Module CH1002

Structure of Molecules
Lecture 5

Dr Jamieson

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Common Fragmentation Patterns

Molecular ion and fragmentation

-Cleavage
McLafferty Rearrangement
Alcohol Dehydration

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McLafferty Rearrangement

McLafferty Rearrangement
H
H2C
O
H2C
CH3
C
H2

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CH2
CH2

H
H2C

O
CH3

m/z = 58

Common Fragmentation Patterns

Molecular ion and fragmentation

-Cleavage
McLafferty Rearrangement
Alcohol Dehydration

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Common Fragmentation Patterns

Alcohols
Molecular ions from alcohols fragment easily and so small molecular ion peak.

Dehydration [M-18]+
OH
CH3CH2CH2CH2CHCH3

-e-

OH

CH3CH2CHCH2CHCH3

m/z = 102

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CH3CH2CHCH2CHCH3
m/z = (102 - 18) = 84

H2O

High-Resolution Mass Spectrometry

High-resolution mass spectrometers can determine the exact molecular mass of
a fragment to a precision of 0.0001 amu.
Bee alarm pheromone has MW 114 with formula C7H14O, but how do we know that
this is the correct formula?
C6H10O2, C6H14N2 or C8H18 would also give a peak at 114!
Calculate the exact mass of the molecule using the exact isotope masses
1H = 1.00783, 12C = 12.00000, 13C = 13.00335, 14N = 14.00307
Composition

Calculated M+

Observed M+

Error in ppm

C6H10O2

114.068075

114.1039

358

C6H14N2

114.115693

114.1039

118

C7H14O

114.104457

114.1039

C8H18

114.140844

114.1039

369

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Structure of Molecules
Valence Shell Electron Pair Repulsion Theory (VSEPRT)
The repulsion of electrons to get as far as possible from each other
H
N

C
H

H
H

O
H
H

H
H

What is an orbital? (Reading - Clayden, Organic Chemistry, pp 81-111)

An atomic orbital is a mathematical expression (wave function) that describes the
wave-like behavior of no more than two electrons in the vicinity of an atomic
nucleus or of a system of nuclei as in a molecule.
Usually depicted as a three-dimensional region within which there is a 95 percent
probability of finding the electron.

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Structure of Molecules
sp3 hybridised carbon atom

Hybridisation

2s

2px

+ 2py +

2pz

Four sp3 orbitals

give a tetrahedral
structure for sp3
hybridised carbon

A sp3 hybrid orbital

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Structure of Molecules
sp2 hybridised carbon atom

Hybridisation

sp 2

py
sp 2

sp 2
2s

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2px

2pz

Three sp 2 hybrid orbitals

at 90o to the py orbital,
the angle between the
sp 2 orbitals is 120 o.

Structure of Molecules
sp hybridised carbon atom

py
Hybridisation

pz
sp

2s

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2px

Three sp 2 hybrid orbitals

at 90o to the py orbital,
the angle between the
sp 2 orbitals is 120 o.