Syllabus for CHEM1908 (Chemistry 1 Life Sciences A)

The order of topics presented here is essentially the order of presentation in the lecture course, although individual lecturers may make some variations from this. Some topics span more than one week.

Week

Topics covered

Assumed Knowledge and Revision Material

- basic mathematical skills

- components of matter: atoms, molecules and ions

- stoichiometry

- gases

- reactions in aqueous solution: precipitation and acid/base reactions including solubility rules

Prologue

- admin. matters

- overview of course

Atomic Structure

- electromagnetic radiation and the nature of matter

- atomic spectrum of hydrogen

- Bohr theory of the hydrogen atom

- wave mechanics

- atomic orbitals and quantum numbers

- electrons in atoms

The Periodic Table

- metals and non-metals

- electron configuration

- d-Block elements

- trends in the periodic table

- elements essential to sustain life

- elements known to destroy life

- elements that have therapeutic value

Chemical Bonding

- ionic and covalent bonds

- Lewis structures and the octet rule

- multiple bonds and resonance structures

The Shapes of Molecules

- VSEPR theory of organic compounds

- hybridisation of organic compounds

- electronegativity, bond polarity and dipole moments

Intermolecular forces

- dipole forces

- hydrogen bonds

- dispersion (London) forces

Acids and Bases

- the nature of the hydrated proton

- the Brønsted Lowry theory of acids and bases

- the dissociation of water and the pH scale

- strong, weak and polyprotic acids and strong and weak bases and salts

- relation between K_a and K_b, conjugate pairs

Introduction to Organic Chemistry

- definition: the chemistry of carbon compounds

- importance of carbon

- hybridisation of C, O, and N

- formal charge

- writing structural formulas, abbreviated structural formulas, use of stick notation

- functional groups

Alkanes

- nomenclature

- s-bonds and structure

- conformational and constitutional isomers

Alkenes

- nomenclature

- p-bonds and structure

- configurational isomers

- addition reactions, mechanism of electrophilic addition

Alkenes (continued)

- classification of nucleophiles and electrophiles

- Markovnikov's rule: carbocation stability

- reaction summary (addition reactions, orientation of addition and carbocation stability)

Aromatic Hydrocarbons

- benzene: aromaticity, resonance and molecular orbital picture

- nomenclature

- toxicity of benzene and aromatic compounds

Heterocyclic Compounds

- pyridine, pyrrole, furan, thiophene, imidazole

- purine, pyrimidine

- relevance to DNA

Organic Halogen Compounds

- alkyl halides: classification as 1°, 2°, 3°

- nomenclature

- nucleophilic substitution reactions of 1° and 2°

- reaction summary

Alcohols, Phenols, Ethers and Thiols

- alcohols: classification as 1°, 2°, 3°

- nomenclature

- hydrogen bonding

- acid-base reactions of alcohols and phenols

- reactions of alcohols: dehydration, oxidation, substitution

- physiological importance; alcohol poisoning

- phenols: acidity and aromatic electrophilic substitution

- thiols: acidity and oxidation to disulfides

- NADH/NAD⁺ cycle and thiol disulfide redox cycle

- biologically important thiols and disulfides

Amines

- amines: classification as 1°, 2°, 3°, 4° and aryl amines (aniline)

- nomenclature

- basicity and alkylation of 3° amines

- conversion to amides

- examples of biologically active amines

Aldehydes and Ketones

- nomenclature

- nucleophilic addition reactions, formation of hemiacetals and acetals

- oxidation and reduction and NADH/NAD⁺

- tautomerism

Spectroscopy

- mass spectrometry

- infrared spectroscopy

- UV-visible spectroscopy

Spectroscopy (continued)

- ¹H NMR spectroscopy

- MRI and medical applications

Carboxylic Acids and Derivatives

- nomenclature

- acidity

- acid derivatives: acid chlorides, esters, thioesters, amides

- relative reactivities, preparation and hydrolysis

- b-keto acids and decarboxylation

- fats, waxes and oils

Stereochemistry

- constitutional isomers and stereoisomers (enantiomers and diastereomers)

- stereogenic centres

- optical activity

- (R), (S) nomenclature and D, L nomenclature

- racemic mixtures and resolution of enantiomers

- compounds with 2 stereogenic centres including meso isomers

- importance of chirality in nature and drug design

Carbohydrates

- monosaccharides: nomenclature and stereochemistry

- Haworth projections, open and closed chain forms

- reactions of monosaccharides

- reducing and non-reducing sugars, mutarotation

- disaccharides and polysaccharides: classification and hydrolysis

Amino Acids, Peptides and Proteins

- structure and classification of amino acids, stereochemistry

- acid base chemistry

- formation and hydrolysis of peptides

- protein structure overview

DNA and Nucleic Acids

- tautomerism in heterocycles

- DNA bases

- nucleosides, nucleotides, ATP, ADP, AMP

- DNA structure

Summary of Classes of Reactions

- acid-base reactions

- addition reactions: electrophilic and nucleophilic elimination

- substitution reactions: electrophilic and nucleophilic

- redox reactions: oxidation and reduction

Examples of Synthetic Transformations