Mass Spectrometry

Introduction EI-MS and CI-MS

Molecular mass amp formulas Principles of fragmentation

Fragmentation patterns Isotopic effects

1

Introduction to MS

bull Mass spectrometry is the method of analysis that involves interaction of sample molecule with fast moving electrons

bull Structural information obtained usually based on fragmentation patterns of the molecule under study

bull The sample studied may be gas liquid or solid bull The information obtained is a molecular mass fragment which does

not depend on EM radiations bull There are two methods that are involved in molecule ionization

ndash Electron ionization and ndash Chemical Ionization

bull Other mass spectrometry techniques include ndash fast atom bombardment (FAB) ndash Matrix-assisted laser desorption ionization (MALDI) ndash Electrospray ionization (ESI)

2

Introduction hellip

bull Molecules are subjected to bombardment by stream of high energy electrons (ca 70eV) converting some of the molecule to ions

bull Accelerated ions are separated according to their mass charge ratio (me or mz) in magnetic field or electric field

bull The ions with particular me that strike a detector are counted

bull The amplified output is recorded as mass spectrum

3

Mass spectrum bull Mass spectrum is a graph of particles detected as

function of me

A Typical MS spectrum showing molecular ion peak (M +) and the base peak (M+)

M

M+re

l a

bundan

ce

100

0me

4

Mass spec

bull The base peak is the most abundant peak assigned an arbitrary intensity of 100

bull The relative abundance of all other ions is reported as a of abundance of the base peak

bull Molecular ion peak is the peak with highest mz which corresponds to mass of the compound

5

Schematic representation of Mass spectrometer

6

Electron Ionization mass spectrometry

(EI-MS)

bull Three distinct regions of MS machine where molecule under investigation

ndash Ionization chamber

ndash Ion analyzer and

ndash Detector

bull For EI-MS Gas-phase molecules enter source through heated probe

bull 70 eV electrons bombard molecules forming M+ ions that fragment in unique reproducible way to form a collection of fragment ions

ie M + ē rarr [M]+ + 2ē

A beam of high-energy electrons emitted from a very hot filament (thousand degrees Celcius) strike the stream of molecules and ionize it

7

Representation of ionizing chamber

8

Note

bull The only detectable fragments are positively charged only

bull Neutral and unpaired electrons without positive charge will NOT be detected

Andash B+ rarr A+ (positive charged fragment) +

B (neutralradical fragment)

9

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Introduction to MS

bull Mass spectrometry is the method of analysis that involves interaction of sample molecule with fast moving electrons

bull Structural information obtained usually based on fragmentation patterns of the molecule under study

bull The sample studied may be gas liquid or solid bull The information obtained is a molecular mass fragment which does

not depend on EM radiations bull There are two methods that are involved in molecule ionization

ndash Electron ionization and ndash Chemical Ionization

bull Other mass spectrometry techniques include ndash fast atom bombardment (FAB) ndash Matrix-assisted laser desorption ionization (MALDI) ndash Electrospray ionization (ESI)

2

Introduction hellip

bull Molecules are subjected to bombardment by stream of high energy electrons (ca 70eV) converting some of the molecule to ions

bull Accelerated ions are separated according to their mass charge ratio (me or mz) in magnetic field or electric field

bull The ions with particular me that strike a detector are counted

bull The amplified output is recorded as mass spectrum

3

Mass spectrum bull Mass spectrum is a graph of particles detected as

function of me

A Typical MS spectrum showing molecular ion peak (M +) and the base peak (M+)

M

M+re

l a

bundan

ce

100

0me

4

Mass spec

bull The base peak is the most abundant peak assigned an arbitrary intensity of 100

bull The relative abundance of all other ions is reported as a of abundance of the base peak

bull Molecular ion peak is the peak with highest mz which corresponds to mass of the compound

5

Schematic representation of Mass spectrometer

6

Electron Ionization mass spectrometry

(EI-MS)

bull Three distinct regions of MS machine where molecule under investigation

ndash Ionization chamber

ndash Ion analyzer and

ndash Detector

bull For EI-MS Gas-phase molecules enter source through heated probe

bull 70 eV electrons bombard molecules forming M+ ions that fragment in unique reproducible way to form a collection of fragment ions

ie M + ē rarr [M]+ + 2ē

A beam of high-energy electrons emitted from a very hot filament (thousand degrees Celcius) strike the stream of molecules and ionize it

7

Representation of ionizing chamber

8

Note

bull The only detectable fragments are positively charged only

bull Neutral and unpaired electrons without positive charge will NOT be detected

Andash B+ rarr A+ (positive charged fragment) +

B (neutralradical fragment)

9

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Introduction hellip

bull Molecules are subjected to bombardment by stream of high energy electrons (ca 70eV) converting some of the molecule to ions

bull Accelerated ions are separated according to their mass charge ratio (me or mz) in magnetic field or electric field

bull The ions with particular me that strike a detector are counted

bull The amplified output is recorded as mass spectrum

3

Mass spectrum bull Mass spectrum is a graph of particles detected as

function of me

A Typical MS spectrum showing molecular ion peak (M +) and the base peak (M+)

M

M+re

l a

bundan

ce

100

0me

4

Mass spec

bull The base peak is the most abundant peak assigned an arbitrary intensity of 100

bull The relative abundance of all other ions is reported as a of abundance of the base peak

bull Molecular ion peak is the peak with highest mz which corresponds to mass of the compound

5

Schematic representation of Mass spectrometer

6

Electron Ionization mass spectrometry

(EI-MS)

bull Three distinct regions of MS machine where molecule under investigation

ndash Ionization chamber

ndash Ion analyzer and

ndash Detector

bull For EI-MS Gas-phase molecules enter source through heated probe

bull 70 eV electrons bombard molecules forming M+ ions that fragment in unique reproducible way to form a collection of fragment ions

ie M + ē rarr [M]+ + 2ē

A beam of high-energy electrons emitted from a very hot filament (thousand degrees Celcius) strike the stream of molecules and ionize it

7

Representation of ionizing chamber

8

Note

bull The only detectable fragments are positively charged only

bull Neutral and unpaired electrons without positive charge will NOT be detected

Andash B+ rarr A+ (positive charged fragment) +

B (neutralradical fragment)

9

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Mass spectrum bull Mass spectrum is a graph of particles detected as

function of me

A Typical MS spectrum showing molecular ion peak (M +) and the base peak (M+)

M

M+re

l a

bundan

ce

100

0me

4

Mass spec

bull The base peak is the most abundant peak assigned an arbitrary intensity of 100

bull The relative abundance of all other ions is reported as a of abundance of the base peak

bull Molecular ion peak is the peak with highest mz which corresponds to mass of the compound

5

Schematic representation of Mass spectrometer

6

Electron Ionization mass spectrometry

(EI-MS)

bull Three distinct regions of MS machine where molecule under investigation

ndash Ionization chamber

ndash Ion analyzer and

ndash Detector

bull For EI-MS Gas-phase molecules enter source through heated probe

bull 70 eV electrons bombard molecules forming M+ ions that fragment in unique reproducible way to form a collection of fragment ions

ie M + ē rarr [M]+ + 2ē

A beam of high-energy electrons emitted from a very hot filament (thousand degrees Celcius) strike the stream of molecules and ionize it

7

Representation of ionizing chamber

8

Note

bull The only detectable fragments are positively charged only

bull Neutral and unpaired electrons without positive charge will NOT be detected

Andash B+ rarr A+ (positive charged fragment) +

B (neutralradical fragment)

9

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Mass spec

bull The base peak is the most abundant peak assigned an arbitrary intensity of 100

bull The relative abundance of all other ions is reported as a of abundance of the base peak

bull Molecular ion peak is the peak with highest mz which corresponds to mass of the compound

5

Schematic representation of Mass spectrometer

6

Electron Ionization mass spectrometry

(EI-MS)

bull Three distinct regions of MS machine where molecule under investigation

ndash Ionization chamber

ndash Ion analyzer and

ndash Detector

bull For EI-MS Gas-phase molecules enter source through heated probe

bull 70 eV electrons bombard molecules forming M+ ions that fragment in unique reproducible way to form a collection of fragment ions

ie M + ē rarr [M]+ + 2ē

A beam of high-energy electrons emitted from a very hot filament (thousand degrees Celcius) strike the stream of molecules and ionize it

7

Representation of ionizing chamber

8

Note

bull The only detectable fragments are positively charged only

bull Neutral and unpaired electrons without positive charge will NOT be detected

Andash B+ rarr A+ (positive charged fragment) +

B (neutralradical fragment)

9

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Schematic representation of Mass spectrometer

6

Electron Ionization mass spectrometry

(EI-MS)

bull Three distinct regions of MS machine where molecule under investigation

ndash Ionization chamber

ndash Ion analyzer and

ndash Detector

bull For EI-MS Gas-phase molecules enter source through heated probe

bull 70 eV electrons bombard molecules forming M+ ions that fragment in unique reproducible way to form a collection of fragment ions

ie M + ē rarr [M]+ + 2ē

A beam of high-energy electrons emitted from a very hot filament (thousand degrees Celcius) strike the stream of molecules and ionize it

7

Representation of ionizing chamber

8

Note

bull The only detectable fragments are positively charged only

bull Neutral and unpaired electrons without positive charge will NOT be detected

Andash B+ rarr A+ (positive charged fragment) +

B (neutralradical fragment)

9

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Electron Ionization mass spectrometry

(EI-MS)

bull Three distinct regions of MS machine where molecule under investigation

ndash Ionization chamber

ndash Ion analyzer and

ndash Detector

bull For EI-MS Gas-phase molecules enter source through heated probe

bull 70 eV electrons bombard molecules forming M+ ions that fragment in unique reproducible way to form a collection of fragment ions

ie M + ē rarr [M]+ + 2ē

A beam of high-energy electrons emitted from a very hot filament (thousand degrees Celcius) strike the stream of molecules and ionize it

7

Representation of ionizing chamber

8

Note

bull The only detectable fragments are positively charged only

bull Neutral and unpaired electrons without positive charge will NOT be detected

Andash B+ rarr A+ (positive charged fragment) +

B (neutralradical fragment)

9

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Representation of ionizing chamber

8

Note

bull The only detectable fragments are positively charged only

bull Neutral and unpaired electrons without positive charge will NOT be detected

Andash B+ rarr A+ (positive charged fragment) +

B (neutralradical fragment)

9

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Note

bull The only detectable fragments are positively charged only

bull Neutral and unpaired electrons without positive charge will NOT be detected

Andash B+ rarr A+ (positive charged fragment) +

B (neutralradical fragment)

9

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Ion (mass) analyzer

bull From ionization chamber the ions passes through the field free-region and enter to the mass analyzer where the ions are separated according to their mass-to-charge ratios

bull Governed by the equation

me = H2r22V

ndash This is the combination of two equations one expressing the kinetic energy of the accelerate electron

mv2 2 = eV and ndash another equation is due to the path of electron in the presence of

magnetic field (H) with radius of curvature r = mveH ndash Where e is the charged ion and V is potential difference of ion-

accelerating plate

10

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

The detector

bull A typical spectrometer consists of a counter that produces a current that is proportional to the number of ions that strike it

bull The current caused by just one ion striking the detector can be measured so accurately though the use of electron multiplier circuits

bull Thereafter the signal from the detector is fed to a recorder which produces the mass spectrum

bull Modern instruments produces data in different formats tabulated and bar graph of relative intensity versus mz

bull Generally a mass spectrometer is designed to do three things ndash Convert neutral atoms or molecules into a beam of positive (or rarely

negative) ions ndash Separate the ions on the basis of their mass-to-charge (mz) ratio ndash Measure the relative abundance of each ion

11

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Chemical Ionization (CI)

bull CI is the ionization that occurs through a reaction

between the sample molecule and the reagent gas (usually methane isobutene or ammonia)

bull Gas is reacted (ie it is ionized) by a stream of electrons before it react with the sample to form positive charge ions that acts like Lewis acid

bull Only molecular ion peak is observed

bull The spectrum of CI-MS have mz value corresponding to M+H a unit greater than M+ (molecular ion)

12

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

+

+

CH4 + e

CH4 2e

CH4 excess

CH5 CH3

Sample M

M+H + CH4

pseudo molecular ion

CH3OH CH3OHe

CH3OH

CH3 + OH

mz = 15mz = 32

+ Hmz = 31

CHO + 2H

mz = 29

EI- ionization Chemical ionization

primary ion

secondary ion

reagent

13

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Difference between EI-MS and CI-MS

EI -MS CI-MS

bullGas-phase molecules enter source

through heated probe or GC column

bull70 eV electrons bombard molecules

forming M+ ions that fragment in

unique reproducible way to form a

collection of fragment ions

bullEI spectra can be matched to library

standards

No ions higher mz than M+

Smaller M+ intensity

Rich family of fragment ions

bullHigher pressure of methane or

amonia leaked into the source

(mtorr)

bullReagent ions transfer proton to

analyte (a much lower energy

process)

Adduct ions higher mz than

MH+ [M+C2H5]+ [M+C3H5]+

[M+NH4]+

Large intensity of M+

Relatively few fragment ions

14

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

A partial mass spectrum of dopamine showing all peaks with intensity equal to or greater than 05 of the base peak

15

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Determination of Molecular Mass and Formulas

Molecular ion peaks

Nitrogen rule

Rule of thirteen

16

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Determination of molecular massamp formulas

bull The value of the mass of any ion accelerated in a mass spectrometer is its true mass and NOT its molecular weight obtained from the use of chemical atomic weights

bull The masses that are observed for molecular ions are the masses of the molecules in which every atom is present as its most common isotopes

bull An error of only one mass unity in the assignment off mass spectral peaks can lead to difficulty in determination of structure

bull Varying (lowering) the energy of the ionizing electron beam may confirm that particular molecular ion peak due to increased intensity as tendency of molecular ion to fragment lessens

17

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Nitrogen Rule

bull The rule states that ndash If a compound has zero or an even number of nitrogen atoms its

molecular ion will have an even mz value bull An odd number of nitrogen atoms its molecular ion will have an odd mz

value ndash Reason N atom has an even mass has an odd-numbered valence

Consequently an extra hydrogen atom is included as a part of the molecule giving it an odd mass For example

bull Ethylamine C2H5NH2 has one nitrogen atom and its mass is an odd number 45 whereas bull Ethylenediamine H2NCH2CH2 NH2 has two nitrogen atoms and its mass is an even number 60 bull A molecule free of nitrogen and gives an ion at mz=201 then that peak

cannot be the molecular ion bull An odd molecular ion is an indication of the presence of nitrogen

bull Note In the case of Chemical Ionization where [M+H]+ is observed need

to subtract 1 then apply nitrogen rule

18

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Facts about molecular ion peaks

bull The peaks must correspond to the ion of highest mass in the spectrum excluding the ldquoisotopic peaksrdquo that occur even at higher masses

bull The ion must have an odd number of electrons (the charge of an ion is one)

bull They must be able to form relatively stable fragments with high mass by loss of logical neutral fragments

bull Special attention in assigning M + must be taken when dealing with

bull Chlorine and bromine due to isotopic effects bull Alcohols due to loss of water (mz = 18) bull Conjugate acids of oxygen and nitrogen due its stability

19

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Determination of Molecular Formula (Precise mass determination)

Resolution bull Resolution is a measure of how well a mass

spectrometer separates ions of different mass ndash ie ability to distinguish the nearest peaks

bull Low resolution Refers to instruments capable of separating only ions that differ in nominal mass ndash ie ions that differ by at least 1 or more atomic mass

units (amu)

bull High resolution Refers to instruments capable of separating ions that differ in mass by as little as 00001 amu

20

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Examples bull C3H6O and C3H8O have nominal masses of 58 and 60 and can be

distinguished by low-resolution MS

bull C3H8O and C2H4O2 both have nominal masses of 60 can be distinguish by high-resolution MS that is

bull C3H8O = 6005754 whereas C2H4O2 = 6002112

bull R = 20000 (which is 5 to 10 times Low -resolution MS) can distinguish these ions

bull Resolution R is calculated using the formula bellow in considering ndash Two adjacent peaks of equal intensity ndash The valley between them being lt 10 ie R = Mn Mn-Mm

ndash Where Mn is higher mass number and Mm is low mass number

bull High-resolution MS provides molecular mass information from which the

user can determine the exact molecular formula directly 21

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Rule of Thirteen

bull Rule of Thirteen may be used to generate possible molecular formulas for a given mass when molar mass information is missing

bull Rule of thirteen is expressed as bull

ndash where M is molecular mass n is a numerator and r is

the remainder thus the formula becomes CnHn+r whose unsaturation index may be calculated from the formula

U = (n - r + 2)2

22

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

For example

bull You are given a molecular mass 94 Then apply Rule of 13

bull U = (n - r + 2)2 bull U = (7 - 3 + 2)2= 3 bull Molecular formula CnHn+r = C7H10

bull The structure that fits this information could be bull

CH3

23

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Fragmentation of molecules

bull For EI-MS the fragmentation occur and only stable cation or cation-radical will be detected

bull The fragmentation involves bond cleaving ether by

ndash homolytic cleavage or

ndash heterolytic cleavage

24

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Typical Homolytic and Heterolystic cleavage

C

H

H

OCH3H3C CH3 H2C OCH3+ H2C OCH3

cationic radical

C

CH3

H

BrH3C

cationic radical

C

CH3

H

H3C + Br

25

Homolytic cleavage

Heterolytic cleavage

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Fragmentation of saturated hydrocarbons bull Cleavage occur at the branched carbon atom to form a

stable carbocation bull Peak M-15 (loss of CH3 ) usually observed followed by loss

of ndashCH2 units (ie fourteen mass unit)

Fragmentation of unsaturated hydrocarbons bull Terminal alkene tend to cleave at the second bond from the

double bond to give an alkyl carbocation of mz = 41 stabilized by delocalization to the double bond

bull (ie cleavage occur at andash and bndash positions)

26

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

McLafferty rearrangement bull For the alkyl group with more carbon long a rearrangement

called McLafferty rearrangement can occur

bull By definition McLafferty rearrangement is the electron impact induced cleavage of carbonyl compounds having hydrogen in the -position to an enolic fragment and olefin eg ketones and aldehydes

O

H

R

R

OH

R

+

R

MacLafferty rearrangementenol

27

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Fragmentation patterns

Alkanes Alkenes Cyclohexenes Alcohols and Cycloalcohols Carboxylic acids aldehydes

Esters ethers Aromatic rings

28

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Fragmentation patterns of alkanes

bull Tends to occur in the middle of unbranched chains rather than at the ends

bull The difference in energy among allylic benzylic 3deg 2deg 1deg and methyl cations is much greater than the difference among comparable radicals

bull Where alternative modes of fragmentation are possible the more stable carbocation tends to form in preference to the more stable radical

bull Characteristically strong M loss of 14 units in series M-14 M-28 M-42 etc

29

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Fragmentation patterns of alkanes

30

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

cycloalkanes

31

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

cycloalkanes

32

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Fragmentation patterns of alkenes

bull Alkenes characteristically show a strong molecular ion peak cleave to form resonance-stabilized allylic cations

strong M mz = 41 M-15 M-29 M-43 M-57 etc

bull Resulting fragmentation ions have formula

corresponding to CnH2n+

or CnHn-1+

33

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Fragmentation patterns of alkenes

CH2=CHCH2CH2CH3 CH2=CHCH2 CH3CH2+

34

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Fragmentation patterns of cyclohexenes

bull Cyclohexenes give a 13-diene and an alkene a process that is the reverse of a Diels-Alder reaction

35

CH3

H3C CH2

H3C CH2

CH3

+

Lemonene

mz = 136

A neutral diene

mz = 68 mz = 68

A radical cation

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

cyclohexene

36

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Fragmentation patterns of alcohol

bull One of the most common fragmentation patterns of alcohols is loss of H2O to give a peak which corresponds to M-18

bull Characteristically weak or absent M M-18 (loss of alkyl group)

bull Cyclic alcohols may undergo dehydration in three different ways

bull Dehydration may occur in two mechanisms for acyclic alcohols ndash 12-elimination (before the molecule it come in contact with

ionizing electros) or ndash 14-elimination (from the molecular ion) a cyclic mechanism

37

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

14-Elimination

38

H2O

dehydartion by 14-elimination

H2C

H2C

CH2

CH

H

O

H

R

H2C

HC

R+ + H2C CH2

12-Elimination

RHC

H H-O

CHR

(CH2)n

n = 1 or 2

CHR

(CH2)n

RHC + H2O

dehydartion by 12-elimination

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Alcohol hellip

bull Another common pattern is loss of an alkyl group from the carbon bearing the -OH group to give a resonance-stabilized oxonium ion and an alkyl radical

39

C

R

R OH

R

R + C

R

R

OH

Loss of alkyl group

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

2o alcohol

40

Loss of ethyl group

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Cyclic alcohols

41

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Cyclic alcohol

42

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Ketones

bull Similar to aldehydes except for cyclic ketones

bull Characteristically

1) strong M

2) Aliphatic M-15 M-29 M-43 mz = 43

mz = 58 72 86

1) Aromatic me= 105 120

43

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Ketone

44

ndash cleavage

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

45

McLafferty rearrangement

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Carboxylic acids

bull Characteristic fragmentation patterns are a-cleavage on either side of a carbonyl to give the ion [CO2H]+ with mz 45 or loss of ndashOH group

bull McLafferty rearrangement is possible with acids containing -hydrogens

bull Characteristically ndash Aliphatic carboxylic acids weak M

M-17 M-45 mz = 45 60 ndash Aromatic carboxylic acids strong M

M-17 M-45 M-18

46

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Esters

bull -cleavage and McLafferty rearrangement

bull Characteristically

ndash weak M

ndash Methyl esters M-31 mz = 5974

ndash Higher esters M-45 M-59 M-73 mz= 7387101 mz= 88 102 116mz= 61 75 86 mz = 77 105 108 M-32 M-46 M-60

47

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Ethers

bull Aliphatic ethers have stronger molecular ion peaks compared to that of alcohols

bull There three principal modes of fragmentations

-cleavage

2) formation of carbocation fragments and

3) loss of alkoxy group

48

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Ethers

49

R CH2 OR H2C OR + R

Formation of carbocation fragment (mz = 43 for diisopropyl ether)

-cleavage (responsible for mz = 87 of diisopropyl ether)

CH O CH

CH3

CH3

H3C

H3C

CH HC

CH3

CH3

H3C

H3C

O +

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Ethers hellip

bull Rearrangement reaction taking place on one of the fragmentations rather than on the molecular ion

bull Particularly favoured when -carbon is branched (mz= 45)

50

R CH O CH2

R

CH2

H

R CH OH HC CH2

R

+

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Phenols

bull Loss of CO to form M-28 peak and loss of HCO to from M-29 peak

bull Example 2-methylphenol

bull Characteristically strong M M-1 M-28 M-29

Aliphatic amines

bull The most characteristic fragmentation pattern of 1deg 2deg and 3deg aliphatic amines is b-cleavage a-cleavage is also common to 1deg amine and mz = 30

51

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Isotopic effect

M+1 M+2 amp M+4 peaks

52

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Example of isotopes and their relative abundance

Element IsotopeRelative abundance

Hydrogen 1H 100 2H 0018

Carbon 12C 100 13C 111

Nitrogen 14N 100 15N 038

Oxygen 16O 100 17O 004

Sulphur 32S 100 33S 078

Chlorine 35Cl 100 37Cl 325

bromine 79Br 100 79Br 980

53

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

M+1

bull Carbon in nature 12C (9890) and 13C (110 )

bull Thus there are 111 atoms of carbon-13 in nature for every 100 atoms of carbon-12

54

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Question

bull What is the maximum number of carbons of

unknown substance can have if the relative abundance of the parent peak is 40 and the M+1 peak is 14

Solution

55

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

M+2

bull Chlorine and bromine are common elements that give rise to M+2 peaks

bull In nature chlorine 35Cl is 7577 and 37Cl is 2423 ndash A ratio of M to M+2 is approximately 31 indicates the

presence of a single chlorine in a compoun

bull Bromine in nature 79Br is 507 and 81Br is 493 ndash A ratio of M to M+2 of approximately 11 indicates

the presence of single bromine in compound

56

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

57

bull One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl eg chloroethane

-35

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

bull One Bromide will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br (eg bromoethane)

58

-79

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak

Note for M+2 and M+4 of 1 or 2 isotopic elements

59

One atom Two atoms

One Chloride will contain a M+2 peak approximately 13 the intensity of the molecular ion peak because of the presence of 37Cl

Two chlorides will contain a M+2 peak approximately 13 the intensity of the molecular ion peak and M+4 peak about 13 of the M+2 peak

One Br will contain a M+2 peak approximately equal the intensity of the molecular ion peak because of the presence of 81Br

Two Bromides will contain M+2 peak approximately twice intensity of the molecular ion peak and M+4 peak about equal to the molecular ion peak