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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

H2C

H2CCH2

O

H

CH3!"

#

CH2

CH2H2C

O

CH3

H

m/z= 58

McLafferty Rearrangement

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Common Fragmentation Patterns

Molecular ion and fragmentation

!-Cleavage

McLafferty Rearrangement

Alcohol Dehydration

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Common Fragmentation Patterns

Alcohols

Dehydration [M-18]+

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

CH3CH2CHCH2CHCH3

OHH

!"#CH3CH2CHCH2CHCH3

m/z= (102 - 18) = 84

H2OCH3CH2CH2CH2CHCH3

OH-e-

m/z= 102

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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, C6H14N2or C8H18 would also give a peak at 114!

Calculate the exact mass of the molecule using the exact isotope masses1H = 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 5

C8H18 114.140844 114.1039 369

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Valence Shell Electron Pair Repulsion Theory (VSEPRT)

The repulsion of electrons to get as far as possible from each other

Structure of Molecules

C

H

H

H

H

N

HH

H

O

H

H

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

An atomic orbital is a mathematical expression (wave function) that describes thewave-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

2s + 2px + 2py 2pz+

Hybridisation

Four sp3

orbitalsgive a tetrahedral

structure for sp3

hybridised carbon

A sp3hybrid orbital

sp3hybridised carbon atom

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Structure of Molecules

2s + 2px + 2pz

Hybridisation

Three sp2hybrid orbitals

at 90oto the py orbital,

the angle between the

sp2orbitals is 120o.

sp2

sp2

py

sp2

sp2hybridised carbon atom

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Structure of Molecules

2s + 2px

Hybridisation

Three sp2hybrid orbitals

at 90oto the py orbital,

the angle between the

sp2orbitals is 120o.

py pz

sp

sp hybridised carbon atom