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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