Modern Analytical Techniques Infra red Spectroscopy.

• Identify absorption peaks in an infrared spectrum. Week 20 • State that absorption of infrared radiation causes covalent bonds to vibrate. • Identify absorption peaks in an infrared spectrum. • State that modern breathalysers measure ethanol levels by analysis using infrared spectroscopy. © Pearson Education Ltd 2008 This document may have been altered from the original

Infra red radiation and molecules When a molecule is exposed to electromagnetic radiation covalent bonds will absorb energy in the infrared region of the spectrum. Since each particular type of bond has its own natural vibrational frequency we can use these analytically. The amount of vibration depends on: the bond strength the bond length the mass of each atom involved in the bond.

For IR radiation to be absorbed the vibrations must cause a change in the dipole moment of the molecule. Symmetrical bonds in e.g. O2 and N2 do not absorb radiation and are not IR active. Since most molecules have several different types of bond molecules will cause many absorptions. The same bond may have many different vibrational modes.

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

Recording a Spectrum An infra red beam is split into 2 and passes through a sample and a reference cell containing solvent only. The solvent absorptions are thus removed from the sample and only the absorptions due to the test molecule are seen. N.B. Frequency is measured using WAVENUMBER which is actually 1/wavelength with the units cm-1. This makes the numbers in the spectrum easy to handle. Absorptions are diagnostic of bonds present.

Schematic diagram of an infrared spectrometer Week 20 Schematic diagram of an infrared spectrometer © Pearson Education Ltd 2008 This document may have been altered from the original

A typical infrared spectrum showing absorption peaks Week 20 A typical infrared spectrum showing absorption peaks © Pearson Education Ltd 2008 This document may have been altered from the original

Even though energy is absorbed and the spectrum consists of several troughs these are still described as peaks (since they represent increasing amounts of energy absorbed). Most organic compounds produce a peak at around 3000 cm-1 due to absorption by C-H bonds which is therefore NOT used diagnostically. However (see table p.168) O-H bonds and C=O bonds can be used diagnostically for alcohols, aldehydes, ketones and carboxylic acids. Very broad absorptions are due to the large amounts of energy absorbed by very polar bonds like O-H.

When interpreting simple spectra: Concentrate on major absorptions only. Remember that absence of an absorption is diagnostic and popular in exam questions. Do not expect to make absolute identifications from IR spectra only.

Week 20 • Identify, using C=O and O–H absorptions, an alcohol, an aldehyde or ketone and a carboxylic acid. © Pearson Education Ltd 2008 This document may have been altered from the original

Infrared spectrum of methanol Week 20 Infrared spectrum of methanol © Pearson Education Ltd 2008 This document may have been altered from the original

Infrared spectrum of propanal Week 20 Infrared spectrum of propanal © Pearson Education Ltd 2008 This document may have been altered from the original

Infrared spectrum of propanoic acid Week 20 Infrared spectrum of propanoic acid © Pearson Education Ltd 2008 This document may have been altered from the original

IR Analysis and Breath Testing The legal limit for blood alcohol in the UK is 80mg of ethanol per 100cm3 of blood. Initial breath testing using a breathalyser involves the use of potassium dichromate absorbed onto crystals. Exhaled breath passes through the crystals and ethanol is oxidised, causing the crystals to go green as the dichromate is reduced to Cr3+ ions. A positive breath test is a cue for an IR test back at the police station. A broad absorption at 3340 cm-1 and a sharp absorption at 2950 cm-1 can be used by the computer to calculate the % of ethanol present.

• Outline the early developments in mass spectrometry. Week 20 • Outline the early developments in mass spectrometry. • Outline the use of mass spectrometry in the determination of relative isotopic masses and for identifying elements. • Interpret mass spectra of elements in terms of isotopic abundances. © Pearson Education Ltd 2008 This document may have been altered from the original

Mass Spectrometry

Simple Mass Spectrometer Early developments in mass spectrometry listed on p. 170 in the text book are NOT required by the syllabus, but make interesting reading, nor are the workings of the machines. The key is that POSITIVE ions are created and accelerated then deflected (by a magnet) round a bend which serves to focus the beam of ions since heavy and light ones will hit the sides. To ensure that all ions are detected the magnetic field is varied. The ions are detected and recorded according to their mass to charge ratio (written m/z). For AS only ions with a single + charge are considered so m/z = Ar The use of mass spectrometers to determine relative isotopic masses are required.

Using the Mass Spectrum of Neon to work out RAM Neon shows 3 isotopes with m/z (mass number) 20,21 and 22. Peak heights show relative abundances as: 90.5, 0.3 and 9.2 respectively. To calculate the RAM remember: RAM = (20 x 90.5)+(21 x 0.3)+(22x9.2) 100 =1810+6.3+202.4 =20.19 (or 20.2 to 3sf) Use the mass spectrum for magnesium on the following slide to calculate the RAM for magnesium.

The mass spectrum of magnesium Week 20 The mass spectrum of magnesium © Pearson Education Ltd 2008 This document may have been altered from the original

Also mentioned: pesticides in the food chain. Syllabus requires that you know that mass spec is used as a method for identifying elements e.g. in the Mars space probe and in monitoring levels of environmental pollution such as lead. Also mentioned: pesticides in the food chain. http://www.bbc.co.uk/radio4/science/smalldog.shtml http://www.azcentral.com/community/westvalley/articles/2009/03/27/20090327gl-nwvvan0328.html http://www.nytimes.com/1986/02/06/business/technology-detecting-food-contaminants.html?sec=health&spon=&pagewanted=all

Week 20 • Use the molecular ion peak in an organic molecule’s mass spectrum to determine its molecular mass. • Explain that a mass spectrum is essentially a molecule’s fingerprint that can be identified using a spectral database. © Pearson Education Ltd 2008 This document may have been altered from the original

Mass Spectrometry and Organic Molecules The value of mass spectroscopy with isotopes of elements is limited. However it is widely used as a routine analytical tool in organic chemistry because the beam of high energy electrons (or whatever the ionising source is) disrupts the covalent bonds within the molecule and fragments it. There is usually a fragment made which represents the MOLECULAR ION where a single electron has been knocked off the molecule leaving it positively charged with the same mass since the mass of an electron is negligible. Energy can cause the molecular ion to vibrate strongly enough to weaken the bonds and cause fragmentation.

Using Fragmentation Patterns to Confirm Molecular Structures The mass spectrum of ethanol has many peaks due to the fragmentation of the molecular ion. These can often be explained from a knowledge of the structure of the molecule under test or used diagnostically to identify unknown or new molecules. Examples include: m/z 15 CH3+ fragment m/z 17 OH+ fragment m/z 29 C2H5+ fragment m/z 31 CH2OH+ fragment m/z 46 M+ C2H5OH+ the molecular ion. Can you suggest fragments for peaks at m/z 45, 43, 27?

Mass spectrum of ethanol Week 20 Mass spectrum of ethanol © Pearson Education Ltd 2008 This document may have been altered from the original

Using Fragmentation Patterns to Confirm Molecular Structures(2) Look at the mass spectra for Pentane and 2-Methyl pentane. Can you identify the key fragments which unambiguously identify which of thesespectra is which? Identify the M+ for A and B. Any ideas for possible identification?

Mass spectra of the isomers of C5H12, pentane and 2-methylbutane Week 20 Mass spectra of the isomers of C5H12, pentane and 2-methylbutane © Pearson Education Ltd 2008 This document may have been altered from the original

Week 20 Spectra A and B © Pearson Education Ltd 2008 This document may have been altered from the original

Week 20 • Suggest the identity of the major fragment ions in a given mass spectrum. • Use molecular ion peaks and fragmentation peaks to identify structures. © Pearson Education Ltd 2008 This document may have been altered from the original

Mass spectrum for an unknown alkane (hexane). Week 20 Mass spectrum for an unknown alkane (hexane). © Pearson Education Ltd 2008 This document may have been altered from the original

Week 20 Equations explaining how some of the peaks arise in the mass spectrum for hexane © Pearson Education Ltd 2008 This document may have been altered from the original

Using Fragmentation Patterns to Confirm Molecular Structures(3) Identify the fragments responsible for the peaks A,B and C for pent-1-ene as follows. Identify the molecular ion peak in the spectrum of the unknown alkane. It is a 2-methyl…… branched chain. Draw structures for the fragment ions represented by the peaks with m/z values of 43, 57 and 71.

Mass spectrum of pent-1-ene Week 20 Mass spectrum of pent-1-ene © Pearson Education Ltd 2008 This document may have been altered from the original

Mass spectrum of an alkane Week 20 Mass spectrum of an alkane © Pearson Education Ltd 2008 This document may have been altered from the original

Combined Techniques It is worth remembering that no one single analytical technique is ever used alone. Mass Spectroscopy is invariably carried out in sequence with Gas Chromatography. IR and NMR are also used with the other 2. The job of a modern analytical chemist is not a lot different to the antics of the various CSI ‘scientists’ on the TV. Any new substance is routinely ‘fingerprinted’ and records of the various spectra stored on databases to enable swift analysis when required.