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Advan'd Level Chemistry Notes: Introduction to mass spectrometry

Doc Brown's Chemistry: Mass Spectrometer - Mass Spectroscopy

The mass spectrometer is an instrument by which you can separate ionised/charged (+) particles of different mass and determine the amounts of each particle in a mixture. The technique is called mass spectroscopy or mass spectrometry ('mass-spec' and 'MS' in shorthand!). How can mass spectrometry be used to measure percentage isotopic composition of an element (isotopic abundance) and determine the relative atomic mass of an element? The examples feature mass spectra of chlorine, bromine, ethanol and strontium and its relative atomic mass determination and calculation.

Sub-index for this page

INTRODUCTION

How a deflection mass spectrometer works and m/z values

Explaining a mass spectrum

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

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

Calculating the relative atomic mass of potassium (from mass spectra data)

Analysing the mass spectrum of bromine

The mass spectra of organic compounds and the molecular ion peak - use in identification of organic molecules

See also Spectroscopy indexes: IR, mass, H-NMR & C-13 NMR spectra of organic compounds

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

Calculation of % isotopic composition from the relative atomic mass of an element

How a time of flight mass spectrometer works



INTRODUCTION

Some abbreviations used: A = mass number,    Ar = relative atomic mass,   Z = atomic number (NOT z)

m/z = relative molecular mass or isotopic mass / electric charge for ions formed in a mass spectrometer

simplified diagram of a mass spectrometerMass spectrometry gives accurate information on the relative masses of isotopes and their relative abundance (proportions).

Mass spectrometry is an important method of analysis in chemistry and can be used to identify elements and compounds by their characteristic mass spectrum pattern - the technique is used in planetary space probes e.g. mass spectrometer instrumentation is incorporated in the Mars explorer vehicles, mass spectrometers can monitor the concentration of air pollution molecules and detect traces of illegal drugs in the urine of athletes.

What is Mass Spectroscopy and a mass spectrum?

A mass spectrometer is an instrument of analysing particles of different relative mass.

The instrument used is called a mass spectrometer, of which there are several types.

All types of mass spectrometers involve vaporising atoms or molecules in high vacuum and subjecting the vapourised particles to electron bombardment to generate a beam of positive ions, a process called ionisation.

The mass spectrometer, by several different means, separates and counts the numbers of different positive ion particles produced.

The resulting data from the detector is called a mass spectrum (plural mass spectra) which gives you lots of data including:

the accurate relative masses (based on 12C = 12.0000) of all the positive ions generated from individual atoms (isotopes), whole molecules and fragments of molecules,

the relative numbers of each particle (listed above) generated by the electron bombardment of the original atoms or molecules.

 

Uses of mass spectrometry include:

the determination of

very accurate relative isotopic masses (these days to at least 9 significant figures with high resolution mass spectrometers,

the relative abundances of the isotopes for a specific element - from this you can calculate the relative atomic mass of an element (which can also be measured from chemical analysis),

identifying molecular formula using a high resolution mass spectrometer

identification of organic molecules from fragmentation patterns (each has a mass spectra fingerprint)

 

Advantages of using mass spectrometry as an analytical technique

Like other modern instrumental analytical techniques used in chemistry in the 20th-21st centuries, mass spectroscopy has several advantages over traditional methods of chemical analysis e.g.

It is a very sensitive technique, only requiring tiny amounts of material for analysis and only tiny amounts might be available e.g. in forensic analysis of a crime scheme.

It is a very accurate technique, but the mass spectrometer does require careful calibration e.g. relative to carbon-12 isotope given a value of 12.0000 atomic mass units and quality instruments rarely make a mistake.

The analysis can be done quickly AND continuously. A sampling plus a mass spectrometer system could monitor pollution or a chemical production process 24/7!

A mass spectrometer can be linked to other analytical instruments e.g. you can set up a mass spectrometer to sample the separate molecules exiting from a gas/liquid chromatograph column.

 


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See also Spectroscopy indexes: IR, mass, H-NMR & C-13 NMR spectra of organic compounds


Method (1) DEFLECTION MASS SPECTROMETER

(NOTE: Most mass spectrometers these days are of the TOF type, and students now, and in the future, should be expected know how a TOF works, the results are ultimately the same, but I've described the older type of mass spectrometer as an introduction to mass spectroscopy of the atoms and molecules of elements and compounds)

My use of the word 'deflection' in describing this type of mass spectrometer is NOT official, but I couldn't think of any other way of distinguishing it from a 'time of flight' mass spectrometer described in method (2) at the end of this page!

The relative paths of light to heavy ions in a mass spectrometer tubeThe substance to be analysed is introduced/injected into a high vacuum (extremely low pressure) tube system (at K left diagram) where the particles are ionised by colliding with beam of high speed electrons (at Q in left diagram).

Note: If the sample is not already a gas, then a liquid or solid substance must be vapourised, i.e. the material must be in the gaseous state to be analysed in a mass spectrometer. The material being analysed must in the form of free moving gaseous atoms or molecules which can be then bombarded with electrons to produce equally free moving positive ions which can rapidly be accelerated in a powerful electric field. It is the manipulation of the stream of gaseous ions that forms the basis of mass spectrometry.

You cannot analyse any liquid or solid material in this way unless it is vapourised.

The resulting (+) ions are accelerated down a tube (from + to - plates, P in left diagram) and then through a powerful magnetic field.

The charged or ionised particles are deflected by this powerful magnetic field (R in left diagram).

How much they are deflected depends on the particle mass and the speed of the particle and the strength of a magnetic field i.e. lighter particles of lower mass (and momentum) are deflected more than heavier particles of bigger mass (see right diagram below) for a given set of conditions.

By varying the strength of the magnetic field, it is possible to bring into focus onto an ion detector (N in left diagram) at the end of the tube (effectively an electrical event is detected), every possible mass in turn and a measure the strength of the ion current, which is a measure of how much of that ion has been formed from the sample under analysis.

A simplified diagram of a mass spectrometer tube system is shown below (left) with further explanation as to what is going on and an extra diagram to show the relative paths of light to heavy ions for a given strength of magnetic field.

simplified diagram of a mass spectrometer The relative paths of light to heavy ions in a mass spectrometer tube

KEY TO DIAGRAM and more detail of each component's function

K = sample injection point, it must be a gas, so a liquid/solid must be vaporised at the injection point.

IONISATION

Q = high voltage (high +/- p.d.) electron gun which fires a beam of high speed/energy electrons from a heated 'metal element' into the vaporised sample under analysis and causes ionization of the atoms (or molecules) forming positive ions (mainly monopositive in charge).

The collision of high KE electrons with atoms or molecules causes another electron to be knocked off the particle leaving a negative deficit i.e. a positively charged particle is formed e.g.

M(g) + e- ==> M+(g) + 2e-, usually written as just

M(g) ==> M+(g) + e- (M might represent e.g. a metal atom or a molecule)

The ions formed should be written as [M]+, a notation that is handy if you are dealing with ionised molecule fragments with an overall single positive charge e.g. [CH3]+ is seen in the mass spectrum of methane gas, CH4.

The low pressure (~vacuum) is needed to prevent the ions from colliding with air particles which would stop them reaching the ion detector system.

ACCELERATION

P = are negative plates which accelerate the positive ions down the tube (there are positive plates at the start of the tube). A moving beam of charged particles creates a magnetic field around itself, and this 'ion beam' magnetic field interacts with the magnetic field at R.

DEFLECTION-SEPARATION

R = the magnetic field that causes deflection of ions, this is can be varied to change the extent of deflection for a given mass and to focus a beam of ions of particular mass down onto the detector. Hence, by programming the mass spectrometer to 'sweep' through all likely particle masses, in terms of the right hand diagram, you can increase the strength of the magnetic field to bring into focus onto the ion detector monopositive ions of increasing mass.

DETECTION

N = an ion detection system which essentially generates a tiny electrical current when the ions hit it. The minute electric current which can be amplified. The strengths of the 'electronic' signals from the various ion peaks are sent to a computer for analysis, computation and display. They tell you the particle masses present and their relative abundance (see the mass spectrum diagram for the element strontium below). The data is then presented as an m/z versus peak height.

m/z means the relative mass of the ion over its charge, which for our purposes the electric charge is +1 (lower case z) and the mass (lower case m) is the relative atomic/formula mass of the particle ionised. You should write the structure of the ion in square brackets and put the charge on the outside of them in the top right - this is an important and universally accepted notation in mass spectrometry.

Examples of m/z values (mass/charge ratio) m/z values apply to ALL methods of mass spectrometry (see TOF later)

ion relative mass (m) positive ion charge (z) m/z ratio
[14N]+ 14 1 14/1 = 1
[56Fe]+ 56 1 56/1 = 56
[56Fe]2+ 56 2 56/2 = 28
[35Cl]+ 37 1 35/1 = 35
[35Cl2]+ 70 1 70/1 = 70
[35Cl2]2+ 70 2 70/2 = 35
[CH3]+ 15 1 15/1 = 15

Note that you can get multiple charged ions, but most mass spectral analysis is based on mono-positive ions.

The are integer m/z values from a low resolution mass spectrometer.

Other terms used in mass spectroscopy:

Monatomic (mononuclear ions) are derived from single atoms eg [35Cl]+ or [88Sr]+ and a molecular ion (polynuclear ion) is derived from more than one atom i.e. a complete but ionised molecule (molecular ion) or broken off 'pieces' (molecular fragment ion) e.g.

Molecular ions: [Cl2]+ from chlorine molecules, [C6H5COOH]+ from benzoic acid molecules

Fragment ions: [CH3CH2]+, an ethyl fragment from the fragmentation of a hydrocarbon in a mass spectrometer.

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See also Spectroscopy indexes: IR, mass, H-NMR & C-13 NMR spectra of organic compounds


Examples of a MASS SPECTRUM explained

The resulting record of the ion peaks is called the mass spectrum or mass spectra. The highest peak is called the base peak and is often given the relative and arbitrary value of 100, particularly in the mass spectra of organic compounds.

MASS SPECTRA

For elements you get a series of signals or ion peaks for each isotope present and the ratio of peak heights gives you the relative proportion of each isotope in the element so that you can calculate the relative atomic mass of an element. This 'simple' spectra of mononuclear ions like [Sr]+ is only true for non-molecular elements like metals (see mass spectrum of strontium diagram below) or noble gases, but for molecular elements like nitrogen or the halogens things are not so simple (see chlorine example below).

The proportions or percentages of all the isotopes of an element is often called the isotopic abundance.

For larger e.g. organic molecules, things can be very complex indeed, as molecules fragment and many different ions can be formed BUT you can get the relative molecular mass of a molecule by identifying what is called the molecular ion peak, that is, when one electron is knocked of the molecule but the molecule retains its full molecular structure.

e.g. (c) doc bbenzoic acid (Mr = 122) gives a molecular ion peak of m/z = 122, due to [C6H5COOH]+

but you also get fragments such as [C6H5]+ with an m/z of 77 as the molecule breaks up on further electron impact.

m/z explained

More highly charged ions show up in mass spectra

You can get multiple ionisation e.g.35Cl2+(m/z = 35/2 = 17.5), 16O2+(m/z = 16/2 = 8), 32S2+(m/z = 32/2 = 16) etc. These more highly charged ions would be deflected or accelerated more in the mass spectrometer than the monopositive ions. In the mass spectrometer the monopositive ions are selected to produce the mass spectrum.

You should note that e.g. the m/z for 32S2+(m/z = 32/2 = 16) is identical to the m/z for 16O+ (m/z = 16/1 = 16). In a low resolution mass spectrometer they would not be distinguishable, but in a very modern high resolution mass spectrometer they would be.


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See also Spectroscopy indexes: IR, mass, H-NMR & C-13 NMR spectra of organic compounds


CHLORINE EXAMPLE

The mass spectrum of chlorine is a good example of a molecular element whose mass spectra can be a bit tricky when first encountered.

Chlorine consists of two principal stable isotopes, chlorine-37 (~25% is 37Cl) and chlorine-35 (~75% is 35Cl).

Ar(Cl) is ~35.5 using the above percentages

from Ar(Cl) = [(75 x 35) + (25 x 37)] / 100

BUT, chlorine consists of Cl2 diatomic molecules, which may or may not split on ionisation, so how can we explain the presence of five peaks and not just two for the two isotopes?

The result of the ionisation process and subsequent fragmentation of chlorine molecules is a series of 5 different mass peaks from the various isotopic monatomic or molecular ion possibilities.

  1. [37Cl37Cl]+ or [37Cl2]+ m/z = 74  (molecular ion)

  2. [37Cl35Cl]+ m/z = 72 (note that you must show the two isotopes separately in the molecular ion)

  3. [35Cl35Cl]+ or [35Cl2]+ m/z = 70  (molecular ion)

  4. [37Cl]+ m/z = 37  (mononuclear ion, monatomic fragment)

  5. [35Cl]+ m/z =35  (mononuclear ion, monatomic fragment)

Reminder: (i) m/z means the relative mass of the ion over its charge (m/z explained), (ii) monatomic/mononuclear ions are derived from one atom, (iii) a molecular ion is derived from more than one atom.

So, the presence of five peaks is explained and the ratio of the peak heights can be explained by considering a simple probability table of all the permutations possible for the monatomic or molecular ions - remember in a mass spectrometer you are dealing with millions of 'randomised' particles.

m/z 35Cl 35Cl 35Cl 37Cl
35Cl 70 70 70 72
35Cl 70 70 70 72
35Cl 70 70 70 72
37Cl 72 72 72 74

The ratio of heights for peaks 1 and 2 is 3 : 1, the ratio of the isotopic abundance.

For the bimolecular ions, (left table of possibilities) we assume (for simplicity) that exactly 3/4 (75%) of the chlorine isotopes are 35Cl and 1/4 (25%) of the isotopes are 37Cl.

This gives an expected ratio of the molecular ions 70 : 72 : 74 of 9 : 6 : 1, and this is what you observe for peaks 3 to 5.

The ratio of the heights of the first set of peaks (1-2) to the heights of the 2nd set (3-5) depends on the energy and intensity of the ionising beam of electrons. The greater this is, the greater the fragmentation of the molecules i.e. peaks 1-2 would increase and peaks 3-5 would decrease relative to each other, BUT, the height ratios would stay the same in each set i.e. the monatomic/mononuclear ions and the diatomic molecular ions.

For identifying molecules from a fingerprint pattern you should operate the mass spectrometer under the same conditions i.e. standards and unknowns compared under the same operating conditions to give reproducible mass spectra.

Other examples and explanation of the calculation of the relative atomic mass of an element using % of isotopes is given in Part 1 of GCSE-AS (basic) calculations.

The simplest and best example on this page of calculating relative atomic mass from a mass spectrum is fully explained for the metallic element strontium.


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See also Spectroscopy indexes: IR, mass, H-NMR & C-13 NMR spectra of organic compounds


STRONTIUM EXAMPLE using mass spectra data to calculate relative atomic mass from the mass spectrum of strontium

A 'simple' element mass spectrum to interpret AND a subsequent relative atomic mass calculation based on the mass spectroscopy of the element strontium

The mass spectrum of the element strontium

The relative atomic mass of an element, Ar, is the weighted average mass of the isotopes present, compared to 1/12th of the relative mass of the carbon-12 isotope. [ 12C is given the relative mass value of 12.0000 ]

Quite often the highest m/e peak is arbitrarily given the relative value of 100, as in this case and referred to as the base peak, but the peak lines might well indicate % abundance of isotopes. The diagram of abundances is sometimes called a stick diagram.

Relative peak height = relative abundance as measured from the ion current detector signal.

The mass spectrum shows strontium consists of four isotopes giving rise to four positive ions - relative peak heights of

84Sr (peak height = 0.68), 86Sr (peak height = 12.0),87Sr (peak height = 8.47) and 88Sr (peak height = 100.0)

The sum of the heights = 0.68 + 12.0 + 8.47 + 100.0 = 121.15

So we can now calculate the weighted average mass of ALL the isotopes.

Therefore Ar = {(0.68 x 84) + (12.0 x 86) + (8.47 x 87) + (100.0 x 88)}/121.15 =  87.7

The book value is 87.62, BUT this calculation does NOT take into account the very accurate relative atomic masses based on the carbon-12 scale, it merely uses the mass numbers, which are always integer.


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See also Spectroscopy indexes: IR, mass, H-NMR & C-13 NMR spectra of organic compounds


Potassium - Another relative mass calculation from mass spectrometry

Potassium has three naturally occurring isotopes, stable 39K and 41K, and the long-lived 40K (half-life of millions of years!)

The mass spectrum of potassium generated the following data:

m/z 39 40 41
relative % abundance 93.258 0.012 6.730

Calculate the relative atomic mass of potassium.

Ar(K) = average mass of all the potassium atoms present.

= {(39 x 93.258) + (40 x 0.012) + (41 x 6.730)} / 100

= {(3637.062) + (0.48) + (275.93)} / 100 = 3913.472 / 100 = 39.13 (4sf, 2dp)

More on relative atomic mass calculations

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The mass spectrum of bromine Br2

You get five peaks in the spectra of bromine molecules. For molecules completely atomised you get two peaks (m/z) of almost equal height from [79Br]+ and [81Br]+ mononuclear ions.

Because its ~50% of each isotope, the relative atomic mass of bromine is ~80 and hence the equality of peaks 1 [79Br]+ and 2 [81Br]+ from the monatomic ions from the fragmentation and ionisation of bromine molecules.

However, as with chlorine, molecular bromine is also ionised without fragmentation, giving rise to three more ion permutations (3 more m/z peaks).

[79Br79Br]+ (158), [79Br81]Br+ (160) and [81Br81Br]+ (162)

So! the presence of all five peaks is explained in the mass spectrum of bromine, and, because you are dealing with millions of randomised ionised atoms, the ratio of the two monatomic peaks can be used to accurately determine the relative atomic mass of bromine.

The data book quotes for the stable isotopes: 79Br (50.69%) and 81Br (49.31)

The ratio of the heights for the monatomic ions in the mass spectrum of bromine would 50.69 : 49.31 ~ 1 : 1 as observed.

Ar(Br) = (50.69 x 79) + (49.31 x 81) / 100 = 79.90

m/z 79Br 81Br
79Br 158 160
81Br 160 162

The ratio of the 2nd set of peaks (3 to 5) can be readily explained with a simple probability table, and a bit simpler than the chlorine example!

This assumes (for simplicity) that we have exactly 50% bromine-79 and 50% bromine-81 isotopes and how they might be combined in the molecular ions on a random basis.

The ratio of peak heights expected for m/z values of 158 : 160 : 162 would be 1 : 2 : 1

 and this is what you observe in the mass spectrum of bromine.


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See also Spectroscopy indexes: IR, mass, H-NMR & C-13 NMR spectra of organic compounds


The mass spectra of organic compounds

These mass spectra can be very complex as the molecules fragment under electron bombardment, but the resulting mass spectra can used to identify compounds from their 'finger-print' pattern of ion peaks of different mass and particular proportions for a given set of experimental conditions.

The largest m/z value gives the molecular mass of a molecule, i.e. the ion of largest mass, prior to fragmentation, is formed when the original whole and neutral molecule, loses one electron e.g. for ethane it would be due to the formation of [C2H6]+, m/z = 30 and is called the molecular ion peak.

Above is the mass spectrum of ethanol where the maximum molecular ion peak has an m/z value of 46 (M),

i.e. [CH3CH2OH]+, and, because it is a singly charged positive ion, this must be equivalent to the whole molecule minus one electron.

This description does ignore the presence of molecular ion of one mass unit more due to some molecules having a carbon-13 isotope in them (M+1 molecular ion)

In a mass spectrometer the ions fragment giving a characteristic set of peaks that can be used to identify a compound. e.g. 15 corresponds to [CH3]+ and 31 corresponds to [CH2OH]+ etc.

The most abundant ion is called the base ion peak and often given the arbitrarily value of 100 and all other ion peak intensities are expressed relative to it.

You can think of possible fragmentations to give m/z values of 15 or 31 e.g.

[CH3CH2OH]+  ==>  [CH3]+ CH2OH     or      [CH3CH2OH]+ ==> CH3  +  [CH2OH]+

and the ethyl fragment can be formed by scission of the C-O bond e.g.

[CH3CH2OH]+  ==>  CH3CH2]+   +   OH

The fragmentation pattern is unique and characteristic of a particular compound, hence mass spectrometry can be used as an identification test procedure.


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See also Spectroscopy indexes: IR, mass, H-NMR & C-13 NMR spectra of organic compounds


ISOTOPIC MASSES - definition and uses - including very accurate molecular ion peaks and use in identifying molecules

The relative isotopic mass of an isotope is the accurate relative mass based on the carbon-12 scale, Ar(12C) = 12.0000

Below is a table of examples compared with the relative atomic mass of the element itself - which takes into consideration ALL of the isotopes in the naturally occurring element and their relative abundances.

ALL relative masses are quoted to four decimal places based on the isotopic carbon-12 value of 12.0000 from the 2015 IUPAC database - an internationally recognised standard system - no matter where you work, everybody is working to the same calibration system so that results are consistent.

The most abundant and next most abundant isotopes and their relative isotopic masses are quoted.

All the relative masses are quoted to four decimal places, but they can all be measured/calculated to more decimal places.

element relative atomic mass isotopic abundance by % mass relative isotopic masses
hydrogen 1.0080  most abundant H isotope (~99.99%)  1H, 1.0078
    next most abundant isotope (~0.01%) 2H, 2.0141
carbon 12.0106 most abundant C isotope (~99%): 12C, 12.0000
    next most abundant isotope (~1%) 13C, 13.0034
nitrogen 14.0069  most abundant N isotope (~99.7%) 14N, 14.0031
    next most abundant isotope (~0.3%) 15N, 15.0001
oxygen 15.9994  most abundant O isotope (~99.8%) 16O, 15.9949
    next most abundant isotope (~0.2%) 18O, 17.9992

Notes for the above data table:

(i) Relative isotopic mass is effectively the relative atomic mass of a single specific isotope.

(ii) The relative atomic mass of the element in these four cases is greater than that for the most abundant isotopic mass, because the next most abundant isotope happens to have a greater mass of 1 or 2 atomic mass units.

(iii) The relative atomic mass quoted is based on all the isotopes found in the naturally occurring element.

(iv) Here we are interested in using the relative isotopic masses of individual atoms and calculating the theoretical mass of the molecular ion [whole molecule - one electron]+ (M ==> [M]+).

You do this by adding up all the individual isotopic masses:

e.g. mass of [C2H4]+ molecular ion peak = (2 x 12.0000) + (4 x 1.0078) = 28.0312 .

BUT, note that isotopes of some elements will give rise to other molecular ion peaks.

In organic chemistry, the most notable extra molecular ion peaks arise from carbon-13 (13C).

Most carbon atoms are carbon-12 (12C), but some molecules will have a 13C atom and give a 2nd bigger molecular ion peak of 1.0034 mass units greater, often denoted by [M+1]+.

18O will give an [M+2]+ molecular ion because although the majority of oxygen atoms are 16O, there is a small percentage of 18O atoms. This ion [M+2]+ ion would be 2.0043 mass units bigger than the [M]+ molecular ion.

Some naturally occurring organic molecules can have slightly different ratios of isotopes, therefore you may need several molecular ion 'markers' in your database. to obtain the molecules molecular formula (and possibly its identity).

 

Very accurate isotopic masses are usually a tiny fraction different from a whole number but provide invaluable information.

Modern mass spectrometers are exceedingly accurate and very sophisticated instruments and can measure mass to at least 4 decimal places.

Therefore high resolution mass spectrometers can readily distinguish molecules with the same integer molecular mass.

e.g. distinguish between N2, CO and C2H4 molecules, all with an integer Mr of 28.

The very accurate molecular ion masses are [N2]+ = 28.0062; [CO]+ = 27.9949 and [C2H4]+ = 28.0312

These values are based on the most abundant isotopic masses of the elements (more on this below).

The most abundant molecular ion will be formed from the most abundant isotopes.

The relative mass of an electron is ~0.0005 and this can usually be ignored when dealing with the actual mass of the isotope to the very slightly smaller mass of a singly charged positive ion.

A very accurate mass spectrometer, for high resolution mass spectroscopy, can even differentiate between organic molecules of the same integer molecular mass but different molecular formula.

e.g. for the relative molecular mass of ~103, some possible, however unlikely, molecular formulae could theoretically be

C5HN3 = 103.0170C3H5NO3 = 103.0269C2H5N3O2 = 103.0382C7H5N = 103.0427CH5N5O = 103.0494

BUT note:

This data will NOT distinguish between structural isomers of the SAME molecular formula forming an identical molecular ion,

but the fragmentation pattern will differ between structural isomers (see the ethanol mass spectrum diagram) because isomers tend to differ in the way they fragment.

 

More on distinguishing different molecules of identical integer molecular masses

 Lets first explore a bit more on relative atomic masses and relative isotopic masses.

So, how you can distinguish different molecules of identical integer molecular masses?

In some textbooks I've noticed that molecular ion masses are computed using four decimal place relative atomic mass values.

This is incorrect.

When calculating the theoretical mass of a molecular ion peak, you should use the accurate relative isotopic masses, NOT the relative atomic mass of the element (Ar).

By this means you can use specific molecular ion peaks to identify specific molecules (*) - even with the same integer relative molecular mass.

(*) Technically, what you actually identify is a molecular formula, if there is only one molecular structure with that particular molecular formula, you can therefore deduce the specific molecule - but cannot distinguish isomers!

This idea has already been briefly mentioned at the start of this section for molecules of relative molecular mass of ~103. I'm now looking at a few more simple examples, but in more detail and typical of examples you see in Advanced A Level textbooks.

 

(a) Three molecules of relative molecular mass ~28

Molecule Molecular formula Relative molecular mass based on relative atomic masses of the elements molecular ion based on the most abundant isotopes molecular ion mass based on the most abundant isotopes
nitrogen N2 28.0138 [14N14N]+ m/z = 28.0062
carbon monoxide CO 28.0100 [12C16O]+ m/z = 27.9949
ethene C2H4 28.0532 [12C21H4]+ m/z = 28.0312

I've shown the precise isotopic composition of the ion that will give the most abundant ion peak.

All three molecular ions show significant relative mass differences within the context of a high resolution mass spectrometer working to an accuracy of at least 4 decimal places.

You can quite clearly distinguish between all three molecules using a high resolution mass spectrometer because you have three different molecular formulae.

For small molecules, it is possible to deduce the molecular formula just from the most prominent molecular ion peak - so it is more than just distinguishing between three different molecules.

You can also see the significant error involved if you incorrectly calculate the mass for a molecular ion peak using the relative atomic masses of the elements in the molecule.

You can see similar data 'errors' in examples (b) and (c) described below.

Note that isomeric molecules (same molecular formula), will give the same m/z molecular ion peak, mo matter how many decimal places you measure it too!

 

(b) Two molecules of relative molecular mass ~44

Molecule Molecular formula and structure Relative molecular mass based on relative atomic masses of the elements molecular ion molecular ion mass based on the most abundant isotopes (*)
propane C3H8

CH3CH2CH3

44.0958 [C3H8]+ m/z = 44.0624
ethanal C2H4O

CH3CHO

44.0526 [C2H4O]+ m/z = 44.0261

(*) Based on the most abundant isotope of each element: 12C, 1H and 16O.

A difference of 0.0363 relative mass units, to distinguish propane from ethanal OR C3H8 from C2H4O.

Again, these m/z values are characteristic of two different molecular formulae, C3H8 and C2H4O. of two different molecules

 

(c) Three molecules of relative molecular mass ~58

Molecule Molecular formula and structure Relative molecular mass based on relative atomic masses of the elements molecular ion molecular ion mass based on the most abundant isotopes (*)
butane C4H10

CH3CH2CH2CH3

58.1224 [C4H10]+ m/z = 58.0780
propanone or propanal C3H6O

CH3CH2CHO or

CH3COCH3

58.0792 [C3H6O]+ m/z = 58.0417
ethene-1,2-diamine (E/Z 1,2-ethenediamine) C2H6N2

H2NCH=CHNH2

58.0830 [C2H6N2]+ m/z = 58.0530

(*) Based on the most abundant isotope of each element: 12C, 1H, 14N and 16O.

Four different molecular formula can be distinguished from the high resolution m/z values.

BUT, the molecular ion m/z values will NOT distinguish between the isomers propanal (an aldehyde) and propanone (a ketone).

 

(d) Three molecules of relative molecular mass ~60

Molecule Molecular formula and structure Relative molecular mass based on relative atomic masses of the elements molecular ion molecular ion mass based on the most abundant isotopes (*)
methoxyethane C3H8O

CH3OCH2CH3

60.0952 [C3H8O]+ m/z = 60.0573
ethanoic acid C2H4O2

CH3COOH

60.0520 [CH3COOH]+ m/z = 60.0210
urea CH4N2O

O=C(NH2)2

60.0558 [O=C(NH2)2]+ m/z = 60.0323

(*) Based on the most abundant isotope of each element: 12C, 1H, 14N and 16O.

Again three different molecules with their different molecular formula can be distinguished by the small, but accurately measured differences, in their m/z values of the most abundant molecular ions.

 

(e) Identifying the molecular formula of large molecules

- just a few alkaloid examples picked up at random from the internet!

Molecular formula m/z theoretical mass m/z empirical mass
C18H20N3O 294.160637 294.160608
C17H21NO 255.162 255.162
C24H27NO4 393.194 393.194

So, high resolution mass spectroscopy can be used to determine a specific molecular formulae and complex ones too!

BUT, remember,

(i) you can only deduce the molecular formula, it could be any one of many structural isomers,

(ii) you cannot deduce any structural information from the molecular ion peaks,

(iii) the bigger the organic molecule, the more likely to give several different molecular ion peaks, e.g. you get a molecular ion peak of +1 unit more than the molecular mass  (from [M+1]+) because of the greater chance of a molecule having a carbon-13 atom (13C) in its structure.


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Calculation of % isotopic composition from the relative atomic mass of an element

The relative atomic mass of an element can be obtained from accurate analytical chemistry.

It is possible to do the reverse of a relative atomic mass calculation if you know the Ar and which isotopes are present.

It involves a little bit of arithmetical algebra.

The Ar of boron is 10.81 and consists of only two isotopes, boron-10 and boron-11

The relative atomic mass of boron was obtained accurately in the past and mass spectrometers can sort out the isotopes present.

If you let X = % of boron 10, then 100-X is equal to % of boron-11

Therefore Ar(B) = (X x 10) + [(100-X) x 11) / 100 = 10.81

so, 10X -11X +1100 =100 x 10.81

-X + 1100 = 1081, 1100 - 1081 = X (change sides change sign!)

therefore X = 19

so naturally occurring boron consists of 19% 10B and 81% 11B (the data books quote 18.7% and 81.3%)

It should be pointed out that the relative ratio of isotopes can be very accurately determined using a modern mass spectrometer AND individual isotopic masses can be measured to four decimal places - which were NOT used in the above calculation.


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Method (2) TIME OF FLIGHT (TOF) MASS SPECTROMETER (the latest design in common use)

Appendix 4b How a Time of Flight Mass Spectrometer Works

Ion mass separation using a time-of-flight mass spectrometer - a more modern instrument

The principles of a simple time of flight (TOF) mass spectrometer involve ionisation, acceleration to give all ions constant kinetic energy, ion drift, ion detection and finally data analysis - all done by computers these days!

  • In a time-of-flight mass spectrometer the ions are formed in a similar manner by electron bombardment, and the resulting ions accelerated between electrically charged plates.

  • Again, the sample must be a gas or vapourised and is bombarded with an electron beam or laser beam to knock off electrons to produce positive ions - the singly charged ions are used for analysis.

  • However, the method of separation due to different m/e (m/z, mass/charge) values is then dependent on how long it takes the ion to travel in the drift region' i.e. in the drift region the particles are NOT under the influence of an accelerating electric field.

    • A time of fight mass spectrometer does NOT use a magnetic field to effect the separation of the positive ions.

  • So ...

    1. Once the sample is vaporised and bombarded with an electron beam, a beam of positive ions is produced

      • M(g) + e- ==> M+(g) + 2e-  (ionisation process, M can be an atom of a molecule)

    2. The ions are accelerated in the same way between positive to negative plates in an electric field of fixed strength i.e. constant potential difference.

    3. The particles are given a constant kinetic energy as they pass into the drift region.

    4. The ions are then collected and detected.

    5. The positive ions cause a tiny electrical effect in the detector which becomes the electronic signal to the computer which analyses and compares the strength of the signal for the different arrival times of the different masses.

  • The smaller the mass of the ionised particle (ionized atom, fragment or whole molecule) the shorter the time of flight in the drift region where no electric field operates.

  • This is because for a given accelerating potential difference, a lighter particle is accelerated more to a higher speed than a heavier ion, so the 'time of flight' down the tube is shorter.

  • Therefore the ions are distinguished by different flight times NOT by different masses being brought into focus with a magnetic field as described in section 4a BUT the separation by time of flight is still determined by the m/e (m/z) value of the ion.

  • The general principles of the separation are required knowledge but the mathematics is NOT needed by A level students, but if you are interested, a simplified summary is given below

    • t = Kinst√(m/q)

    • t = time of flight, m = mass of ion, q = charge on ion, = square root of

    • Kinst = a proportionality constant based on the instrument settings and characteristics e.g. the electric field strength, length of analysing tube etc.

    • Therefore t is proportional to the square root of the mass of the ion for particles carrying the same charge - the bigger the mass the longer the 'flight time'.

    • The first equation is derived partly from the extra mathematics outlined below.

    • KE = qV, the kinetic energy imparted to the ion is given by its charge x the potential difference of the accelerating electric field.

    • The acceleration, for a fixed electric field, results in an ion having the same kinetic energy (KE) as any other ion of the same charge q but the velocity v of the ion depends on the m/e (m/z) value.

    • v = d/t (or t = d/v), where v = velocity of accelerated particle in the drift region, d = length of tube in the drift region. (or t = d/v)

    • KE = 1/2mv2, so the bigger m, the smaller is v in the drift region and hence the basis of detecting ions of different mass by different 'flight times'.

    • The diagram makes the method look simple, but far from it, the instrument works in a pulsed manner i.e. pulsed electric field, and some pretty sophisticated electronics are used to analyse the signals from the detector and the software calculates the mass of the ion based on the drift flight time.

  • Ultimately the data for analysis and subsequent calculations is the same as that derived from a deflection mass spectrometer described in method (1).

  • Most mass modern mass spectrometers are of the 'time of flight' type.

    • They come in all sizes eg a small scale version was on board an orbiter called Cassini which was carried by the Cassini-Huygens mission spacecraft to investigate and analyse the upper atmosphere of Titan, one of Saturn's moons. A miniature mass spectrometer was also in the probe Huygens which actually landed on Titan. In both cases gases were identified from mass spectra data and the mass spectrometer was coupled with a gas chromatograph to provide more analytical data.

      •  Gases such as hydrogen, nitrogen, methane, argon, carbon dioxide were found in the upper atmosphere of Titan.

      • Near the surface of Titan, the gases detected included hydrogen, methane, nitrogen ,argon, carbon dioxide, C2N2 (interesting!) and other small organic molecules.

    • -


(c) doc b Basic GCSE/IGCSE/O/A Level Atomic Structure Notes

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