2024/25 Undergraduate Module Catalogue

CHEM2221 Organic Chemistry: Introduction to Pericyclic, Heterocyclic and Bioorganic Chemistry

10 creditsClass Size: 200

Module manager: Prof Paul Taylor
Email: p.c.taylor@leeds.ac.uk

Taught: Semester 2 (Jan to Jun) View Timetable

Year running 2024/25

Pre-requisite qualifications

Level 1 Chemistry or equivalent

Co-requisites

CHEM2121

Organic Chemistry: Conformation, Configuration & Reactivity

Module replaces

CHEM2241 Organic Structure and Mechanism

This module is not approved as a discovery module

Module summary

This module will introduce how the molecular orbitals govern the shape, structure and reactivity of molecules. It will introduce a new class of reactions, pericyclic reactions and describe how these can be understood in terms of the interaction of molecular orbitals. The module will then explore the fundamental physical basis for molecular interactions involving these species, the chemical basis for catalysis and how the electronic structure of the molecules is responsible for their characteristic behaviour. The second half of the module will then describe the principles of how introduction of heteroatoms (atoms other than C and H) to molecules changes their properties and reactivity. The final part of the module will build on this knowledge to cover the key roles that heterocyclic molecules have in biological systems including in DNA, enzymes and coenzymes.

Objectives

- To understand the basis for pericyclic reactions and their use in synthetic transformations; 
- To understand key principles in aromatic heterocyclic chemistry; 
- Knowledge of key reactions in organic chemistry including the Diels-Alder reaction, 1,3-dipolar cycloadditions and reactions involving heterocycles; 
- To introduce major concepts in physical organic chemistry relevant to laboratory and biological settings including principles of enzymatic catalysis; 
- To understand the structure of key biological polymers including peptides, oligonucleotides and oligosaccharides and the major classes of natural products.

Learning outcomes
Students will be able to: 
1. Draw mechanisms for pericyclic reactions; 
2. Rationalise the stereochemical and/or regiochemical outcome of reactions by considering the overlap of relevant orbitals and steric demands; 
3. Describe the bonding in aromatic heterocycles and understand and predict the change of reactivity in aromatic heterocycles as a result of introducing heteroatoms to the ring system; 
4. Describe the microscopic basis for specific intermolecular interactions in solution; 
5. Describe the structure of key biologically-derived materials including peptides, oligonucleotides, oligosaccharides and lipids; 
6. Understand the chemical basis for catalysis by enzymes and small molecules in buffered solutions; 
7. Understand the structural basis for reactivity of common synthetically-useful coenzymes and their application in biochemistry and synthesis.

Skills outcomes
Students will gain skills in: rationalising and predicting reaction outcomes for pericyclic reactions by consideration of orbital symmetry, identification of heterocyclic molecules and prediction of their reactivity; identifying elements in molecules leading to favourable intermolecular interactions; identifying experimental conditions to probe the mechanisms of organic chemical reactions; identifying the properties of different biomolecules.

Syllabus

PERICYCLIC CHEMISTRY (lectures 1-5): 
- The Diels-Alder reaction. Stereospecificity: retention of diene and dienophile geometry. Stereoselectivity: the endo rule. Predicting the stereochemical outcome of Diels-Alder reactions. The ortho/para rule to predict regiochemistry. Ozonolysis; use to make carbonyl compounds from alkenes. Other 1,3-dipolar cycloadditions, eg SPAAC. Sigmatropic rearrangements e.g. Claisen, Cope. 

PHYSICAL ORGANIC CHEMISTRY (lectures 6-9):
- Hydrogen bonding, electrostatic interactions (including pi-pi and cation-pi interaction), van der Waals interaction and the hydrophobic effect, energy profile diagrams and different types of catalysis.

HETEROCYCLIC CHEMISTRY (lectures 10-12):
- Introduction to heterocyclic chem: structure and bonding (azoles vs azines), reactivity in SEAr and SNAr – halopyridines and pyridones. Introduction to classes of Examples of heterocyclic compounds in key biomolecules e.g. nucleic acids and nucleotide cofactors. 
 
BIOLOGICAL CHEMISTRY (lectures 13-18): 
- Revision of structure of major classes of biomolecules including proteins and nucleic acids. Introduction/revision to intermolecular interactions relevant to biological and supramolecular chemistry.
- Introduction to the structure and chemistry of sugars and lipids. Anomeric effect. General and specific acid base catalysis. Nucleophilic catalysis. Role of key enzymes in biological catalysis exemplified by proteases and glycosidases. 
- Introduction to classes of enzymes and coenzymes (exemplified by coenzyme A, pyridoxal and nicotinamide cofactors), role in catalysis and stereoelectronic basis for action. Use of enzymes in synthesis. Introduction to the use of whole organisms for catalysis.

Teaching methods

Delivery type	Number	Length hours	Student hours
Examples Class	8	1.00	8.00
Lecture	14	1.00	14.00
Seminar	2	1.00	2.00
Independent online learning hours			15.00
Private study hours			61.00
Total Contact hours			24.00
Total hours (100hr per 10 credits)			100.00

Private study

76h (including 15h online study - quizzes, note-taking, additional reading)

Opportunities for Formative Feedback

Regular examples classes for which worked solutions will be available.
Two tutorials where written feedback will be available on students’ work.

Methods of assessment

Exams

Exam type	Exam duration	% of formal assessment
Open Book exam	2 hr	100.00
Total percentage (Assessment Exams)		100.00

Normally resits will be assessed by the same methodology as the first attempt, unless otherwise stated

Reading list

The reading list is available from the Library website

Last updated: 18/07/2024

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