Organic Chemistry: Techniques & Spectra — IAL Edexcel Linear (Chemistry) Revision Notes & Topical Questions

Section 1 of 19Principle of mass spectrometry

A small sample is bombarded with high-energy electrons, which remove an electron to form a positive molecular ion with one unpaired electron.

The molecular ion can fragment into new ions, molecules and radicals: M⁺ → X⁺ + Y•.

• Only the positive fragments are detected.

The fragment ions are accelerated by an electric field and deflected into the detector according to their mass-to-charge ratio, m/z.

Most ions have a 1+ charge, so m/z equals the mass.

• An ion of mass 16 with a 2+ charge has m/z = 8.

Smaller and more highly charged ions are deflected more, so a small m/z can mean a small fragment, a high charge or both.

Base peak

• Base peak the peak of the most abundant ion.

Section 2 of 19Isotopes and relative abundance

Isotopes

• Isotopes atoms of the same element with the same number of protons but different numbers of neutrons.

Relative abundance

• Relative abundance the proportion of each isotope in a natural mixture, shown by peak heights.

Chlorine is 75% ³⁵Cl and 25% ³⁷Cl; boron is 19.9% ¹⁰B and 80.1% ¹¹B.

Section 3 of 19Molecular ion and M+1 peak

Molecular ion and M+1 peak

The peak with the highest m/z (apart from M+1) is the molecular ion, giving the relative molecular mass.

The M+1 peak is due to ¹³C, which has about 1.1% natural abundance.

• The more carbon atoms in the molecule, the taller the M+1 peak.
• Hexane has a taller M+1 peak than ethane.

The M+1 peak is not the molecular ion; for example, pent-1-ene (C₅H₁₀) has M = 70 and but-1-ene (C₄H₈) has M = 56.

Section 4 of 19Isotope patterns of halogen compounds

Isotope patterns of halogen compounds

Halogenoalkanes show several peaks around the molecular ion because of halogen isotopes.

Chlorine compounds show M and M+2 peaks in the ratio 3:1.

Bromine compounds show M and M+2 peaks in the ratio 1:1.

• CH₃Br shows equal peaks at m/z 94 and 96.

Section 5 of 19Fragmentation

1

Different compounds can have the same molecular mass, so fragments are used to work out the structure.

2

The difference between M⁺ and a fragment shows the neutral group lost, e.g. 15 = CH₃.

3

Loss of small molecules gives peaks at M−18 (H₂O), M−28 (CO) and M−44 (CO₂).

4

Stable cations (acylium ions, tertiary carbocations) give tall peaks.

m/z	Fragment ion
15	CH3+
29	C2H5+ or CHO+
31	CH2OH+
43	C3H7+ or CH3CO+
45	COOH+

Fragmentation

Alkanes fragment by breaking C-C bonds.

Alcohols often lose water, giving a peak at M−18, and a peak at 31 from CH₂OH⁺.

• Propan-1-ol fragments to m/z 59 (loss of H•), 42 (loss of H₂O), 31 (loss of •C₂H₅) and 29 (loss of •CH₂OH).

Isomers can be distinguished by fragments: propanone gives a strong peak at 43 (CH₃CO⁺) and 15, whereas propanal gives m/z 29.

Section 6 of 19Infrared spectroscopy

Infrared spectroscopy

Infrared radiation is absorbed by covalent bonds, which vibrate by stretching and bending at specific frequencies.

Absorptions are reported as wavenumber (cm⁻¹), the reciprocal of wavelength, and have characteristic width and intensity.

Hydrogen bonding makes O-H absorptions broad, whereas C=O absorptions are strong and sharp.

Bond	Wavenumber / cm-1	Appearance
O-H (alcohol)	3200-3550	Broad
O-H (carboxylic acid)	2500-3300	Very broad
N-H	3300-3500	Medium
C-H	2850-3100	Strong, sharp
C=O	1680-1750	Strong, sharp
C=C	1620-1680	Medium

• The fingerprint region below about 1500 cm⁻¹ is unique to each compound and is compared with a reference spectrum.

Section 7 of 19Using IR spectra to identify functional groups

1

Look first for a broad O-H, a strong C=O near 1700 cm⁻¹ and N-H.

2

An alcohol shows O-H but no C=O.

3

A carboxylic acid shows both a very broad O-H and C=O.

4

An aldehyde, ketone or ester shows C=O only.

5

Propanone shows a sharp absorption near 1710 cm⁻¹; propan-2-ol shows a broad absorption at 3200–3550 cm⁻¹.

6

IR can confirm oxidation of an alcohol: the O-H disappears and a C=O appears.

7

Absorptions can overlap, so IR is combined with mass spectrometry to identify an unknown compound.

Section 8 of 19More from the specification

1Anhydrous chemical drying agents

• Anhydrous chemical drying agents adding anhydrous magnesium sulfate or calcium chloride removes trace water from organic extracts prior to distillation.

2Heating under reflux

• Heating under reflux a condenser returns vapour to the flask so a reaction mixture can boil for a long time without loss.

3Distillation

• Distillation separates a product by boiling point, collecting the fraction at the temperature that corresponds to it.

4Separating funnel

• Separating funnel separates immiscible layers, with the organic layer run off from the aqueous layer.

5Drying

• Drying an anhydrous salt such as magnesium sulfate removes traces of water from the organic product.

6Purity check

• Purity check a sharp boiling or melting point indicates a pure product; spectra confirm structure.

7Separating funnel

• Apparatus for separating two immiscible liquids.

8Drying agent

• An anhydrous salt that removes water from an organic liquid.

9Primary alcohol

• An alcohol in which the C–OH carbon is attached to one other carbon.

10Boiling

• Liquid to gas throughout the liquid at the boiling point.

11Distillation

• Separating a liquid from a solution by boiling and condensing the vapour.

12Condenser

• Apparatus that cools gas back to liquid.

13Reflux

• Heating with a condenser to stop volatile liquids escaping.

14Temperature

• A measure of the average kinetic energy of the particles.

15Fragmentation

• Breaking of the molecular ion into a smaller cation and a radical.

16Liquid

• A state with a fixed volume that flows, particles sliding past each other.

Section 9 of 19More on this topic

• Alcohols oxidise according to their class.

Section 10 of 19Heating under reflux

1

Organic reactions are often slow at room temperature, so the mixture is heated under reflux.

2

A vertical condenser returns vapours to the flask, so the mixture reacts fully without loss of reactants, products or solvent.

3

Examples

• Oxidation of a primary alcohol to a carboxylic acid with acidified potassium dichromate.
• Making an ester from an alcohol and an acid with an acid catalyst;
  • ethyl ethanoate needs about 15 minutes of reflux.

4

The aim is to keep all chemicals inside the reaction vessel.

Section 11 of 19Reflux apparatus and method

1

Place the mixture in a pear-shaped or round-bottomed flask with anti-bumping granules for smooth boiling.

2

Heat with an electric heating mantle or a water bath, not a Bunsen burner, because organic liquids are flammable.

3

Clamp a Quickfit condenser vertically, with lightly greased joints and an open top (never a closed system).

4

Run water in at the bottom and out at the top of the jacket so it stays full.

5

Boil the mixture for the required time.

6

Stop heating and let the mixture cool to room temperature.

Section 12 of 19Distillation

1

Distillation separates a product from a mixture by boiling point; the lowest-boiling liquid distils first.

2

It is used when a reaction does not go to completion or when other chemicals form.

3

Apparatus

• A flask with anti-bumping granules.
• A still head with the thermometer bulb level with the side arm, where vapour enters the condenser.
• A downward-sloping condenser with water entering at the bottom, with greased joints.
• A receiving flask.

4

Heat with an electric heating mantle, because the temperature is controllable and the liquids are flammable.

5

Collection

• Collect the distillate within ±2 °C of the boiling point of the desired product.
• Discard any distillate below this range in a separate vessel.
• Stop collecting if the temperature rises above the range.

6

To make an aldehyde from a primary alcohol, heat the alcohol with acidified dichromate and distil the aldehyde off as it forms.

7

The aldehyde boils lower than the alcohol because it has lost hydrogen bonding, so it distils before further oxidation.

Section 13 of 19Boiling point determination

1

The boiling point of a liquid indicates its purity and identity.

2

Heat the sample gently, record the temperature at which it boils and compare it with literature or database values.

3

Impurities cause two effects.

• The boiling point appears higher than the literature value.
• The sample boils over a range of temperatures instead of at one temperature.

4

A pure liquid boils at a fixed temperature at a given pressure.

5

It can be measured by distillation (steady thermometer reading) or by heating a sample with an inverted capillary tube,

• where the boiling point is when bubbles stop and liquid enters the capillary on cooling.

Section 14 of 19Solvent extraction with a separating funnel

Solvent extraction with a separating funnel

Water often forms with the organic product, giving an aqueous layer and an organic layer.

Identify the organic layer by adding a little water and seeing which layer grows.

Wash with sodium carbonate solution to neutralise acidic by-products and remove other impurities.

1

Transfer the mixture to a separating funnel and add the stopper.

2

Invert the funnel and open the stopcock to release pressure; repeat 15–20 times.

3

If neutralisation is occurring, open the stopcock slowly to avoid losing product.

4

Allow the two layers to separate.

5

Run off the lower layer and collect the organic layer in a clean beaker.

Section 15 of 19Drying organic liquids

1

Drying agents remove traces of water from an organic liquid.

2

They are anhydrous inorganic salts that readily hydrate.

3

Anhydrous calcium chloride is used for hydrocarbons.

4

Anhydrous calcium sulfate or magnesium sulfate are general-purpose drying agents.

1

Add a spatula of drying agent and swirl.

2

Stopper the flask if the product has a low boiling point.

3

If the agent clumps together, water remains, so add more.

4

Stop when some agent stays dispersed as a fine powder and the liquid is clear.

5

Decant or filter off the dry liquid.

Section 16 of 19Safety and evaluation

1

Choose electric heating mantles and water baths rather than Bunsen burners.

2

Hazards include corrosive, irritant, flammable and toxic liquids, so wear gloves and goggles and use a fume cupboard where needed.

3

A typical preparation is: reaction (reflux), separation (distillation or funnel), purification (washing, drying, redistillation) and analysis (boiling point, spectra).

4

Typical sources of loss: product lost in transfers, incomplete reaction and a boiling range wider than expected, which shows impurity.

Section 17 of 19More from the specification

More from the specification

Mass Spectrometry and the Molecular Ion Peak

• In mass spectrometry, vaporized organic molecules are bombarded with high-energy electrons to form a radical cation called the molecular ion (M+);
  • the m/z value of the molecular ion peak directly corresponds to the relative molecular mass of the molecule.

Fragmentation Patterns and Structural Elucidation

• The molecular ion undergoes fragmentation, breaking into smaller positively charged fragment ions and neutral radicals;
  • characteristic fragment peaks at specific m/z values identify particular functional groups and carbon skeleton arrangements.

Isotope Peaks in Mass Spectroscopy

• Small peaks appearing at (M+1)+ arise from the natural abundance of carbon-13 isotopes,
  • (approximately 1.1% of carbon atoms)
• allowing analysts to estimate the number of carbon atoms in an organic molecule.

Mass-to-Charge Ratio (m/z) and Ion Detection

• Mass spectrometers separate particles according to their mass-to-charge ratio (m/z);
• because most fragment ions carry a single positive charge (+1), the measured m/z value directly corresponds to the fragment ion's mass.

Relative abundance

• Percentage of each isotope.

Isotopes

• Atoms of the same element with the same number of protons but different numbers of neutrons.

Molecule

• Two or more atoms held together by covalent bonds.

Fragmentation

• Breaking of the molecular ion into a smaller cation and a radical.

Charge

• Q = It, measured in coulombs.
  What the symbols mean: Q = charge (C) · I = current (A) · t = time (s)

Abundance

• The percentage or proportion of atoms of an element that are a particular isotope.

Compound

• Two or more elements chemically combined in a fixed ratio.

Section 18 of 19Key terms

Term	Meaning
Molecular ion peak	The peak at highest m/z (ignoring M+1), giving the relative molecular mass.
Base peak	The peak of the most abundant ion.
Fragmentation	Breaking of the molecular ion into a smaller cation and a radical.
m/z	The mass-to-charge ratio of an ion.
Wavenumber	The reciprocal of wavelength in cm-1, used to report IR absorptions.
Fingerprint region	The IR region below about 1500 cm−1 that is unique to each compound.
Isotope	Atoms of an element with the same protons but different neutrons.

Term	Meaning
Reflux	Heating with a vertical condenser so that vapour condenses and returns to the flask.
Distillation	Separating liquids by boiling point.
Anti-bumping granules	Small pieces added to promote smooth boiling.
Separating funnel	Apparatus used to separate two immiscible liquids.
Drying agent	An anhydrous salt that removes water from an organic liquid.
Boiling point range	The span of temperatures over which an impure liquid boils.

Section 19 of 19Exam technique

1

Taking the M+1 peak as the molecular ion — the molecular ion is the highest m/z apart from the M+1 peak.

2

Expecting a 3:1 pair for bromine compounds — chlorine gives 3:1 and bromine gives 1:1.

3

Forgetting that only cations are detected — the radical fragment does not appear.

4

Describing the O-H absorption of a carboxylic acid as sharp — it is very broad.

1

Heating a closed system under reflux — the top of the condenser must be open.

2

Using a Bunsen burner for flammable organic liquids — use a heating mantle or water bath.

3

Collecting all the distillate regardless of temperature — collect only within ±2 °C of the boiling point.

4

Adding the drying agent once without checking for clumping — add more until some stays free-flowing.