# Mass Spectrometry. 1. Calculation of Molecular Ion or Fragment Composition

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1 Mass Spectrometry 1 alculation of Molecular Ion or Fragment omposition a ommon Isotopes Nominal Abundance, Isotope Mass % Exact Mass (or D) N N F Si Si Si P S S S Br Br where m is the mass of the particle in emu, e is the charge in esu, and V is the potential of the electric field that accelerates the particle Note that a singly-charged particle (more common), M, with a mass of 58 would appear at the same location in the spectrum as a doubly-charged particle, M of mass 116 c Exact mass calculations [Agreement should be to within less than 10 millimass units, 1 ± 0010 mass units)] Example: : 3 x = : 6 x = : 1 x = alculated exact mass = emu The nominal mass of an ion is the sum of the nominal masses for the most abundant isotopes (usually the isotopes with the smallest nominal masses) Thus, for 3 6, the nominal mass would be: (3 x 1) (6 x 1) (1 x 16) = 58amu Note that the particles,, =, N, and N each have nominal masses of 8 emu owever, these particles are readily distinguishable by exact mass measurements: particle nominal mass exact mass N = N I Please note that these values are not the same as the usual chemical atomic weights (eg, 101 for is the average value for all isotopes) used in chemical calculations b Measurement of mass to charge ratio m/e for molecular ions and fragment ions is in atomic mass units (amu) For a spectrometer employing a magnetic field,, to cause particles to follow a circular path of radius, r, the relationship is: m r = e V d Intensities of Isotope Peaks ( M1, M, etc) elative to the Molecular Ion Peak M (taken to be 100 for this discussion) For a particle containing n atoms with isotope fractions a and b the relative intensities of the M, M1, M, etc peaks is given by the expression (a b) n For example in a fragment containing one l atom ( a = 3/4 for 35 l ) b = 1/4 for 37 l) the relative intensities of the fragments would be: M = 100; M1 = 0; M = 33; M3 = 0 1

2 In a fragment containing two l atoms the relationship (a b) = a ab b or 9/16 6/16 1/16 corresponds to the following intensity distribution: M = 100 M1 = 0 M = 67 M3 = 0 M4 = 11 For n atoms of isotope distribution (a b) and M atoms of isotope distribution (c d), the intensity ratios are given by the relationship; (a b) n (c d) m For most organic compounds that do not contain one of the elements Si, S, l or Br, the following approximation will suffice to predict the intensities of the M1 and M peaks relative to the M peak peak % of M M1 (No of s) 11% (No of N s) 036% M (No of s) 01% (No of s) 00% In practice, the observed M1 and M peaks are often somewhat larger than the values predicted above because of some contribution from intermolecular ion-molecule collisions in which M abstracts a proton from an unionized molecule to give M- The expected intensity ratios for M, M1 and M may also be complicated if the parent ion, M, has a significant tendency to lose one or two atoms to form appreciable amounts of M-1 or M- ions Although some workers recommend use of the relative intensities of the peaks M, M1 and M to derive molecular formulas for compounds containing the elements and N, in practice, this method is of limited reliability especially as the size of the molecule becomes large Therefore, any definitive determination of a molecular formula using mass spectrometry should always employ an exact mass measurement rather than the intensity ratios of M, M1 and M peaks Location and use of Molecular Ion Peaks a Location of molecular ion M It is always unwise simply to assume that the highest peak of appreciable intensity in the mass spectrum of an unknown is the molecular ion This peak could arise from an unsuspected impurity, as a fragment from a M of higher mass, or as a thermal decomposition product (eg, dehydration, dehydrohalogenation, etc) of the original sample formed when the sample was heated ( o or more) to introduce it or while the sample was stored in the hot (150 o ) inlet system Slow thermal decomposition in the inlet system can be detected by making repeated scans at successively longer times and then extrapolating the changes in relative peak intensities back to time zero Thermal decomposition during the introduction of the sample is more probable but is more difficult to detect This possibility should always be suspected for mass spectra obtained from relatively high-melting or relatively high molecular weight compounds since these samples are likely to have been heated for as long as 0-30 min as they are being distilled or sublimed into the inlet system ne method to explore possible thermal decomposition during sample introduction is to compare spectra obtained when the sample is introduced normally and when the sample is introduced by the direct inlet procedure where thermal decomposition may be minimized Substantial difference in the two spectra suggests that the sample is decomposing thermally during the conventional introduction procedure The intensity of a M peak, relative to fragment peaks in a spectrum, is determined by the ease of formation of the molecular ion on electron impact (e - lost most easily from non-bonded electron pairs or from electrons in π-bonds) and by the tendency of the initially formed ion to fragment (especially likely at "weak" bonds in M or if fragmentation can lead to very stable radicals or positive ions) The following list contains types of molecules listed in the usual order of decreasing relative intensity of the M peak Exceptions to this general order are to be expected 1 aromatic compounds olefins 3 ketones decreasing relative 4 amines intensity of M peak 5 ethers 6 esters and acids 7 alkanes 8 alcohols If a peak arises from a molecular ion, its location and the location of nearby fragment peaks will usually meet the following criteria (i) the nitrogen rule No of N atoms Nominal mass Nominal mass of most in ion of ion fragment peaks zero or even even odd odd odd even (ii) high-mass fragment peaks (M-1, M-, etc) (1) The loss of 1 or hydrogen atoms (M-l, M- peaks) from M is relatively probable especially with compounds of the type - -X- or with dihydroaromatic systems

3 () The loss of 15 mass units (eg, 3 ) or more (M-15, M-17, M-t8, etc) from M is relatively probable (3) The loss of 3 to 14 mass units from M (M-3 to M-4, M-14) are very improbable events For example, the loss of - - (14 amu) from M would require the simultaneous breaking of two bonds Thus, if a peak, suspected to be M, shows appreciable fragment peaks in the range M-3 to M-14, it is probable that the peak "M " is not a molecular ion but rather a fragment from some higher mass molecular ion 3 Study and Use of Fragmentation Patterns a Methods for studying fragmentation patterns easonable mechanistic pathways for the conversion of a molecular ion, M, to the various abundant fragment peaks that appear in a mass spectrum can often be suggested based on the generalizations and on analogous fragmentations described subsequently (section c of this section) owever, one must recognize that these mechanistic speculations in previously unstudied systems may be totally wrong and should not serve as the basis of any rigorous structural assignment To remove such mechanistic proposals from the realm of speculation, several types of experimental evidence can be obtained (i) Exact mass measurements to establish the composition of fragments ften the nominal mass m/e values obtained in routine mass spectra will not distinguish between two different compositions that have the same nominal mass (eg, m/e 8 for both and = ) Since the composition of the fragment ion (ie, the reaction product) must be known for any meaningful mechanistic speculation, the first step in any serious mechanistic study is to determine the compositions of any fragments of interest by exact mass measurement In many cases involving low-mass fragments, the nominal mass peaks included two ions of different composition that are not resolved in a routine spectrum For example, the routine mass spectrum of ( 5 ) 5 exhibits an abundant fragment peak at m/e 71 which could arise from either of the two fragments indicated below : ( 5 ) -- 5 m/e 14 ( 5 ) 5 - m/e 71 (710861) 5 - ( 5 ) m/e 71 (710497) Examination of this m/e 71 peak at high resolution easily resolved this peak into two components of comparable abundance with the measured exact mass values indicated (ii) Use of metastable ion peaks If an ion (either a molecular ion or a fragment) of mass m 1 is produced in the spectrometer ion source and decomposes to a lower mass ion, m, as it passes from the ion source to the magnetic field, this metastable ion will appear in the spectrum as a broad, low-intensity peak that often will have a non-integral m/e value even in a routine spectrum The m/e value for this metastable ion, m*, is predicted by the relationship: m * = ( m ) 1 m The presence of such a metastable peak provides experimental evidence for a fragmentation mechanism that involves the transformation m 1 m For example, in the mass spectrum of the following trimethylsilyl enol ether (m/e 186 for M ) a fragment was observed at m/e 143 which was shown by exact mass measurement (143089) to have the composition Si The spectrum contained a metastable peak at m/e 1100 which corresponds to the fragmentation of the parent ion (m/e 186) to a fragment, m/e 143 The calculated position of the metastable peak is: 3 m* = It should be noted that the absence of a metastable peak, m*, does not provide any evidence concerning the possible occurrence of a fragmentation m 1 m (iii) Use of isotopic labeling Perhaps the most convincing evidence for the mechanism of a fragmentation arises from comparing the mass spectra of an unlabelled compound and the corresponding compound that has been synthesized in such a way that one or more stable isotopes [typically (or D), 18 0 or 13 ] has been incorporated at a specific position in the labeled molecule From the relative abundances of the fragment peaks and their isotope peaks, it is possible to trace where the labeled atom has gone during the fragmentation process As a simple example, when the routine mass spectra of ketone A and the trideuterated analog, ketone B, are measured the m/e value from the fragments indicated are clearly consistent with the structures shown ( 143) 186 or n =--Si ( 3 ) 3 =--Si ( 3 ) 3 n- 3 7 m/e 186 m* = 1100 m/e 143 3

4 3 ( 3 ) -- 3 A, m/e 100 ( 3 ) ( 3 ) m/e 71 3 m/e 57 ( 3 ) D m/e 7 b Use of mass spectra to establish the identity of two compounds hemists often have need to provide experimental evidence that two substances (eg, an unknown and an authentic sample) are identical If the substances are covalent solids that melt without decomposition, lack of depression in the melting point of a mixture of the two substances is often used as one piece of evidence In general at least two independent types of experimental evidence for identity should be obtained A second common type of evidence for identity consists of measuring a spectrum of each of the two substances on the same instrument under the same experimental conditions and showing that the two spectra are superimposable This criterion becomes increasingly rigorous with an increasing number of peaks in the spectrum since the probability of two different compounds having the same spectrum is very small if different spectral peaks all coincide For this reason comparison of mass spectra provides one of the most reliable tests for the identity of two substances omparison of infrared spectra (with fewer peaks than mass spectra) is somewhat less reliable and comparison of NM spectra, uv spectra, or gas chromatographic (G) retention times are distinctly less reliable tests for identity The fact that good mass spectra can be obtained with only 1- µg of material also recommends use of this technique for establishing identity Normally, sufficient sample for an adequate mass spectrum can be collected in one passage of sample through a G column Thus, this spectroscopic technique provides an ideal method for establishing the identity of G peaks that have been tentatively identified by comparison of retention times c General types of fragmentation observed 3 D m/e 59 ( 3 ) D--D 3 B, m/e D When a number of neutral molecules, M, suffer impact with a relatively high-energy electron beam (ca 70 ev equivalent to ca 160() kcal/mol), the molecular ions, M, will be formed with energies ranging from an energy just sufficient to ionize M to an energy sufficient to rupture one or more bonds in M forming various fragment ions, F 1, F, etc, and various neutral fragments, F 3, F 4, F 5, etc The most abundant fragments will be those formed either by rupture of one of the weakest bonds in M or by the rupture of one or more bonds in M to form fragment ions, F, or neutral fragments, F, that are much more stable than M In many cases, initially formed fragment ions, F 1, can be shown either to rearrange to new structures, F, or fragment further forming lower mass neutral and ionized fragments, F 3, and F 4 The following paragraphs list some of the more common fragmentation processes that ( 3 ) D are observed For any particular class of compound, the student is advised to read the appropriate section in a mass spectrometry monograph for a description of the important fragmentation processes observed in that class of compound Within any class of compounds, the abundance of fragment ions, F, relative to the molecular ion, M, is increased by: (1) decreasing unsaturation; () decreasing the number of rings present; and (3) increased branching in carbon chains (i) leavage of a single bond in M (1) -X bonds (where X is a heteroatom) [-X] X X () - bonds in alkvl groups [--] - (usually predominates) (becomes significant if X is relatively stable eg 1 ) ( charge with more stable carbonium ion) In both processes (1) and () the ease of cleavage increases as the stability of the carbonium ion increases (ie 3 < < < 3 < = < Ph Thus in an alkyl chain: favored sites of cleavage (3) --X or -=X bonds (where X =, N, or S) : = - - N =N 1 : 1 -- (where 1 is larger than ) Note that with N, the favored mode of cleavage places the () charge on the more stable ion, =N 1 4

5 (ii) leavage of a single bond in a fragment ion, F -- = (Especially favorable if is a very stable carbonium ion) - = (iii) leavage of two bonds in M to eliminate a neutral (or charged) even-electron fragment Small, even-electron fragments commonly eliminated include: -X (X is a heteroatom),= (mass 8), = (mass 8), = (mass 6), (mass 44), N (mass 7), = (mass 31), and =N (mass 30) N N - N - - X - ( ) n ( ) n -X - - (n = 0 to 4) (where X is a heteroatom) X -X (iv) earrangement of molecular ion, M, or fragmentation, F (may be followed by loss of even-electron fragments) The following four fragmentation processes in which an atom is transferred during fragmentation are examples of a general process known as the McLafferty rearrangement - : - : S : S 5

6 = X = X where X is a heteroatom 3 3 N - N = 3 3 Ph Ph- == 6

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