The formed ions are separated by Deflection in magnetic
field according to their Mass to charge (m/z)
Ions formed Further break up into smaller ion
(Fragment ions or Daughter ions formed)
Mass Spectroscopy
Basic Principles
3
Molecules converted into highly energetic positively charged
ions (Molecular ions or Parent ions)
Organic Molecules are bombarded with electron
Mass Spectrum
m/z ratio Vs intensity (relative abundance of peak)
AISC/SBS/MSc-I
Working of MS
•There are four key stages in the process for
Mass Spectrometry.
–Ionization
–Acceleration
–Deflection
–Detection
7AISC/SBS/MSc-I
Stage 1: Ionisation
8
•Theinitialsamplemaybeasolid,liquid,orgas.
•Thesampleisvaporizedintoagasandthenionizedbytheionsource,usuallyby
losinganelectrontobecomeacation
•ElectroIonisationisthemostcommontypeofionisation.
•Thesampleisbombardedbyelectronswhichcomefromaheatedfilament.
•Whenthesamplepassesthroughtheelectronstream,thehighenergyelectronsin
thestreamknockelectronsoutofthesampletoformions.
•Theionizationchamberiskeptinavacuumsotheionsthatareproducedcan
progressthroughtheinstrumentwithoutrunningintomoleculesfromair.
Stage 2: Acceleration
•Acceleration is a simple step where the ions are placed between a set of charges
parallel plates.
•Theionswillthenberepelledbyoneplateandattractedtotheother.
•Thereisaslitcutintheplatewhichtheionsareattractedto.theforceof
attractionandrepulsionforcestheionsthroughtheslitatanacceleratedrate.
•Thespeedofaccelerationcanbeadjustedbychangingthechargeontheplates.
•Thepurposeofaccelerationistogiveallspeciesthesamekineticenergy,like
startingaracewithallrunnersonthesameline.
AISC/SBS/MSc-I
Stage 3: Deflection
•Ions are deflected by the magnetic field surrounding the instrument.
•Theamountofdeflectiondependsonthemassandchargeoftheions.
•Lightercomponentsorcomponentswithmoreionicchargewilldeflectinthefield
morethanheavierorlesschargedcomponents.
•Theheavierions,aredeflectedtheleast(IonstreamC)
•Thelightestionsaredeflectedthemost(IonStreamA)
•Theionsatthecorrectmassandchargetraveltothedetector.(IonStreamB)
•Themasstochargeratio(m/z)isdeterminedfromtheionthathitsthedetector.
9
Step 4: Detection
•Whentheionstreamreachedthedetectorthehitawire.Onhittingthe
wiretheybecomeneutralisedbyanelectronjumpingfromthemetalwire
totheion.
•Theamplifierpicksuponthiscurrentbeingcreatedbetweenthewireand
theionandamplifiesthesignalbeingdetected.
•Thecomputerpicksuponthisandconvertsittomass/chargeratioanda
spectrumisproduced.
AISC/SBS/MSc-I
•Ionizing technique and their source in MS
There are many types ofionizationmethods are used in mass spectrometry
methods.
Gas Phase Sources. (Sources)
• Electron Impact Ionization (EI). (By Energetic electrons)
• Chemical Ionization (CI). (By reagent gaseous ions)
• Field Ionizations (FI). (By high potential electrodes)
Desorption Sources.
• Field Desorption (FD). (By high potential electrodes)
• ElectrosprayIonization (ESI). ( by high electric field)
• Matrix assisted desorption/Ionisation(MALDI). (By laser beam)
• Plasma desorption (PD). (by fragments from
253
Cf)
• Fast Atom Bombardment (FAB). (by energetic atomic beam)
• ThermosprayIonization (TS). (By high temperature)
• Secondary Ion Mass Spectrometry (SIMS). (energetic atomic beam)
10AISC/SBS/MSc-I
Mass Spectrum
AISC/SBS/MSc-I 11
Types of Peaks in MS
•Molecular ion Peak
•Base Peak
•Metastablepeak
•Fragmention peak
•Rearrangemention peak
•Multichargedion
•Negative ion peak
12AISC/SBS/MSc-I
Molecular ion Peak
•Whenaanysampleisbombardedwithelectronsof9
to15eVenergy,themolecularionisproducedbyloss
ofsingleelectron.ItisdenotedbyM
(orM
)
•Whenthevaporizedorganicsamplepassesintothe
ionizationchamberofamassspectrometer,itis
bombardedbyastreamofelectrons.Theseelectrons
haveahighenoughenergytoknockanelectronoffan
organicmoleculetoformapositiveion.Thisionis
calledthemolecularion.(sometimestheparention.)
•Molecularionpeakgivesmolecularweightof
compounds
M M 2e+
e
molecular ion
13AISC/SBS/MSc-I
Molecular Ion peak in Ethanol
14AISC/SBS/MSc-I
Mass spectrum of Pentane
(Molecular weight = 72)
15AISC/SBS/MSc-I
High Resolution Molecular ion peak
•Auniquemolecularformulacanoftenbederivedaccurate
massmeasurementaloneinHighResolutionMass
spectrometry(HRMS).SomolecularioninHRMSarecalled
highresolutionmolecularionpeak.InHRMSmasses
obtaineduptofourorfivedecimalplaces.
•Theuniquemolecularformulapossiblebecausethenuclide
massesarenotinteger.
•Exactmassesofsomenuclides
H1.00783
C12.0000
N14.0031
O15.9949
•
AISC/SBS/MSc-I 16
Precise mass determination
•if we have molecular formula C
6H
12O then its HRMS molecular ion
mass is unique at 100.0888
•Mass = (number of Carbon X Mass of Carbon) + (number of hydrogen X
Mass of Hydrogen )+ (number of Oxygen X mass of Oxygen)
•Mass = 6 X Mass of Carbon + 12 X Mass of Hydrogen + 1 X mass of Oxygen
= 6 x 12.0000 + 12 x 1.00783 + 1 x 15. 9949
= 72.0000 + 12.09396 + 15.9949
=100.08886
•For molecular formula C
5H
8O
2
•Mass = 5 x Mass of Carbon + 8 x Mass of Hydrogen + 2 x mass of Oxygen
= 5 x 12.0000 + 8x 1.00783 + 2 x 15. 9949
= 60.0000 + 8.06264 + 31.9898
= 100.05244
AISC/SBS/MSc-I 17
Significance / Use of the Molecular Ion (M
)
•Byusingrulethirteenformolecularionpeak,onecandeterminethe
molecularformula.
•FromMolecularionpeak,itgivesideaofisotopicelementifpresent.
•Itgivesideaofoddnitrogenpresentincompound(nitrogenrule).
•ThemolecularionalongwithotherinformationfromIRandNMRspectra
canallowtheidentityofanunknowntobedetermined.
•Nowadays,Oncetheidentityofthemolecularionhasbeendetermined
muchcanbelearnedaboutthecompound.Oneextremelyvaluablepiece
ofinformationthatcanbedeterminedfromahighresolutionmass
spectrometeristhemolecularformulaofanunknownanalyte.
•Ifamolecularionwasidentifiedtobeatm/z80onaninstrumentwith
unitresolutionlittlecouldbedeterminedaboutthemolecularformula.
Forexample,someofthemanypossiblemolecularformulasinclude
C
4H
4N
2(80.0375),C
5H
4O(80.0262),andC
6H
8(80.0626).
•Ahighresolutioninstrumentmeasurementofthispeakat80.0372±
0.0005wouldindicatethattheempiricalformulaisC
4H
4N
2.
18AISC/SBS/MSc-I
Base peak in pentane
20
In the mass spectrum for pentane, the positive ion with m/z = 43 produces
the tallest spectrum. It is base of given spectrum.
AISC/SBS/MSc-I
Mass Spectrum of ethyl Benzene
(Base peak = 91)
21AISC/SBS/MSc-I
Fragment ion peak
•MolecularionpeakinMSfurtherundergo
fragmentationgivesnewdaughterionpeaks
suchpeakproducedinMScalledasfragment
ionpeaks.
24AISC/SBS/MSc-I
Negative ion peak
25
•Negativeionsareformedfromelectronbombardmentof
sample.Theseresultsduetothecaptureofelectronbya
moleculeduringcollisionofmolecules.
•Molecularionsobservedinnegativeionchemicalionization
massspectraareusuallyM
n
or[M-H]
-
.
•Inthenegativeionmodeoperationpeakscorrespondingto
deprotonatedanalytemoleculesareobserved.
•Theformationofnegativeionsisveryrare.
AISC/SBS/MSc-I
Calculate Mass and tally with Nitrogen rule
28
NH
2 NO
2 NH
2
mass
nitrogen
odd / even
odd / even odd / even odd / even
odd / even
odd / even
H
3C H
3C
H
2N
AISC/SBS/MSc-I
Calculate Mass and nitrogen
29
NH
2 NO
2 NH
2
NO
2
mass
nitrogen
odd / even
odd / even odd / even odd / even
odd / even
odd / even
AISC/SBS/MSc-I
*Rule of 13*
•TheRuleof13isasimpleprocedurefortabulatingpossible
chemicalformulaforagivenmolecularmass.
•Thefirststepinapplyingtheruleistoassumethatonlycarbonand
hydrogenarepresentinthemoleculeandthatthemolecule
comprisessomenumberofCH"units"eachofwhichhasanominal
massof13.
•IfthemolecularweightofthemoleculeinquestionisM,the
numberofpossibleCHunitsisnand
• where r is the remainder.
•The base formula for the molecule is C
nH
n+r
30AISC/SBS/MSc-I
31AISC/SBS/MSc-I
Q2 ) for a m
+
= 106,
n=8 (106/13) with r of 2.
A possible molecular formula for this ion C
8H
8+2= C
8H
10
Other way Rule of 13
32AISC/SBS/MSc-I
The nominal mass of a substance is 140.
What is its molecular formula?
•By using The rule of 13:
•Divide the nominal mass by 13:
•A hydrocarbon with this molecular weight
would have 10 Catoms
•Multiply the remainder by 13: 0.769*13 = 9.997 or 10;
•A hydrocarbon with this molecular weight
would have (n+r) (10+10) or 20 hydrogens
•‘CH’Molecularformula will be C
10H
20
33AISC/SBS/MSc-I
By using rule of 13, molecular formula
determination with other element.
•Fromparenthydrocarbonwhichisderived
fromruleof13,otherelements(likeO,N)can
beaddedtothathydrocarbon.
•Foradditionofoxygen/nitrogenwehaveto
removesamemassofoxygenornitrogenfrom
hydrocarbonformula.
•Foradditionof‘O’removeCH
4
•Foradditionof ‘N’removeCH
2
•Foradditionof ‘C’remove12H
34AISC/SBS/MSc-I
Q) A carboxylic acid of molecular ion peak (m/z) at 122. find its
molecular formula with the help of rule of 13.
•M = 122
•Therefore become
:. CH Molecular formula C
nH
n+r= C
9H
14
Carboxylic acid contain at least 2oxygen to form –COOH group
C
9H
14
+O -CH
4
C
8H
10O
+O -CH
4
C
7H
6O
2
35
:. Molecular formula for give mass 122 is C
7H
6O
2
AISC/SBS/MSc-I
Q) A hydrocarbon compound with mass 128 and 8 hydrogen.
find its molecular formula with the help of rule of 13
36
•M = 128
•Therefore become
:. CH Molecular formula C
nH
n+r= C
9H
20
C
9H
20
remove12H add C
C
10H
8
AISC/SBS/MSc-I
Q) A hydrocarbon compound with mass 109 and PMR shows
7 hydrogen. find its molecular formula with the help of rule
of 13
37
•M = 109
•Therefore become
:. CH Molecular formula C
nH
n+r= C
8H
13
mass is odd there it contain odd no. of Nitrogen (Nitrogen Rule)
C
8H
13
+N -CH
2
C
8H
11N
+O -CH
4
C
7H
7ON
:. Molecular formula for give mass 109 is C
7H
7ON
AISC/SBS/MSc-I
Formation of molecular ion M
+
and
Fragmentation of the molecular ion
AISC/SBS/MSc-I 39
•Whenaanymolecule/sampleisbombardedwithelectrons,the
molecularionisproducedbylossofsingleelectronwithsamemassofits
molecularweight.Molecularionisalsodenotedbyaradicalcationas
below
AB
e
AB
Molecular ion
M
2 e
•TheseMolecularionoraradicalcationundergofragmentationtobreaka
bondbetweenA&Btoformaradicalandacationasgivenbelow.
•Only cationsor fragment with positive charge is detected in MS.
Molecular ion
a radical cation
AB
A + B
A + B
radical
radical cation
cation
Fragmentation of Alkanes
40AISC/SBS/MSc-I
•Fragmentation of straight chain alkane is observed by
breaking of any C-C bond from molecular ion.
•Alkane gives following m/z fragments due loose of
group
M-15(due to loose of -CH
3methyl group)
M-29(due to loose of –CH
2CH
3ethyl group)
M-43(due to loose of -CH
2CH
2CH
3propylgroup)
•Lose of largest substituent is more fevered due to
stability .
•Stability of cation:
•methyl < primary < secondary < tertiary
Q.2) Give the genesis for pentane
Mass (m/z): 15, 29, 43(100%), 57, 72
42AISC/SBS/MSc-I
Molecular ion
m/z = 72
CH
3CH
2CH
2CH
2CH
3
e
CH
3CH
2CH
2CH
2CH
3
MW =72
Answer
Another way it is also written like this
AISC/SBS/MSc-I 43
Genesis for Hexane
AISC/SBS/MSc-I 44
Fragmentation of Branched alkane
•Genesis of 2-methyl pentane:
•m/z = 15, 29, 43 (100%),71, 86
AISC/SBS/MSc-I 45
Q) Show the genesis for following branched alkanes.
AISC/SBS/MSc-I 46
Fragmentation of Cycloalkanes
•Loss of side chains if present, by cleavage
•Loss of ethylene or double bond fragment
from ring
•Cleavage takes place by homolyticfasion
(show single headed arrow mechanism)
AISC/SBS/MSc-I 47
Fragmentation in cyclopentane
AISC/SBS/MSc-I 48
e
- +
MW = M/Z =
molecular ion
70 70
+
M/Z =70
+
+
CH
2
CH
2
m/z =42
28
C
3H
6
C
5H
10
C
5H
10
Fragmentation in cyclohexane
AISC/SBS/MSc-I 49
e
- +
MW =
M/Z =
molecular ion
84
84
+
M/Z =84
+
+
CH
2
CH
2
m/z =56
28
C
4H
8
C
6H
12
+ +
m/z =42
C
3H
6
i)
ii)
iii)
C
6H
12
Genesis of 1-metyl cyclopentane
AISC/SBS/MSc-I 50
e
-
+
MW = M/Z =
molecular ion
84 84
+
+ +
CH
2
CH
2
m/z =56
28
C
4H
8
C
6H
12
CH
3 CH
3
+
M/Z =84
C
6H
12
+
CH
3
m/z = 69
M/Z =84
C
6H
12
i)
ii)
iii)
-cleavage in alcohol
•The most important fragmentation reaction in
alcohols is the loss of an alkyl group which are
.
•Example
or
AISC/SBS/MSc-I 53
e
-
molecular ion
i)
ii)
OH
+
+
OH
+
OH OH
a-cleavage
•In tertiary alcohol, there are chances of
braking each all three -bond to alcohol
•Alcoholsalsoundergodehydrationtoloss
watermoleculeeither1,2eliminationoe1,4
eliminationresulting(M-18)peak.
AISC/SBS/MSc-I 54
1,2 elimination
1,4 elimination
•Alcoholsalsofrequentlyundergotherearrangementresultingina
M-18peakfromthelossofwater.Thispeakismosteasilyvisiblein
primaryalcoholsbutcanbefoundinsecondaryandtertiary
alcoholsaswell.Primaryalcoholsalsocanlosebothwaterandan
alkene.
•Alcoholcontainingfourormorecarbonmayundergosuch
rearrangementsimultaneouslosswaterandethyleneas
AISC/SBS/MSc-I 55
Or
Genesis of 1-butanol
mass (m/z) = 31, 43, 73, 74.
AISC/SBS/MSc-I 57
AISC/SBS/MSc-I 58
•Q1. Give Genesis of 1-pentanol
mass (m/z) = 31, 42 (100%), 55, 70, 87,88.
•Q2. Give Genesis of 2-pentanol
mass (m/z) = 42, 45 (100%), 55, 73, 87,88.
•Q3. Give Genesis of 2methyl-2-butanol
mass (m/z) = 31, 43, 55, 59 (100%),70, 73, 88.
Q4) Give the genesis for following base
peak fragments for their molecular ion.
AISC/SBS/MSc-I 59
Cyclic alcohol may undergo fragmentation by at least
three different pathway
60AISC/SBS/MSc-I
Fragmentation of Amines
61AISC/SBS/MSc-I
The fragmentation reaction in amines are similar to
alcohol
•-cleavage in amines:
Questions to solve
64AISC/SBS/MSc-I
•Q1. Give Genesis for Ethyl amine
mass (m/z) = 30 (100%) , 44, 45.
•Q2. Give Genesis for diethyl amine
mass (m/z) = 30, 58 (100%) , 72, 73.
•Q1. Give Genesis for triethylamine
mass (m/z) = 30, 58, 86 (100%) , 100, 101.
Applications of Mass Spectrometry
•MassSpectrometry as a technique can be coupled with
other techniques such as HPLC and GC.
•As it is used in the identification of compounds it is
used in all areas of science.
•Some of its uses are:
•Trace Gas Analysis
•Pharmaceutical Industry
•Space Exploration
•Forensic Toxicology
•Archaeological Dating.
65AISC/SBS/MSc-I
Question from question papers
66AISC/SBS/MSc-I
i)
ii)
iii)
iv)
AISC/SBS/MSc-I 67
i)
iii)
AISC/SBS/MSc-I 68
Calculation of intensity of isotopic (M+1) peak
•M+1peakpossibleduetoisotopesofC,H,andN.
M+1peakintensitycanbecalculatedbynumberof
atomspresentwiththeirisotopicabundance
•Theformulaforcalculatingtheintensityofthe
M+1peakisasfollows
•% (M+1) = 1.1 X number of C atoms +
0.016 X number of H atoms +
0.38 X number of N atoms +…
AISC/SBS/MSc-I 69
What will be the M+1 intensity for
propeneC
3H
6
•PropeneC
3H
6
•% (M+1) = 1.1 X number of C atoms + 0.016 X number of H atoms +
0.38 X number of N atoms +…
% (M+1) = 1.1 x 3 + 0.016 x 6
= 3.3 + 0.096
= 3.396 %
Calculate intensity of M+1 peak for Aniline
Aniline C
6H
7N
% (M+1) = 1.1 X number of C atoms + 0.016 X number of H atoms +
0.38 X number of N atoms +…
% (M+1) = 1.1 x 6 + 0.016 x 7 + 0.38 x 1
= 6.6 + 0.112 + 0.38
= 7.1 %
AISC/SBS/MSc-I 70