Molecular Interactions and Catalysis

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 a solid knowledge of the theoretical bases of catalysis.
  • Provide an understanding of the importance of non-covalent interactions in chemical and biological systems, and describe some applications in modern chemical research.
  • 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.



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

 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

Molecular Machines (G. De Bo, 8 lectures)

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




Knowledge and understanding

 Students should be able to:

  • 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.
  • Understand non covalent interactions and their importance in chemical and biological systems.
  • Understand how to design and synthesize rudimentary artificial molecular machines, including appreciating the principles governing their operation.

Intellectual skills

Students should be able to:.

  • 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.
  • Describe the different types of non covalent interactions.
  • Describe how knowledge of fundamental interactions can be explained in medical chemistry and biocatalysis
  • Design and outline synthetic stratergies to various types of artificial molecular switches, motors and other machines.

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

  • Bures J.* Topics in Catalysis 2017, 60, 631-633
  • J.J Murdoch J.  Chem.Ed. 1981, 32
  • D.G Blackmond Angew. Chem. Int..Ed, 2005, 4302
  • Bures, J.* Agnew.  Chem.Int. Ed. 2016, 55, 2028-2031.
  • Bures. J,* Agnew.  Chem.Int. Ed. 2016, 55, 16084 - 16087.
  • P. Mendes, S. Hoops, S. Sahle, R. Gauges, J. Dada and U. Kummer, Methods in Molecular Biology, Systems Biology, 2009, 17
  • Molecular recognition in chemical and biological systems.  E Persch, O. Dumele and F.Diederich, Agnew. Chem. Int. Ed, 54, 3290-3327 (2015)
  • Design of protein catalysts, D Hilvert, Annu. Rev. Biochem, 82, 447 - 470 (2013)
  • 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).
  • Bruns, C.J,.  Stoddart, J.F. The Nature of the Mechanical Bond.  John Wiley & Sons, Inc: Hoboken, NJ, USA, 2016. Print ISBN: 9781119044000, Online IBSN: 9781119044123, DOI: 10.1002/978119044123 

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

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