Spectroscopic Techniques (3) Gas Chromatography and Mass Spectrometry (GC-MS)

I have already written extensively in this blog about Mass Spectrometry here

So what I want to do in this blog is take mass spectrometry (MS) to the next level as it were. 

I am going to discuss the “time of flight” mass spectrometer.

I am also going to discuss how mass spectrometry is used to analyse organic molecules – the organic molecules separated out from a sample using gas chromatography (GC).

I am also going to discuss how gas chromatography works.

Time of Flight Mass Spectrometer

This is the simplest type of mass spectrometer and they have been sent on space missions such as that on the Philae lander that made the first soft landing on a moving comet in November 2014. 

How does this type of mass spectrometer work?

The sample is injected into the machine and it is subjected to fast electron bombardment.

An electric field then accelerates (it actually pushes the positive ions since the ions experience a positive field) the resultant positive ions towards a negatively charged plate but the ions do not then enter a magnetic field instead they enter a long tube or flight tube (see diagram) which is about 0.6—2.0m in length.

All ions acquire the same kinetic energy but some travel faster because they are lighter than others.

This tube is field free and it is the momentum of the ions that means they reach the detector.

So the lighter ions have greater velocity than the heavier ions.

The lighter ions take a shorter time to travel down the tube so that they are detected first at the ion detector.

Other heavier ions take a longer time to travel to the detector.

Flight times are proportional to the square root of the mass of the positive ion

Flight time =  drift length  = drift length × √(mass/2×energy)

                           velocity

Knowing the flight time means the mass of that positive particle can be determined and a mass spectrum plotted. 

As a result, the different fragment ions from the sample can be determined.

For example, a mass spectrometer with a 0.6m flight tube will mean that a molecule of mass 26amu will take 6 × 10^–6 seconds to complete the flight path.

For good distinction between different masses, the instrument’s timing electronics must be capable of measuring the time of flight to a resolution of 0.25 ns (0.25 x 10^-9 seconds).

Ions of different mass arrive at the detector one after the other so that it is possible to detect all the ions that were derived from the source.

Ions are detected by gaining electrons.

The abundance of any one particular isotope is measured by the size of the current flowing in the detector.

This is why a time of flight mass spectrometer can have a very high overall sensitivity compared to other MS systems.

It also means that time of flight spectrometers have no difficulties with high mass ions; it is just a matter of waiting for them to arrive.

The high mass limit is then determined by the ability of the detector to register the arrival of the high mass ion.

This means they can determine the mass of large molecules such as proteins with some degree of accuracy say 0.01%

If you are studying AQA A level there are extensive notes on Time of Flight mass spectrometers here .

The time of flight instrument on the Philae lander was coupled to a Gas Chromatograph. 

This is a common analytical combination.

Here is how the gas Chromatograph operates

Gas Chromatograph

It works like this:

The chromatograph column contains an inert solid and it is between 1.5 and 10m long with an internal diameter of about 4mm.

On the surface of the powder in this column there is adsorbed a liquid called the liquid stationary phase because it does not move.

A chemically inert gas is flowing through the column–gases used include carbon dioxide, nitrogen and argon–the choice of gas depends on the sample under test and the kind of detector being used.   

The sample under test is vaporised and injected into the column.

As the sample mixture passes along the column, some parts of it are retained on the column for longer than others.

The separated components of the mixture emerge from the column according to their retention time (R_t  )

It’s very important to prevent molecules like water entering the column.

A small sample is usually used, say 20 μlitres, and injected as a “plug” of vapour.

There is usually a flash vaporizer at the head of the column that operates at about 50^oC above the known boiling point of the least volatile component in the sample. 

You will see in the diagram that the column is in an oven and the temperature of the oven is controlled very precisely to within tenths of a degree Celsius. 

The time taken for the sample to pass through the column is called the elution time. 

If the GC is linked to a Mass Spectrometer as on the Philae lander then the sample is directly transferred to the MS after separation in the GC. 

Other wise a flame, ionisation detector picks up the different samples from the mixture.

The output from the column is mixed with hydrogen and air, and ignited.

Organic compounds burning in the flame produce ions and electrons.

The electrons can conduct electricity through the flame.

The resultant current is measured. 

The only problem with this approach is that the sample is destroyed. 

If the samples are put through a mass spectrometer they are also destroyed. 

How to analyse the mass spectra of organic molecules.

So you have analysed your organic sample in the Gas Chromatograph and each of the components of your sample mixture has been put through the Mass Spectrometer.

Your Gas Chromatogram might look like this::

It looks like a drugs test sample: note the amphetamine peak.

Note the peak at 2.055ms.

The individual components are identified by their retention times compared with standards already known. 

Note the horizontal scale is a labeled “time” i.e. retention time on the column. 

And the Mass Spectrum of one of the samples in the mixture might look like this:

But how do you analyse mass spectra like this?

The mass spectrum reveals the fragmentation pattern of the molecule on bombardment with high energy electrons.

Take this sample of an alkane:

You can find most molecules at the site above: http://webbook.nist.gov/chemistry

First, note the highest mass peak at 142.

This is the M⁺ peak or molecular ion or parent ion peak.

It represents the ionised decane molecule or the  C₁₀H₂₂⁺ ion.

Now I want you to see the pattern that follows in the masses of the higher peaks that occur in little clusters.

These masses are:

113

99

85

71

57

43

First note how each is separated by 14 mass units: that's a —CH₂— or methylene group.

You can see how this molecules a linear alkane is fragmenting as —CH₂— groups are broken off one at a time.

So what positive ion does each mass represent?

113 is 142–29 so it must be C₈H₁₇+

99 is 113–14 so it must be C₇H₁₅+

85 is 99-14 so it must be C₆H₁₃+

71 is 85–14 so it must be C₅H₁₁+

57 is 71– 14 so it must be C₄H₉+

and 43 is 57-14 so it must be  C₃H₇+  etc…….

This is the distinctive pattern of fragmentation of a linear alkane molecule or alkane type side chain in a molecule.

Lastly, note too the very small peak at m/z 143

It is a tenth the size of the parent ion peak and represents the abundance of the molecular ion with one C13 carbon isotope in it. 

e.g. the C₉C¹³H₂₂ +  ion.

Lets look now at a typical halogenoalkane: chloroethane C₂H₅Cl

Again we can see the alkane fragmentation pattern but the significant thing here is the signature of chlorine.

Look at the peaks at m/z 66 and 64

66 is one third the height of 64

This reflects the abundance of chlorine isotopes in the environment where Cl³⁵ is three times more abundant than Cl³⁷

Both these peaks represent molecular or parent ions

66 is C₂H₅Cl³⁷   and  64  is C₂H₅Cl³⁵

Here is a neat way if detecting the presence of one chlorine atom in a molecule.

This is a likely question in a college or school advanced exam paper.

Knowing how alkanes fragment you should be able to work out what ions the other major peaks represent.

Here is another mass spectrum this time it's a bromo compound

This is the mass spectrum of bromoethane.

What is distinctive about this mass spectrum is that there are two parent or molecular ion peaks at m/z 108 and 110.

These two peaks reflect the relative abundance in nature of the two bromine isotopes Br⁷⁹ and Br⁸¹.

You can see the two very small peaks at 79 and 81 showing the bromine atoms that have fragmented as cations from the molecule.

The isotopes are about equally abundant so the two parent ion peaks are of about the same intensity. 

Here is another signature mark on a mass spectrum that tells you there is one bromine atom in the molecule.

Here is another mass spectrum this time of an aromatic compound

This is the mass spectrum of benzyl alcohol: C₆H₅CH₂OH

The characteristic feature of the mass spectra of aromatics is that they usually carry a peak at 77 as you can see here.

Why 77?

77 corresponds to a phenyl ion C₆H₅+

Aromatic molecules tend to fragment by the ring substituents breaking off one at a time. 

This leaves the phenyl ring at 77.

updated 30th October 2017

Spectroscopic Techniques (2) Infrared (IR) Spectroscopy

Infra–red spectroscopy was one of the first spectroscopic techniques developed to analyse samples of molecules non–invasively.

The essential principle of infrared spectroscopy is that polar covalent bonds resonate at energies and frequencies in the infra–red region of the electromagnetic spectrum. 

And basically that’s it. 

But note that the molecule visible to this spectroscopy must contain polar covalent bonds.

So molecules like chlorine do not interact with infra red radiation because the Cl—Cl bond is not polar.

Whereas molecules with covalent bonds in which the two atoms have a difference in electronegativity do resonate with infrared radiation and vibrate like those in water H2O.

So what happens in molecules when their bonds resonate with infra-red radiation?

Essentially, the bond in question vibrates.

Infrared energy lifts the bond into a higher vibrational energy state. 

The quanta of energy needed for this process is related the bond’s strength or its force constant. 

You will notice from this equation that the force constant f is proportional to 1/λ the inverse of the wavelength of infra-red resonance energy absorbed. 

This property 1/λ is called the wave number and is also proportional to the energy ∆E absorbed since

     c  =  ν λ   and therefore  c/λ= ν

and from Planck’s equation: ∆E =  h ν

therefore combining these two equations we have ∆E  =  hc/ λ

therefore ∆ E  ∝ 1/λ

Wavenumber has units of cm^–1

So what sort of vibrational modes occur when infra-red energy is absorbed?

Bonds can either stretch or bend.

In polar diatomic molecules like CO NO and HCl the polar covalent bond stretches

So     H — Cl

         ↔︎

H and Cl atoms pulsate in and out along the bond axis and the interatomic distances change.

It is as if the bond were a spring joining the two atoms together and one end of the spring is pulled allowing the atoms to move together then move apart. 

In polar non-linear molecules the bonds have different vibrational modes.

Not only can the bonds stretch either symmetrically or asymmetrically they can also bend

A good example to show these modes is the water molecule and you can find many illustrations of water’s molecular vibrational modes on the Internet e.g.

When we examine organic molecules we find that they also behave in similar ways because most of their bonds are polar. 

Certain functional groups have particular absorption bands in the infra-red region.

If you are studying chemistry at school or college level you will know that your institution or examination authority provides tables of these absorption bands related to functional groups in organic molecules.

Here is typical example from the UK’s Royal Society of Chemistry:

All you need to do is then take you infra-red spectrum and examine it in the light of these absorption bands.

At school and college level you will have fairly straightforward examples to deconstruct and they will usually be part of a question in which you have other information about the example molecule as well as its IR spectrum. 

For example here is a simple example that of methanol (formaldehyde)

Here is a typical ketone showing the carbonyl absorption

here is  carboxylic acid

and here is an alcohol