CHM312

INSTRUMENTAL ANALYSIS
CHAPTER 1

MASS SPECTROMETRY
LEARNING OUTCOMES
1. Better understanding of Mass
spectrometry.

2. Gain experience in the acquisition,

processing, and displaying MS data.

3. Interpret MS data in order to establish

structure for unknown
 CONTENTS

Introduction Theory

The Mass The Mass

Spectrometer Spectrum

Interpretation of
spectrum
MASS SPECTROMETRY (MS)

 MS is an analytical chemistry technique that helps to

identify the amount and type of chemicals present in a
sample by measuring the mass-to-charge ratio and
abundance of gas-phase ions.
 A mass spectrum is a plot of the ion signal as a
function of the mass-to-charge ratio.
• MS is an analytical technique for measuring the mass-to-charge
ratio (m/z) of ions in the gas phase.

 Mass spectrometry is the most valuable analytical tool for

determining accurate molecular masses.
 Also able to give information about structure.
 One of the most sensitive and versatile analytical tools
 More sensitive than other spectroscopic methods (e.g. IR
spectroscopy)
 Only a microgram or less of materials is required for the
analysis
Mass spectrometric analysis involves:
1. the conversion of molecules to ions
2. separation of the ions formed according to their mass-
to-charge (m/e) ratio
 m is the mass of the ion in atomic mass units and
e is its charge
3. Finally, the number of ions of each type (i.e. the
relative abundance of ions of each type) is determined
4. The analysis is carried out using a mass spectrometer
 A MASS SPECTROMETER
• A mass spectrometer is designed to do three things:
1. Convert neutral atoms or molecules into a beam of
positive (or rarely negative) ions.
2. Separate the ions on the basis of their mass-to-charge
(m/z) ratio.
3. Measure the relative abundance of each ion.
Components of a mass spectrometer
 PRINCIPLES OF MASS
SPECTROMETER
Sample (solid/liquids/ gases)

+
_

Ionizer Mass Analyzer Detector

 MASS SPECTROMETER
SCHEMATIC
Turbo pumps
High Vacuum System
Diffusion pumps
Rough pumps
Rotary pumps

Ion Mass Data

Inlet Detector
Source Filter System

Sample Plate MALDI TOF Microch plate PC’s

Target ESI Quadrupole Electron Mult. UNIX
HPLC IonSpray Ion Trap Hybrid Detec. Mac
GC FAB Mag. Sector
Solids probe LSIMS FTMS
EI/CI
 VOLATILIZATION CHAMBER (GAS
PHASE VS DESORPTION )
 Gas phase source
sample is vaporized then ionized. Restricted to
thermally stable compounds (temperature less than
300°C)
 Desorption source
solid or liquid sample is converted directly into gaseous
ions (do not require volatilization)- applicable to non
volatile and thermally unstable samples
 IONIZATION CHAMBER
 There are a few different Ionization methods (different way of producing
parent/molecular ions M+) which can be divided into two types:
 Hard ionization (extensive fragmentation)
a) Electron Impact (small molecules, 1-1000 Daltons)
b) Chemical ionization
c) Fast Atom Bombardment (FAB – Semi-hard) (peptides, sugars, up to
6000 Daltons)

 Soft ionization (little or no fragmentation)

a) Electrospray Ionization (ESI - Soft) (peptides, proteins, up to 200,000
Daltons)
b) Matrix Assisted Laser Desorption (MALDI-Soft) (peptides, proteins,
DNA, up to 500 kD)
 (Soft ionization techniques keep the molecule of interest fully intact)
 This give rise to different type of MS
a) Electron Ionization Mass Spectrometry (EI-MS). Hard
ionization
b) Fast Atom Bombardment (FAB-MS).
c) Chemical Ionization (CI).
d) Matrix-Assisted Laser Desorption ionization Soft
(MALDI). ionization
e) Electrospray ionization (ESI).
HARD IONIZATION METHODS

EI
a) Electron Impact Ionization (EI)
• Utilize heat or no heat .
• Use electron gun under vacuum. Sample introduced into
instrument by heating it until it evaporates
• Gas phase sample is bombarded with electrons coming from
rhenium or tungsten filament (energy = 70 eV to 100 eV)
• Molecule is “shattered” into fragments (70 eV >> 5 eV bonds)
• Fragments (cations) sent to mass analyzer
EI Fragmentation of CH3OH
CH3OH CH3OH+
CH3OH CH2O=H+ + H

CH3OH
+ CH3 + OH

CH2O=H+ CHO=H+ + H
15
b) Chemical ionization
• Utilize gases such as NH3 or methane
• The gases when heated produce/generate reactive chemical
species such as NH3. or NH3+ which are potential proton donors
or hydride extractors:
• Ions produced through chemical ionization are much more stable
than molecular ions generated from EI
 SOFT IONIZATION METHODS

337 nm UV laser

Fluid (no salt)

+
_

cyano-hydroxy Gold tip needle

cinnamic acid

MALDI ESI
a) Electrospray Ionization (ESI)
• Sample is in the form of microdroplets. (sample is coated with solvent
(polar, volatile buffer (no salts)) and pumped through a stainless steel
capillary (70 - 150 mm) at a rate of 10-100 mL/min
• Strong voltage (3-4 kV) applied at tip along with flow of nebulizing gas
causes the sample to “nebulize” or aerosolize
• Aerosol is directed through regions of higher vacuum until droplets
evaporate to near atomic size (still carrying charges)

18
b) Matrix-Assisted Laser Desorption/Ionization (MALDI)
• The analyte is mixed with a matrix compound, usually solid aromatic
compound with carboxylic acid
• The solid matrix is placed on a solid probe, inserted into the ionization
chamber (under vacuum) and exposed to a short UV laser pulse
• Intact gaseous molecular ions of the analyte are formed.
• Useful for large biomolecules (proteins)
• Can only be used with TOF mass analyzer
• Very expensive (requires powerful laser)

19
 ELECTROSPRAY IONIZATION
• Samples of MW up to 1200 Da usually produce singly charged
ions with observed MW equal to parent mass + H (1.008
Daltons)
• Larger samples (typically peptides) yield ions with multiple
charges (from 2 to 20 +)
• Multiply charged species form a Gaussian distribution with those
having the most charges showing up at lower m/z values

20
 IONS SOURCE : EI VS ESI
• Electron Impact (EI) • Electrospray (ESI)
1. Ions produced under vacuum 1. Ions produced at atmospheric
condition condition
2. Spectrum shows plenty of 2. Spectrum shows prominent
fragments ions and less intense protonated molecular ion
molecular ions observed with only insignificant
3. Suitable for thermally stable fragment ions
compounds
 MASS SPECTROMETER
SCHEMATIC
Turbo pumps
High Vacuum System
Diffusion pumps
Rough pumps
Rotary pumps

Ion Mass Data

Inlet Detector
Source Filter System

Sample Plate MALDI TOF Microch plate PC’s

Target ESI Quadrupole Electron Mult. UNIX
HPLC IonSpray Ion Trap Hybrid Detec. Mac
GC FAB Mag. Sector
Solids probe LSIMS FTMS
EI/CI
 DIFFERENT MASS ANALYZERS
• Magnetic Sector Analyzer (MSA)
▫ High resolution, exact mass, original MA
• Quadrupole Analyzer (Q)
▫ Low (1 amu) resolution, fast, cheap
• Time-of-Flight Analyzer (TOF)
▫ No upper m/z limit, high throughput
• Ion Trap Mass Analyzer (QSTAR)
▫ Good resolution, all-in-one mass analyzer
• Ion Cyclotron Resonance (FT-ICR)
▫ Highest resolution, exact mass, costly
1. Magnetic Sector Analyzer

24
Mass Spec Equation (Magnet Sector)

m B2 r2
=
z 2V

M = mass of ion B = magnetic field

z = charge of ion r = radius of circle
V = voltage
QUADRUPOLE MASS ANALYZER
 QUADRUPOLE MASS ANALYZER
• A quadrupole mass filter consists of four parallel metal rods with
different charges
• Two opposite rods have an applied potential of (U+Vcos(wt)) and
the other two rods have a potential of -(U+Vcos(wt))
• The applied voltages affect the trajectory of ions traveling down the
flight path
• For given dc and ac voltages, only ions of a certain mass-to-charge
ratio pass through the quadrupole filter and all other ions are thrown
out of their original path
 TOF
• A time of flight (TOF) mass analyzer measures the time it takes
for an ion to pass through a field-free zone called a drift tube at a
constant voltage so as they have the same kinetic energy.
• The ions are released into the gas phase in a single burst, the
ions are accelerated by an electric field and ions of different
mass to charge ratio will have different velocities.
NANOSPRAY MCP
TIP DETECTOR

PUSHER

HEXAPOLE
HEXAPOLE
COLLISION
CELL TOF
QUADRUPOLE

SKIMMER REFLECTRON
ION HEXAPOLE
SOURCE
Mass Spec Equation (TOF)

m 2Vt 2
=
z L2

m = mass of ion L = drift tube length

z = charge of ion t = time of travel
V = voltage

30
 ION TRAP MASS ANALYZER
• Ion traps are ion trapping
devices that make use of a
three-dimensional quadrupole
field to trap and mass-analyze
ions
• invented by Wolfgang Paul
(Nobel Prize1989)
• Offer good mass resolving
power, and even MSn capability.

31
ION TRAP MASS ANALYZER
 MASS SPECTROMETER
SCHEMATIC
Turbo pumps
High Vacuum System
Diffusion pumps
Rough pumps
Rotary pumps

Ion Mass Data

Inlet Detector
Source Filter System

Sample Plate MALDI TOF Microch plate PC’s

Target ESI Quadrupole Electron Mult. UNIX
HPLC IonSpray Ion Trap Hybrid Detec. Mac
GC FAB Mag. Sector
Solids probe LSIMS FTMS
EI/CI
MASS DETECTORS

Electron Multiplier (Dynode)

 MS DETECTORS
• Early detectors used photographic film
• Today’s detectors (ion channel and electron multipliers) produce
electronic signals via 2o electronic emission when struck by an ion
• Timing mechanisms integrate these signals with scanning voltages to
allow the instrument to report which m/z has struck the detector
• Need constant and regular calibration
 DIFFERENT TYPES OF MS
• ESI-QTOF
▫ Electrospray ionization source + quadrupole mass filter + time-of-
flight mass analyzer
• MALDI-QTOF
▫ Matrix-assisted laser desorption ionization + quadrupole + time-
of-flight mass analyzer
• GC-MS - Gas Chromatography MS
▫ separates volatile compounds in gas column and ID’s by mass
• LC-MS - Liquid Chromatography MS
▫ separates delicate compounds in HPLC column and ID’s by
mass
• MS-MS - Tandem Mass Spectrometry
▫ separates compound fragments by magnetic field and ID’s by
mass
 TANDEM MASS
SPECTROMETER
NANOSPRAY MCP
TIP DETECTOR

PUSHER

HEXAPOLE
HEXAPOLE
COLLISION
CELL TOF
QUADRUPOLE
SKIMMER REFLECTRON
ION HEXAPOLE
SOURCE
TANDEM MASS SPECTROMETRY
• Purpose is to fragment ions from parent ion to provide structural
information about a molecule
• Also allows separation and identification of compounds in
complex mixtures
• Uses two or more mass analyzers/filters separated by a collision
cell filled with Argon or Xenon
• Collision cell is where selected ions are sent for further
fragmentation
 TANDEM MASS SPECTROMETRY
• Different MS-MS configurations
▫ Quadrupole-quadrupole (low energy)
▫ Magnetic sector-quadrupole (high)
▫ Quadrupole-time-of-flight (low energy)
▫ Time-of-flight-time-of-flight (low energy)
• Fragmentation experiments may also be performed on single
analyzer instruments such as ion trap instruments and TOF
instruments equipped with post-source decay

Lecture 2.1

39
 DIFFERENT MS-MS MODES
• Product or Daughter Ion Scanning
▫ first analyzer selects ion for further fragmentation
▫ most often used for peptide sequencing
• Precursor or Parent Ion Scanning
▫ no first filtering, used for glycosylation studies
• Neutral Loss Scanning
▫ selects for ions of one chemical type (COOH, OH)
• Selected/Multiple Reaction Monitoring
▫ selects for known, well characterized ions only

Lecture 2.1

40
In Mass spectrometric analysis:
1. Sample molecules is first vaporized into gaseous state in the
vaporization chamber
2. The vapor is ionized by bombarding with a beam of high
energy electrons.
3. Energy from the collisions with the energetic electrons excite
the molecules
4. Relaxation from excited state occur via fragmentation of part
of the molecular ions producing ions of lower masses.
5. Positive ions are attracted through a slit and separation of
the ions formed according to their mass-to-charge (m/e) ratio
is done by mass analyzer
6. The number of ions of each type (i.e. the relative abundance
of ions of each type) is determined
 STEPS IN MASS SPECTROMETER
1. In the vaporization chamber :The sample is heated until
it vaporizes
 changes to the gaseous state
2. In the ionization chamber: Ionization and fragmentation
The molecules in the gaseous state are bombarded
with a beam of fast-moving electrons (using
electrons with energies of approximately 70 eV
[6750 kJ (1600 kcal)/mol].
 Collisions between these electrons and the sample result in
loss of electrons from sample molecules and formation of
positive ions.
 One of the electrons of the molecule is knocked
off/removed the molecular ion contains a single
unpaired electron
 the molecular ion is not only a cation, it is also a free
radical
a) Molecular ion (M+. ): Parent ion

A radical cation formed by the removal of a single electron

from a parent molecule in a mass spectrometer.
▫ a plus sign to show that it is a cation.
▫ a dot to show that it has an odd number of electrons.
[M]+.

H H +
H C H + e H C H +2 e
H H
Molecular ion
(a radical cation)
b) M+2 and M+1 Peaks
• Sulfur is the only element common to organic compounds
that gives a significant M+2 peak

32S = 95.02% and 34S = 4.21%

• Because M+1 peaks are relatively low in intensity compared

to the molecular ion and often difficult to measure with any
precision, they are generally not useful for accurate
determinations of molecular weight.
c) Fragmentation

▫ The energy used for bombardment is sufficient not

only to dislodge one or more electrons from a molecule,
but also to cause extensive fragmentation.
▫ These fragments may be unstable as well and, in turn,
break apart to even smaller fragments.
▫ Fragmentation of a molecular ion, M, produces a
radical and a cation.
▫ Only the cation is detected by MS.
 A • + B+
+ Radical Cation
A-B •

Molecular ion
A+ + •B
(a radical cation)
Cation Radical

• The way that a molecular ion fragments

give us highly useful information about the structure of a complex
molecule

Example: a molecule of methanol (CH3OH) is bombarded with a beam of fast-moving

electrons
▫ Where fragmentation occurs to form new cations, the
mode that gives the most stable cation is favored.
▫ The probability of fragmentation to form new carbocations
increases in the order.

+
2° 3°
CH3 < 1° < 1° allylic < 2° allylic < 3° allylic
1° benzylic 2° benzylic 3° benzylic
d) The base peak

• the largest peak and is assigned the value of 100. Heights

of the other peaks is calculated as a percentage of the
base peak
Formation of Fragments
• The molecular ions formed in the ionization chamber are
energetically unstable
 Some of them may break up into smaller fragments
 Called the daughter ions
Formation of Fragments
• The peak at m/e 31
 corresponds to the ion H2C = OH+
 formed by losing one hydrogen atom from the
molecular ion
Formation of Fragments
• The peak at m/e 29 corresponds to the ion HC  O+
 formed by losing two hydrogen atoms from the
ion H2C = OH+
Formation of Fragments
• The peak at m/e 15 corresponds to the ion H3C+
 formed by the breaking of the C  O bond in the
molecular ion
3. Acceleration and deflaction of cations:
 The positivelycharged ions formed are then accelerated by
electric field and deflected by magnetic field
 causes the ions to arrive the ion detector
 The lighter the ions, the greater the deflection
 Positively charged ions of higher charge have
greater deflection
 Ions with a high m/e ratio are deflected to smaller
extent than ions with a low m/e ratio
4.In the ion detector
 the number of ions collected is measured electronically
 The intensity of the signal is a measure of the relative
abundance of the ions with a particular m/e ratio
 MASS SPECTRUM
 Mass spectrum: A plot of the relative abundance of ions
versus their mass-to-charge ratio.
 Base peak: The most abundant peak.
 Assigned an arbitrary intensity of 100.
 The relative abundance of all other ions is reported as a
% of abundance of the base peak.
 Mass spectrum of pentan-3-one
• The fragmentation pattern of pentan-3-one is
summarized below:
Mass spectrum of pentan-3-one
Interpretation of the mass spectrum of methanol
Corresponding ion m/e ratio
H3C+ 15
H  CO+ 29
H2C = OH+ 31
CH3OH 32
  The peak at m/e 31
 the most intense
peak
 Arbitrarily assigned an
intensity of 100%
 Called the base
peak

Mass spectrum of methanol

 Corresponds to the
most common ion
formed
 RESOLUTION
• Resolution: A measure of how well a mass spectrometer
separates ions of different mass.
▫ Low resolution: Refers to instruments capable of
separating only ions that differ in nominal mass; that is
ions that differ by at least 1 or more atomic mass units
(amu).

▫ High resolution: Refers to instruments capable of

separating ions that differ in mass by as little as 0.0001
amu.
 RESOLUTION
▫ C3H6O and C3H8O have nominal masses of 58 and 60, and
can be distinguished by low-resolution MS.
▫ C3H8O and C2H4O2 both have nominal masses of 60.
▫ distinguish between them by high-resolution MS.

Molecular N ominal Precise

Formula Mass Mas s
C3 H8 O 60 60.05754
C2 H4 O2 60 60.02112
 ISOTOPES
Atomic Mas s Relative
Element w eigh t Isotope (amu ) A bun dance
Virtually all hydrogen 1.0079 1H
2
1.00783 100
elements H 2.01410 0.016
carbon 12.011 12 C 12.0000 100
common to 13
C 13.0034 1.11
organic nitrogen 14.007 14 N
15
14.0031 100
N 15.0001 0.38
compounds are oxygen 15.999
16
O 15.9949 100
mixtures of 18
O 17.9992 0.20
isotopes. su lfu r 32.066
32
34
S 31.9721 100
S 33.9679 4.40
ch lorine 35.453 3 5Cl 34.9689 100
37
Cl 36.9659 32.5
bromine 79.904 79Br 78.9183 100
81
Br 80.9163 98.0
 ISOTOPES
▫ Carbon, for example, in nature is 98.90% 12C and 1.10%
113C.
▫ There are 1.11 atoms of carbon-13 in nature for every
100 atoms of carbon-12.

13 100 13 12
1.10 Cx x 100 = 1.11 atoms C per 100 atoms C
12
98.90 C
 M+2 and M+1 Peaks
• The most common elements giving rise to significant M + 2
peaks are chlorine and bromine.
▫ Chlorine in nature is 75.77% 35Cl and 24.23% 37Cl.
▫ A ratio of M to M + 2 of approximately 3:1 indicates the
presence of a single chlorine in a compound, as seen in the
MS of chloroethane.
 M+2 and M+1 Peaks
▫ Bromine in nature is 50.7% 79Br and 49.3% 81Br.
▫ A ratio of M to M + 2 of approximately 1:1 indicates the
presence of a single bromine atom in a compound, as
seen in the MS of 1-bromopropane.
 INTERPRETING A MASS
SPECTRUM
• The only elements to give significant M + 2 peaks are Cl and
Br.
▫ If no large M + 2 peak is present, these elements are
absent.
• Is the mass of the molecular ion odd or even?
• Nitrogen Rule: If a compound has
▫ zero or an even number of nitrogen atoms, its molecular
ion will have an even m/z value.
▫ an odd number of nitrogen atoms, its molecular ion will
have an odd m/z value.
 69

The Mass Spectrum

Relative Intensity of Molecular Ion Peaks
Imagine a sample containing 10,000 methane molecules...

Molecule # in sample m/z Relative abundance

12C1H 9889 12 + (4 x 1) = 16 100%
4

13C1H
4
110 13 + (4 x 1) = 17 (110/9889) x 100% = 1.1%*
14C1H
4
~1 14 + (4 x 1) = 18 (1/9889) x 100% = < 0.1%*

*Contributions from ions with 2H are ignored because of its very small
natural abundance

CH4 mass spectrum

m/z = 16 (M; 100%), m/z = 17 (M+1; 1.1%), m/z = 18 (M+2; < 0.1%)
 Formula from Mass Spectrum
M+1 Contributors
Comparing many mass spectra reveals M+1 intensity  ~1.1% per C in
formula
•Examples: C2H6 M = 100%; M+1 = ~2.2%
C6H6 M = 100%; M+1 = ~6.6%

Working backwards gives a useful observation...

When relative contribution of M = 100% then relative abundance of
M+1/1.1% gives the approximate number of carbon atoms in the
molecular formula

Other M+1 contributors

•15N (0.37%) and 33S (0.76%) should be considered
•2H (0.015%) and 17O (0.037%) can be ignored
 71

Formula from Mass Spectrum

M+2 Contributors

Anything useful from intensity of M+2?

Isotopes Natural abundances Intensity M : M+2

32S : 34S 95.0 : 4.2 100 : 4.4
35Cl : 37Cl 75.8 : 24.2 100 : 31.9
79Br : 81Br 50.7 : 49.3 100 : 97.2

Conclusion: Mass spectra of molecules with S, Cl, or Br have significant

M+2 peaks
 72

Formula from Mass Spectrum

M+2 Contributors
CH3

H C Cl C3H7Cl
CH3

C H Cl
M: 36 + 7 + 35 = 78
M+2: 36 + 7 + 37 = 80

78 80 M:M+2
abundance
~3:1

m/z
 73

Formula from Mass Spectrum

M+2 Contributors

C3H7Br
Relative abundance (%)

Br

C H Br
M: 36 + 7 + 79 = 122
M+2: 36 + 7 + 81 = 124

M:M+2
122 124
abundance
~1:1

m/z
 74

Identifying the Molecular Ions

Which peaks are molecular ions?
•Highest m/z not always M
Br
C7H7Br
•M+1 has m/z one more than m/z of M M: m/z = 170
 75

Formula from Mass Spectrum

Summary of Information from Mass Spectrum

M: Reveals mass of molecule composed of lowest mass isotopes

M+1: Intensity of M+1 / 1.1% = number of carbons
M+2: Intensity reveals presence of sulfur, chlorine, and bromine

Next lecture: procedure for deriving formula from mass spectrum

 76

Mass Spectrum  Formula  Structure

How do we derive structure from the mass spectrum?

CH3
?
 H C Cl

CH3

•Not trivial to do this directly

•Structure comes from formula; formula comes from mass spectrum

CH3

 C3H7Cl  H C Cl

CH3
 77

Mass Spectrum  Formula  Structure

How do we derive formula from the mass spectrum?
•m/z and relative intensities of M, M+1, and M+2

M: m/z = 78
C2 H6 O 3
C3H7Cl
M C5 H4 N
C6 H6
etc.

•A few useful rules to narrow the choices

 78

How Many Nitrogen Atoms?

Consider these molecules:
CH3 O
CH3
O2N NO2 H3C N
N
NH3 H2NNH2
O N N

NO2 CH3

Formula: NH3 N2 H4 C7 H5 N3 O 6 C8H10N4O2

m/z (M): 17 32 227 194

Conclusion
•When m/z (M) = even, number of N in formula is even
} The Nitrogen Rule
•When m/z (M) = odd, number of N in formula is odd
 79

How Many Nitrogen Atoms?

A Nitrogen Rule Example

Example: Formula choices from previous mass spectrum

M: m/z = 78 m/z even

C2 H6 O 3 even nitrogen count

C3H7Cl even nitrogen count

discarded C5 H4 N odd nitrogen count

C6 H6 even nitrogen count

 80

How Many Hydrogen Atoms?

One pi bond Two pi bonds

HC C

C6H14 C6H12 C6H10

max H for 6 C H count = max - 2 H count = max - 4

Conclusion: Each pi bond reduces max hydrogen count by two

 81

How Many Hydrogen Atoms?

One ring Two rings

C6H14 C6H12 C6H10

max H for 6 C H count = max - 2 H count = max - 4

Conclusion: Each ring reduces max hydrogen count by two

 82

How Many Hydrogen Atoms?

One nitrogen Two nitrogens
NH2 NH2

NH2
CH3

N H3C N
N CH3

CH3

C6H14 C6H15N C6H16N2

max H for 6 C H count = max + 1 H count = max + 2

Conclusion:
•Each nitrogen increases max H count by one
•For C carbons and N nitrogens, max number of H = 2C + N + 2
The Hydrogen Rule
 83

Mass Spectrum  Formula

Procedure
 Chem 14C atoms: H C N O F S Cl Br I
 M = molecular weight (lowest mass isotopes)
 M+1: gives carbon count
 M+2: presence of S, Cl, or Br
 No mass spec indicator for F, I (Assume absent unless otherwise
specified)
 Accounts for all atoms except O, N, and H
 MW - mass due to C, S, Cl, Br, F, and I = mass due to O, N, and H
 Systematically vary O and N to get formula candidates
 Trim candidate list with nitrogen rule and hydrogen rule
 84

Mass Spectrum Formula

Example #1
m/z Molecular ion Relative abundance Conclusions
102 M 100% Mass (lowest isotopes) = 102
Even number of nitrogens
Given information

103 M+1 6.9% 6.9 / 1.1 = 6.3 Six carbons*

104 M+2 0.38% < 4% so no S, Cl, or Br

Oxygen?

*Rounding: 6.00 to 6.33 = 6; 6.34 to 6.66 = 6 or 7; 6.67 to 7.00 = 7

 85

Mass Spectrum Formula

Example #1

Mass (M) - mass (C, S, Cl, Br, F, and I) = mass (N, O, and H)
102 - C6 = 102 - (6 x 12) = 30 amu for N, O, and H

Oxygens Nitrogens 30 - O - N = H Formula Notes

0 0 30 - 0 - 0 = 30 C6H30 Violates hydrogen rule

1 0 30 - 16 - 0 = 14 C6H14O Reasonable

2 0 30 - 32 - 0 = -2 C6H-2O2 Not possible

0 2* 30 - 0 - 28 = 2 C6 H2 N2 Reasonable
*Nitrogen rule!
•Other data (functional groups from IR, NMR integration, etc.) further trims the list
 86

Mass Spectrum Formula

Example #2

m/z Molecular ion Relative abundance Conclusions

157 M 100% Mass (lowest isotopes) = 157
Odd number of nitrogens

158 M+1 9.39% 9.39 / 1.1 = 8.5

Eight or nine carbons

159 M+2 34% One Cl; no S or Br

 FRAGMENTATION PATTERN
1. Straight-chain Alkanes

• Simple alkanes tend to undergo fragmentation by

 the initial loss of a • CH3 to give a peak at M – 15

 This carbocation can then undergo stepwise cleavage

down the alkyl chain
• Take hexane as an example:
 Alkanes

▫ Mass spectrum of octane.

2. Branched-chain Alkanes
Tend to cleave at the “branch point”
 more stable carbocations are formed
 Alkanes
▫ Mass spectrum of 2,2,4-trimethylpentane.
 Alkenes
▫ show a strong molecular ion peak.
▫ cleave to form resonance-stabilized allylic cations.
+
[CH2 =CHCH2 CH2 CH3 ] • CH2 =CHCH2 + + • CH2 CH3
 Alkynes
▫ show a strong molecular ion peak.
▫ cleave readily to form the resonance-stabilized propargyl
cation or substituted propargyl cations.
3-Propynyl cation + +
HC C-CH2 HC C=CH2
(Propargyl cation)
 Alcohols
• One of the most common fragmentation patterns of alcohols
is loss of H2O to give a peak which corresponds to M-18.
• Another common pattern is loss of an alkyl group from the
carbon bearing the OH to give a resonance-stabilized
oxonium ion and an alkyl radical.

R'
• + + + ••
R C O H R• + R' -C= O- H R' -C ••O H
••
R" R" R"
Molecular ion A radical A resonance-stabilized
(a radical cation) oxonium ion
 Alcohols
• In addition to the loss of a proton and the hydroxyl radical,
 alcohols tend to lose one of the  alkyl groups (or
 hydrogen atoms)
 form oxonium ions
 Alcohols
▫ Mass spectrum of 1-butanol.
 Aldehydes and ketones
• Frequently undergo fragmentation by losing one of the
side chains
 generate the substituted oxonium ion
 often represents the base peak in the mass
spectra
 Aldehydes and ketones
• Characteristic fragmentation patterns are
▫ -cleavage
▫ McLafferty rearrangement O
+ + •
+
• m/z 43
O
-cleavage
O
m/z 128 +
CH3 • +
m/z 113

+
• McLafferty +
H H •
O rearrangement O
+

Molecular ion m/z 58

m/z 114
 Aldehydes and ketones
▫ Mass spectrum of 2-octanone.
▫ Most show an intense molecular ion peak.
▫ Most alkylbenzenes show a fragment ion of m/z 91.
H
+• H
- H• H
CH3 + H Tropylium cation
H (m/z 91)
H
Toluene radical H
cation