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Learning outcome

Understand MS concept
Capable to read the mass spectrum

Mass Spectrometry (MS)

Mass spectrometry (MS) is an analytical technique
that ionizes chemical species and sorts the ions
based on their mass to charge ratio. In simpler
terms, a mass spectrum measures the masses within
a sample.

Mass Spectrometry (MS)

m/e= H2r2/2v

Mass Spectrometry (MS)

Electron Ionization MS
 In

the ionization chamber, the sample is bombarded with a
beam of high-energy electrons.
 Collisions between these electrons and the sample result in
loss of electrons from sample molecules and formation of
positive ions.
H C H + e

+2 e
Molecular ion
(a radical cation)


Gas Chromatography-Mass Spectroscopy (GC-MS)   Gas chromatography–mass spectrometry. Gas chromatography–mass spectrometry (GC-MS) is an analytical method that combines the features of gas-chromatography and mass spectrometry to identify different substances within a test sample Drawback.need a rapid scanning by MS (the scanning must be done before all compound exist from the GC column) .

Base peak: The most abundant peak.Mass Spectrum    Mass spectrum: A plot of the relative abundance of ions versus their mass-tocharge ratio. The relative abundance of all other ions is reported as a % of abundance of the base peak. . Assigned an arbitrary intensity of 100.

.5% of the base peak.MS of dopamine A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 0.

Determination of molecular weight    Molecular ions-accelerated-sent to magnetic fielddetect Life time at least 10-5/s can react with the detector without breaking.can detect direct m/e=mw Consideration-isotopes / bombardment .

Molecular peaks       Mass higher in spectrum (M+ intensity) Ion has odd no of electron Forming important fragment ions in spectrum (highly branched substances undergoes fragmentation easily) Nitrogen rule Halogens Molecular ions life times .

CH4N2O (compared with chemical method in chapter 1) . C2H8N2.Determination of molecular formula    Precise mass determination Eg: mw=60 will have many possibility C3H8O.

 Low Resolution MS (LR-MS): Refers to instruments capable of separating only ions that differ in nominal mass.  High resolution MS (HR-MS): Refers to instruments capable of separating ions that differ in mass by as little as 0.0001 amu.Resolution  Resolution: A measure of how well a mass spectrometer separates ions of different masses. . that is ions that differ by at least 1 or more atomic mass units (amu).

 distinguish between them by high-resolution MS. Molecular N ominal Precise Formula Mass Mas s C3 H8 O 60 60.  C3H8O and C2H4O2 both have nominal masses of 60 which occurs due to isotopes of the same elements.02112 60 .05754 C2 H4 O2 60. and can be distinguished by low-resolution MS.Resolution  C3H6O and C3H8O have nominal masses of 58 and 60.

9659 32.11 14.0 .453 3 5Cl 34.40 ch lorine 35.01410 0.Determination of molecular formula of Isotopes Virtually all elements common to organic compounds are mixtures of isotopes with different relative abundances.5 bromine 79.9163 98.9679 4.0031 100 nitrogen 14.007 14 N 15 N 15.999 O 15.0034 1.016 12 carbon 12.066 32 S 31.9721 100 34 S 33.38 16 oxygen 15.011 13 C 12.904 79Br 78.9689 100 37 Cl 36.0079 1H 1.00783 100 2 H 2.20 su lfu r 32.0000 100 C 13.9183 100 81 Br 80.9949 100 18 O 17.9992 0.0001 0. Atomic Mas s Relative Element w eigh t Isotope (amu ) A bun dance hydrogen 1.

 Carbon. .11 atoms of carbon-13 in nature for every 100 atoms of carbon-12.90% 12C and 1.  There are 1.10% 113C.Determination of molecular formula of Isotopes for example. in nature is 98. So low intensity M+1 peak is very likely to appear along with M+ peak.

of H atoms)2/200+ 0.38 no of N atoms.  Formula for calculating the intensity of M+2 peak is as follows: %(M+2)= 100[(M+2)/M]= (1.1x no.20 no of O atoms. of C atoms)2/200+ (0.  . of H atoms+ 0. of C atoms+ 0.1x no.....0016 no.Determination of molecular formula Isotope ratio data  Formula for calculating the intensity of M+1 peak is as follows: %(M+1)= 100[(M+1)/M]= 1.0016 no.

containing ions .isotope peak patterns for Cland Br.

Fragmentation Patterns   Molecules ion which has life time greater than 105/sec =peaks refer to molecular ion appear in mass spectrum Molecules ion which has life time less than 10-5/sec. break apart into fragment before they are accelerated within the ionization chamber .

M. produces a radical and a cation. + • Molecular ion (a radical cation) A• + B+ Radical Cation A+ + • B Cation Radical .Fragmentation of M+  Fragmentation of a molecular ion.  Only A-B the cation is detected by MS.

Fragmentation Patterns Fragmentation involves the loss of an electrically neutral fragment  Mode of fragmentation: #One bond CH3+<RCH2+<R3C+<CH2=CH-CH2+<C6H5-CH2+ #Two bond  .

Mc Lafferty rearrangement 3. Heterolytic cleavage 3. Retro Diels-Alder reaction * Rearrangement reactions accompanied by transfer of atoms. Elimination . Homolytic cleavage 2.General modes of fragmentation: Fragmentation of the molecular ion takes place in following modes: * Simple cleavage 1. Scrambling 2. 1.

Simple cleavage .

Homolytic cleavage   Here fragmentation is due to electron redistribution between bonds.1. R ─ CH2 ─ CH2 ─ R' R ─ CH2 : CH2 ─ Rꞌ e- R ─ CH2+ + CH2 ─ R' . .

It is designated by a conventional arrow (↶ or ↷) to signify the transfer of a pair of electrons in the direction of the charged site.2.Heterolytic cleavage Fragmentation by movement of two electrons: In this type of cleavage both the electrons of the bond are taken over by one of the atoms. the fragments are an even electron cation and a radical with the positive charge residing on the alkyl group. .

.3. Retro Diels-Aldel reaction Elimination by multiple  bond rupture: cyclohexene is broken down to Diene and Dienophile.

Rearrangement .

Scrambling Fragmentation giving rise to stable carbocation: In certain cases fragmentation takes place at bond.Molecular ion from the alkyl benzene undergoes fragmentation at the benzylic bond and final product is seven membered cyclic ion known as Tropylium ion. which gives stable carbocation. Ex.1. .

Mc Lafferty rearrangement:  Fragmentation due to rearrangement of Molecular or Parent ion:  Compounds containing hydrogen atom at position gamma to carbonyl group have been found to a relative intense peak. The rearrangement results in the formation of charged enols and a neutral olefins . This rearrangement is known as McLafferty rearrangement.2. This is probably due to rearrangement and fragmentation is accompanied by the loss of neutral molecule.

. a molecule must posses: a.oxygen) b. To undergo McLafferty rearrangement. An abstractable Hydrogen atom which is γ (gamma) to C=O system. An appropriately located heteroatom (ex. A double bond c.

Table for the common McLafferty peak in the spectra of carbonyl group. Compound type Substituent (R) McL peak Aldehyde -H 44 Methyl ketone -CH3 58 Amide -NH2 59 Acid -OH 60 Ethyl ketone -CH2CH3 72 Methyl ester -OCH3 74 .

3. . CO.An alcohol readily looses H2O molecule and shows a peak 18 mass units less than the peak of molecular ion.C2H4 from molecular ion during fragmentation. elimination Fragmentation due to loss of small molecule: Loss of small stable molecules such as H2O. Ex. CO2.

Fragmentation Patterns  Alkane (octane) .

Fragmentation adjacent to the branching point In case of branched alkanes. bond fission takes place adjacent to the branching point. Hence this leads to the formation of more stable carbocation Ex: 3-methyl pentane .

Fragmentation Patterns  Alkane (isooctane) .

Fragmentation Patterns  cycloalkane .

 cleave to form resonance-stabilized allylic cations. + [CH2 =CHCH2 CH2 CH3 ] • CH2 =CHCH2 + + • CH2 CH3 .Fragmentation Patterns  Alkenes characteristically  show a strong molecular ion peak.

CH3 + • CH3 H3 C C H3 C C + • + CH2 CH2 Limon ene (m/z 136) A neu tral d iene (m/z 68) A radical cation (m/z 68) .3-diene and an alkene. a process that is the reverse of a Diels-Alder reaction.Fragmentation Patterns  Cyclohexenes give a 1.

 cleave readily to form the resonance-stabilized propargyl cation or substituted propargyl cations.Fragmentation Patterns  Alkynes typically  show a strong molecular ion peak. + + 3-Propynyl cation (Propargyl cation) HC C-CH2 HC C=CH2 .

 This may eliminate a neutral acetylene molecule to give a peak at m/e 65. .Fragmentation Patterns Aromatic compounds:  It shows prominent mol ion peak. This is as a result of the stabilizing effect of the ring. as compared to the alkanes and alkenes containing same number of C atoms. m/z 91.  If aromatic ring is substituted by an alkyl groups a prominent peak is formed at m/z 91. +  Here benzyl cation (C6H5C H2) formed rearranges to tropylium cation (C7H7+).

91 M (92) Mass spectrum of toluene .

e.  The CH2=OH+ ion is the most significant peak in the spectra of 1º alcohols. corresponding to the loss of water.  Secondary alcohols cleave to give prominent peaks due R-CH=OH at m/z=45.   The fragmentation of C-C bond (alkyl group) adjacent to oxygen atom is the preferred fragmentation mode i.59. 1º alcohols shows M-18 peaks.Fragmentation Patterns Alcohols:  The molecular ion peak of 1º and 2ºalcohol is usually of low abundance or may not detected in 3º alcohols. α cleavage.73 .

H is small. Cresols form very intense peak due to the formation of hydroxyl tropylium ion. The peak due to the loss of hydrogen radical. H H + m/z=79 +CO . M+ . The fragment ion due to the loss of carbon monoxide is significant. OH OH + m/z=107 +H.Fragmentation Patterns Phenols: The molecular ion peak is intense.


. the positive charge being retained on the carbon rather than on oxygen (loss of an alkoxy group).Fragmentation Patterns Ethers:  Aliphatic ethers undergo facile fragmentation and exhibit a weak molecular ion peak because the resultant ion is highly stabilized by resonance   The major fragmentation modes occur through cleavage α- α cleavage : Cleavage of a bond α to oxygen occurs.


Second common feature of Aliphatic Aldehyde is β cleavage. (m/e=29) R-C≡O+ + H. end group gives rise to characteristic M-43 peaks. For ex: Aldehyde with R+ + CH2=CHO. McLafferty rearrangement-occurred when the carbon chain attached to carbonyl group contains at least three carbon   .  Aromatic Aldehydes shows moderate intense peak at: H-C=O+ + R. (M-1) By α-cleavage.Fragmentation Patterns Aldehydes  The Molecular ion peak of aliphatic Aldehydes is observable.

Β-cleavage (M-43) R + CH2=CHO. .

Fragmentation Patterns Ketones:  Molecular ion peaks are intense than Aldehyde. .  Most of the abundant ions in the mass spectra of Ketones can be accounted by α cleavage and Mc Lafferty rearrangement.


RCO+ McLafferty rearrangment: . α-cleavage : loss of alkoxy group to form corresponding acylium ion.Fragmentation Patterns Ester:    Most of the abundant ions in the mass spectra of ester can be accounted by α cleavage and Mc Lafferty rearrangement.

Mass spectrum of methyl butyrate: .

α-cleavage : loss of OH. COOH through α-cleavage on either side of the C=O group McLafferty rearrangment: .Fragmentation Patterns Carboxylic acid:    Principal modes of fragmentation resemble those of methyl ester.

Mass spectrum of butanoic acid .

Fragmentation Patterns amines:  Compound with odd no. of MW. of Nitrogen must have odd no.  α-cleavage :  Β-cleavage:  McLafferty rearrangement: Amides:  α-cleavage :  McLafferty rearrangement: Nitrile:  M-H  McLafferty rearrangement .

m/z=46 (NO2+ ion) aromatic nitro compound (nitrobenzene) .Fragmentation Patterns Nitro Compounds: Aliphatic Nitro compounds fragment by loss of NO2 m/z= 30 (NO+ ion).

38.Fragmentation Patterns Halogen Compounds:      A compound with 1 chlorine atom gives a M+2 peak. In a mono bromo derivative the M+2 peak is almost of equal intensity to the molecular ion and is due to the presence of molecular ion containing 81Br isotope. which is one third the intensity of the molecular ion peak due to the presence of Molecular ion containing 37Cl isotope. Fluorine and Iodine being mono isotopic do not give these patterns. Aliphatic chlorine compounds fragment mainly by the loss of HCl to give peaks at M-36 and M-38. HCl peaks can also be seen at m/z 36. The relative abundance of the Molecular ion decreases with increase in chain length and increase in branching. .

determine the m/z values for the base peaks  3. propose the structure.Compound X contains a single oxygen atom but it does not show any significant IR absorption peak above 3000 cm-1. determine the m/z values for the molecular ion peaks  2. And show how the fragmentation ions at m/=59 and m/z=31 are formed. Generate the molecular formula for the compound X using rule of thirteen  4. The MS spectrum of compound X is shown:  1. .