Molecular Interactions in Organic Chemistry

Unit code: CHEM40422
Credit Rating: 10
Unit level: Level 4
Teaching period(s): Semester 2
Offered by School of Chemistry
Available as a free choice unit?: N




 The course unit aims to:

  • Provide an understanding of the principles and theory behind making and operating machines at the molecular level. The mechanisms behind biological molecular machines serve as inspiration for the design of synthetic systems.
  • Provide an understanding of the importance of non-covalent interactions in chemical and biological systems, and describe some applications in modern chemical research.
  • Provide a solid knowledge of the theoretical bases of catalysis.




Molecular Machines (D. Leigh/G. De Bo, 8 lectures)

  • Principles governing the operation of molecular machines.
  • Design and synthesis of molecular switches, motors and other machines.
  • Chemical topology

Molecular Interactions of Proteins with Small Molecules Chemistry (A. Green, 8 lectures)

  • Types of non-covalent interactions
  • Optimization of small molecule ligands for protein receptors
  • Directed evolution to optimize enzymes for non-natural reactions

Kinetics in Catalysis (J. Bures, 8 lectures)

  • Basic Concepts of Chemical Kinetics.
  • Basic Concepts of Catalysis
  • Rate Laws for Catalytic Cycles
  • Reaction Progress Kinetic Analysis
  • Modelling of catalytic reaction kinetics



Knowledge and understanding

 Students should be able to:

  • Understand how to design and synthesize rudimentary artificial molecular machines, including appreciating the principles governing their operation.
  • Understand non-covalent interactions and their importance in chemical and biological systems.
  • Understand kinetic concepts in catalysis, and how to use these to obtain mechanistic information, and to gain insights into recent catalytic reactions of both academic and industrial importance.

Intellectual skills

Students should be able to:

  • Design and outline synthetic strategies to various types of artificial molecular switches, motors and other machines.
  • Describe the different types of non-covalent interactions.
  • Describe how knowledge of fundamental interactions can be exploited in medicinal chemistry and biocatalysis.
  • Derive rate laws for catalytic cycles.
  • Design experiments and analyse the results in order to extract mechanistic information of catalytic reactions using the reaction progress kinetic analysis.
  • Use kinetic simulation software to visualize the effects that different parameters have in complex catalytic systems.

Transferable skills and personal qualities

Students will be able to:

  • Participate in related research projects and have discussions with researchers in the field.

Assessment methods

  • Written exam - 100%

Recommended reading

  • Organic Chemistry J Clayden, N Greeves, S Warren and P Wothers (Oxford University Press, 2001) ISBN 0198503466
  • Synthetic Molecular Motors and Mechanical Machines, E. R. Kay, D. A. Leigh and F. Zerbetto, Angew. Chem. Int. Ed., 46, 72-191 (2007).
  • Molecular recognition in chemical and biological systems, E. Persch, O. Dumele and F. Diederich, Angew. Chem. Int. Ed., 54, 3290-3327 (2015).
  • Design of protein catalysts, D. Hilvert, Annu. Rev. Biochem., 82, 447-470 (2013).

Feedback methods

 Students are expected to work through problems issued during the lectures (and available on Blackboard). Answers will be disscussed in lectures and questions answered. Model answers will be placed on BlackBoard.

Study hours

  • Assessment written exam - 2 hours
  • Lectures - 24 hours
  • Independent study hours - 74 hours

Teaching staff

Anthony Green - Unit coordinator

▲ Up to the top