with either quadrupole or ion trap mass filters. Applying single-ion monitoring (SIM) of a few characteristic fragments of the halocarbon molecules, the sensitivity is equal to or better than that of the ECD. 

Depending on the efficiency of the high vacuum pump, one major modification of the P T method may be necessary to keep the pressure in the ion source within acceptable limits. The optima] gas flow into the mass spectrometer is usually l-2mL/min, which means that a miniaturized P T system with a microtrap and a narrow-bore GC column is needed. Techniques for measuring halocarbons in the atmosphere by mass spectrometry have been used for several years (e.g., O Doherty et al., 1993), whereas systems for seawater measurements were developed more recently. Either a constant flow of seawater equilibrates with a gas which is subsampled for analysis (7. Butler, personal communication), or a modified P T system is used which allows for a larger range of halocarbons to be determined (Ekdahl and Abrahamsson, 1997). 

The intensity of a peak is usually determined by integrating the area underneath. However, measuring the peak height may yield better results in cases when the base of the peak is influenced by nearby eluting peaks. Examples are the CH2CII peak in Fig. 23-3 and its neighbour. 

A secondary standard is prepared by mixing the substances in a dilution chamber with a voliune of more than 10 m. The larger the better, since the final concentrations of individual components have to be very low. Most of the halocarbons are liquids at room temperature, and are mixed at about the same relative ratios as found in seawater. The gaseous methyl chloride, methyl bromide and CFC-12 are released into the dilution chamber from glass ampoules. The toxicity of methyl halides deserves special attention. An evacuated stainless-steel cylinder, electropolished inside, with a volume of 1-5 L, is opened in the chamber. The gas mixture let into the cylinder is then pressurised with nitrogen gas to reach the required concentration level (mixing ratio). 

The detector of a mass spectrometer converts the intensity of the ion beam into an electronic signal that can be transformed by the processor into useful formats for storage or display. The intensity of the ion beam and thus of the signal is determined by the number of the ions of a given m/z that reach the detector. A common way to display the processed information is as a mass spectrum, in which the intensity of the signal is displayed as a function of the m/z of the ions arriving at the detector (Fig. 8.59). From such a display, molar mass and, in some cases, structural features can be determined. 

O +1 ions, larger m/z represented by darker fill color. 

To illustrate the value of mass spectrometry, let s consider how the peaks in the mass spectrum of methane (Fig. 8.59) can be related to its structure. This simple example is presented to assist you in making the connection between the spectrum and the molecular structure. It also serves to introduce you to some of the basic principles of the technique. 

When bombarded with high-energy electrons, for example, methane can be ionized to produce a radical cation, CH4, a positively charged species having an unpaired electron. This process is illustrated in general in Equation 8.2 and specifically in Equation 8.16. 

As you might surmise, molecules more complex than methane produce more complicated fragmentation patterns, as illustrated by the mass spectrum of 2-methylbutane (Fig. 8.60). A generalized representation of the fragmentation of the parent ion and daughter ions into combinations of smaller charged and neutral species for such molecules is shown in Equations 8.18 and 8.19. In these equations and the subsequent discussion, the radical cations are represented in a simplified form in which we omit the symbol for the unpaired electron. 

Low resolution El mass spectral studies of pyrimidine, cytosine and derivatives of cytosine and isocytosine has been reviewed [54 refs].  

This year has seen a number of mass spectrometric applications to oligosaccharide characterizations. Uqmd secondary ion mass spectrometry (LSIMS) has been used in characterization of tetra-, hexa- and octasaccharides derived from porcine intestinal heparin. Laser desorption time-of-flight MS of heparin fragments complexed with (Arg-Gly)io and (Arg-Gly)is overcomes the problem 

The 1 - 2, 1 - 3 or 1 - 4 linkage type of xylobioses has been distinguished using unimolecular decomposition spectra (MIKE) of the [M+NH4] ions or CID-MS of [M+MeNHa] ions or permethylated derivatives.  

A matrix of 2,5-dihydroxybenzoic acid and 1-hydroxyisoquinoline (wt ratio of 3 1) proved most suitable for MALDI-MS of oligosaccharides. A new study of the use of electrospray ionization MS of cyclodextrins and guests shows that some amino adds least likely to form inclusion complexes show the most intense complex ions. This suggests previous data identifying complexes in this way are probably due to electrostatic adducts formed in the electrospray process.  

Solid SIMS has proved useful in the study of acetylated precursors of a series of glycosylated porphyrins (solid SIMS spectra are not complicated by chemical noise or matrix reactions).  

FIGURE 18.13 Partial mass spectrum of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D), which may be found as a water pollutant. 

The use of mass spectrometry for the exact determination of molecular weight of compounds in limited supply is a technique routinely applied to new coumarins. The results of a number of investigations have shown that characteristic fragmentation patterns are obtained from differently substituted coumarins. These are particularly useful for distinguishing between isomeric structures 58, 110, 337, 419, 502, 603, 605—607). 

The electron ionization (El) mass spectral behavior of pyridazine, pyridazin-3(2//)-one, and phthalazine was discussed in CHEC(1984) 1984CHEC(2)1 . In CHEC-II(1996) 1996CHEC-II(6)1 the comparison of the high-resolution El mass spectra of pyridazin-3(2//)-one, phthalazin-l(2//)-one and cinnolin-3(2//)-one was mentioned. 

For a discussion of the basic mass spectral fragmentation of several of these classes of compounds, the reader is encouraged to consult the treatment by Chadwick 84CHEC-I(3)I55 . 

Pyrroles and their Benzo Derivatives Structure CO2H 

A mass spectral study of several other isoindole derivatives has been reported 90KGS923). Rationalizations of the fragmentation patterns of -methyl- and JV-phenylisoindole are included in 

There are correlations between mass spectral fragmentations and thermal and photochemical fragmentations and rearrangements see Sections 4.02.1.2.1 and 4.02.1.2.2. 

Understanding mass spectrometry-since this technique does not involve the production and measurement of electromagnetic spectra and is not based on quantum principles, it should not really be referred to as a spectroscopic technique. 

Mass-to-charge ratios - in the overwhelming majority of simple cases the ion detected is a monopositive cation thus z = 1 ar,d the peaks seen on a low-resolution spectrometer equate to the mass of the ion. 

Determination of exact molecular mass -high-resolution instruments enable the molecular formula of a compound to be determined by summation of the masses of the individual isotopes of atoms, e.g. both ethane and methanal have integral 

Electron impact mass spectrometry has been employed to study the fragmentation patterns of isoxazolylmethyl- and bis(isoxazolylmethyl)-isoxazoles and the results are in agreement with proposed pathways (79AC(R)8l). Electron impact studies of nitrostyryl isoxazole (6) show fragmentation in a variety of ways. The standard loss of NO2 from the molecular ion 

Quasiequilibrium statistical theory was applied to the negative ion mass spectra of diphenylisoxazoles. Electron capture by the isoxazole leads to molecular ions having excited vibrations of the ring and of bonds attached to it. The dissociation rate constants were also calculated (77MI41615, 75MI416U). 

The chemical potentials and free energies of the 2-isoxazolines have also been studied and the electron impact and chemical ionization mass spectra determined (77MI41614). Fragmentation pathways and retrocycloadditions of various derivatives were discussed in these reports. 

Electron impact fragmentation studies on 1,2-benzisoxazoles and benzoxazole indicate that isomerization takes place before degradation. Shape analysis and metastable ion abundances in the mass spectra indicate that isomerization to o-cyanophenols occurred prior to degradation by loss of CO or NCH (75BSB207). 

Extensive mass spectral and electron impact studies have been reported for 3-hydroxy-1,2-benzisoxazole and its ethers. Similar work was also carried out with the isomeric A-alkyl-l,2-benzisoxazol-3-one (71DIS(B)4483). 1,2-Benzisoxazole A-oxide showed a mass spectral pattern than more closely resembled furoxans. The loss of NO predominated over the loss of O (Aft intense, [M— weak, [Af-30] strong). 

The early use of mass spectrometry as a tool for structural elucidation based on analysis of fragmentation patterns has gradually evolved to its present significance in natural product chemistry and biochemistry. This relies largely on soft ionization techniques, for example, matrix-assisted laser desorption ionization (MALDI) and electrospray ionization 

Carbon dioxide protected pyrroles and indole (carbamates), generated by treatment of the iV-lithiated heterocycles with gaseous CO2, can be easily tracked by negative ion electrospray ionization mass spectrometry (ESI-MS) revealing invariable loss of CO2 from the anion 2002JMP541 . 

The gas-phase ion chemistry of simple indoles by using several mass spectrometric methods has been reviewed 2003MI174, 2004MI398 . 

The origin of main fragments from cycloalkan[ ]indoles, 3-cyanoalkylindoles, and 2 -nitrovinylindoles has been extensively discussed 1996IJM97 . 

4-Benzyloxyindole-2-carboxylic acid hydrazide and arylidene hydrazides undergo fragmentation with significant loss of hydrazine and arylidenehydrazine radicals as well as of neutral isocyanates 2005JHC985 . 

The combination of a gas chromatograph with a mass spectrometer provides one of the most specific and sensitive means of analyzing and identifying the numerous pyrolysis products from lignin (see Chap. 9.1). The mass spectrometer acts as a detector and records the mass spectrum of each compound eluting from a GC column. This information, together with the retention time, allows unequivocal product identification to be made in most instances. 

Basically, mass spectrometers can be classified as magnetic sector and quadrupole instruments. For analytical pyrolysis, all instruments are useful provided the scan rate is fast enough (at least 1 scan/s) to record the narrow peaks eluting from the high-resolution GC column. 

The recent innovations in mass spectrometry involve methods for enhancing the vaporization, more accurately termed desorption, of relatively nonvolatile samples without derivatization. Even more significant are those advances that now allow for direct ionization of the sample to occur on the probe with subsequent desorption of the ions. As the efficiency of these new techniques improves, arguments begin to arise as to whether ionization of the sample components actually occurs prior to or subsequent to desorption (34, 35, 153, 154). Such arguments, however, need not concern us here. 

This chapter describes how mass spectrometry is used to determine the relative molecular mass of individual molecules and obtain information about their structure. After you have studied this chapter, you should be able to  

MS does not only allow precise determination of the molecular mass of oligonucleotides with their high molecular weight, but does permit sequencing of nucleic acids when using extremely small amounts of sample material. 

Some discussion on the use of mass spectrometry for end group deteniiination can be found in recent texts. Traditionally mass speclromelric lechniques have required polymers of relatively low molecular weight. Meisters et a/. reported that fast atom bombardment mass spectrometry (FAB-MS) can be applied in the analysis of MM A oligomers to at least hexadecamer. For polymers that degrade by unzipping, pyrolysis GCMS has provided extremely useful data on initiation processes. Thus, Farina et 7/. and Ohtani et described the 

Two relatively new techniques, matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDl-TOF) and electrospray ionization (RSI), offer new possibilities for analysis of polymers with molecular weights in the tens of thousands. PS molecular weights as high as 1.5 million have been determined by MALDI-TOF. Recent reviews on the application of these techniques to synthetic polymers include those by Hanton and Nielen. The mctliods have been much used to provide evidence for initiation and termination mechanisms in various forms of living and controlled radical polymerization. Some examples of the application of MALDl-TOF and ESI in end group determination are provided in Table 3.12. The table is not intended to be a comprehensive survey. 

Conventional - with catalytic chain transfer MALDI-TOF PMMA, copolymers  

Conventional, AIBN - with transfer to solvent. MALDI-TOF FNVP-  

Recent advances in the field of mass spectrometry now extend the applicability of this method to the analysis of macromolecules such as proteins. Using electrospray mass spectrometry, it is now possible to determine the molecular mass of many proteins to within an accuracy of 0.01 per cent. A protein variant missing a single amino acid residue can easily be distinguished from the native protein in many instances. Although this is a very powerful technique, analysis of the results obtained can 

The classical area of application of mass spectrometry has been with small volatile compounds, although non-volatile samples could be analysed if they were suitably derivatised. The application of mass spectrometry to large complex molecules like proteins has been made possible by the development of novel ionisation techniques which enable large molecules ( 200 kDa) to be introduced into the mass spectrometer in an intact form suitable for analysis (Siuzdak 1996 Dass 2000). Of the various techniques that have been developed, electrospray ionisation (ESI) and matrix-assisted laser desorption ionisation (MALDI) are the ones best suited for use with macromolecules and macromolecular complexes. 

A fine spray of sample solution is dried in a stream of warm nitrogen. This produces ions which are analysed in the mass-analyser. 

In MALDI, the sample is embedded in a non-volatile matrix such as nicotinic acid or 2,5-dihydroxybenzoic acid. The sample matrix is introduced into the mass spectrometer, charged to high-voltage and exposed to a high-energy laser beam. The matrix material is chosen to absorb the laser radiation and the radiation causes the matrix and sample molecules to vaporise or sputter into the gas phase. 

In these ionization procedures, the sample is split up into individual molecules and ionised under as gentle conditions as possible. Ideally, the sample should be dissolved in pure solvent, but this is often not possible since, for most biological macromolecules, salt and buffer solutions are needed to ensure the solubility and structural integrity of the sample. Since the ionic species generated from salts and buffers in the sample can interfere with the mass spectrum produced these need to be kept as dilute as possible. 

The resolution of the mass spectrometric analysis is a measure of its ability to distinguish between species with different m/z ratios for example, a resolution of 1000 implies that the system can distinguish between species with m/z ratios of 1000 and 1001. Different modes of analysis are used, depending on the specific experimental needs and also on the method of ionisation. 

One of the issues that is raised when data from mass spectrometry are applied to determining the character of coal is its non volatility. However, this should not be a deterrent to using this valuable technique. It is the interpretation that is derived from the data that should be suspect. Many workers have erroneously assumed that the volatile material is truly representative of the nonvolatile sample, and thereby hangs the error  

The use in coal analysis of gas chromatography-mass spectroscopy as well as pyrolysis-mass spectrometry and pyrolysis gas chromatography-mass spectroscopy has enabled low-molecular-weight benzenes, phenols, and naphthalenes to be identified as well as the C27 and C29-C30 hopanes and C15 sesquiterpenes (Gallegos, 1978 Smith and Smoot, 1990 Blanc et al., 1991). 

Curie point pyrolysis mass spectrometry has also been valuable in providing information about the chemical types that are evolved during the thermal decomposition of coal (Tromp et al., 1988) and, by inference, about the nature of the potential chemical types in coal. However, absolute quantification of the product mixtures is not possible, due to the small sample size, but the composition of the pyrolysis, product mix can give valuable information about the metamorphosis of the coal precursors and on the development of the molecular structure of coal during maturation. However, as with any pyrolysis, it is very important to recognize the nature and effect that any secondary reactions have on the nature of the volatile fragments, not only individually but also collectively. 

Application of mass spectrometry to the identification of methyl esters of the organic acids obtained by the controlled oxidation of bituminous coal 

The mass spectrometer (Section 3.6.2) has become a very important detector in gas chromatography. The mass spectrometry (MS) instrument basically consists of an ionization unit (ion source), a mass/charge (m/z) separation unit (analyzer), and an ion detector. The MS is a mass-sensitive detector, where the signal (S) depends on 

The MS can provide structural information, which can be used for identification of the compounds in addition to quantiflcation. 

The very high sensitivity inherent to MS (10-100 pg) and compatibihty with GC makes a GC-MS combination extremely valuable. Mass spectrometers may be classed as low-resolution (LR) or high-resolution (HR) instruments. The LR instruments provide mass measurements to the closest whole unit mass. Since many combinations of atoms may give the same unit mass, LR MS may provide the molecular weight of a compound but does not provide elemental composition. HR instruments provide sufficiently accurate mass measurements to permit determination 

Mass spectrometty is generally used in the flavor area to either determine the identity of an unknown or to act as a mass-selective GC detector. As mentioned, MS as an identification tool is unequaled by other instruments. The systems have largely become turn-key systems that require little or no operator expertise. If the operator can do GC, he/she can do MS. Comprehensive MS libraries and efficient searching algorithms make identification simple however, here lies a danger. A MS will provide a best match (suggest identity) for any unknown irrespective of the validity of the match. The neophyte often accepts the proposed identifications without question and obtains incorrect identifications. It is essential that all MS identifications be supported by other data, for example, GC retention data, IR, or nmr. 

FIGURE 3.9 Reconstructed mass chromatograms, a) Total ion current plot b) SIM plot c) Total ion chromatogram with full mass spectra. (From Holland, J.F., B.D. Gardner, Flavor, Fragrance, and Odor Analysis, R. Marsili, Ed., Marcel Dekker, New York, 2002, p. 107. With 

Tin has ten naturally occurring isotopes, more than any other element. The relative abundances are given in Table 2-5. In the mass spectrum, these isotopes give rise to the characteristic pattern of peaks which is illustrated in the Table. 

Rather limited use has been made of mass spectrometry in the study of organotin compounds,23-24 though MS linked to gas-liquid chromatography is now being used for the identification of organotin compounds, particularly in environmental studies. Most of the early work involved electron ionisation (El), but in recent years, other techniques such as chemical ionisation (Cl),25 fast atom bombardment (FAB),26, 27 field desorption,28 surface ionisation,29 and, particularly, electrospray (ES),30 31 have been used. 

Me4Sn + Decays by progressive loss of Me and MeMe, but with P-H available in the alkyl group, the alkene R(-H) is eliminated, and the hydrides Bu2SnH+ and BuSnH2+, and Sn + are major products from Bu4Sn. 

The most precise technique for the determination of moiar mass is mass spectrometry, and we need to know how to adapt traditionai techniques deveioped for smali moiecuies to the study of bioiogical macromoiecules. 

This sample is then irradiated with a laser pulse. The pulse of electromagnetic energy ejects matrix ions, cations, and neutral macromolecules, thus creating a dense gas plume above the sample surface. The macromolecule is ionized hy coUisions md complexation with H+ cations. 

A note on good (in this case, common) practice Strictly, the units of m/z are kilograms however, it is conventional to interpret m as the ratio of the molecular mass to the atomic mass constant m , in which case m/ (strictly mizmf) is dimensionless. 

Consider an ion of charge ze and mass m that is accelerated from rest hy an electric field of strength E applied over a distance d. The kinetic energy, of 

Answer Two distinct biopolymers because the feature at lower m/z probably does not arise from the unfragmented -I-2 cation of the species that gives rise to the feature at higher m/z. 

Looking back on my work in MS over the last 40years, I believe that my major contribution has been to help convince myself, as well as other mass spectrometrists and chemists in general, that the things that happen to a molecule in the mass spectrometer are in fact chemistry, not voodoo and that mass spectrometrists are, in fact, chemists and not shamans. 

Seymour Meyerson, Research Department, Amoco Corporation 

Of the many analytical techniques now available to the lipid chemist, mass spectrometry (MS), is probably the one that has experienced the fastest growth in the last two decades. This is due both to the development of new techniques (gas and liquid chromatography combined with MS, soft-ionization MS, field desorption MS, atmospheric pressure MS etc.) and to the refinement of more traditional methods and their successful application to very complex problems, e.g. the elucidation of glycolipid structure, or the study of structures in lipid mixtures. Much progress has been made since the pioneering work of Ryhage and Stenhagen (1963) on fatty acid methyl esters. 

Perhaps the main reason for MS success is its ability to detect and characterize organic compounds, giving definite structural information from minute amounts of material. The combination of gas chromatography (GC) and mass spectrometry (GC-MS) is particularly useful for lipid studies because of the ease with which complex mixtures may be separated and identified. In general, any compounds which are volatile enough for GC separation are sufficiently volatile for MS analysis. Compounds which are not sufficiently volatile for GC-MS analysis can usually be studied either after derivatization or with the help of new techniques, such as field-desorption MS. 

Mass spectra are generally obtained by bombarding the molecules of a compound in the vapour phase at low pressure with electrons of low energy. If the electrons have sufficient energy to cause ionization the molecular ion is formed  

The radius of the path described by ion of mass M and of charge e depends upon the accelerating potential V and the magnetic field H. The potential energy eV of the ion will equal the kinetic energy after full acceleration where v is the velocity  

In the field H the ion experiences a centripetal force Hev which is balanced by a centrifugal force Mv lr  

The appearance potentials of HPC+ and DPC+ from methylidynephosphine (155) and its deuteriated analogue are close to the theoretical values.21 The mass spectra and ion-molecule reactions of phosphiran (156) and of mixtures of phosphiran with ammonia and deuterio-ammonia show that all the important product ions are formed by PH group-transfer reactions where ethane is generated as a neutral particle. 

The molecular ion appears to retain its cyclic structure, but several ions with two or three phosphorus atoms can be detected.192 The fragmentation patterns of a number of dialkylphosphines (157) show initial loss of an alkyl group as a neutral particle formed by the transposition of hydrogen.193 Some six-membered cyclic phosphites (158 X = OEt, OPh, or Cl) have been studied.194 The mass spectra of a wide variety of phosphine sulphides (159 Z = Ph, Me, CH2Ph, COPh, NH2, N=CHPh, or 

A comparison of the basicities of Group VA element organic derivatives in nitro-methane solution showed that trioctylphosphine oxide (165 R = octyl) is a much weaker base than the corresponding amine oxide or hexamethylphosphoric triamide. 

All the methods of analysis described above, with the exception of some of the mass spectrometry applications, measure concentrations relative to a standard of known composition or to a calibration curve, drawn on the basis of standards of known composition. The standards used in the construction of calibration curves are either ultra-pure chemical reagents or, where matrix effects are important in some rock samples, well-analysed in-house samples and international reference samples (Govindaraju, 1984 Abbey, 1989). In either case the standards should be analysed using the most precise technique possible. Qearly the accuracy of the final analysis depends upon the accuracy of the standards used in calibration and systematic effbis can easily be introduced. 

In most analytical techniques used in geochemistry there is little attempt to separate the element to be analysed from the rest of the rock or mineral sample. The only exception is in mass spectrometry. Thus there is the possibility of interference of spectral lines or peaks so that the value measured is spuriously high due to overlap from a subsidiary peak of another element present in the rock. The effect of these interferences must be calculated and removed. 

Errors in one s own data can be detected by running well-analysed in-house or international standards through the sample preparation and analytical system. Errors in published data are more difficult to spot unless the author has cited values for international reference standards. 

Arithmetic mean x The arithmetic mean of a sample x (p. for die population) is 

A closed array is a data array where the individual variables are not independent of each other but are related by, for example, being expressed as a percentage (Section 2.6). 

However the fractions are separated, the next step is fiieir analysis by various mass-spectrometry techniques, directly or in combination with gas chromatography. What follows are the methods used for detailed hydrocarbon type analysis. 

Since physical properties of diesel fuels are directly related to their chemical composition, it is of great importance to be able to rely on the results provided by any of the methods used for hydrocarbon type analysis. As with separation methods, we have done some work on comparing our MS results 

The results for total saturates and aromatics from different class-type separations for these fuels were shown previously in Tables 1 and 2. The results in Table 5 provide a more detailed composition. Methods like supercritical fluid chromatography (SFC) and high performance liquid chromatography (HPLC) can only determine the aromatic subgroups (mono-, di-, and polyaromatics). We used these data to evaluate the reliability of hydrocarbon t)q)es determined by both EIMS and FIMS methods. In all cases there is a very good agreement between the methods. There are no independent techniques that would allow estimation of the MS performance 

To confirm the reliability of FIMS results in a different way, we analyzed a large number of diesel blends by the GC-FIMS method. The blends were manually prepared fi om individual diesel components. Before using GC-FIMS results for the model development, the GC-FIMS method was first verified by comparing the chemical composition of blends analyzed by GC-FIMS with the calculated weight averaged chemical composition derived from original components by the following equation  

Analysis of diesel blends on one hand helped to establish the GC-FIMS method as being a reliable tool for quick diesel analysis, and on the other hand provided valuable data for the general product quality model database 

Conventional, AIBN - wnth transfer to solvent MALDI-TOF PNVp. M 

The general fragmentation pattern of monocyclic 1,2,3-triazines shows peaks for [M+-N2], for an acetylene, and for a nitrile, in accordance with the results of thermolysis and photolysis. The mass spectrum of the parent triazine showed peaks as follows 81 (M+, 47%), 53 (M+-N2, 69%), 27 (HCN, 

2-Pyridone undergoes fragmentation by loss of CO and formation of the pyrrole radical cation. 3-Hydroxypyridine, on the other hand, loses HCN to give the furan radical cation while 4-pyridone 

The development of methods for ionising molecules that are far less drastic than the traditional route of vaporising them, and then bombarding them with electrons from an electron gun, has enabled the mass spectra of underivatised carbohydrates to be studied. Moreover, tandem techniques have enabled ions to be selected, made to undergo collision-induced dissociation by the presence of an inert gas such as argon or helium and the fragments examined. The 

Three soft ionisation methods are in use for earbohydrates, fast atom bombardment (FAB), eleetrospray ionisation (ESI) and matrix-assisted laser desorption/ionisation (MALDI). FAB is the oldest and involves directing a high-energy beam of Cs ions or Xe atoms at the sample dissolved in a nonvolatile solvent such as m-nitrobenzyl alcohol. The atoms sputter the sample and matrix [M + H] or [M + Na] ions are commonly observed. With an upper limit of M of about 2000, FAB is not that soft, and is usually used for small oligosaccharides it has the further disadvantage that the sample is prepared and then directly introduced into the mass spectrometer, so that it cannot be combined with liquid chromatography. 

MALDI occurs from a solution of the sample in a UV-absorbing matrix 2,5-dihydroxybenzoic acid is the current favourite for carbohydrate analysis. A pulse of laser light directed on the matrix gives rise to both positive and negative ions, which can be further analysed. In the positive mode, [M + Na] is commoner than [M + H]+. 

Nuclear Magnetic Resonance spectrometry is used for many types of analytical work but is key in the elucidation of structures of chemical compounds. When used in conjunction with mass spectrometry and infrared spectroscopy, the three techniques make it possible to determine the complete structures of novel compounds. Mass spectrometry is used to determine the size of a molecule and its molecular formula and infrared spectroscopy help identify the functional groups present in a molecule. NMR spectroscopy is used to determine the carbon-hydrogen framework of a molecule and works with even the most complex molecules. NMR is now being used to elucidate complicated protein structures  

While mainly used as a qualitative technique for identification, NMR has been used for quantitative analysis. Examples include the determination of glyphosate in biological fluids, ions in serum and fluoroquinolones in aqueous samples . 

Obviously, the easiest sample to work with is a gas or volatile sample. However, there are now many ionisation and desorption techniques that can drive gas ions from a condensed liquid or solid phase. These allow even very large thermally labile molecules to be ionised and separated according to their m/z values. The sample can be introduced into a mass spectrometer in a number of ways. Two of the most common are by direct inlet probe and infusion by syringe at a set (slow) flow rate. Another common means of delivery is straight from another instrument, such as a high performance liquid chromatograph (HPLC) where a stream of liquid is infused from the outlet of the HPLC into the MS via the ion source chamber. 

The ion source is where the sample of interest is both ionised with a positive or negative charge and converted into the gas phase. There are a number of ion sources available  

Electron impact The gaseous sample enters the electron impact (El) chamber via the inlet and is immediately bombarded by a beam of electrons. These electrons impact the sample molecules causing the loss of electrons, rendering the neutral molecules positively charged (Eigure 2.31). With this positive charge, the ions are now attracted to the extraction plate, from where they pass on to the mass analyser. El is considered to be a hard  

Hint First of all, never make the mistake of calling it mass spectroscopy. Spectroscopy involves the absorption of electromagnetic radiation, and mass spectrometry is different, as we will see. The mass spectrometrists sometimes get upset if you confuse this issue [25]. 

Indeed, there is almost no book using the term mass spectroscopy and all scientific journals in the field bear mass spectrometry in their titles. You will find such highlighted rules, hints, notes, and definitions throughout the book. This more amusing one - we might call it the zeroth law of mass spectrometry - has been taken from a standard organic chemistry textbook. The same author completes his chapter on mass spectrometry with the conclusion that despite occasional mysteries, mass spectrometry is still highly useful [25]. 

The large variety of ionization techniques and their key applications can be roughly classified by their relative hardness or softness and (molecular) mass of suitable analytes (Fig. 1.2). 

Atmospheric Pressure Chemical Ionization (APCI) Atmospheric Pressure Photoionization (APPI) 

Matrix-Assisted Laser Desorption/lonization (MALDI) Electrospray Ionization (ESI) 

Another direct, and in this case, well established, method of following the course of a reaction is by mass spectrometry. The application of mass spectrometry to analysis of organic compounds has been dealt with by Beynon and Reed ° and two volumes are concerned with the advances in this field . The mass spectrometry of free radicals has been reviewed by Cuthbert .  

Apart from the direct following of the rate of a reaction, identification and quantitative estimation of the transient species, the mass spectrometer may also be 

One method for the detection of free radicals depends upon the principle that the electron energy required to ionise the free radical is less than that required to produce the ionised radical from the parent or other compound. Eltenton used this method to detect free radicals in pyrolytic and combustion reactions up to pressures, in the RV, of 160torr. His RV and ion source are shown in Fig. 65. The ionisation and ion accelerating chambers were evacuated by two, separate, large diffusion pumps ( 2 and P3), while the filament and the analysing chambers were separately evacuated by smaller pumps (P. ). The RV consisted of a spirally-wound double quartz tube Q down the centre of which the reactant was introduced. The reaction zone 

The errors involved in estimating net peak heights depend on the relative size of contributing peaks, the identification of all peaks and the assumption of 100 % material balance. The problems involved in the detection of free radicals in mass spectrometry have been discussed by Tossing  

The oxidation of acetaldehyde has been studied by means of a continuous scanning technique The system was capable of producing 60 spectra per second, scanning from 12 to 80 mass units. The RV and ionisation chamber are shown in Fig. 67. Samples flow through a Tossing type quartz leak from the cylindrical RV into the ionisation chamber, from where they are evacuated by a high-speed 

Polymers are not easily converted to gas-phase ions but this is a requirement for compounds analyzed by mass spectrometry. Despite this difficulty, mass spectrometry has been utilized to study various aspects of polymers polymers can be characterized - among others - with respect to their chemical composition, to their end groups, and to their molecular weight. Moreover, mass spectrometry can be used to study polymer surfaces. 

MALDI measures the mass very accurately, and it gives an absolute measurement of mass. Still, sample and solution conditions must be optimized for the best performance of the matrix and therefore, it cannot yet be used as a routine method. Also, characterization of synthetic polymers by MALDI is sometimes 

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 information that mass spectrometry provides. The most intense peak in the mass spectrum is called the base peak and is assigned a relative intensity of 100. Ion abundances are 

FIGURE 13.35 The mass spectrum of benzene. The peak at m/z = 78 corresponds to the CgHs molecular ion. 

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

Smaller proportions of benzene molecules contain in place of one of the atoms 

Magnetic field separates particles according to their mass-to-charge ratio 

Electric field accelerates particles toward magnetic region 

Ionization and fragmentation produce a mixture of particles, some neutral and some positively charged. To understand what follows, we need to examine the design of 

These three techniques make the identification of surfactants a simple and straightforward matter in the majority of cases, although mixtures can present problems, and some degree of separation is usually necessary. The high cost of mass spectrometers puts that technique beyond all but the biggest research laboratories. 

Analysis of surfactant mixtures almost always requires separation of at least some components. The techniques outlined here are all useful and are all described more fully later. 

This topic was the subject of the occasional review in last year s volume. Pulsed electron beam high energy source pressure mass spectrometry has been used in combination with photoelectron spectra to determine the gas-phase basicities of methyl and phenyl tertiary phosphines and also primary phosphines. Fragmentation patterns in the mass spectra of various phosphanes, cyanophosphines, and the naphthyldiphosphine (90) have been described. 

An improved method of obtaining the appearance potential of phosphorus trichloride from electron impact spectra is reported. The mass spectra of various diazadiphosphetidines (at 20 and 70 eV) have been analysed as have the 

The mass spectra of a number of heterocyclic compounds have been reported. The fragmentation patterns of thiophosphoryl derivatives of phosphorinanes are sensitive to stereochemistry, thus for the series (95) facile loss of the HS radical is indicative of an axial PS bond. The seven-membered heterocycles (96 Ch = S, Se) undergo a remarkable migration of sulphur or selenium from phosphorus to carbon with ring cleavage. While exocyclic P-C bonds of five-and six-membered heterocycles in the phosphonic class may be readily cleaved with retention of the phosphorus ring system, the seven-membered ring (97) exhibits facile expulsion of a phosphorus radical.  

Field desorption mass spectrometry has been applied to the identification of phosphamide metabolites, whilst negative ion mass spectra was found to be the most suitable method of identifying zinc dithioate oil additives. Abundant 

Pulsed ion cyclotron double resonance spectroscopy was used to study the enthalpy of deuteriation abstractions from dimethyl phosphonate by various bases.  

The behavior of ion-radicals in the mass spectrometer chamber opens up principal venues of their alteration. However, liquid-phase reactions (typical for ion-radical organic chemistry) have many peculiarities and mass-spectrometry methods of ion-radical transformations are not inevitably reproducible. This is quite evident and needs no further comments. 

Mass spectral data have also been employed for biological studies aimed at determining the distribution of quinolizidine alkaloids within a plant. For instance, the analysis of stem sections of Lupinus polyphyllus and Cytisus scoparius by laser desorption mass spectrometry led to the conclusion that these alkaloids are restricted to the epidermis and probably also to the neighboring one or two subepidermal cell layers 1984MI230 . 

MS has evolved in the past few decades. There have been several milestone discoveries and inventions (Table 1.1). They encompass fundamental physical phenomena related to ion formation, as well as technical aspects - including the constmction of ion sources and mass analyzers. Since the operation of these two components is crucial for the measurements conducted in the time domain, they will be discussed extensively in the following chapters. 

1918 Electron ionization, first modern mass spectrometer A. Dempster [49] 

1919 Accurate determination of the masses of individual atoms F. Aston [50] 

1957 Time-resolved mass spectrometry of flash photolysis G.B. Kistiakowsky, P.H. Kydd [36] 

1985 Matrix-assisted laser desorption/ionization F. Hillenkamp [55] 

Low ionizing potentials or soft ionization methods are necessary to observe the parent ions in the mass spectra of many S-N compounds because of their facile thermal decomposition. Mass spectrometry has been used to investigate the thermal breakdown of S4N4 in connection with the formation of the polymer (SN). On the basis of the appearance potentials of various S Ny fragments, two important steps were identified  

Mass spectrometry played an important role in the recent characterization of small cyclic sulfur imides that are formally derived from the unstable cyclic sulfur allotropes Se and S7 by the replacement of one sulfur atom by an NR group. The compounds SsNOct and SeNOct (Section 6.2.2), which are yellow oils, exhibit molecular ions of medium intensity in their mass spectra.  

Chivers, B. McGarvey, M. Parvez, I. Vargas-Baca and T. Ziegler, Inorg. Chem., 35, 3839 (1996). 

Xiaoqing, F. Fengyi, S. Qiao, G. Maofa, Z. Jianping, A. Xicheng, M. Fingpeng, Z. Shijun and W. Dianxun, Inorg. Chem., 43, 4799 (2004). 

Andrews andP. Flassanzadeh, J. Chem. Soc., Chem. Commun., 1523 (1994). 

The primary use of NMR is in the determination of the structure of unknown organic compounds. It is often used in conjunction with other spectrometric techniques (FTIR and mass spectrometry, for example) in this determination. NMR spectra are molecular fingerprints, however, and by comparison with data files of known spectra, the structure of an unknown can be determined independent of other data. 

Instrumentation for gas analysis has been reviewed by Lodding [144] and is also discussed in the biannual reviews by Murphy [145]. The most widely applied techniques of EGA have been mass spectrometry and gas chromatography. 

Qualitative or quantitative mass spectrometric analysis can be made by one of two alternative configurations. Either the sample is decomposed in the high vacuum chamber of the mass spectrometer (MS) itself or reaction proceeds in an external system at higher pressure (e.g. a microbalance) 

The quadrupole mass spectrometer has been found to be particularly suitable for EGA in thermal analysis. Published reports include descriptions of the various systems used [153—155] and applications in studies of the pyrolysis of polymers [155], minerals [156] and many inorganic solids [157—159]. 

The high sensitivity of the MS [160] makes it a particularly appropriate tool for the investigation of nucleation and growth processes, since it is possible to measure rates during the early part of the reaction using small samples or individual crystals. The influence of residual gases [160] on the initiation of reaction can also be determined. Short scan times enable very rapid reactions e.g. detonations, to be studied, and it is also possible to measure simultaneously the rate of evolution of several different product molecules. 

A novel application [161] of EGA is in the study of crystal transformations by detection of the release of organic molecules occluded by the reactant solid during preparation. 

It is possible to determine the masses of individual ions in the gas phase. Strictly speaking, it is only possible to measure their mass/charge ratio (m/e), but as multi charged ions are very much less abundant than those with a single electronic charge (e= 1), m/e is for all practical purposes equal to the mass of the ion, m. The principal experimental problems in mass spectrometry are firstly to volatilise the substrate (which implies high vacuum) and secondly to ionise the neutral molecules to charged species. 

The most common method of ionisation involves Electron Impact (El) and there are two general courses of events following a collision of a molecule M with an electron e. By far the most probable event involves electron ejection which yields an odd-electron positively charged cation radical [M]+ of the same mass as the initial molecule M. 

The cation radical produced is known as the molecular ion and its mass gives a direct measure of the molecular weight of a substance. An alternative, far less probable process, also takes place and it involves the capture of an electron to give a negative anion radical, [M] . 

Electron impact mass spectrometers are generally set up to detect only positive ions, but negative-ion mass spectrometry is also possible. 

The energy of the electron responsible for the ionisation process can be varied. It must be sufficient to knock out an electron and this threshold, typically about 10-12 eV, is known as the appearance potential. In practice much higher energies ( 70 eV) are used and this large excess energy (1 eV = 95 kJ mok ) causes further fragmentation of the molecular ion. 

A comparative analysis of the El breakdown of arylsulfonyl-1//-azepines and IV-carboxymethyl-azepines carried out by Kulkami et al. 88OMS(23)240 indicates the primary breakdown is one of, respectively, N—S and N—C cleavage. In the latter case there is little indication of a competitive hydrogen capture by the azepine ring, a process preferred in the fragmentation of the isomeric aniline derivatives, nor could a correlation between mass spectral behavior and thermal and photochemical reactions be established. 

It is unlikely that the laboratory organic chemist will be required to record mass spectra of compounds produced in the laboratory as they will normally be obtained through a centralised service. This section therefore concentrates on the interpretation of spectra rather than on the techniques for obtaining the spectra. For further information on this aspect of mass spectrometry the reader should consult the sources listed in the references at the end of this chapter.4 

Probably the most common use of mass spectrometry by the organic chemist is for the accurate determination of molecular weight. A second important use is to provide information about the structure of compounds by an examination of the fragmentation pattern. 

The numbers by the signals indicate the numbering of the carbon atoms. Values relative to TMS = 0. Data reproduced from E. Breitmaier, G. Jung and W. Voelter (1971). Angew. Chem. Internat. Edit., 10,667. 

To shed light on the mechanism of formation of silsesquioxane a7b3, to identify the species formed during the process, and to try to explain the high selectivity towards structure a7b3 of the optimised synthetic method described above (64% yield in 18 h), the synthesis of cyclopentyl silsesquioxane a7b3 was monitored by electrospray ionisation mass spectrometry (ESI MS) [50-52] and in situ attenuated total reflection Fourier-transform infrared (ATR FTIR) spectroscopy [53, 54]. Spectroscopic data from the latter were analysed using chemometric methods to identify the pure component spectra and relative concentration profiles. 

The mechanistic study by means of mass spectrometry was performed by analysing samples of the reaction mixture at regular intervals throughout the experiment. The MS spectra recorded between t=0 and 1440 min show peaks corresponding to cyclopentyl silsesquioxane structures with l o 13. 

Peaks due to a=7 species (m/z=839.3, 857 3, 875.3, 893.3) are present in all the recorded spectra (see Fig. 9.8 for an example). The relative abundance of these peaks compared to that of the peaks of other silsesquioxane species is rather low at any reaction time, indicating a low concentration in solution. Knowing that the precipitate produced by the synthesis is mainly silsesquioxane 7F3, it can be inferred that this compound has a low solubility in the reaction mixture and tends to precipitate as it is formed. Its lower solubility with respect to other cyclopentyl silsesquioxanes is probably due to the tendency of silsesquioxane alkS to form dimers [37, 55], which are insoluble in polar solvents such as acetonitrile. This is in agreement with the observed formation of a white precipitate after 1 h of reaction. 

The concentration of the a=7 species in solution can, therefore, be considered approximately constant during the course of the reaction. This assumption allows one to normalise the intensity of the peaks of the other silsesquioxanes relative to the o=7 peaks, making it possible to compare the spectra measured at the various reaction times. (A normalisation of the MS data is necessary because the mass spectrometer produces plots in which the intensities of the peaks are not absolute but normalised to the most intense peak, the value of which is set at 100%.) The relative concentrations of the principal silsesquioxane species with increasing o 

The concentration of silsesquioxanes with o=4 decreased less rapidly. These species were still present in small amounts after 10 h and were only fully consumed close to the end of the reaction, after 24 h. 

The FT n.m.r. spectrum at 15.08 MHz of C-enriched methyl palmi-toleate (50), which was isolated from the lipid fraction, was recorded on 1.2 mg in CHCI3 solution. The spectrum showed enhanced signal intensities for the eight alternate carbon atoms (C-2, C-4, C-6, C-8, C-10, C-12, C-14, and C-16). This is the expected labelling pattern for the fatty acid derived from CH3C02Na. Mass spectrometry of the C-enriched ester indicated a 32% enrichment for the eight alternate sites. 

General.—Since the electron-impact fragmentation patterns of many classes of natural products are now known, mass spectrometry can be used in conjunction with heavy isotopes in biosynthetic studies. A study of the fragmentation pattern of a metabolite with and without isotopic labelling yields direct information on the position of the labelled atom in the molecule without recourse to wet chemical degradation. Essential requirements for the biosynthetic application of mass spectrometry are (0 thermal stability of the metabolite at the probe inlet temperatures and (ii) a reasonably simple fragmentation pattern. 

Recent practical applications of mass spectrometry of metabolites labelled with the stable isotopes H, C, N, and 0 will be reviewed. 

Determining the structure of an organic compound was a difficult and time-consuming process in the nineteenth and early twentieth centuries, but extraordinary advances have been made in the past few decades. Powerful techniques are now available that greatly simplify the problem of structure determination. In this and the next two chapters well look at four of the most useful techniques—mass spectrometry (MS), infrared spectroscopy (IR), nuclear magnetic resonance spectroscopy (NMR), and ultraviolet spectroscopy (UV)—and we ll see the kind of information that can be obtained from each. 

A small amount of sample is vaporized into the mass spectrometer, where it is bombarded by a stream of high-energy electrons. The energy of the electron beam can be varied but is commonly around 70 electron volts 

At one time, the molecular weight of a compound was determined by its vapor density or freezing-point depression, and molecular formulas were determined by elemental analysis, a technique for measuring the relative proportions of the elements in the compound. These were long and tedious procedures that required a relatively large amount of a very pure sample of the compound. Today, molecular weights and molecular formulas can be rapidly determined from a very small sample by mass spectrometry. 

In mass spectrometry, a small amount of a compound is introduced into an instmment called a mass spectrometer, where it is vaporized and then ionized (an electron is removed from each molecule). The sample can be ionized in several ways. Electron ionization (El), the most common method, bombards the vaporized molecules with a beam of high-energy electrons. The energy of the beam can be varied but is typically about 70 electron volts. When the electron beam hits a molecule, it knocks out an electron, producing a molecular ion. A molecular ion is a radical cation, a species with an unpaired electron and a positive charge. 

Electron bombardment injects so much kinetic energy into the molecular ions that most of them break apart (fragment) into cations, radicals, neutral molecules, and other radical cations. Not surprisingly, the bonds most likely to break are the weakest ones and those that result in formation of the most stable products. 

CHAPTER 14 Mass Spectrometry, Infrared Spectroscopy, and Ultraviolet/Visible Spectroscopy 

A mass spectrum records only positively charged fragments. 

Structure of Five-membered Rings with One Heteroatom 

The He(Ia) photoelectron spectra of the parent heterocycles have been the subject of much study. Initially the assignment of the ionization energies to appropriate occupied molecular orbitals was confused by the unexpected reversal in the sequence of the two highest occupied MOs in tellurophene relative to the other heterocycles. The reported values are compared in Table 24. The assignments are based upon comparisons with the spectra 

Molecular orbital Pyrrole Furan Thiophene Selenophene Tellurophene 

Most of the ions in the spectrum of isothiocyanate derivatives of cyclo-phosphazenes are cyclic. The CNS group fragments to give abundant ions M — S, M — S2, and M — CSj. 

A great deal of interest has been shown in the mass spectral analysis of natural products. In most cases it is desirable to develop techniques incorporating g.l.c. to enable the separation of the components obtained in extracts from natural products. The volatility required for g.l.c. is 

Atomization energies of CP, CgP, CPj, and CgPg have been determined using high-temperature Knudsen cell mass spectrometry.  

In terms of HTS campaigns, there has been a move toward screening purified natural products libraries.6,7 Although more chemical diversity can be sampled from crude extract libraries or partially purified natural product libraries, pure 

LC-MS is quite widely used, although it is not nearly so popular a technique as GC-MS. The main difficulty in LC-MS is in introducing a sample which is dissolved in a liquid flowstream running at around 1 ml min into the MS, whilst maintaining a high vacuum within the MS. A number of techniques have been developed for coupling HPLC with MS, and a variety of systems are in commercial production. Others which promise significant improvements in performance are under development. 

Thomas Annesley) Ph.D., Alan L. Rockwood Ph.D., and Nicholas E. Sherman, Ph.D, 

Mass spectrometry (MS) is a powerful qualitative and quantitative analytical technique that is used to measure a wide range of clinically relevant analytes. When MS is coupled with either gas or liquid chromatographs, the resultant analyzers have expanded analytical capabilities with widespread clinical applications. In addition, because of its ability to identify and quantify proteins, MS is a key analytical tool that is used in the emerging field of proteomics. 

We begin this chapter with a discussion of the basic concepts and definitions of MS followed by discussions of MS instrumentation and cUnical applications. 

All MS techniques require an ionization step in which an ion is produced from a neutral atom or molecule. In fact development of versatile ionization techniques has led to MS being the excellent analytical tool it is today. In 2002 the Nobel prize was shared by John Fenn and Koichi Tanaka for their development of electrospray and laser desorp-tion ionization, respectively. 

Chemical, electron field desorption, laser desorption, photon, plasma desorption, spark, and thermal ionization are all used as primary ionization processes. Secondary ionization is the term used to describe a process in which ions are ejected from a surface as a result of bombardment by a primary beam of atoms or ions. If low energy or soft ionization techniques are used, the mass of the target molecule can be determined. Advances in soft ionization techniques have extended the use of MS to the direct measurement of peptide and protein mass. Ionization at higher energy results in more extensive fragmentation of target molecules. 

The electron that is ejected from the molecule will be of relatively high energy. For example, from a lone pair, which is not involved in bonding. Examples 

The molecular ions then pass between the poles of a powerful magnet, which deflects them (the deflection depends on the mass of the ion), before hitting an ion detector. Since the molecular ion has a mass that 

If the bombarding electrons have enough energy, this can lead to the fragmentation of the molecular ion into smaller radicals and cations (called daughter ions). Only charged particles (i.e. radical cations and cations) can be recorded by the detector. 

A mass spectrum determines the masses of the radical cation and cations and their relative concentrations. The most intense peak is called the base peak, and this is assigned a value of 100%. The intensities of the other peaks are reported as the percentages of the base peak. The base peak can be the molecular ion peak or a fragment peak. 

The apparent loss of the phthalazinone carbonyl band in the IR spectrum of a phthalazinone nitration product (10), initially thought to be consistent with the formation of the 1-nitroxy derivative, was shown by model studies to be due to a high frequency shift of the band on nitration at N-2 (from 1644 to 1719 cm ) causing the band to overlap with that of an ethoxycarbonyl group also present in the molecule 92CPB3327 . 

Detector Application/ selectivity Limit of detection [g/s] Linearity Comments 

This is a measure of the response characteristics towards the various compounds. Some detectors respond to almost all compounds and are referred to as universal . Others only respond to certain types of compounds and enable the user to determine these compounds in a complex matrix. For this reason, GC detectors are divided into three groups  

The FID responds to compounds that yield electrically charged species on combustion in a hydrogen/air flame, the free-radical reaction being 

These charged species, under die influence of an electric field, are captured on a collecting electrode and measured by an electrometer, whose output is amplified. The field of application of the FID is very large, as it responds to almost all organic compounds. A disadvantage is that it is often too unspecific and insensitive for environmental analysis and the analysis of residues. 

The beta-rays emitted from the cathode ionize the carrier gas, thereby liberating electrons. If a pulsed voltage is applied to the electrode in the cell, these electrons are captured, so producing an electric current. If electrophilic molecules are introduced into the cell, these absorb electrons and become negatively ionized. The electron density in the detector therefore decreases, so that a smaller number of electrons are captured at each pulse. The total number of electrons captured per unit of time (i.e. the current) can be kept constant by increasing the pulse frequency when the number of electrons decreases. The pulse frequency is then proportional to the concentration of the electrophilic molecules passing through the detector [8]. 

In most NMR spectra of stereoregular polymers, the key factor for the analysis is the methylene group in the polymer chain. In an isotactic molecule, the two methylene protons are not identical, and therefore, two resonances must be observed. For a syndiotactic chain, the two protons in the methylene group are identical by symmetry, so only one resonance is observed [27]. 

The spectra of stereoregular polymers show a single sharp line for each chemically distinct carbon because, within each type of chain, each monomer residue is identical. However, the chemical shifts for isotactic and syndiotactic chains are not the same. 

MS is a useful analytical technique to analyze and determine the molecular structure of an organic compound by observing its fragmentation pattern. This can be applied to qualitative or quantitative analysis. 

A mass spectrum is a two-dimensional representation of signal intensity of a fragment and the ratio between mass (m) and charge (z) of the fragment (m/z). The intensity of the peak correlates with the abundance of the corresponding ion. 

Often but not always, the molecular ion peak can be appreciated in the mass spectrum, resulting from the detection of the intact ionized molecule. It is usually accompanied by several peaks at lower miz caused by fragmentation of the molecular ion to yield fragment ions. 

Michael Przr bylski, Wolfgang Weinmann, and Thilo A. Fli e 

In the gas phase, both the a- and P-anomers of methyl 3-0-benzyl-2,6-dideoxy-D-arabino-hexopyranoside undergo ready deprotonation of the 4-hydroxyl, and collision activated dissociation (CAD) of these anions leads to E2 elimination, decarbonylation and ring opening fragmentations. Study of the trideuteromethyl a-glycoside, 2,2-dideutero- and dideuterobenzyl a-glycosides support the mechanism proposed.  

EI-MS of alkyl and phenyl A -alkyl- and A, iV-dialkyl-2-amino-4,6-0-benzyl-idene-2-deoxy-D-hexopyranosides and benzyl and phenyl 2,3-di-0-alkyl-4,6-0-benzylidene-D-hexopyranosides leads to three different fragmentation pathways, and definitive chemical evidence for these different pathways is presented.  

FAB and El spectra of some acenaphtho[l,2-e][l,2,4]triazines and acenaphtho[l,2,4]triazolo[4,3-Z ] and [3,4-c][l,2,4]triazines attached to acyclic monosaccharide derivatives have been reported. The reaction of iV-a-acetyl-L-lysinamide and glucose has been examined with the assistance of electrospray mass spectrometry (along with capillary zone electrophoresis), providing evidence for a number of products exhibiting different degrees of dehydration and oxidation and for species with two lysines per glucose (relevant to cross-linking of 

di- and tri-saccharides appear to be volatile compounds under the conditions of field desorption (f.d.)-m.s., as evidenced by energy deficit measurements. The electric field has been shown to play an essential role in the desorption of [M+H] ions 

Peracetylated xylo-oligosaccharides have been studied by e.i. 

A number of reports have appeared on the coupling of h.p.l.c. and m.s. systems for the analysis of sugars. The technique of thermospray ionization permits the use of standard h.p.l.c. columns 

Izatlon of the -substituents (from h.p.l.c. retention time). Micro-bore fused-slllca column h.p.1.c.-m.s. has also been investigated. With conventional amine-bonded silica or reversed-phase columns of 0.22 mm l.d., and a direct capillary inlet, monosaccharides and cardiac glycosides gave interpretable e.i.- or 3 3 

Fast atom bombardment (FAB) m.s. of glucose and sucrose in the presence of various metal complexes have been studied. Potassium hexacyano ferrate(II) gave useful [M+K] lons. Components of the polyoxins, a fermentation-produced complex of nucleoside peptide antibiotics, have been identified by FAB m.s. following separation by h.p.l.c, The FAB m.s. of the natural ribo- and deoxyrlbo-nucleosldes and -nucleotides and some cytosine analogues have been Investigated. The use of the negative ion mode reduced interference from positive counter-ions (e.g., Na ) and permitted rapid 

Molecular secondary ion m.s. of the constituent pentasaccharide vlridopentaoses of the antibiotic sporavirldin gave informative 

The presence of molecular ions from field desorption (f.d.)-m.s. of glucose and sucrose is taken to indicate that these sugars are volatile, and a mechanism for ion formation is discussed.It has been claimed, however, that molecular ions seen by others are not 

In the c.i.-m.s. of mono- and dl-saccharides and cycloalkanedlols using trimethylborate as reagent gas, the reagent reacts with 1,2- 

Isomers to be distinguished. Anomeric hexoslde tetraacetates have been examined by e.l.- and c.l. (CH, 1-Cj Hj q, and NH2)-m.s. While practically no fragmentation was observed with NH -c.l., minor differences in relative intensities of common ions between spectra of anomeric pairs were enhanced by CH j- and i-C H g-c.i., 

PROBLEM 12.14 Which of the following aromatic compounds do you expect to absorb at the longer wavelength  

PROBLEM 12.15 Naphthalene is colorless, but its isomer azulene is blue. Which compound has the lower-energy pi electronic transition  

Mass spectrometry (MS) differs from the other types of spectroscopy discussed in this chapter, in that it does not depend on transitions between energy states. Instead, a mass spectrometer converts molecules to ions, sorts them according to 

The beam of these parent ions then passes between the poles of a powerful magnet, which deflects the beam. The extent of the deflection depends on the mass of the ion. Since M has a mass that is essentially identical to the mass of the molecule M (the mass of the ejected electron is trivial compared to the mass of the rest of the molecule), mass spectrometers can he used to determine molecular weights. 

Frequently, mass spectra show a peak one or two mass units higher than the molecular weights. How can this be Recall that the isotope (one mass unit higher than ordinary C) has a natural abundance of about 1.1%. This gives rise to an (M -I- I) peak in carbon compounds. The intensity of this peak relative to the peak is approximately 1.1% times the number of carbons in the compound (because the chance of finding a atom in a compound is proportional to the number of carbon atoms present). 

Worked example 4.2 Three-stage decomposition of CaC204 H2O 

TGA data for hydrated calcium oxalate, CaC204 H2O, are shown below  

09 mg of CaC03 loses 43.97% of its weight when heated from 298 to 1100 K. Confirm that this corresponds to the formation of CaO. 

When 2.50 g of CUSO4 5H2O are heated from 298 to 573 K, three decomposition steps are observed. The % weight losses for the consecutive steps with respect to the original mass are 14.42,14.42 and 7.21%. Rationalize these data. 

Explain the shape of the curve, and give a series of equations to summarize the thermal decomposition. 

Many organic compounds such as lycopene are colored because their HOMO- LUMO energy gap is small enough that Xmax appears in the visible range of the spectrum. All that is required for a compound to be colored, however, is that it possess some absorption in the visible range. It often happens that a compound will have its Xin x in the UV region but that the peak is broad and extends into the visible. Absorption of the blue-to-violet components of visible light occurs, and the compound appears yellow. 

An important enzyme in biological electron transport called cytochrome P450 gets its name from its UV absorption. The P stands for pigment because it is colored, and the 450 corresponds to the 450-nm absorption of one of its derivatives. 

Diagram of a mass spectrometer. Only positive ions are detected. The cation X+ has the lowest mass-to-charge ratio and its path is deflected most by the magnet. The cation Z+ has the highest mass-to-charge ratio and its path is defiected least. (Adapted, with permission, from M. Silberberg, Chemistry, McGraw-Hill 

Although still a challenging task, structure determination has been greatly simplified by modem instrumental methods. These techniques have both decreased the time needed for compound characterization, and increased the complexity of compounds whose structures can be completely determined. 

A mass spectrum plots the amount of each cation (its relative abundance) versus its 

TABLE 10.4 Infrared Correlation Chart for Common Organic Functional Groups 

Mass spectra do not involve electromagnetic radiation as do the other techniques discussed here. A molecule is ionized with a high energy electron beam and the resulting ionic fragments are sorted by mass and their abundance 

This activity is designed to be completed in a 1 Vi-hour laboratory session or two classroom sessions. 

Model 1 Frictionless, Tireless, Reproducible Shot-Putter 

A shot-putter throws two balls with all her might. 

Assume the distance each ball goes is an exact and reproducible quantity (i.e., a 10-lb ball always goes the same distance, and she never gets tired. 

To show which ball went farther, label the 10- and 15-lb balls drawn in Model 1. 

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Using Mass Spectrometry for Determining Distribution by Chemical Families... 

The resulting mass spectrometry analysis is an analysis by chemical... 

Separation of families by merely increasing the resolution evidently can not be used when the two chemical families have the same molecular formula. This is particularly true for naphthenes and olefins of the formula, C H2 , which also happen to have very similar fragmentation patterns. Resolution of these two molecular types is one of the problems not yet solved by mass spectrometry, despite the efforts of numerous laboratories motivated by the refiner s major interest in being able to make the distinction. Olefins are in fact abundantly present in the products from conversion processes. 

Mass spectrometry allows analysis by hydrocarbon family for a variety of petroleum cuts as deep as vacuum distillates since we have seen that the molecules must be vaporized. The study of vacuum residues can be conducted by a method of direct introduction which we will address only briefly because the quantitative aspects are ek r metiy difficult to master. Table 3.6 gives some examples the matrices used differ according to the distillation cut and the chemical content such as the presence or absence of olefins or sulfur. 

Non-exhaustive summary of analytical methods using mass spectrometry. 

Interest in this method has decreased since advances made in gas chromatography using high-resolution capillary columns (see article 3.3.3.) now enable complete identification by individual chemical component with equipment less expensive than mass spectrometry. 

As the temperatures of the distillation cuts increase, the problems get more complicated to the point where preliminary separations are required that usually involve liquid phase chromatography (described earlier). This provides, among others, a saturated fraction and an aromatic fraction. Mass spectrometry is then used for each of these fractions. 

Before ehding this presentation on mass spectrometry, we should cite the existence of spectrometers for which the method of sorting ions coming from the source is different from the magnetic sector. These are mainly quadripolar analyzers and, to a lesser degree, analyzers measuring the ion s time of flight. 

One has seen that the number of individual components in a hydrocarbon cut increases rapidly with its boiling point. It is thereby out of the question to resolve such a cut to its individual components instead of the analysis by family given by mass spectrometry, one may prefer a distribution by type of carbon. This can be done by infrared absorption spectrometry which also has other applications in the petroleum industry. Another distribution is possible which describes a cut in tei ns of a set of structural patterns using nuclear magnetic resonance of hydrogen (or carbon) this can thus describe the average molecule in the fraction under study. 

Other techniques for predicting the cetane number rely on chemical analysis (Glavinceski et al., 1984) (Pande et al., 1990). Gas phase chromatography can be used, as can NMR or even mass spectrometry (refer to 3.2.1.l.b and 3.2.2.2). 

The spectroscopic methods, NMR and mass spectrometry for predicting cetane numbers have been established from correlations of a large number of samples. The NMR of carbon 13 or proton (see Chapter 3) can be employed. In terms of ease of operation, analysis time (15 minutes), accuracy of prediction (1.4 points average deviation from the measured number), it is... 

With regard to mass spectrometry, accuracy is not as high with an average error of 2.8 points, but on the other hand, the sample required is very small, being around 2 jl1. 

Fisher, I.P. and P. Fisher (1974), Analysis of high boiling petroleum streams by high resolution mass spectrometry . Talanta, Vol. 21, p. 867. 

W. V. Ligon, Jr., Evaluating the Composition of Liquid Surfaces Using Mass Spectrometry, in Biological Mass Spectrometry, Elsevier, Amsterdam, 1990. 

Ions are also used to initiate secondary ion mass spectrometry (SIMS) [ ], as described in section BI.25.3. In SIMS, the ions sputtered from the surface are measured with a mass spectrometer. SIMS provides an accurate measure of the surface composition with extremely good sensitivity. SIMS can be collected in the static mode in which the surface is only minimally disrupted, or in the dynamic mode in which material is removed so that the composition can be detemiined as a fiinction of depth below the surface. SIMS has also been used along with a shadow and blocking cone analysis as a probe of surface structure [70]. 

Benninghoven A, Rudenauer F G and Werner FI W 1987 Secondary ion Mass Spectrometry Basic Concepts, instrumentai Aspects, Appiications, and Trends (New York Wiley)... 

Chang C-C and Winograd N 1989 Shadow-cone-enhanced secondary-ion mass-spectrometry studies of Ag(110) Rhys. Rev. B 39 3467... 

The hydration of more inert ions has been studied by O labelling mass spectrometry. 0-emiched water is used, and an equilibrium between the solvent and the hydration around the central ion is first attained, after which the cation is extracted rapidly and analysed. The method essentially reveals the number of oxygen atoms that exchange slowly on the timescale of the extraction, and has been used to establish the existence of the stable [1 10304] cluster in aqueous solution. 

Most ion-molecule techniques study reactivity at pressures below 1000 Pa however, several techniques now exist for studying reactions above this pressure range. These include time-resolved, atmospheric-pressure, mass spectrometry optical spectroscopy in a pulsed discharge ion-mobility spectrometry [108] and the turbulent flow reactor [109]. 

Castleman A W and Mark T D 1986 Cluster ions their formation, properties, and role in eluoidating the properties of matter in the oondensed state Gaseous Ion Chemistry and Mass Spectrometry ed J FI Futrell (New York Wiley)... 

Viggiano A A 1993 In-situ mass spectrometry and ion chemistry in the stratosphere and troposphere Mass Spectron. Rev. 12 115-37... 

Arnold F and Viggiano A A 1986 Review of rocket-borne ion mass spectrometry in the middle atmosphere Middie Atmosphere Program Handbook, Voi. 19 ed R A Goldberg (Urbana, IL SCOSTEP)... 

Schlager H and Arnold F 1985 Balloon-borne fragment ion mass spectrometry studies of stratospheric positive ions unambiguous detection of H (CH3CN), (H20)-clusters Pianet. Space Sc/. 33 1363-6... 

The basic principle behind TOP mass spectrometry [36] is tire equation for kinetic energy, ze V... 

Harrison A G 1992 Chemical Ionization Mass Spectrometry (Boca Raton, FL Chemloal Rubber Company)... 

Busoh K L, Gllsh G L and MoLuokey S A 1988 Mass Spectrometry/Mass Spectrometry (New York VCH)... 

Dawson P H 1976 Quadrupole Mass Spectrometry and its Applications (Amsterdam Elsevier)... 

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