MASS Ions MKR 6 6 11

Mass Spectrometry:

1 Mass Spectrometry TYPES OF IONS, ITS FORMATION AND THEIR SIGNIFICANCE IN MASS SPECTRA

Mass Spectrometry:

2 Mass Spectrometry Types of ion peaks in mass spectra: 1) The molecular ion peak (M+ peak) 2) Base peak. 3) Isotope ion peak. 4) Fragment ion or Daughter ion peaks. 5) Rearrangement ion peak. 6) Metastable ion peak. 7) Multicharged ion peak. 8) Negative ion peak.

1) The Molecular Ion Peak (M+ Peak): :

3 1) The Molecular Ion Peak (M + Peak): When the vaporized organic sample passes into the ionization chamber of a mass spectrometer, it is bombarded by a stream of electrons with energy of 10-15 eV. The electron readily comes out from the highest occupied orbital of aromatic system, non bonding electron orbitals on oxygen and nitrogen atoms, double bond or triple bond. The ionization of C-C sigma bond is easier than C-H bond in alkanes. The formation of molecular ion and its peak:

Slide 4:

4 These electrons have a enough high energy to knock an electron of an organic molecule to form a positive ion. This ion is called the molecular ion. M + e – M + + 2 e – Where M represents the molecule and M + represents the molecular ion or parent ion. For example, in the mass spectrum of methanol, the heaviest ion has an m/z value of 32.

Slide 5:

5 CH3OH + 1 electron CH3OH + . + 2 electrons (note:  the symbols  +. indicate that a radical cation was formed)

1) The Molecular Ion Peak (M+ Peak): [2–4]:

6 1) The Molecular Ion Peak (M + Peak): [2–4] M (g) M + (g) +2e -

1) The Molecular Ion Peak (M+ Peak)::

7 1) The Molecular Ion Peak (M + Peak): Here, for n-pentane we can reasonably assume that this is the molecular ion. Because the relative mass of the compound is 72. This is the first ion to appear from the removal of an electron from the molecule, hence is called molecular ion or parent ion .

1) The Molecular Ion Peak (M+ Peak)::

8 1) The Molecular Ion Peak (M + Peak): The molecular ions or parent ions remain intact long enough (about 10 -6 sec) to reach the detector, only then a molecular ion peak is observed. This peak gives the molecular weight of the compound. With unit resolution, this molecular weight is the molecular weight to the nearest whole number. The molecular ion peak is usually the peak of highest mass number except for the isotope peak. This is an important parameter in the identification of a compound. In case of about 80-90 % organic compounds, the molecular ion peak is readily recognizable.

1) The Molecular Ion Peak (M+ Peak)::

9 1) The Molecular Ion Peak (M + Peak): If the energy of the beam is lowered, the tendency of the molecular ion to fragment lessens, as a result the intensity of the molecular ion peak increases. Similarly soft ionization techniques (i.e. chemical ionization and field desorption method) uses less energy compared to electron impact method and hence molecular ion becomes less susceptible for fragmentation.

1) The Molecular Ion Peak (M+ Peak): [2–4]:

10 1) The Molecular Ion Peak (M + Peak): [2–4] The intensity of the molecular ion peak depends upon the stability of molecular ion. The molecular ion is stabilized by the presence of π electron system which are capable of accommodating a loss of one electron more easily, therefore intensity of the molecular ion decreases with chain branching and increases with unsaturation and with number of rings. The intensity also increases by the presence of hetero atom having easily ionisable outer shell electron. If substituents that have favorable modes of cleavage are present, the molecular ion peak will be less intense, and fragment peaks will be more intense. The intensity of molecular ion peak:

Slide 11:

11 Molecular ion stability order: Aromatic compounds > conjugated alkenes > alicyclic compounds > sulphides > unbranched hydrocarbons >mercaptans >ketones >amines > esters > ethers > carboxylic acids > branched hydrocarbons > alcohols.

1) The Molecular Ion Peak (M+ Peak): [2–4]:

12 1) The Molecular Ion Peak (M + Peak): [2–4] Intensity of Molecular Ion In The Mass Spectrum Strong Medium Weak/not detectable Aromatic hydrocarbon, Aromatic Fluorides, Chlorides, Nitriles and amines, Saturated cyclic compounds. Aromatic Bromide and Iodides, Conjugated alkenes, Straight chain ketones and aldehydes, Acids, esters, amides, ethers, Alkyl halides. Aliphatic alcohols, amines and Nitriles, Branched chain compounds, Nitro compounds.

1) The Molecular Ion Peak (M+ Peak)::

13 1) The Molecular Ion Peak (M + Peak): Abundant molecular ions: Aryl amines, nitriles, fluorides and chlorides give more abundance. Aromatic hydrocarbons and heteroaromatic compounds give strong M+ peaks. Aryl bromides and iodides lose halogen too readily to give strong molecular ion peaks. Other classes with weakened M+ peaks are aryl ketones (which fragments easily to ArCO + ) and benzyl compounds such as side chain hydrocarbons (ArCH 2 R) or ArCH 2 X (both of which fragment at benzylic carbon).

Slide 14:

14 Naphthalene (MW = 128.17) The intensity of the peak is strong in aromatic systems

1) The Molecular Ion Peak (M+ Peak)::

15 1) The Molecular Ion Peak (M + Peak): This is the characteristic of highly branched molecules whatever the functional class. Alcohols and molecules with long alkyl chains also fragment easily and lead to very weak M+ peaks. Absence of molecular ion: (an extremely weak M+ peak)

Slide 16:

16 An alcohol's molecular ion is small or non-existent.  Cleavage of the C-C bond next to the oxygen usually occurs.

1) The Molecular Ion Peak (M+ Peak)::

17 1) The Molecular Ion Peak (M + Peak): It is difficult to find the molecular ion peak because the peak may be very weak or it may not appear at all. Hence the “nitrogen rule” is often helpful in recognition the molecular ion peak. Recognition of Molecular Ion Peak:

1) The Molecular Ion Peak (M+ Peak)::

18 1) The Molecular Ion Peak (M + Peak): The molecular ion peak in the aromatic compounds is relatively much intense due to the presence of pi- electron system. Unsaturated compounds give more intense peak as compared to the saturated or the cyclic molecule. The relative abundance of the saturated hydrocarbon is more than the corresponding branched chain compound with the same number of C atoms. For example, the molecular ion peak for n- pentane is more intense than that of neopentane. It helps in the determination of molecular weight of compound. Important Features/ Significance of molecular Ion Peak:

Important Features/ Significance of molecular Ion Peak::

19 Important Features/ Significance of molecular Ion Peak : The ion must have an odd number of electrons. When a molecule is ionized by an electron beam. The ion must be capable of forming the important ions in the spectrum The stability can be predicted by the molecular ion peak. Absence of molecular ion peak in the mass spectrum means that the compound is highly branched or tertiary alcohol. Primary and secondary alcohols give a very small molecular ion peaks.

1) The Molecular Ion Peak (M+ Peak)::

20 1) The Molecular Ion Peak (M + Peak): Conjugated olefins show more intense molecular ion peak as compared tot the corresponding non conjugated olefins because of their stability. The substituent groups like –NH 2 , -OH, -OR etc., which lower the ionization potential increase the relative abundance in case of aromatic compounds whereas the groups like –NO 2 , -CN, etc., decreases the relative abundance of aromatics. In case of chloro or bromo compounds, isotope peaks are also found along with the molecular ion peak. Important Features/ Significance of molecular Ion Peak:

1) The Molecular Ion Peak (M+ Peak):-:

21 1) The Molecular Ion Peak (M + Peak):- SIGNIFICANCE: Its help us to obtain molecular formula of a compound. Since atomic masses are not exact integers, each combination of atoms will have unique non- integers value. For example, CH 2 O and C 2 H 6 both have integral mass of 30 but the accurate masses are 30.010565 and 30.46950 respectively. Accurate mass measurement will therefore distinguish between these two molecules Literature/library contains enough amounts of data to reduce the problem of relating accurate masses to possible molecular formula. The abundance/intensity of the molecular ion peak tells something about its stability.

NITROGEN RULE::

22 NITROGEN RULE: It states that, “if a compound has an even number of nitrogen atoms (or no nitrogen atoms), its molecular ion will appear at an even mass value. On the other hand a molecule with an odd number of nitrogen atoms will form a molecular ion with an odd mass”. This rule holds for all compounds containing C, H, N, O,S and halogens as well as less usual atoms like P, B, Si, As, etc., 1) The Molecular Ion Peak (M + Peak):

NITROGEN RULE::

23 NITROGEN RULE: The nitrogen rule stems from the fact that nitrogen has an even atomic weight and an odd valance whereas all the other elements encountered in organic mass spectrometry have either an even mass and an even valance or an odd mass and an odd valence. NOTE: An important corollary is that the fragmentation at a single bond gives an odd numbered ion fragment from an even numbered molecular ion and vice versa. For this corollary to hold, the ion fragment must contain all of the nitrogen (if any) of the molecular ion

Slide 24:

24 Ions with no nitrogen or an even # N atoms odd-electron ions even-number mass even-electron ions odd-number mass Ions having an odd # N atoms odd-electron ions odd-number mass even-electron ions even-number mass

Slide 25:

25 4-methyl-3-pentene-2-one N,N-diethylmethylamine

NITROGEN RULE::

26 NITROGEN RULE: COMPOUND NUMBER OF NITROGEN MASS Ethylamine (C 2 H 5 NH 2 ) 1 45 Ethylenediamine (H 2 NCH 2 CH 2 NH 2 ) 2 60 Nitrobenzene (C 6 H 5 NO 2 ) 1 123 Fragments at m/z =46 & m/z=30 2,4- dinitrophenol (C 6 H 4 (NO 2 ) 2 ) 2 184 Fragment M + – H m/e 183 M + – H – C O m/e 155 1) The Molecular Ion Peak (M + Peak):

1) The Molecular Ion Peak (M+ Peak)::

27 1) The Molecular Ion Peak (M + Peak): A third indication that an ion, indeed the molecular ion, may be obtained by looking for the presence of an M-15 peak (loss of CH3), or an M-18 peak (loss of H2O) or an M-31 peak (loss of OCH3 from ethyl esters). If a molecular ion loses a methyl radical, the mass spectrum will show an ion 15 mass units below the molecular ion, so we can write this process as

1) The Molecular Ion Peak (M+ Peak)::

28 1) The Molecular Ion Peak (M + Peak): Molecular ion may also result in; M-1 peak: common M-2 peak: occur occasionally, due to the loss of H2 M-13 to M-14: presence of contaminants or the presumed molecular ion is actually a fragment ion. M-16(loss of O), M-17(loss of OH), M-18(loss of H2O). M-19 to M-25: very uncommon (except for the loss of Fluorine or HF).

1) The Molecular Ion Peak (M+ Peak)::

29 1) The Molecular Ion Peak (M + Peak): The ring rule explains the number of unsaturation and the number of rings present in the given molecule. R is equal to the number of rings in the molecule plus the number of double bonds plus twice the number of triple bonds. The ring rule for the molecule CwHxNyOz can be stated as follows: RING RULE: R = w + 1 + ((y-x) / 2)

1) The Molecular Ion Peak (M+ Peak)::

30 1) The Molecular Ion Peak (M + Peak): Eg: 1: C6 H6 (w = 6; x = 6; y = 0; z = 0) R = 6 + 1 – 3 = 4 (one ring +three double bonds) 2: C2 H5 O C2 H5 (w = 4; x = 10; z = 1) R = 4 + 1 – 5 = 0 (no rings; no unsaturation) 3: C6 H5 CH3 (w = 7; x = 8) R = 7 + 1 – 4 = 4 (one ring + three double bonds) 4: C6 H5 C O C6 H5 (w = 13; x = 10; z = 1) R = 13 + 1 – 5 = 9 (two rings + seven double bonds) RING RULE:

2) Base peak:-:

31 2) Base peak:- The largest peak in the mass spectrum corresponding to the most abundant ion or the most intense peak in the spectrum is called the base peak and is assigned a value of 100 %. The base peak will be the most stable ion peak (fragment ion or some times molecular ion peak) The molecular ion peak and all other peaks are reported as percentages of the base peak. Depending on the nature of the compound it may be either a fragment ion peak or the parent ion peak. Sometimes molecular ion peak may be the base peak.

2) Base peak:-:

32 2) Base peak:- Example:- The following diagram displays the mass spectra of three simple gaseous compounds, carbon dioxide, propane and cyclopropane. The molecules of these compounds are similar in size, CO 2 and C 3 H 8 both have a nominal mass of 44 amu, and C 3 H 6 has a mass of 42 amu. The molecular ion is the strongest ion in the spectra of CO 2 and C 3 H 6 , and it is moderately strong in propane. The unit mass resolution is readily apparent in these spectra (note the separation of ions having m/z=39, 40, 41 and 42 in the cyclopropane spectrum).

Slide 33:

33 Example: CO 2 = 44 C 3 H 8 = 44 C 3 H 8 = 42 M+ peak is base peak M+ peak is base peak Fragment ion peak is base peak 2) Base peak:-

3) ISOTOPE ION /ISOTOPE PEAKS:-:

34 3) ISOTOPE ION /ISOTOPE PEAKS:- Isotopes: These are the atoms of the same element that have similar atomic number (i.e. same number of protons) but vary in their atomic masses (i.e. different number of neutrons). Most atoms have several naturally occurring isotopes, but not all the isotopes are equally abundant in nature. Isotones: These are the atoms of the different element that have same number of neutrons but vary in atomic number and atomic masses. Isobars: These are the atoms of the element that have similar atomic masses (i.e. same number of neutrons) but vary in their atomic number (i.e. different number of protons).

3) ISOTOPE ION /ISOTOPE PEAKS:-:

35 3) ISOTOPE ION /ISOTOPE PEAKS:- NATURAL ABUNDANCE OF ISOTOPES OF COMMON ELEMENTS Element Isotope Exact mass Natural abundance (%) %relative to most abundant isotope Hydrogen 1 H 2 H 1.00783 2.01410 99.985 0.015 100 0.015 Carbon 12 C 13 C 12.00000 13.00336 98.89 1.11 100 1.08 Nitrogen 14 N 15 N 14.00307 15.00011 99.89 1.11 100 0.36 Oxygen 16 O 17 O 18 O 15.99491 16.99914 17.99916 99.79 0.037 0.204 100 0.04 0.20 Fluorine 19 F 18.99840 100 100 Chlorine ( 3:1 ) 35 Cl 37 Cl 35.96885 36.9690 75.537 24.47 100 32.40 Bromine ( 1:1 ) 79 Br 81 Br 78.9183 80.9163 50.54 49.48 100 97.85 Sulfur 32 S 33 S 34 S 100 0.78 4.40 Silicon 28 Si 29 Si 30 Si 100 5.10 3.35 Phosphorous 31 P 100 100

3) ISOTOPE ION /ISOTOPE PEAKS:-:

36 3) ISOTOPE ION /ISOTOPE PEAKS:- The presence of these isotopic elements in the molecules, there is an observable peak known as isotope peak at different mass units beyond the molecular ion peak. Percentage of natural abundance refers to the quantity of a specific isotope that occurs in natural sample of an element. It has been established that the distribution of the elements on earth is such that a natural sample of an element will contain the same percent of abundance of given isotope, no matter where the sample was obtained.

Slide 37:

37 Because of the presence of these elements, there is an observable peak (known as isotope peak) one/two/four/six mass units beyond the molecular ion peak. The number of isotope peaks and the relative intensity of each peak depend on the chemical formula of the ionic fragment and the natural isotopic composition of its constituent elements.

Slide 38:

38 Mass spectrometers are capable of separating and detecting individual ions even those that only differ by a single atomic mass unit. As a  result molecules containing different isotopes can be distinguished. This is most apparent when atoms such as bromine or chlorine are present (79Br : 81Br, intensity 1:1 and 35Cl : 37Cl, intensity 3:1) where peaks at "M" and "M+2" are obtained. The intensity ratios in the isotope patterns are due to the natural abundance of the isotopes. "M+1" peaks are seen due the the presence of 13C in the sample.

3) ISOTOPE ION /ISOTOPE PEAKS:-:

39 3) ISOTOPE ION /ISOTOPE PEAKS:- In high resolution mass spectrum and a complete (rather than a simplified) mass spectrum , we will find a small line one m/z unit to the right of the molecular ion peak; this small peak is called as M+1 Peak. The isotopes which are heavier by one mass unit generally give M+1 peak. M+1 Peak:

3) ISOTOPE ION /ISOTOPE PEAKS:-:

40 3) ISOTOPE ION /ISOTOPE PEAKS:- 13C is stable isotope of carbon (don’t confuse it with 14C isotope which is radioactive) In simple compound like Methane (CH4), 1.11 (≈1) in every 100 of these molecules will contain carbon-13 rather than the more common carbon -12. This means that one in every 100 of the molecules will have a mass of 17(13+4) rather than 16(12+4). The mass spectrum will therefore have a line corresponding to the molecular ion [ 13 CH4] + as well as [ 12 CH4] +, whose intensity will be in the ratio 1:100.

Slide 41:

41 The line at m/z=17 will be much smaller than at m/z=16 because the carbon-13 isotope is much less common. Statistically we will have a ratio of approximately 1 of the heavier ions to every 99 of the lighter ones, that’s why the intensity of M+1 peak is much smaller than the M+ peak.

3) ISOTOPE ION /ISOTOPE PEAKS:-:

42 3) ISOTOPE ION /ISOTOPE PEAKS:- Ethane (C2H6) has a molecular weight of 30 amu when it contains the most common isotopes of carbon and hydrogen. Its molecular ion peak should appear at a position in the spectrum corresponding to a mass of 30. Occasionally, a sample ethane yields a molecule in which one of the carbon atoms is replaced by heavy isotope of carbon i.e. 13C. This molecule would appear in the mass spectrum at 31. The relative abundance of 13C atom in nature is 1.11% of the 12C atoms.

3) ISOTOPE ION /ISOTOPE PEAKS:-:

43 3) ISOTOPE ION /ISOTOPE PEAKS:- Since there are two carbon atoms in ethane, a molecule show the M+1 peak at 31 amu and the intensity of molecular ion peak in its spectra would be 2.22% (1.11 x 2). This mass 31 peak is called the M+1 peak . M+1 peak of ethane also could form from another manner. If a deuterium atom (2H) is replaced one of the hydrogen atoms in a molecule, the molecule would also have a mass of 31 the natural abundance of deuterium is only 0.016% of the abundance of 1H atoms. The intensity of the M+1 peak would be 0.096% (6 x 0.016) of the intensity of molecular ion peak.

3) ISOTOPE ION /ISOTOPE PEAKS:-:

44 3) ISOTOPE ION /ISOTOPE PEAKS:- Significance of M+1 peak: The intensity of M+1 peak allows an estimate to be made for the number of carbon and nitrogen atom present in molecule. E.g. 12 C has an isotope 13 C, their abundance are in the ratio 100:1.11 So if a compound contains 6 carbons, then each atom has a 1.1% abundance of 13 C. Therefore if molecular ion peak has an intensity of 100% then the isotope peak (one mass unit higher) will have an intensity of 6 X 1.1= 6.6%. But if the molecular ion peak is not 100% then we can calculate the relative abundance of the isotope peak to the molecular ion peak,

Slide 45:

45 Number of carbon atoms will be = If M+ peak and M+1 peak has an intensity of 34% and 2.3% respectively, Then the relative abundance of the isotope peak to M+ will be = 2.3/34 X 100 = 6.8%. Therefore 6.8/1.1 = 6 carbons

3) ISOTOPE ION /ISOTOPE PEAKS:-:

46 3) ISOTOPE ION /ISOTOPE PEAKS:- M+2 Peaks : A small line at two m/z units to the right of the main molecular ion is called as M+ 2 peak. The M+2 peak is given by the isotopes which are heavier by two mass units to M+. a) Compounds containing chlorine atoms: The molecular ion peaks (M+ and M+2) each contain one chlorine atom - but the chlorine can be either of the two chlorine isotopes, 35 Cl and 37 Cl. The molecular ion containing the 35 Cl isotope has a relative formula mass of 78. The one containing 37 Cl has a relative formula mass of 80 - hence the two lines at m/z = 78 and m/z = 80 .

3) ISOTOPE ION /ISOTOPE PEAKS:-:

47 3) ISOTOPE ION /ISOTOPE PEAKS:- Notice that the peak heights are in the ratio of 3:1. That reflects the fact that chlorine contains 3 times as much of the 35 Cl isotope as the 37 Cl has. That means that there will be 3 times more molecules containing the lighter isotope than the heavier one.

3) ISOTOPE ION /ISOTOPE PEAKS:-:

48 3) ISOTOPE ION /ISOTOPE PEAKS:- You might also have noticed the same pattern at m/z = 63 and m/z = 65 in the mass spectrum above. That pattern is due to fragment ions also containing one chlorine atom - which could either be 35 Cl or 37 Cl. The fragmentation that produced those ions was:

Slide 49:

49 bromine vinyl chloride methylene chloride Methyl bromide

3) ISOTOPE ION /ISOTOPE PEAKS:-:

50 3) ISOTOPE ION /ISOTOPE PEAKS:- Ions containing one bromine atom display lines of roughly equal intensity (1:1) and separated by two mass units. Similarly for ions containing one chlorine atom, the relative intensity of lines, separated by two mass units, is 3:1 .

Slide 51:

51 Note the isotope pattern at 122 and 124 that represent the M amd M+2 in a 1:1 ratio. Loss of 79Br from 122 or 81Br from 124 gives the base peak a m/z = 43, corresponding to the propyl cation. Note that other peaks, such as those at m/z = 107 and 109 still contain Br and therefore also show the 1:1 isotope pattern.

3) ISOTOPE ION /ISOTOPE PEAKS:-:

52 3) ISOTOPE ION /ISOTOPE PEAKS:- If one is certain about the molecular formula then we can calculate the approximate intensity of M+1 peak and M+ 2 peak as follows: Note : The formulae are only applicable to molecules containing C, H, N, O, F, P, I.

3) ISOTOPE ION /ISOTOPE PEAKS:-:

53 3) ISOTOPE ION /ISOTOPE PEAKS:- The usefulness of M+1 and M+ 2 peaks can be better illustrated using following examples Compound Molecular mass M + intensity (%) M+1 relative intensity (%) M+2 relative intensity (%) Carbon monoxide (CO) 28 100 1.12 0.2 Nitrogen (N 2 ) 28 100 0.76 - Ethylene (C 2 H 4 ) 28 100 2.23 0.01 Propane (C 3 H 6 ) 42 100 3.426 0.0564 Diazomethane (CH 2 N 2 ) 42 100 1.08 0.01

3) ISOTOPE ION /ISOTOPE PEAKS:-:

54 3) ISOTOPE ION /ISOTOPE PEAKS:- The intensity ratio of molecular ion clusters owing to halogen isotopes may be calculated by means of binomial expression (a +b) n Where ‘a’ is the % of natural abundance of lighter isotope; ‘b’ is the % of natural abundance of heavier isotope; ‘n’ number of isotope atoms present in the ion. When n = 2 , then a 2 +2ab+b 2 is the binomial expression and when n =3 , then a 3 +3a 2 b+3ab 2 +b 3 is the binomial expression .

3) ISOTOPE ION /ISOTOPE PEAKS:-:

55 3) ISOTOPE ION /ISOTOPE PEAKS:- When the ionic structure has two chlorine atoms then the expression for the number and relative abundances of peaks becomes a 2 +2ab+b 2 Since 35Cl and 37Cl are in the ratio of 3:1, i.e., a:b = 3:1 and the above expression becomes 3 2 + 2 X 3 X 1 + 1 2 = 9:6:1 Thus, for any ionic structure containing two chlorine atoms there will be three peaks in abundance ratio 9:6:1 and separated by two mass units ( first peak contains 35Cl atoms and each successive peak has 35Cl is replaced by 37Cl until the last peak contains two 37Cl atoms). Example:-1

3) ISOTOPE ION /ISOTOPE PEAKS:-:

56 3) ISOTOPE ION /ISOTOPE PEAKS:- The above ratio can also be calculated by multiplying the ratios of the individual chlorine atoms, (3:1) X (3:1) 9 : 3 3 : 1 ------------------------------- 9 : 6 : 1 ------------------------------- M+ M+2 M+4 Combination of chlorine and bromine atoms may be treated in a similar manner by using the product of the binomial expressions for chlorine and bromine (a + b) n (c + d) m , where n is the number of chlorine and m is the number of bromine atoms.

3) ISOTOPE ION /ISOTOPE PEAKS:-:

57 3) ISOTOPE ION /ISOTOPE PEAKS:-

4) FRAGMENT IONS/ DAUGHTER IONS:-:

58 4) FRAGMENT IONS/ DAUGHTER IONS:- The ions produced from the molecular ion by cleavage of bonds are called as fragment ions. Fragmentation of molecular ion may occur by cleavage of bonds in two ways: heterolytic or homolytic. M 1 + M 2 + + M 3

Slide 59:

59

4) FRAGMENT IONS/ DAUGHTER IONS:-:

60 4) FRAGMENT IONS/ DAUGHTER IONS:- The line at m/z = 57 , is obtained by the fragment C4H9 + i.e. [CH3CH2CH2CH2] + and this would be produced by the following fragmentation: Hence the loss of methyl group from pentane gives a peak at m/e=57 .

4) FRAGMENT IONS/ DAUGHTER IONS:-:

61 4) FRAGMENT IONS/ DAUGHTER IONS:- Similarly, the line at m/z = 43 is the fragment obtained from following: The line at m/z = 43 is due to a break producing a 3-carbon ion. Where as the line at m/z = 29, is typical of an ethyl ion , [CH3CH2] + : Many of the peaks in mass spectrum due to fragment ions. The greater the potential energy i.e. electron impact, smaller the fragments.

Slide 62:

62 If you remember, the m/z = 57 peak in pentane was produced by [CH3CH2CH2CH2]+. If you look at the structure of pentan-3-one, it's impossible to get that particular fragment from it.

Slide 63:

63 Work along the molecule mentally chopping bits off until you come up with something that adds up to 57. With a small amount of patience, you'll eventually find [CH3CH2CO]+ - which is produced by this fragmentation: You would get exactly the same products whichever side of the CO group you split the molecular ion. The m/z = 29 peak is produced by the ethyl ion - which once again could be formed by splitting the molecular ion either side of the CO group.

Slide 64:

64 Look first at the very strong peak at m/z = 43. This is caused by a different ion than the corresponding peak in the pentane mass spectrum. This peak in 2-methylbutane is caused by:

Slide 65:

65 The ion formed is a secondary carbocation - it has two alkyl groups attached to the carbon with the positive charge. As such, it is relatively stable. The peak at m/z = 57 is much taller than the corresponding line in pentane. Again a secondary carbocation is formed - this time, by:

Slide 66:

66

Slide 67:

67

Slide 68:

68

4) FRAGMENT IONS/ DAUGHTER IONS:-:

69 4) FRAGMENT IONS/ DAUGHTER IONS:- Many of the peaks in the mass spectra are due to the fragments which are designated as fragment peaks. The greater the fragmentation of molecular or parent ion the greater is the loss in its peak intensity. The fragmentation ions should be examined for characteristic mass losses from the parent ion because it helps us to conclude tentatively about the functional group lost from the parent ion during fragmentation.

Slide 70:

70 Probability of fragmentation decreases in order: Alcohols > branched hydrocarbons > carboxylic acids > ethers > esters > amines > ketones > thiols > straight chain hydrocarbons > sulphides > alicyclic compounds >conjugated dienes > aromatic compounds.

4) FRAGMENT IONS/ DAUGHTER IONS:-:

71 4) FRAGMENT IONS/ DAUGHTER IONS:- Ion m/e a Neutral fragment lost Tentative Inference M-1 H Aldehyde M-15 CH 3 Methyl group M-18 H 2 O Alcohol M-28 C 2 H 4 ,CO,N 2 b Mc Lafferty rearrangement, CO etc. M-29 CHO,C 2 H 5 Aldehyde, Ethyl group M-31 OCH 3 Methyl ester M-34 H 2 S Thiol M-35,M-36 Cl, HCl Chlorides M-43 CH 3 CO,C 3 H 7 b Methyl ketone, Propyl group M-45 COOH Carboxylic acid M-60 CH 3 COOH Acetate a M = mass of the molecular ion , b Alternatives can be distinguished by high resolution MS.

4) FRAGMENT IONS/ DAUGHTER IONS:-:

72 4) FRAGMENT IONS/ DAUGHTER IONS:- Common Mass Spectrum Fragments

4) FRAGMENT IONS/ DAUGHTER IONS:-:

73 4) FRAGMENT IONS/ DAUGHTER IONS:- A peak at mass 19 always indicates fluorine; mass 30 is always for primary amines. The peaks at masses 31, 45, 59 indicate the presence of oxygen as alcohol or ether, mass 33 shows a thiol, mass 77 corresponds to the presence of benzene ring, mass 91 indicates a monobasic carboxylic acid or the presence of a tolyl group. The peak at mass 29 may be in part C2 H5+ and in part of C4 H10+2. The peaks at masses 59, 44 and 30 indicate the fragments C4 H10+, C3 H7+, C2 H5+ respectively of which either one hydrogen is replaced by a heavier isotope deuterium or C12 is replaced by C13. Significance:

4) FRAGMENT IONS/ DAUGHTER IONS:-:

74 4) FRAGMENT IONS/ DAUGHTER IONS:- The peak at mass 29 may be in part C2 H5+ and in part of C4 H10+2. The peaks at masses 59, 44 and 30 indicate the fragments C4 H10+, C3 H7+, C2 H5+ respectively of which either one hydrogen is replaced by a heavier isotope deuterium or C12 is replaced by C13. Fragment peaks give valuable information regarding molecular structure, because fragmentation is specific to the structures. We can predict the no. of carbon atoms in the ion. They are also used as building blocks to reconstruct the molecular structure. Significance :

5) REARRANGMENT ION:-:

75 5) REARRANGMENT ION:- Rearrangement ions are fragments whose origin can not be described by simple cleavage of bonds in the molecular ion, but are a result of intra-molecular atomic rearrangement during fragmentation. These are the ions which are formed from the molecular ion by redistribution of atoms at the moment of decomposition of the molecular ion. These peaks also occur at mass numbers in mass spectrum but not by simple fragmentation. These are probably due to recombination of fragment ions. Rearrangements involving migration of hydrogen atoms in molecules that contain a heteroatom are common. One important example is the McLafferty rearrangement.

5) REARRANGMENT ION:-:

76 5) REARRANGMENT ION:- Hydrogen –transfer rearrangements are very common, though migration of an alkyl group can also occur. In hydrocarbons, the rearrangement is non-specific and unpredictable. On the other hand, the rearrangement is specific in molecules containing a hetero atom; this may result in a very intense peak.

5) REARRANGMENT ION:-:

77 5) REARRANGMENT ION:- For example: a prominent peak in the spectrum of diethyl ether occurs at m/e =31. This peak is due to the ion CH 3 O + which is formed by rearrangement of C 2 H 5 O + ion .

6) METASTABLE ION:-:

78 6) METASTABLE ION:- The ions resulting from decomposition between the source region and magnetic analyzer are called as Metastable Ions . As we know that molecular ions formed in the ionization chamber do one of the things: Either they decompose completely and very rapidly in the ion source (ionization chamber) and never reach the collector (as in case of highly branched molecular ions with lifetimes less than ≈10 -5 s). Or else they survive long enough to reach the collector and be recorded there (life times longer than ≈10 -5 s). Depending on the inherent stability of an ion, and on the amount of excitation energy absorbed on bombardment, ion lifetimes will vary in a complex manner

6) METASTABLE ION:-:

79 6) METASTABLE ION:-

6) METASTABLE ION:-:

80 6) METASTABLE ION:-

6) METASTABLE ION:-:

81 6) METASTABLE ION:- Suppose that a large number of molecules of M are converted to M+., then not all of the M+. will possess the same excitation energy and therefore some will have longer lifetimes than others. Since the translational energy of the daughter ion A+/ (m*) is lower than that of the parent ion, therefore this A+/ (m*) will arrive at the collector differently from the ‘normal’ A+/ m ion.

The most important characteristics of metastable peaks are: :

82 These peaks are much broader, that is, they spread over several mass units. These peaks appear in the mass spectrum usually at non-integral m/e values. These peaks are of relatively low abundance or low intensity. The metastable ions can be detected by a double focusing mass spectrometer. If an ion fragments after acceleration but before entering the magnetic field a metastable peak is observed in the mass spectrum . The most important characteristics of metastable peaks are :

6) METASTABLE ION:-:

83 6) METASTABLE ION:- The apparent mass of metastable ion A+ / m* can be calculated using following relation Where, m* is apparent mass of metastable ion, m is mass of the normal daughter ion, M + is mass of the molecular ion.

6) METASTABLE ION:-:

84 6) METASTABLE ION:- Consider the formation of metastable peaks in the spectrum of toluene. Two strong peaks at m/e 91 and at m/e 65 are formed. The peak at m/e 91 is due to the formation of tropylium cation which loses a molecule of acetylene (26 mass units) to give C 5 H 5 + (m/e 65). Example:-

6) METASTABLE ION:-:

85 6) METASTABLE ION:- Suppose the transition C 7 H 7 + (91) to C 5 H 5 + (65) occurs in the second field free region , then a metastable peak is determined as = 65 X 65/ 91 = 46.4 A metastable peak in case of toluene appears at 46.4 in the mass spectrum.

6) METASTABLE ION:-:

86 6) METASTABLE ION:- It help to establish whether two or more ions in the spectrum are related by a fragmentation process or not. SIGNIFICANCE:-

7) MULTIPLY CHARGED IONS:-:

87 7) MULTIPLY CHARGED IONS:- In mass spectrometry, the ions are generally carrying a single positive charge. However sometimes doubly or even triply charged ions are found in mass spectrum The molecular ions that becomes multiply charged during the ionization processes, will generate a peak in the mass spectrum at an m/z value numerically equal to 1/2 (for doubly charged) or 1/3 (for triply charged) of m/z value of their actual mass number.

7) MULTIPLY CHARGED IONS:-:

88 7) MULTIPLY CHARGED IONS:- Example:- Mass spectrum of chrysene (mol.wt. 228) exhibits a relatively intense peak at m/z 114 for the doubly charged molecular ion.

7) MULTIPLY CHARGED IONS:-:

89 7) MULTIPLY CHARGED IONS:- The formation of these multiply charged ions are common in hetero atomic molecules, also they are common in inorganic mass spectrometry. E.g. fixed gases such as CO 2+ , N2 2+ , CO2 2+ and O2 2+ . In hydrocarbons the abundance of these ions varies inversely with degree of saturation i.e. higher the unsaturation, higher will be the abundance of multiply charged ions. Thus spectral intensities increase in the order, Paraffins, Olefins and aromatic. Multiply charged ions are in general, insignificant in mass spectra of compounds. However the peaks pertaining to stable multiply charged ions, may sometimes be useful in data interpretation.

8) NEGATIVE ION:-:

90 8) NEGATIVE ION:- In addition to positive ions, negative ions may be formed from electron bombardment of the sample. This results due to the capture of electron by a molecule during collision of molecules. Negative ions can be produced in three ways:-

8) NEGATIVE ION:-:

91 8) NEGATIVE ION:- The formation of negative ions is very rare, since the production of cations is favored over production of anions by a factor of about 10 4 . Examples:- Negative ions formed in mass spectrometry are O - , OH - and C 2 H - . The negative ions are not useful in the structural determinations; hence they are generally ignored during studies.

References:-:

92 References:- B K Sharma, Instrumental Methods of Chemical Analysis. Goel Publishing House.       Meerut. XXIV; 2005: S-844-89. www.chemguide.co.uk/analysis/masspecmenu.html William Kemp, Organic Spectroscopy, Hamshire, III; 1991: 293-307. Silverstein R M, Clayton Bassler G, Terence C M, Spectrometric Identification of      Organic Compounds, John Wiley & Sons, New York. V; 1991: 03-39. Donald L. Pavia, Gary M. Lampman, George S. Kriz. Introduction to Spectroscopy.      III; Harcourt College Publishers; 390-404. http://www.chem.uic.edu/web1/ocol/spec/MS2.html Introduction to Mass Spectroscopy, Editors; S K Agarwal & H C Jain, ISMAS                  Publication; 139-56.

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93 Jagmohan, Organic Spectroscopy principles and applications, Narosa Publishing House, NewDelhi, II; 2005: 340-1, 358-64. Vogel’s Textbook of Practical Organic Chemistry, Addison Wesley Longmann Ltd, England,V; 1989:362-70. http://www.chem.uoa.gr/applets/AppletMS/Appl_Ms2.html-isotope Sharma Y.R, Elementry Organic Spectroscopy Principles and Chemical Applications. S.chand, NewDelhi, I;2006;239-45. http://www.chemguide.co.uk/analysis/masspec/mplus.html#top Kenneth A Connurs, A text book of Pharmaceutical Analysis, John Wiley and sons, NewYork, III; 1982: 310-1, 316-7. Gurdeep R Chatwal, Sham K Anand, Instrumental Methods of Chemical Analysis, Editor-M Arora Aseem Anand, Himalaya Publishing House, Mumbai,V; 2002:2.285-9.