Structure and reactivity of organic molecules

Unit code: CHEM20412
Credit Rating: 10
Unit level: Level 2
Teaching period(s): Semester 2
Offered by School of Chemistry
Available as a free choice unit?: N




 To extend the concepts presented in previous courses to the structural, mechanistic, physical and biological properties of organic molecules.


 Weeks 1-4: Structure and Mechanism (Dr Nathan Owston)

  • Rates and barriers in organic reactions - bond rotation, kinetics and NMR
  • Rings and stereoelectronics: ring formation and ring stability, kinetic and thermodynamic considerations.  Thorpe-Ingold effect and Baldwin's rules.
  • Neighbouring group participation 
  • Carbocation rearrangements, migration and fragmentation.

Weeks 5-8 Introduction to Primary Metabolites (Dr Jenny Slaughter)

  • Monosaccharides: Stereochemistry and hemiacetals, cyclic structures, anomeric centre, mutarotation, glysosylation. Reactions of alcohols: synthesis and protecting groups.
  • Disaccharides & oligosaccharides: Glycosylation, position of glycosyl linkage and strategies for synthesis
  • α-Amino acids: Structure and stereochemistry (enantiomers,  diastereoisomers). Reactivity-  zwitterionic behaviour, pKa, isoelectric point, side chains.
  • Peptides & oligopeptides: structure and nomenclature, peptide synthesis (multi-step), protecting groups.
  • Analysis of polypeptides: composition and sequence analysis, secondary structure.

Weeks 9-12: Retrosynthetic Analysis (Dr Andrew Regan)

  • Retrosynthetic analysis of compounds containing one functional group:
  • Disconnections of alcohols and α-alkylated carbonyl compounds. Control of enolate reactions.
  • Retrosynthetic analysis of compounds containing two functional groups
  • Disconnections of 1,2- 1,3- 1,4- 1,5- and 1,6-difunctional compounds. Disconnections of difunctional compounds in rings: intramolecular cyclisation reactions
  • Functional group interconversions

Learning outcomes

Students successfully completing this unit should have developed the ability to:

  • Apply knowledge of structure and bonding to the kinetics associated with bond rotation and their consequences for spectroscopy and mechanism.
  • Describe  organic reaction mechanisms taking into account stereoelectroniceffects.
  • Predict whether organic reactions will occur through consideration of stereoelectronic effects, basic kinetics and thermodynamics.
  • Evaluate and propose strategies for the synthesis of cyclic organic molecules based on consideration of stereoelectronic effects, basic kinetics and thermodynamics.
  • Apply the concepts of reactivity, stereochemistry and stereoelectronics to evaluate the nature of carbohydrates.
  • Use knowledge of the nature of amino acids, protecting group stratergies and solid phase synthesis. carbohydrates and protecting group strategies to evaluate the outcomes of reactions and construct synthetic routes to oligosaccharides.
  • Apply the concepts of reactivity, stereochemistry and stereoelectronics to evaluate the nature of amino acids and select methods appropriate for their synthesis.
  • Use knowledge of the nature of amino acids, protecting group strategies and solid phase synthesis to generate synthetic strategies for the synthesis of oligopeptides.
  • Use knowledge of oligopepetide analysis, for sequencing and composition, to evaluate the primary (and secondary) structure of oligopeptides.
  • Choose appropriate disconnections for difunctional target molecules, based on stabilities of the synthons generated
  • Analyse the relationships between functional groups in difunctional compounds
  • Choose appropriate synthetic equivalents for synthons resulting from retrosynthetic analysis
  • Choose appropriate reagents for the reactions involved in planned syntheses
  • Decide whether any extra methods of control are required for a synthesis to proceed as planned


Transferable skills and personal qualities

  • Problem-solving skills: Manipulation of chemical structures and using multiple models, e.g. 2D into 3D and vice versa. Determination of reaction mechanisms and rationalizing reaction selectivity by consideration of steric and electronic factors. Evaluating synthetic routes and choosing and proposing syntheses and retrosyntheses using a logical, analytical approach.
  • Numeracy and mathematical skills:(e.g.determination of mole fraction from polarimetry & graphical information)
  • Analytical skills (e.g. spectroscopy and link to mechanism, analysis of chromatographic evidence for peptide composition)
  • Communications skills (written and oral communication using chemical terminology and technical vocabulary)

Assessment methods

  • Written exam - 100%

Recommended reading

  • J. Clayden, N. Greeves, and S. Warren, Organic Chemistry, 2nd edition (Oxford University Press, 2012), ISBN 978-0199270-29-3.
  • S. Doonan, Peptides and Proteins, RSC Tutorial Chemistry Texts (RSC, Cambridge, 2002), ISBN 0-85404-692-5
  • S. Warren, Organic Synthesis: the Disconnection Approach, Wiley, 2nd edition, 2008; classmark 545.9/W55). The first edition is also useful: (1982); classmark 545.9/W8. Workbook at 545.9/W5 (also available as an online e-book).
  • S. Warren, Designing organic syntheses : a programmed introduction to the synthon approach, Wiley, (1978) (classmark: 545.9/W9) (9 copies)

The following Oxford University Press Chemistry Primers are recommended, and are freely available to students as e-books via the University Library catalogue and Bibliotech:

  • A. J. Kirby, Stereoelectronic Effects, 1996.
  • B. G. Davis & A. G. Fairbanks, Carbohydrate Chemistry, 2002.
  • C. M. Dobson, J. A. Gerrard & A. J. Pratt, Foundations of Chemical Biology, 2001
  • J. Jones, Amino Acid & Peptide Synthesis, 2002.
  • C. L. Willis and M. Wills, Organic Synthesis, 1991.
  • R. S. Ward, Bifunctional Compounds, 1994.
  • J. Jones, Core Carbonyl Chemistry 1997.

A set of molecular models is also highly recommended.

Feedback methods

  • Answers and written feedback for tutorials and workshops
  • Worked solutions to unseen and seen problems.
  • Online support materials including test exercises (formative assessments) that allow students to engage in problem-solving activities, with the provision of answers and feedback

Study hours

  • Assessment written exam - 2 hours
  • Lectures - 24 hours
  • Tutorials - 3 hours
  • Independent study hours - 71 hours

Teaching staff

Andrew Regan - Unit coordinator

Jennifer Slaughter - Unit coordinator

Nathan Owston - Unit coordinator

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