MASS SPECTROSCOPY (MS)

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1 MASS SPECTOSCOPY (MS) Castor seeds icin (toxic protein)

2 INTODUCTION Does not involve absorption of electromagnetic radiation. It is a spectroscopic technique, by virtue of its use in structure elucidation. MS is used to determine:- 1) Molecular weight (from Low esolution Mass Spectroscopy, LMS). 2) Molecular formula (from igh esolution Mass Spectroscopy, MS). 3) To detect within a molecule the places at which it is preferred to fragment (recognizable groupings can be deduced). 4) To identify unknown compounds by comparison with MS of standards (fingerprint comparison).

3 The Mass Spectrometer The three essential components of a mass spectrometer are:- 1. The Ion Source A small sample of a compound is ionized (individual molecules are changed into ions), usually to cations by loss of an electron. 2. The Mass Analyzer The ions are sorted and separated according to their mass to charge ratio (m/z). 3. The Detector The separated ions are then detected and tallied, and the results are displayed on a chart.

4 Ions are very reactive and short-lived, their formation and manipulation is conducted in a vacuum. Different types of ionization are known. The most common method is:- Electron Ionization Mass Spectroscopy (EIMS) ionization is effected by a high energy beam of electrons, and ion separation is achieved by accelerating and focusing the ions in a beam, which is then bent (deflected) by an external magnetic field. The ions are then detected electronically and the resulting information is stored and analyzed in a computer.

5 EIMS SPECTOMETE

6 IONIZATION POCESS A high energy electron collides with a molecule, it ionizes it by knocking away one of the molecular electrons (either bonding or non-bonding). This results in the formation of a molecular ion. esidual energy from the collision may cause the molecular ion to fragment, (into neutral pieces and smaller fragment ions).

7 adical cation molecular ion (adical cation) cation fragment ions (radical) Only cations are detected in normal MS spectra; the presence of neutral fragments is recognized through inference.

8 The Nature of Mass Spectra Vertical bar graph, in which each bar represents an ion having a specific mass-to-charge ratio (m/z) and the length of the bar indicates the relative abundance of the ion. Modern mass spectrometers easily distinguish (resolve) ions differing by only a single atomic mass unit (amu), and thus provide completely accurate values for the molecular mass of a compound. and lower-mass ions are fragments from the molecular ion, assuming the sample is a single pure compound.

9 % abundance (relative abundance) base peak 106 Molecular ioṇ mass-to-charge ratio (m/z) The most intense ion is assigned an abundance of 100, and it is referred to as the base peak. Most of the ions have a single charge, so the m/z value is equivalent to mass itself esolution is, at least, to a single atomic mass unit (amu). The highest-mass ion is normally the molecular ion.

10 The Molecular Ion 80-90% of organic compounds give rise to spectrum in which the peak with the highest m/z value corresponds to the molecular ion. The stability of the molecular ion and consequently the intensity of the molecular ion peak is related to molecular structure. Conjugated systems show stable molecular ion. Cyclic structures give rise to a relatively strong molecular ion peak, (two bonds have to be broken before the m/z ratio change). molecular ion will be a weak peak, if fragmentation results in the formation of neutral molecule or stable fragment ion.

11 True molecular-ion peaks are of even m/z ratio, unless an odd number of nitrogen atoms are present in the molecule. ISOTOPES Since a mass spectrometer separates and detects ions of slightly different masses, it easily distinguishes different isotopes of a given element. The molecular ion is composed of the most abundant isotopes in the molecules. Molecular ion [M]. [M1]. [M2]. etc... Due to the presence of isotopes

12 106 Molecular ion (m/z) [M1]. at 107

13 [M] at 158 [M2] at 160 [M4] at 162 Bromine: 50.50% 79 Br and 49.50% 81 Br natural bromine consists of a nearly 50:50 mixture of isotopes having atomic masses of 79 and 81 amu respectively. Br 2 may be composed of two 79 Br atoms (mass 158 amu), two 81 Br atoms (mass 162 amu) the more probable combination of 79 Br- 81 Br (mass 160 amu). Fragmentation of Br 2 to a bromine cation then gives rise to equal sized ion peaks at 79 and 81 amu.

14 [M] at 62 [M2] at 64 [M] at 84 chlorine is also composed of two isotopes, the more abundant having a mass of 35 amu, and the minor isotope a mass of 37 amu. Chlorine: [M2] at 86 [M4] at % 35 Cl and 24.23% 37 Cl From the pattern of the clusters around the molecular ion peak, one can predict the presence of certain hetro-atoms in a molecule

15

16 FAGMENTATION POCESS In EIMS bombardment by an electron beam between ev results in the formation of molecular ion ev molecular ions breakdown into various fragments. The fragmentation process is not random and leads to well-established fragments.

17 M. Similarly, loss of water:- [M- 2 O]. or [M-18]., loss of carbon mono-oxide:- [M-CO]. or [M-28]. etc.. Fragmentation in Alkanes C 2 -C 2 C 2. C 2 :C 2 C 2 AND/O. C 3 [M-C [M-15] 3 ] O Molecular ions are weak, especially for long chain e C 2. 2e C 2 C 2. C 2 The driving force is usually the formation of alkenes.

18 : = [M]. [M-1] e 2e. Intensity of the fragment ions depends on carbocation stability 3 C > 2 C > 2 C > 3 C [M-2] etc.... primary secondary m/z = 43 m/z = 57 [M-43] [M-Me] [M]. m/z

19 Effect of of eteroatoms Cleavage occurs near functional group :X: e 2e :X. :X It is easier to ionize non-bonding electrons than s-electrons; because they are in an orbital of higher energy.. Complete arrow: two electrons movement alf arrow: one electron movement

20 ALCOOLS In 1º and 2º alcohols, the molecular ion is weak In 3º alcohols, molecular ion is often undetectable 1) Cleavage of C-C bond next to the oxygen ' :O. 1º :O. 3º :O oxonium ion :O. ' oxonium ion. :O. 2º :O oxonium ion The largest group is expelled most readily.

21 2) Loss of water is common in alcohols.. 2 O O 3) Loss of water with alkene :O. g ' b :O. ' :O:. '. '

22 Ethers 1) b-cleavage occurs principally 2) Followed by elimination of alkene, if b- is present

23 Fragmentation in Alkenes Molecular ion peaks are normally observed 1) The commonest fragmentation in alkenes involves rupture of the allylic bond (b-to double bond) allylic bond e 2e Loss of one p-electron. C. C Allyl carbocation stabilized by resonance

24 [M-Me] 69

25 2) McLafferty rearrangement in alkenes Occurs if the g-carbon has hydrogen on it g ' b 2 C e. 2e '.. ' ' 2 C. ' The driving force is the formation of the neutral alkene. '

26 Fragmentation in Cyclohexenes Elimination of neutral molecule by two s-bond rupture; etro-diels-alder (DA) reaction mechanism followed ' e 2e ' ṘDA Diels-Alder diene monoene The diene is almost always contains the radical cation; Except when the monoene has a heteroatom/conjugation. ' X e 2e X. DA X.

27 adical Mechanism ' e 2e. ' DA. diene ' monoene e 2e DA X X.

28 Carbonyl Compounds 1) -cleavage X Y C O Acylium ion X Y O. X Y C O Acylium ion X C O Y C O The driving force is the formation of carbon mono-oxide

29 2) McLafferty rearrangement in carbonyl compounds (b-cleavage) Occurs if the g-carbon has hydrogen on it O g b ' e 2e O '. O keto. O enol The driving force is the formation of the neutral alkene. '

30 Identify the principal fragment ions and propose mechanism for their formation

31 Aromatic ydrocarbon Groups Molecular ion is strong Benzyl cleavage is the most common fragmentation

32 .. C 2 Benzyl cation m/z 91 Tropylium ion (aromatic).. m/z 92 through McLafferty rearrangement

33 Aromatic ethers Molecular ion is prominent Aromatic esters and acids O O X. C X O. O = alkyl group or

34 Amines Weak molecular ion Tropylium ion [M-Me]

35 IONIZATION POCESSES EI CI FD FAB ESI MALDI

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