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Unit information: Intermediate Organic & Biological Chemistry in 2020/21

Unit name Intermediate Organic & Biological Chemistry
Unit code CHEM20180
Credit points 30
Level of study I/5
Teaching block(s) Teaching Block 4 (weeks 1-24)
Unit director Professor. Crump
Open unit status Not open

CHEM10003, CHEM10900 (or equivalent mathematics unit as approved by the School).



School/department School of Chemistry
Faculty Faculty of Science


This unit develops the introduction to organic chemistry given in CHEM10003 to provide the essential base of organic chemistry required for advanced study at Levels 6 and 7 (Years 3 and 4). It covers the main areas of the subject e.g. the chemistry of carbanions, carbocations, monofunctional and difunctional carbonyl compounds, aromatic, carbocyclic and heterocyclic compounds, amine derivatives and reaction mechanisms and kinetics. This is followed in the second half of the year with modern aspects of synthesis, stereochemistry and molecular conformation and protein/biological chemistry. Workshops are integral to the unit.

Intended learning outcomes

  • Judge the different strengths of a range of bases and be able to recall pKa values of commonly used bases;
  • Illustrate how bases can be used to make anions and enolates and acids can form enols;
  • Be able to draw mechanisms for the reactions of enolates and various carbonyl compounds;
  • Employ enolate chemistry in reactions to yield a given synthetic target;
  • Describe the factors affecting the general stability and reactivity of carbocations and apply these to chemical syntheses and explaining reaction outcomes;
  • Describe what is meant by electrophilic and nucleophilic aromatic substitutions and the factors that influence reactivity; Utilise these principles to devise syntheses of simple substituted aromatic rings. Understand how the properties of aromatic heterocyclic rings are modified by the presence of a heteroatom. Understand a simple synthesis of a heterocyclic aromatic ring.
  • Leading to aliphatic and aromatic amine chemistry. Identify protecting groups for amines and acids and utilise these in organic synthesis;
  • Define resonance, acidity and basicity and identify kinetic vs thermodynamic control of reactions and utilise this to solve synthetic challenges. Identify reversibility in reactions;
  • Be able to explain the ways in which solvents can influence reactions;
  • Be able to determine the order of a reaction from kinetic data and determine features of mechanistic steps from physical chemistry data;
  • An appreciation of selectivity in synthesis including stereoselectivity, regioselectivity and chemoselectivity and use of protecting groups;
  • Identify and employ oxidation/reduction reactions and recognise and use functional group interconversions to design syntheses of organic targets;
  • Understand factors that control molecular conformation/stereochemistry and the influence on chemical reactivity;
  • An appreciation of protein structure and the relationship between structure and function;
  • Understand the basic features of enzyme catalysis and apply this to related examples;
  • To understand the basic steps in solid phase peptide synthesis and how these are applied these to design syntheses of short peptides. Appreciate how to assay protein concentration, secondary structure and mass.

Teaching details

Teaching will be delivered through a blended combination of synchronous and asynchronous sessions. Synchronous sessions include lecture style and interactive delivery and workshops. Workshops will in particular provide opportunity for live interaction with groups of students, feedback on exercises set as independent study and preparation for forthcoming material. There will be associated asynchronous activity involving independent study, problem solving and self-directed exercises. NMR workshops involving a mixture of content delivery, problem solving and discussion will also be delivered synchronously. Synchronous revision sessions as well as drop-in clinics will be offered.

Assessment Details

End-of-TB1 timed, open-book examination (50%) End-of-TB2 timed, open-book examination (50%)

Reading and References

Essential reading will be from the following books:

Organic Chemistry, 2nd Edition, J Clayden, N. Greeves, S Warren, Oxford University Press, 2012.

Further reading from:

Aromatic heterocyclic chemistry, D. T. Davies, Oxford Chemistry Primer 1992; Organic Synthesis, The Disconnection Approach, P. Wyatt and S. Warren, Wiley 2008; Workbook for Organic Synthesis The Disconnection Approach, P. Wyatt and S. Warren, Wiley 2009; Organic Synthesis, C. L. Willis and M. Wills, Oxford Chemistry Primer 1995; How Proteins Work, Williamson, Garland Science; The Molecules of Life, Kuriyan, Konforti and Wemmer, Garland Science.