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Advanced Organic Chemistry: 15.1.1 Mass spectroscopy - How it all works!

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15.1 Mass spectrometry - How it all works

Doc Brown's Chemistry Advanced Level Pre-University Chemistry Revision Study Notes for UK IB KS5 A/AS GCE advanced A level organic chemistry students US K12 grade 11 grade 12 organic chemistry courses involving molecular spectroscopy analysing mass spectra

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15.1.2 Uses and applications of mass spectroscopy, mainly in organic chemistry

15.1.3 Index of mass spectra of organic compounds


Sub-index for this page

Before writing the spectroscopy section, I had already written an extensive introduction to mass spectroscopy, therefore I refer to this page via links, but adding some extra details on this page if needed.

(a) Sections already written on mass spectroscopy (sub-index of sections not repeated on this page)

Extra notes for advanced level chemistry students

(b) More on fragmentation patterns and mass spectra

(c) More on the nature of fragments formed in a mass spectrometer

(d) Equations describing the possible formation of positive ion fragments



(a) Sections I'd already written on mass spectroscopy

Each section opens up in a new window for convenience (close after use)

1. INTRODUCTION to mass spectrometry

2. How a magnetic field deflection mass spectrometer works and m/z values

3. Explaining a mass spectrum - the basics

4. The mass spectrum of chlorine - peak ratios and relative atomic mass

5. The mass spectrum of strontium - peak ratios and relative atomic mass

6. Calculating the relative atomic mass of potassium from mass spectra data

7. Analysing the mass spectrum of bromine

8. Introduction to the mass spectra of organic compounds and the molecular ion peak and fragmentation - use in identification of organic molecules

9. Isotopic masses and accurate molecular ion peaks to identify molecules and molecular formulae

10. Calculation of % isotopic composition given the relative atomic mass of an element

11. How a time of flight (TOF) mass spectrometer works


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(b) More on fragmentation patterns and mass spectra

In a mass spectrometer, of whatever design, the basic initial mechanism of forming a positive ion is the removal of one electron from the parent molecule to form the molecular ion.

This is achieved in two ways:

(i) With a laser beam:  M + h  ===>  [M]+  +  e-

(ii) Electron bombardment: M + e-  ===>  [M]+  +  2e-

The molecular ion is subsequently broken down into smaller fragments, which themselves can be further broken down into even small fragments.

The higher the energy of the laser beam or bombarding electrons, the greater the fragmentation, and the more complex the fragmentation pattern.

Also, the bigger more complex molecules will give more complex fragmentation patterns e.g. you can readily see this with the two hydrocarbon molecules ethane and hexane whose mass spectra are shown below.

mass spectrum of ethane C2H6 CH3CH3 fragmentation pattern of m/z m/e ions for analysis and identification of ethane image diagram doc brown's advanced organic chemistry revision notes

Both mass spectra are unique for each molecule, but comparisons should only be made under the same experimental conditions.

Note it is convention to called the ion of greatest intensity, the base peak ion, and usually given the arbitrary value of 100.

This is also an important feature of comparing spectra obtained under the same experimental conditions.

mass spectrum of hexane fragmentation pattern of m/z m/e ions for analysis and identification of hexane image diagram doc brown's advanced organic chemistry revision notes


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(c) More on the nature of fragments formed in a mass spectrometer

At pre-university level, only the structure of certain fragments is expected e.g. expressed as simple molecular formula.

e.g. [CxHyOz]+ where x, y and z express the number of atoms of each element in the fragment ion.

You must be aware that different ions can have the same m/z value see m/z 28 or m/z 43 below - but these can readily be distinguished with a high resolution mass spectrometer.

Examples of mass spectrum ions with their m/z values (assume atomic masses C = 12, H = 1 and O = 16)

m/z 1 [H]+  m/z 13 [CH]+   m/z 14 [CH2]+  m/z 15 [CH3]+    m/z 17 [OH]+    m/z 18 [H2O]+    m/z ? [?]+   m/z 25 [C2H]+   

m/z 26 [C2H2]+  m/z 27 [C2H3]+  m/z 28 [C2H4]+could be  [CH2=CH2]+  or  [CH3CH]+  and also  [CO]+

m/z 29 [CH3CH2]+    m/z 29   or [HC=O]+   [CH2NH2]+  m/z 28 [CO]+  m/z 30 [H2C=O]+ or [C2H6]+  m/z 31 [CH2OH]+ 

m/z 31 [H3CO]+  m/z 32 [O2]+   m/z 39 [C3H3]+   m/z 40 [CCO]+  [C2H3N]+   m/z 41 [C3H5]+   m/z 41 [CHCO]+  

m/z 42 [C3H6]+   m/z 42 [CH2CO]+   m/z 43 [C2H3O]+ structure [CH3C=O]+ , also m/z 43 [C3H7]+ could be  [(CH3)2CH]+ 

m/z 43 [CH3CH2CH2]+  m/z 44 [C3H8]+   m/z 44 [CH2=CH-OH]+  m/z 44 [O=C-NH2]+  m/z 44 [CO2]+   

m/z 45 [COOH]+  m/z 45 [CH3CH2O]+  m/z 45 [CH2CH2OH]+  or  [CH3CHOH]+   m/z 45 [CH2CH2=OH]+  m/z 45 [C2H5O]+

m/z 50 [C4H2]+     m/z 51 [C4H3]+   m/z 55 [C4H7]+  m/z 55 [C3H3O]+   m/z 56 [C4H8]+  m/z 57 [CH2CH2CHO]+  

m/z 57 [CH3CH2C=O]+  m/z 57 [C4H9]+   m/z 58 [C3H8N]+   m/z 59 [C3H7O]+   m/z 59 [CH3CH2OCH2]+   

m/z 59  [CH3CH2CH2O]+  m/z 59 [CH3CH2CHOH]+   m/z 63 [C5H3]+    m/z 65 [C5H5]+   

m/z 73 [C3H5O2]+  possible structure  [C2H5O-C=O]+     m/z 77 [C6H5]+  m/z 91 [C7H7]+ 

Many of these ions do not normally occur in 'test-tube' chemistry.

You are dealing with highly energised particles that can take many forms prior to, and after, fragmentation.


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(d) Equations describing the possible formation of positive ion fragments

When the parent molecular ion fragments, there are two possible outcomes, and either fragment might carry the positive charge, but only one of two possibilities can be the positive ion.  e.g.

[M]+  ===>  [A]+  +  [B]   or   [M]+  ===>  [A]  +  [B]+

The most stable and most energetically favoured A or B structure will predominate, often one much more than the other.

For all the mass spectra pages I've outlined possible fragmentation equations e.g.

In the mass spectrum of propanone (shown below) there are two possibilities of bond scission of the parent molecular ion:

Formation of m/z 43 ion: [CH3COCH3]+  ===>  [CH3CO]+  +  CH3

Formation of m/z 15 ion: [CH3COCH3]+  ===>  [CH3]+  +  CH3CO

mass spectrum of propanone fragmentation pattern of m/z m/e ions for analysis and identification of acetone image diagram doc brown's advanced organic chemistry revision notes

It is pretty obvious that the m/z 43 ion predominates more than the m/z 15 after bond scission of the parent molecular ion.


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Key words & phrases: Fragmentation of molecular ion, structure of ion fragments, equations to show possible fragmentation reactions


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