Organic Chemistry and Instrumental Analysis

Organic Chemistry and Instrumental Analysis is the second unit within the Advanced Higher Chemistry course. It consists of six subtopics; Molecular orbitals, Molecular structure, Stereo chemistry, Synthesis, Experimental determination of structure and Pharmaceutical chemistry.

Molecular orbitals

 * Formation of bonding molecular orbitals.
 * Hybridisation sp3, sp2 hybrid orbitals and their role in the formation of sigma and pi bonds.
 * The symmetry and position of bonding orbitals between atoms determines types of bonding Ionic, polar and non-polar covalent bonding.
 * Absorption of visible light by organic molecules.
 * An explanation of why organic compounds are colourless or coloured with reference to molecular orbital theory including HOMO and LUMO or conjugated systems.
 * Describe a Chromophore and explain its role in the colour exhibited by the compound.

Molecular structure

 * Draw and convert between molecular, structural and skeletal formulae with no more than 10 carbon atoms in their longest chain.

Stereo chemistry

 * Stereoisomerism
 * Geometric isomerism.
 * cis and trans. Physical and chemical properties of geometric isomers
 * Optical isomerism.
 * Non-superimposable mirror image, chiral/enantiomers. Racemic mixture and effect on polarised light.
 * Physical and chemical properties of optical isomers.

Synthesis

 * From given equations identify: substitution, addition, elimination, condensation, hydrolysis, oxidation, reduction reactions.
 * Devise synthetic routes, with no more than three steps, from a given reactant to a final product.
 * Deduce possible reactions from molecular structures.
 * Homolytic and heterolytic fission.
 * Electrophiles and Nucleophiles.
 * Reactions involving heterolytic bond fission. Nucleophiles or electrophiles as attacking groups.
 * Use of double-headed, single-headed and curly arrows to show electron movement.
 * Haloalkanes
 * Classification of monohaloalkanes as primary, secondary or tertiary.
 * Monohaloalkanes undergo nucleophilic substitution reactions:
 * alkalis to form alcohols
 * alcoholic alkoxides to form ethers
 * ethanolic cyanide to form nitriles which can be hydrolysed to carboxylic acids
 * Monohaloalkanes- elimination reactions to form alkenes.
 * The reaction mechanism for SN1 and SN2 reactions and associated factors.
 * SN1 and SN2 reactions using curly arrows and mechanisms with particular attention given to the transition state/intermediate.
 * Alcohols
 * The preparation properties and reactions of alcohols.
 * Preparation from alkenes, haloalkanes and reduction of carbonyl compounds using lithium aluminium hydride.
 * Physical properties related to bonding.
 * Dehydration, reaction with metals, reactions with carboxylic acids and acid chlorides.


 * Ethers
 * Naming and general structure. Boiling point related to bonding. Preparation using haloalkanes with alkoxides. Chemical and physical properties of ethers linked to molecular size and uses.
 * Alkenes
 * Preparation:
 * dehydration of alcohols
 * base-induced elimination of hydrogen halides from monohaloalkanes
 * Electrophilic addition reactions:
 * catalytic addition of hydrogen to form alkanes
 * Including mechanisms for addition of halogens to form dihaloalkanes
 * addition of hydrogen halides according to Markovnikov’s rule, to form monohaloalkanes
 * acid-catalysed addition of water according to Markovnikov’s rule, to form alcohols

Preparation by:
 * Carboxylic acids
 * oxidising primary alcohols and aldehydes
 * hydrolysing nitriles, esters, amides
 * Reactions:
 * formation of salts by reactions with metals or bases
 * condensation reactions with alcohols to form esters in the presence of an acid catalyst
 * reaction with amino groups to form amide links
 * reduction with lithium aluminium hydride to form primary alcohols
 * Amine
 * Classification as primary, secondary or tertiary.
 * Physical properties related to structure.
 * Amines as weak bases and their use in salt formation.
 * Aromatic hydrocarbons
 * Aromatic hydrocarbons and reactions of benzene.
 * Structure, bonding and stability of the benzene ring. Substitution reactions of benzene (phenyl); alkylation, nitration, sulfonation and halogenation as examples of electrophilic substitution in benzene and other aromatic compounds.

Experimental determination of structure

 * Elemental microanalysis
 * Determination of the masses of C, H, O, S and N in a sample of an organic compound in order to determine its empirical formula.
 * Mass spectrometry
 * Interpretation of fragmentation data from mass spectra to gain structural information.
 * Infra-red spectroscopy
 * Interpretation of spectral data from IR to gain structural information.
 * 1H NMR
 * Interpretation of 1H NMR spectra.
 * Interpretation of spectral data to gain structural information.
 * Draw and analyse low resolution proton NMR spectra and to analyse high resolution proton NMR spectra.

Pharmaceutical chemistry

 * Effect of drugs on the body.
 * Classification of drugs as agonists or as antagonists.
 * How drugs work.
 * Identify the types of interaction between drug functional groups and receptor sites.
 * Recognise the active structural fragments in drug molecules which confer pharmacological activity
 * % solution by mass, % solution by volume and ppm, calculations.