Modern Analytical Techniques

mass spectrometry

technique used by chemists to determine the formulae and structure of molecules

radical

a (neutral) species with an unpaired electron

mass spectrum

plots relative ion intensity against mass to charge ratio

base peak

the peak with the highest intensity, produced by the fragment in greatest abundance (most stable)

fragmentation pattern

the pattern of peaks produced on the mass spectrum

• molecule absorbs lots of energy during bombardment - may cause bonds in molecular ion to break

• fragments = stable

• usually fragment into tertiary carbocations

• fragment next to a carbonyl group - allows positive charge to be spread over C and O / lone pair on O donated (resonance)

• C6H5+ is stable

molecular ion peak

• the peak with the highest m/z ratio (furthest to the right)

• may not always be visible if molecular ion is unstable (fragmented into more stable ions)

infrared spectroscopy

• stronger / double bonds / bonds to lighter atoms vibrate at a higher frequency

• absorb photons on IR radiation at higher energy

• corresponds to a higher wavenumber on the IR absorption spectrum

relative transmittance against wavenumber (1 / wavelength)

IR spectra

• C=O - strong peak

• O-H - strong, broad, smooth peak / COOH - broad, jagged peak

• C-H - strong, sharp peak - under 3000 for saturated vs above 3000 for unsaturated, 2 peaks for aldehydes

• C=C - medium, sharp peak

• N-H - medium, broad peaks - 2 peaks for primary amines / amides, 1 for secondary and 0 for tertiary (no N-H bonds)

• fingerprint region below 1500 cm-1 - unique to each molecule

high resolution mass spectrometry

• measure relative isotopic mass to 4 / 5dp

• can calculate relative atomic and molecular mass

• distinguish between compounds with the same nominal integer mass

• C = 12.0000 amu exactly

13C NMR

• number of peaks = number of different C environments

• chemical shift = type of C environment / bond

• no spin spin coupling - probability of 2 13C next to each other is very low

• much less sensitive than 1H NMR due to low abundancy of 13C

• sample dissolved in solvent (CDCl3) + contain tetramethylsilane TMS (standard reference compound producing single sharp peak)

• more helpful to look at peaks beyond 100 ppm

1H NMR

• number of peaks = number of different H environments

• chemical shift = type of H environment / bond

• area under peak is proportional to number of H atoms in the environment

• number of peaks it is split into (multiplicity) = number of adjacent Hs + 1

• only non-equivalent protons on adjacent C atoms couple with each other

• sample dissolved in solvent (CDCl3 or CCl4) + contain tetramethylsilane TMS (standard reference compound producing single sharp peak)

labile protons

• labile protons = protons that are rapidly moved / exchanged from one molecule to another due to hydrogen bonding

• if H bonded to O, N or F, the corresponding peak is a singlet and they don’t split other peaks

• detect labile protons by measuring NMR spectrum in the presence of deuterium oxide D2O

  • D nuclei exchange rapidly with labile protons + don’t show up in proton region of NMR spectrum

  • peaks of any labile protons disappear

chromatography

used for

• separating and identifying components in a sample / mixture

• determining purity of sample

• identifying impurities (using Rf values)

• purify a chemical product

• check progress of reaction

generally

• components separate due to different affinities for mobile and stationary phases

• different equilibrium between adsorped onto stationary phase and dissolved in mobile phase

• eg if substance has higher polarity, greater forces of attraction, it will adsorp onto silica to a greater extent and form H bonds with exposed OH groups on silica → move slower

thin layer chromatography

• stationary phase = silica (supported on glass / plastic plate)

• mobile phase = solvent

• quick, cheap, only needs a very small sample for analysis, widely used in labs and industry

• use capillary tube to place spot, dry and repeat

• pencil line higher than solvent level - substance don’t wash off paper and dissolve in solvent

• put chromatography paper into tank, cover tank with lid

  • ensures atmosphere in tank is saturated with solvent vapour, stops solvent from evaporating as it rises up

  • avoid contamination from external environment / changes in environment

column chromatography

• column is packed with stationary phase (silica)

• pour in sample at the top of the column

• eluent (mobile phase) is added slowly and continuously to run through the column

• separate into components and collect each fraction in test tubes at different times

locating agents

• eg amino acids appear colourless on chromatogram

• spray with ninhydrin spray which reacts with amino acids on chromatogram

• dry with hairdryer / in oven

• produce purple spots that turn brown with time

• may use TLC plate impregnated with fluorescent chemical, then look at chromatogram under UV light - the whole plate glows except organic compounds which show up as dark spots

• may place plate in covered beaker with iodine crystals - iodine vapour stains the spots

high performance liquid chromatography

• similar to column chromatography

• very small particles of silica is tightly packed into the steel column - provides greater surface area for adsorption (more OH groups exposed) so greater adsorption occurs

• components move through the column more slowly so there is greater + more efficient separation

• can separate components that are very similar + that decompose when heated (to bp) as is carried out at room temperature

• requires high pressures pump to force the mobile phase through the silica particles

• can test urine and blood samples to study drug metabolism + combine with mass spectrometry

gas chromatography

• stationary phase = silica / silica coated in solvent

  • gas-liquid chromatography uses liquid as stationary phase (inert solid coated with thin film of liquid) - separate by solubility

• mobile phase = carrier gas eg nitrogen, helium, argon which are inert, unreactive at high temperatures, non-flammable

• small sample is injected, chemicals turn to gas and mix with carrier gas, mixture carried through long coiled column inside an oven

• used to separate volatile substances that vaporise on heating without decomposing

  • tracking down oil pollution

  • presence of chemicals in industrial process

  • level of alcohol in blood / anti-doping

  • pesticides in river

• substances separate by polarity and boiling points (if higher bp, then spend less time in gas phase so retention time is longer)

• the components reach a detector which sends a signal to a recorder

• computer generates peaks with different retention times; area under peak is proportional to the (relative) amount of substance

chromatography combined with MS

• gas chromatography or HPLC

• drug detection in sport, forensics, airport security

• each component of the mixture is collected and separately ionised

• separate mass spectrum produced for each component

• computer receives data - compares mass spectrum to those in known library, reports list of likely identifications

• can distinguish between similar components with similar retention times + may identify new chemicals (as no standards to determine retention times)