Thin layer chromatography:
- The stationary phase is the coating on the TLC plate
- The mobile phase is the solvent
- Separation of compounds is by adsorption to the surface of the plate. Using this an Rf value can be calculated:
Distance migrated by the compound / distance of solvent front from starting point.
- The stationary phase is the coating on the inside of the column. In gas-liquid chromatography this is liquid, meaning separation is by soluability and in gas chromatography this is solid, meaning separation is by adsorption
- The mobile phase is the gas
- Retention time= the time between a compound entering and leaving the GC column
- GC can also be connected to mass spectrometer; Gas chromatography separates the compounds and mass spec indentifies them
Structure of Benzene
- Formula C6H6.
In 1865 Kekule suggested that the structure of benzene was a ring of 6 carbons with alternating single and double bonds. Kekule was wrong, the reasons people began to doubt Kekule were:
- All bond lengths between carbons appeared equal
- Benzene will not decolourise bromine water
- The hydrogenation of benzene has a lower enthalpy than would be expected
In fact, benzene is a 6 carbon ring, but each carbon is only making 3 bonds.
- Each carbon in benzene makes 3 sigma bonds: 1 X C-H and 2 X C-C
- Sideways overlap of p-orbitals on adjacent carbons results in electron density above and below the ring; this is known as the pi system
- The 6 pi electrons in benzene are all delocalised around the ring
- These pi electrons are therefore evenly distributed between all the carbon atoms
- All bons lengths between carbons are equal
Relative Reactivity of Benzene
Cyclohexene > phenol > benzene
- The most reactive because its 2 pi electrons are localised between 2 carbon atoms
- Therefore there is sufficient electron density to induce a dipole in a halogen
- Less reactive than cyclohexene but more reactive than benzene
- 1 lone pair from the oxygen atom is delocalised into the pi system
- This creates sufficient electron density to induce a dipole in a halogen
- Bromination of phenol causes a white precipitate of 2,4,6-tribromophenol to form
- The least reactive because its 6 pi electrons are delocalised across all carbons
- Therefore there is insufficient electron density to induce a dipole in a halogen. A halogen carrier is needed.
Carbonyl compounds contain a C=O, this does not include carboxylic acids, but mainly aldehydes and ketones.
- 2,4-DNPH tests for aldehydes and ketones
- A positive result is an orange precipitate
- To find out the exact compound that is present the orange precipitate must be recrystallised. The melting point of the compound can then be found and compared to a databank of values
- Tollen's (ammonical silver nitrate) tests for aldehydes
- The suspected aldehyde should be heated with Tollen's, positive result is a silver mirror
- Tollen's is a weak oxidising agent and works like so:
Aldehyde + 2Ag+ + H2O = Carboxylic acid + 2Ag + 2H+
Aldehydes and ketones can also be reduced back to primary or secondary alcohols, sodium tetrahydrioborate (NaBH4) is the reducing agent for this reaction and releases hydride (H-) ions.
Aldehyde + 2[H] = primary alcohol
Carboxylic acids dissolve in water as they can hydrogen bond. They are also weak acids and so partially dissociate in solution:
CH3COOH -------- CH3COO- + H+
Carboxylic acids are also able to undergo acid-base reactions and will react with alkali metals, hydroxides and carbonates:
- Reacted with an alkali metal- carboxylate salt and hydrogen formed
- Reacted with a hydroxide- carboxylate salt and water formed
- Reacted with a carbonate- carboxylate salt, carbon dioxide and water formed
Carboxylic acids also form esters when reacted with alcohols in the presence of concentrated sulfuric acid. However, acid anhydrides instead of carboxylic acids can be used; this method not only gives a better yield but can be carried out without the need for a catalyst:
(CH3CO)2O + C3H7OH = CH3COOC3H7 + CH3COOH
Amines are closely related to ammonia, they act as bases and can accept protons via the lone pair on the nitrogen atom to form a dative colvalent bond. There are two types of amines, aromatic and aliphatic. Aromatic amines have their amine group attatched directly to a benzene ring.
- Aliphatic amines can be synthesised by reacting a halogenoalkane with an excess of ethanoilc ammonia NH3 (EtOH). This is a nucleophilic substitution reaction.
CH3CH2Cl + NH3 (EtOH) = CH3CH2NH2 + HCl
- Aromatic amines can be synthesised by reduction of nitrobenzene, tin and concentrated hydrochloric acid are catalysts for this reaction
C6H5NO2 + 6[H] = C6H5NH2 + 2H2O
Aromatic amines can then be used to form an azo dye. Firstly the amine must be reacted with nitrous acid (HNO2) and HCl. This gives the diazonium ion with the distinctive N triple bond N.
Nitrous acid is very unstable, therefore it must be made in situ and the reaction mixture must be kept below 10 degrees:
NaNO2 + HCl = HNO2 + NaCl
The diazonium ion can then be coupled with a phenol in alkaline conditions to form the azo dye.
Alpha amino acids have the general formula RCH(NH2)COOH. They have both the amine group and the carboxylic acid group attatched to the same carbon.
- Amino acids can form internal salts called zwitterions these only form at a particular pH called the isoelectric point, which is different for every amino acid
- The zwitterion sees a a proton accepted via the lone pair on the nitrogen and a proton lost on the OH part of the carboxylic acid. This gives the zwitterion no overall charge
- At alkaline pH proton concentration is low, everything that can be deprotonated on the amino acid is, including side chains
- At acid pH proton concentration is high, therefore everything that can be protonated is.
- These rules determine the isoelectric point of each amino acid
All but one of the amino acids show optical isomerism.
- Optical isomerism occurs if the molecule has a chiral centre. A chiral carbon is a carbon with 4 different groups attatched to it
- Optical isomers form non-superimposable mirror images of each other
- This is a type of sterioisomerism, so the isomers have the same structural formula but a different arrangement in space.
Chirality in pharmaceuticals
Chirality is a big problem in the pharmaceutical industry because:
- One isomer may be biologically inactive, meaning that you must administer double the dose
- One isomer may have harmful side effects, which may mean that the optical isomers have to be separated; a complicated and costly process
Fortunately, there are some ways round this:
- You could use a naturally occuring enzyme to help synthesise the drug if there is one; enzymes only synthesise a single isomer of a compound
- You could use chiral pool synthesis. Which involves using an optically pure starting material
- As a last resort the optical isomers can be separated by chromatography, but it is difficult to separate isomers that are chemically and physically very similar. This is also extremely expensive.