Spectroscopy in a suitcase

A Spectroscopy workshop kindly funded by the Royal Society of Chemistry (RSC) in collaboration with Imperial College London.

Hosted by Ben (PhD student) and Leila (undergraduate) at Imperial College

We were very fortunate that Rooks Heath Chemistry and Physics A level students were able to take part in this workshop last December. Spectroscopy is a very important method for helping chemists to identify chemical compounds but the principles behind the methods are important to physicists.

The aims of the workshop was to give the students a ‘hands on’ experience with Spectroscopic equipment that is found in a University Lab (UV, IR) and to ‘problem solve’ with real spectra.

As an introduction the students were asked about what they knew about spectroscopy.

Spectroscopy is the study of the interaction between light (electromagnetic radiation) and matter.’

Radiation is energy in the form of waves or moving subatomic particles.

Matter is a substance of which physical objects are composed.

Looking at a substance only tells us if it is a solid, liquid or a gas. Trying to identify it by taste or small could be very dangerous so we rely on spectroscopy to do the job for us.

In reality spectroscopy means we can characterise matter by the way it interacts with different frequencies of energy.

Our students learn about the electromagnetic spectrum quite early on in their school career. They learn about the relationship between the speed, wavelength and frequency at GCSE:

c = fl where c is the speed of the electromagnetic wave, f (or n if you are a chemist) is the frequency of the wave and l is the wavelength

http://blog.rafaelcorrales.com/

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http://en.wikipedia.org/wiki/Electromagnetic_spectrum

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The wavelengths and frequencies in the electromagnetic spectrum vary widely and these dictate the use that can be made for each type of wave.

For example radiowaves are as large as buildings and in contrast the wavelength of visible light is as large/small as unicellular organisms and X-rays even as small as atoms.

The smaller the wavelength the larger the energy this can be seen in a formula which the A level physics students meet:

hc/l where h is Planck’s constant

http://en.wikipedia.org/wiki/Planck_constant

This means that radiowaves with their large wavelengths are harmless compared with UV and gamma radiation.

The following is a list of the technologies involved in spectroscopy:

Infra-Red (IR)

UV / Visible (UV/Vis)

Mass Spectrometry (MS)

Nuclear Magnetic Resonance (NMR)

With this combination of techniques you can identify the structures of unknown substances.

Infra-red

http://en.wikipedia.org/wiki/Infrared

Infrared (IR) light is electromagnetic radiation with longer wavelengths than those of visible light, extending from the nominal red edge of the visible spectrum at 700 nanometers (nm) to 1 mm.

In spectroscopy it is used to identify functional groups. A functional group is responsible for the characteristics of a molecule.

http://en.wikipedia.org/wiki/Functional_group

http://www.youtube.com/embed/lZ7sC1t00Cs?feature=player_detailpage

http://www.le.ac.uk/spectraschool/ then select IR video

A graph is produced of IR absorption. IR spectra are usually easy to identify by the large troughs that result from particular bonds in the molecule absorbing radiation.

Transmittance is plotted against the wavenumber. The term wave number refers to the number of complete wave cycles of an electromagnetic field (EM field) that exist in one meter (1 m) of linear space. Wave number is expressed in reciprocal meters (m^-1).

http://whatis.techtarget.com/definition/wave-number

http://en.wikipedia.org/wiki/Wavenumber

http://www.chemguide.co.uk/analysis/ir/interpret.html

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The troughs actually show how good the substance is at absorbing the infra-red.

Certain individual bonds in a molecule absorb IR radiation and become excited. Some will “bend” and some will “stretch”.

‘‘Peaks and Troughs’’ – Spectrum produced in wavelengths (λ) or wavenumbers (cm^-1)

Functional Groups (OH etc) are identified by characteristic ‘bends and stretches’

http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/InfraRed/infrared.htm

http://en.wikipedia.org/wiki/Molecular_vibration

Ultraviolet and visible light

The visible region which is used in UV/Vis spectroscopy is between 300-700 nm, ranging from blue (400 nm) to red (700 nm). The Beer-Lambert law, which is used in UV/Vis spectroscopy to convert the absorbance of a compound (A, this is what is measured) into the concentration, (which is what you want to know). L (cuvette or sample size) and e (compound specific constant) are always constant and c (concentration) is the only variable. Light of a certain intensity (I(0)) enters the sample, some of which will be absorbed by the molecules in solution and light with less intensity (I(1)) is transmitted through the sample and is measured by the spectrometer. I(1) can be converted into A (A = ln(I(0)/I(1)) and then the Beer-Lambert law is applied.

The information obtained is the sample concentration.

http://en.wikipedia.org/wiki/Beer%E2%80%93Lambert_law

In UV/Vis spectroscopy you observe peaks rather than troughs as the absorbance is measured vs. the wavelength (this is the opposite of an IR spectrum). When a compound absorbs a certain wavelength we will only see what is reflected. For example chlorophyll in plants absorbs in the red region of the spectrum, this is why leaves appear green.

http://en.wikipedia.org/wiki/Chlorophyll

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Absorbance spectra of free chlorophyll a (blue) and b (red) in a solvent. The spectra of chlorophyll molecules are slightly modified depending on specific pigment-protein interactions.

Mass Spectrometry

Our A level physics students learn how a mass spectrometer functions.

Mass spectrometry provides information about molecule fragmentation (in addition to RMM), which can help to identify the structure of the compound, but not always.

Mass spectrometry does not use electromagnetic radiation and is therefore called Mass Spectrometry but is often called Mass Spectroscopy!

Molecules are ionised then fragmented.

The information obtained is the mass of molecule (RMM) and often its molecular structure.

http://en.wikipedia.org/wiki/Mass_spectrometry

http://lawrencekok.blogspot.co.uk/2012/10/ib-chemistry-on-mass-spectrometer-and.html

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A mass spectrometer is highly sensitive and operates under high vacuum. When the sample is injected into the mass spectrometer it is firstly heated and therefore vapourised, next it will be ionised and depending on the MS method this is done with electrons or other particles. The ions are then accelerated through an electric field and deflected by a magnetic field, which has the effect that their retention time measured is dependent on their size, with small molecules arriving first and heavier ones last.

In a MS spectrum the peak with the largest mass per unit charge (m/e or m/z) number is generally the parent ion, although you can occasionally get a smaller peak with a mass of M+1 where a proton has been added to the molecular ion (dependent upon the ionisation technique used). The difference between two peaks can be used to calculate possible fragments, which can provide us with information on molecular structure.

Identifying Propanone using MS

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http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis/Chapter__4%3A_Structure_Determination_I/Section_4.4%3A_Mass_Spectrometry

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Nuclear Magnetic Resonance (NMR)

http://en.wikipedia.org/wiki/NMR_Spectroscopy

The information gained from this process is about the hydrogen environment of the molecule.

In effect this process is like a jigsaw puzzle where the spectra generate the jigsaw pieces which are fitted together therefore generating the whole molecule. 1H (Proton NMR) and 13C (Carbon 13)

The jigsaw pieces show the environment of each different Hydrogen e.g.

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It can distinguish between hydrogens attached to oxygen and hydrogens attached to carbons etc.

Using NMR to identify propanal

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http://en.wikipedia.org/wiki/Propionaldehyde

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The graph above is of signal height (y axis) against chemical shift d/ppm (x axis). The left signal is CHO (1H), the middle signal is CH2 (2H) and the right signal is CH3 (3H)

Where the H is bonded determines its position. The area of the peak shows the number of protons present (not easy to see in the above diagram).

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Combination of Techniques

Infra Red gives the Functional Groups (alcohol, acid etc)

Mass Spec gives the Molecular Mass / Molecular Structure

UV gives the Concentration

All the techniques outlined have to be combined as no single technique can tell you everything you need to know. Together they can tell you the structure of a substance or identify an unknown substance.

If the compound is known, substances can be confirmed when an identical spectrum is produced. For example, IR machines are taken to festivals (Glastonbury) to confirm random drug tests through use of a pre-existing database (library) or used in Formula 1 in the pit lane to conduct random oil tests during and after the race.

The students get to work

The students were lucky to be able to use spectroscopy techniques to carry out to practicals:

IR & MS (Hands on) – solving a crime scene

This activity involved using ATR (attenuated total reflectance) IR spectrometer to find out what killed a man found dead in a lab. The students first had to work out how many carbons, hydrogens, oxygens and nitrogenswere in the suspected chemicals and the relative molecular mass (gmol^-1) of the suspected chemicals. They them had to use mass spectrometry and IR data to narrow the possibilities down to two possibilities.

The mass spectrometry data recorded was molecular weight, abundance and assignment (fragment/parent ion etc). The infrared data recorde was important peak values, functional group and specific wavelength of the functional group.

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The above picture shows Leila explaining the process to some of the students and Ms Ibrahim.

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Leila running the process watched by the students.

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The above picture shows the students helping out.

The picture below shows the resultant spectrum.

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At the end of the activity the students were able to gather all the information together to identify the unknown compounds including the one that caused the death.

IR & MS (Paper based) – determining unknown compounds

In this activity the students were given information and asked to use it to draw out the possible organic compound structures identifying the numbers of carbons, hydrogens and oxygens in each and also their relative molecular masses.

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Knowing the relative molecular masses of the chemicals and given IR and MS data the students were able to narrow down the possibilities to just two compounds.

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Ben giving the students some pointers

The MS data gave the molecular weight, % abundance and assignment.

From the two possible compounds the students then used IR data to identify the functional group by looking at the wavenumber and strength of signal. They were then in a position to identify the unknown compound.

A summary

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Thank you RSC for use of your pictures! http://www.le.ac.uk/spectraschool/

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