Fragmentation rule MASS

Mass
Spectrometry
Prepared By :
Mahendra G S
M-Pharm,Pharmaceutical
Chemistry
JSSCP, MYSURU
Fragmentation Rules

Background
 Mass spectrometry (Mass Spec or MS)
uses high energy electrons to break a
molecule into fragments.
 Separation and analysis of the fragments
provides information about:
 Molecular weight
 Structure

Background
 The impact of a stream of high energy
electrons causes the molecule to lose an
electron forming a radical cation.
 A species with a positive charge and
one unpaired electron
+ e
-
C H
H
H
H H
H
H
HC + 2 e
-
Molecular ion (M+)
m/z = 16

Background
 The impact of the stream of high energy
electrons can also break the molecule or
the radical cation into fragments.
(not detected by MS)
m/z = 29
molecular ion (M
+
) m/z = 30
+ C
H
H
H
+ H
HH C
H
H
C
H
H
H C
H
H
C
H
H
H C
H
H
+ e
-
H C
H
H
C
H
H
H
m/z = 15

Background
 Molecular ion (parent ion):
 The radical cation corresponding to the
mass of the original molecule
 The molecular ion is usually the highest
mass in the spectrum
 Some exceptions w/specific isotopes
 Some molecular ion peaks are absent.
H
H
H
HC H C
H
H
C
H
H
H

Background
 Mass spectrum of ethanol (MW = 46)
SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of
Advanced Industrial Science and Technology, 11/1/09)
M+

Background
 The cations that are formed are
separated by magnetic deflection.

Background
 Only cations are detected.
 Radicals are “invisible” in MS.
 The amount of deflection observed
depends on the mass to charge ratio
(m/z).
 Most cations formed have a charge of
+1 so the amount of deflection
observed is usually dependent on the
mass of the ion.

Background
 The resulting mass spectrum is a graph
of the mass of each cation vs. its
relative abundance.
 The peaks are assigned an abundance as
a percentage of the base peak.
 the most intense peak in the spectrum
 The base peak is not necessarily the
same as the parent ion peak.

Background
M+
base peak
The mass spectrum of ethanol

Background
 Most elements occur naturally as a
mixture of isotopes.
 The presence of significant amounts of
heavier isotopes leads to small peaks
that have masses that are higher than
the parent ion peak.
 M+1 = a peak that is one mass unit
higher than M+
 M+2 = a peak that is two mass units
higher than M+

Easily Recognized Elements in MS
 Nitrogen:
 Odd number of N = odd MW
CH3CN
M
+
= 41

 Bromine:
 M+ ~ M+2 (50.5% 79Br/49.5% 81Br)
2-bromopropane
M+ ~ M+2
SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of Advanced Industrial
Science and Technology, 11/1/09)

 Chlorine:
 M+2 is ~ 1/3 as large as M+
Cl
M+2
M+

 Sulfur:
 M+2 larger than usual (4% of M+)
M+
Unusually
large M+2
S

 Iodine
 I+ at 127
 Large gap
Large gap
I+
M+
ICH2CN

Fragmentation Patterns
 The impact of the stream of high energy
electrons often breaks the molecule into
fragments, commonly a cation and a
radical.
 Bonds break to give the most stable
cation.
 Stability of the radical is less
important.

 Alkanes
 Fragmentation often splits off simple
alkyl groups:
 Loss of methyl M+ - 15
 Loss of ethyl M+ - 29
 Loss of propyl M+ - 43
 Loss of butyl M+ - 57
 Branched alkanes tend to fragment
forming the most stable carbocations.

 Mass spectrum of 2-methylpentane

 Alkenes:
 Fragmentation typically forms
resonance stabilized allylic carbocations

 Aromatics:
 Fragment at the benzylic carbon, forming a
resonance stabilized benzylic carbocation
(which rearranges to the tropylium ion)
M+
CH
H
CH Br
H
C
H
H
or

Aromatics may also have a peak at m/z = 77 for
the benzene ring.
NO2
77
M+ = 123
77

 Alcohols
 Fragment easily resulting in very small or
missing parent ion peak
 May lose hydroxyl radical or water
 M+ - 17 or M+ - 18
 Commonly lose an alkyl group attached to
the carbinol carbon forming an oxonium
ion.
 1o alcohol usually has prominent peak at
m/z = 31 corresponding to H2C=OH+

 MS for 1-propanol
M+M+-18
CH3CH2CH2OH
H2C OH

 Amines
 Odd M+ (assuming an odd number of
nitrogens are present)
 a-cleavage dominates forming an
iminium ion
CH3CH2 CH2 N
H
CH2 CH2CH2CH3 CH3CH2CH2N CH2
H
m/z =72
iminium ion

86
CH3CH2 CH2 N
H
CH2 CH2CH2CH3
72

 Ethers
 a-cleavage forming oxonium ion
 Loss of alkyl group forming oxonium ion
 Loss of alkyl group forming a
carbocation

H O CHCH3
MS of diethylether (CH3CH2OCH2CH3)
CH3CH2O CH2
H O CH2

 Aldehydes (RCHO)
 Fragmentation may form acylium ion
 Common fragments:
 M+ - 1 for
 M+ - 29 for
RC O
R (i.e. RCHO - CHO)
RC O

 MS for hydrocinnamaldehyde
M+ = 134
C C C H
H
H
H
H
O
133
105
91
105
91

 Ketones
 Fragmentation leads to formation of
acylium ion:
 Loss of R forming
 Loss of R’ forming RC O
R'C O
RCR'
O

 MS for 2-pentanone
CH3CCH2CH2CH3
O
M+
CH3CH2CH2C O
CH3C O

 Esters (RCO2R’)
 Common fragmentation patterns
include:
 Loss of OR’
 peak at M+ - OR’
 Loss of R’
 peak at M+ - R’

Frgamentation Patterns
M+ = 136
C
O
O CH3
105
77 105
77

Rule of Thirteen
 The “Rule of Thirteen” can be used to
identify possible molecular formulas for an
unknown hydrocarbon, CnHm.
 Step 1: n = M+/13 (integer only, use
remainder in step 2)
 Step 2: m = n + remainder from step 1

Rule of Thirteen
 Example: The formula for a hydrocarbon
with M+ =106 can be found:
 Step 1: n = 106/13 = 8 (R = 2)
 Step 2: m = 8 + 2 = 10
 Formula: C8H10

Rule of Thirteen
 If a heteroatom is present,
 Subtract the mass of each heteroatom
from the MW
 Calculate the formula for the
corresponding hydrocarbon
 Add the heteroatoms to the formula

Rule of Thirteen
Example: A compound with a molecular ion
peak at m/z = 102 has a strong peak at
1739 cm-1 in its IR spectrum. Determine
its molecular formula.

GC-Mass Spec: Experiment 23
 Mass Spec can be combined with gas
chromatography to analyze mixtures of
compounds.
 GC separates the components of the
mixture.
 Each component is analyzed by the
Mass Spectrometer.

 Assignment:
 Observe the GC-mass spec experiment
 Record experimental conditions
 Analyze the mass spectrum of each
component of your mixture:
 Parent ion peak?
 Heteroatoms apparent from
spectrum?
 A minimum of 1 or two significant
fragments and their structures

 Assignment (cont.):
 Using the Mass Spec data, retention
times, and boiling points, identify the
components of your mixture.
 Write three paragraphs (one per
compound) summarizing and interpreting
all data. See your data sheet for
more details.

Fragmentation rule MASS

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