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Structure and Reactivity of Organic Compounds II

Module titleStructure and Reactivity of Organic Compounds II
Module codeBIO2085
Academic year2024/5
Module staff

Dr Mark Wood (Convenor)

Duration: Term123
Duration: Weeks


Number students taking module (anticipated)


Description - summary of the module content

Module description

A vital aim of organic chemistry is to be able to synthesise biologically active molecules. With this in mind, you will explore some of the most important organic reactions used in research laboratories. These reactions, along with those introduced in earlier modules, are then studied in the laboratory. Having been introduced to modern spectroscopic methods for determining the structures of organic molecules, these techniques are then used to identify the compounds which have been prepared in the laboratory. Aromatic compounds are central to the structure of a vast number of important organic molecules and the chemistry of these species will also be studied.

This module builds on your knowledge of the basic principles of organic (and inorganic and physical) chemistry (including practical) learned in the first year. In particular, it is assumed that you will have a thorough working knowledge of the basic principles of structural representation, mechanism, reactivity, functional group chemistry and stereochemistry.

Module aims - intentions of the module

This module aims to show you how chemists determine and confirm the structures of organic compounds spectroscopically and to describe a number of key, basic reactions, particularly of molecules that contain carbonyl groups and aromatic compounds. Each part of the module is designed to reinforce and build on earlier material, thereby giving you a sound understanding of the fundamentals of modern organic chemistry.

Intended Learning Outcomes (ILOs)

ILO: Module-specific skills

On successfully completing the module you will be able to...

  • 1. Recall the large variety of carbonyl-containing functional groups and understand their basic reactivity
  • 2. Describe (and estimate) the acidity of ?-hydrogen atoms in the common carbonyl group-containing compounds
  • 3. Discuss the formation of enols and enolates from carbonyl compounds
  • 4. Illustrate the basic reactions of enols and enolates, including their use in C-C bond formation
  • 5. Describe in some detail and use basic spectroscopic techniques (ultraviolet, infrared and NMR [1H and 13C] spectroscopies and mass spectrometry)
  • 6. Explain the synthesis and reactivity of benzenoid aromatic compounds (including substituted derivatives)
  • 7. Explain the synthesis and reactivity of 5 and 6-membered ring aromatic heterocyclic compounds
  • 8. Understand how basic practical techniques and spectroscopic methods are used in the laboratory in the preparation of organic molecules

ILO: Discipline-specific skills

On successfully completing the module you will be able to...

  • 9. Describe and evaluate approaches to our understanding of organic chemistry with reference to primary literature, reviews and research articles
  • 10. Describe in some detail essential facts and theory across a subdiscipline of the chemical and biosciences
  • 11. Identify critical questions from the literature and synthesise research-informed examples from the literature into written work
  • 12. With some guidance, deploy established techniques of analysis, practical investigation and enquiry within the chemical and biosciences

ILO: Personal and key skills

On successfully completing the module you will be able to...

  • 13. Communicate ideas, principles and theories fluently by written means in a manner appropriate to the intended audience
  • 14. Develop, with some guidance, a logical and reasoned argument with valid conclusions
  • 15. Collect and interpret appropriate data, drawing on a range of sources, with limited guidance

Syllabus plan

Syllabus plan

Section 1 – The first part of the module will examine the influence that the carbonyl group has on other positions in a molecule and in particular, the -carbon. The concept of a-hydrogen acidity will be introduced and illustrated using the pKa values of commonly encountered molecules that contain carbonyl groups. An emphasis will be placed on how this acidity is affected by electronic effects. The generation of enols and enolates will be explained and their use in a wide range of reactions will be explained. These reactions will include, a-hydrogen exchange, racemisation, -halogenation and C-C bond formation. The latter category of reaction will include the common acid and base-catalysed condensation reactions.

Section 2 – Concurrently with part 1 (above), this module will cover the principles behind the spectroscopic techniques which are commonly used in the study and determination of the structure of organic molecules, namely ultraviolet, infrared and NMR (1H and 13C) spectroscopy and mass spectrometry.

Section 3 – The structure and reactivity of benzenoid aromatic compounds will be covered after introduction of the general concept of aromaticity. This section of the module will focus mainly on electrophilic substitution but will also examine the special cases of nucleophilic substitution within these systems. Regiochemical issues associated with the use of substituted benzene derivatives will also be explained.

Section 4 – After introducing the key, basic molecules, the synthesis and reactions of 5 and 6-membered ring heterocyclic systems will be compared and contrasted with the benzene derivatives.

Section 5 – The basic practical techniques learned in the first year will be used to synthesise a range of organic molecules. The reactions used will draw on the chemistry covered in sections 1, 3 and 4 (above) and the experiments will use the spectroscopic techniques covered in section 2 for identification of the reaction products.

Where appropriate, all of the sections above will be illustrated with examples of biological relevance.

Accessibility Statement:

As part of this module you will undertake laboratory sessions in the large teaching laboratory (of up to 80 students) that are of 3 hrs in duration. These sessions will be undertaken in groups of three students and they involve fine laboratory work, chemical handling (with appropriate PPE and safety considerations) and heating chemical reactions with high-temperature hotplates. Breaks are possible and students are able to leave the laboratory for short periods.

Learning and teaching

Learning activities and teaching methods (given in hours of study time)

Scheduled Learning and Teaching ActivitiesGuided independent studyPlacement / study abroad

Details of learning activities and teaching methods

CategoryHours of study timeDescription
Scheduled Learning and Teaching22Lectures
Scheduled Learning and Teaching15Laboratory practicals (5 x 3 hours)
Guided Independent Study66Lecture consolidation and associated reading and reading for practical classes
Guided Independent Study6Practical interpretation and write-up
Guided Independent Study6Completion of written coursework
Guided Independent Study35Examination revision


Formative assessment

Form of assessmentSize of the assessment (eg length / duration)ILOs assessedFeedback method
Discussion of problem sheets2 hours1-7, 9-11, 13-15Oral in lectures

Summative assessment (% of credit)

CourseworkWritten examsPractical exams

Details of summative assessment

Form of assessment% of creditSize of the assessment (eg length / duration)ILOs assessedFeedback method
Problem-based examination602 hours1-7, 9-11, 13-15Written via tutor
Problem sheet 1103 hours1-7, 9-11, 13-15Written, model answers
Problem sheet 2103 hours1-7, 9-11, 13-15Written, model answers
Laboratory report 110800 wordsAllWritten
Laboratory report 2101200 wordsAll Written


Details of re-assessment (where required by referral or deferral)

Original form of assessmentForm of re-assessmentILOs re-assessedTimescale for re-assessment
Problem-based examinationProblem-based examination (60%)1-7, 9-11, 13-15August Ref/Def
Problem sheet 1Problem sheet 1 (10%)1-7, 9-11, 13-15August Ref/Def
Problem sheet 2Problem sheet 2 (10%)1-7, 9-11, 13-15August Ref/Def
Laboratory report 1Analysis and interpretation of results and spectroscopic data from a laboratory experiment involving the synthesis of an organic compound (10%)AllAugust Ref/Def
Laboratory report 2Analysis and interpretation of results and spectroscopic data from a laboratory experiment involving the synthesis of an organic compound (10%)AllAugust Ref/Def

Re-assessment notes

Deferral – if you miss an assessment for certificated reasons that are approved by the Mitigation Committee, you will normally be either deferred in the assessment or an extension may be granted. If deferred, the format and timing of the re-assessment for each of the summative assessments is detailed in the table above ('Details of re-assessment'). The mark given for a deferred assessment will not be capped and will be treated as it would be if it were your first attempt at the assessment.

Referral - if you have failed the module (i.e. a final overall module mark of less than 40%) and the module cannot be condoned, you will be required to complete a re-assessment for each of the failed components on the module. The format and timing of the re-assessment for each of the summative assessments is detailed in the table above ('Details of re-assessment'). If you pass the module following re-assessment, your module mark will be capped at 40%.


Indicative learning resources - Basic reading

  • J. Clayden, N. Greeves and S. Warren, Organic Chemistry (Second Edition), Oxford University Press, 2012, ISBN 0-19-927029-5 (essential core text)
  • J. H. Jones, Core Carbonyl Chemistry, (Oxford Chemistry Primer 47), Oxford University Press, 1997, ISBN 0-19-855959-3
  • D. T. Davies, Aromatic Heterocyclic Chemistry, (Oxford Chemistry Primer 2), Oxford University Press, 1992, ISBN 0-19-855660-8

Indicative learning resources - Web based and electronic resources

ELE - 

Module has an active ELE page

Indicative learning resources - Other resources

Lecture notes will be made available via ELE after the lectures have been delivered and all lecture handouts, coursework, past examination papers and practical instructions will also be available at the appropriate time. Model answers to coursework problems will also be provided.

Key words search

Synthesis, structures of organic molecules

Credit value15
Module ECTS


Module pre-requisites

BIO1345 Structure and Reactivity of Organic Compounds I or NSC1003 Foundations in Natural Science

Module co-requisites


NQF level (module)


Available as distance learning?


Origin date


Last revision date