What's In A Medicine?

6.5 Mass Spectrometry cont.

The heaviest ion in a mass spectrum is the molecular ion, X+. Other ions result from fragmentation- the breakdown of X+ into positively charged, smaller ions
The most abundant ion gives the strongest detector signal, which is set to 100% in the spectrum. This is the base peak and the intensities of all the other peaks are expressed as a % of its value
For each fragmentation, one of the products keeps the positive charge, which means there are always two possibilities
Some elements have more than one naturally occurring stable isotope, which can explain why there can be several peaks in a narrow range

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Chromatography is an analytical technique for separating and identifying the components of a mixture
There are two phases- the stationary phase (which stands still) and the mobile phase (which moves over the stationary phase). Different compounds distribute themselves between the two phases differently, and so move along the mobile phase at different speeds
Thin layer chromatography (Tlc)- A sample of a mixture is dotted onto a solid support material- the stationary phase. A suitable solvent rises up the plate- the mobile phase
The developed plate will show a series of spots. Ninhydrin is the locating agent for amino acids, and uv light and iodine locate other substances
The distance a substance travels depends on the nature of the substance, the total distance travelled by the solvent front and the conditions. The Rf value for a substance is the distance the substance travels relative to the solvent
A substance with a greater affinity to the mobile phase will be moved further, and a substance with a greater affinity to the stationary phase will not be moved as far

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Acids have the ability to transfer H+ ions to something else. A base accepts these H+ ions. The reaction where an acid donates H+ ions to a base is an acid-base reaction.
The Bronsted-Lowry theory- an acid is a H+ (proton) donor and a base is a H+ (proton) acceptor
The oxonium ion (H3O-) is present in every acidic solution. The formula is often shortened to H+
An alkali is a base that dissolves in water to produce hydroxide, OH-, ions
Once it has donated an H+ ion, the acid may take it back. CH3COOH -> CH3COO- + H+. But when a strong acid is added CH3COO- + H+ -> CH3COOH
The ethanoate ion is behaving as a base- the conjugate base of ethanoic acid. Every acid has a conjugate base and every base has a conjugate acid. They are called a conjugate acid-base pair.
Substances which can be acids or bases are described as amphoteric.
Strong acids are powerful H+ donors, and have weak conjugate bases
Strong alkalis will have weak conjugate acids

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Carboxylic acids contain the carboxyl group. Acids can be represented by the general formula R-COOH.
The names of carboxylic acids end in -oic acid. When two carboxyl groups are present, the ending -dioic acid is used
The -OH in the carboxylic acid can be replaced by other groups to give a range of carboxylic acid derivatives.

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The hydroxyl group, -OH, can be attached to an alkane chain in alcohols, to a benzene ring in phenols or as part of a carboxyl group in carboxylic acids.
Reaction with water- R-OH + H2O -> R-O- + H3O+. Water behaves as a weak acid.
The order of acid strength is ethanol < water < phenol < carboxylic acid. It is the stability of the R-O- ion which determines how strong the acid is eg. where the position of equilibrium lies. If the negative charge can be shared with other atoms, then the R-O- is more stable
In the phenols and carboxylic acids, the electric charge gets spread out by delocalisation. They are strong enough to react with bases to form salts
Phenol will form a purple complex with Fe3+ ions in neutral solution. Iron (III) chloride is a test for phenol groups
Alcohols react with carboxylic acids to form esters. Needs to be heated with concentrated sulphuric/hydrochloric acid. The reaction is reversible
Esters can be made from phenols by reacting them with an acyl chloride or acid anhydride.

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Esters are formed when carboxylic acids and alcohols react. The ester link is formed by the condensation of the hydroxyl group in the alcohol and the carboxyl group in the acid- this process is esterification.
The reaction is reversible and will come to equilibrium. To improve ester yield, alcohol is added to drive the equilibrium to the right. The reverse reaction is ester hydrolysis.
-thyl from the alcohol, then -oate from the carboxylic acid
Polyesters are condensation polymers made from reacting a diol with a dicarboxylic acid
The -OH group in phenol is less reactive to esterification. When ethanoic acid is involved the process is ethanoylation, and ethanoic anhydride is a more vigorous ethanoylating agent, and ethanoyl chloride is even better
Ethanoic anhydride and ethanoyl chloride are acylating agents.
The reverse of esterification is hydrolysis. A dilute sulphuric acid can be used as a catalyst. An alkali such as sodium hydroxide is also a catalyst, but produces a carboxylate salt instead of a carboxylic acid

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Aldehydes and ketones both have the carbonyl group.
Aldehydes are named using the suffix -al. Ketones are named using the suffix -one, and ketones with five or more carbons have structural isomers.
Aldehydes and ketones can be produced by oxidising an alcohol through heating with acidified potassium dichromate (VI). The orange dichromate (VI) ion, Cr2O7-, is reduced to green Cr3+.
Oxidation of alcohols and aldehydes are redox reactions
The hydrogen atom attached to the carbonyl group means that aldehydes are easily oxidised to carboxylic acids by weak oxidising agents (eg. Cu2+ in Fehlings solution). Ketones are not oxidised by Fehling's or potassium dichromate
A powerful reducing agent (a complex metal hydride called NaBH4) is needed to reduce aldehydes to primary alcohols, and ketones to secondary alcohols
The carbonyl groups in both aldehydes and ketones undergo addition reactions. Hydrogen cyanide (HCN), in the presence of an alkali, adds across the C=O bond to form 2-hydroxynitriles
The cyanide ion is a nucleophile and is attracted to the C atom in the carbonyl with is partially +ve. A new C-C bond forms and a pair of e- in the C=O bond moves onto the new O atom, which has a -ve charge. It then takes up H+ from the water solvent

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