Module proposal
UNIVERSITY OF WARWICK
Proposal Form for New or Revised Modules (MA1- version 3)
For consideration by the Undergraduate Studies Committee/Sub-Faculty or Graduate
Studies Committee only.
NB:
1.
1.
If it is unclear whether or not a change to an existing module should be
proposed on this form, the Chair or Secretary of the Undergraduate
Studies Committee/Sub-Faculty or Graduate Studies Committee should
be consulted.
2.
In order to reduce printing costs please delete the text provided as
guidance in the body of the form before submission to the Faculty
Secretariat. However, all sections must be completed to the satisfaction of
the Faculty Undergraduate/Graduate Studies Committee.
Title of Module:
CH264 Organic Chemistry II
2.
New or Revised Module:
New module?
[]
Revised module?
[X]
Level: D (Doctorate)
M (Masters)
H (Honours)
I (Intermediate)
C (Certificate)
[ ]
[ ]
[X]
[ ]
[ ]
If this new module replaces an existing approved module specify the code and
title of the module to be discontinued and date on which change will occur:
CH246 Mechanism and Stereochemistry in Organic Chemistry (7.5 CATS) and CH247
Aromatic and Heterocyclic Chemistry (7.5 CATS) are replaced with this new 15 CATS
module. October 2009.
If this is a proposal for a revised module, specify which sections have been
amended, and give an outline rationale for the changes:
The syllabus has been changed slightly in line with restructured first year and the two
modules CH246 and CH247 have been combined to obtain a better cohesion of the
syllabus.
3.
Date of Introduction of new module or revised version of existing module:
October 2009
4.
Department Responsible for Teaching:
Chemistry
If the module is taught by more than one department please indicate this (for
matrix purposes):
1
Module proposal
Department
Department
%
%
Name of Module Leader:
Dr. Andrew Marsh
If the module leader is not a member of Warwick staff and has not previously
been appointed as a module leader/tutor, please include a C.V with this form.
5.
Availability/Location of module within courses:
List the degree courses on which this module is available, indicating the year of
study, whether the module is core or an option and the credit weighting in each
case. Include any part-time or 2+2 degrees on which this module is available.
Degree
Code
F100
F101
F102
F105
F106
F107
F108
F121
F122
F125
F126
F127
F128
F1N1
F1N2
BF91
B9F1
FC11
F1C1
Title
Chemistry BSc
Chemistry BSc with Intercalated year
General Chemistry BSc
Chemistry MChem
Chemistry MChem with Professional Experience
Chemistry MChem with Intercalated Year
Chemistry MChem with Industrial Training
Chemistry with Medicinal Chemistry BSc
Chemistry with Medicinal Chemistry BSc with
Intercalated Year
Chemistry with Medicinal Chemistry MChem
Chemistry with Medicinal Chemistry MChem with
Professional Experience
Chemistry with Medicinal Chemistry MChem with
Intercalated Year
Chemistry with Medicinal Chemistry MChem with
Industrial Training
Chemistry with Management BSc
Chemistry with Management BSc with Intercalated
Year
Biomedical Chemistry BSc
Biomedical Chemistry BSc with Intercalated Year
Chemical Biology MChem
Chemical Biology MChem with Intercalated Year
Visiting Students
Year of
study
2
2
2
2
2
2
2
2
2
Core Optional Option list CATS*
core?
A,B or C
Core
15
Core
15
Core
15
Core
15
Core
15
Core
15
Core
15
Core
15
Core
15
2
2
Core
Core
15
15
2
Core
15
2
Core
15
2
2
Core
Core
15
15
2
2
2
2
Core
Core
Core
Core
15
15
15
15
15
*Credit should be in one of the following tariffs:
6, 12, 18, 24, 48 credits; or
7.5, 15, 30, 45, 60 credits; or
(for postgraduate courses only) 10, 20, 30, 40, 50,60 credits
6.
Consultation with other Departments:
It is important that any departments affected by the introduction of this
module are consulted before the module is considered by the relevant
Faculty committee.
2
Module proposal
Which other departments will be affected by the introduction/revision of this
module (i.e. other departments offering the module as an option in their degree
courses, including joint degree courses involving the department proposing the
module)? Please give details of any consultations undertaken and indicate
whether the other departments have approved the proposal.
7.
Context:
Describe the relationship to any other modules with which the new module has a
close connection and any prerequisite relationships.
Pre-requisite
CH161 Introduction to Organic Chemistry is a pre-requisite.
Post-requisites
CH3E3, CH3E4 and CH3E5 as Post-requisites.
8.
Module Aims:
These should identify the module’s broad educational purposes. Indicate how the
module will contribute to the achievement of the aims of the degree courses on
which it is available.
This module builds on first year organic chemistry, using the three-dimensional shapes of
molecules (a ground state effect) to begin to understand their influence upon chemical reactivity (a
transition state effect). It lays the foundations for understanding many organic reactions and the
mechanisms by which they take place. Stereochemistry is of crucial importance in understanding
how molecules interact with, or are part of, biological systems. We learn to use hybrid molecular
orbitals to predict shapes and reactivity of aliphatic, alicyclic and saturated heterocyclic molecules.
Extending this approach to aromatic systems, module aims also include illustrating both the
electrophilic and nucleophilic substitution reactions of benzene. The effects of ring substituents on
these reactions will also be discussed in detail. The concept of aromaticity is further developed by
examining the effect of incorporating heteroatoms into aromatic systems and the study broadened
to look at the synthesis and reactivity of aliphatic heterocyclic compounds.
9.
Learning Outcomes:
Successful completion of the module leads to the learning outcomes. The
learning outcomes identify the knowledge, skills and attributes developed by the
module. Learning Outcomes should be presented in the following format using the
table below:
By the end of the module students should be able to...
Learning Outcomes should include reference to subject knowledge and
understanding, key skills, cognitive skills and subject-specific practical and
professional skills and be clearly relevant to fulfilling the educational aims.
Learning Outcomes should be measurable by the assessment methods for the
module. Indicate how the module will contribute to the achievement of degree
course learning objectives.
(a)
Subject knowledge and understanding
The knowledge and understanding that a student will be expected to have
upon completion, such as : ‘a theoretical knowledge of the principles and
methods of archaeology’ or ‘a knowledge of the major types of chemical
reaction and the main characteristics associated with them.’
(b)
Key Skills
3
Module proposal
Communication (written, verbal, graphical...)
Numeracy
Use of information technology (e.g. WP, www, databases, spreadsheets,
specialist packages)
Ability to learn
Others (e.g. teamwork)
(c)
Cognitive Skills
For example: ability in critical analysis; the ability to formulate and test
concepts and hypotheses.
(d)
Subject-Specific/Professional Skills
For example: laboratory skills; scientific support writing; research skills
and methods.
4
Module proposal
LEARNING OUTCOMES
(By the end of the module the student should be
able to....)
Which teaching and learning methods enable
students to achieve this learning outcome?
Which assessment methods will measure the
achievement of this learning outcome?
Assign C-I-P (R/S) nomenclature to a range of
stereogenic centres including non-carbon centres.
Lectures, computer-aided workshop and tutorials.
Be able to competently draw a range of threedimensional molecules in two dimensions and
appreciate key stereochemical conventions.
Appreciate that stereochemistry is not necessarily
associated with a stereogenic centre. Give
examples of helically and axially chiral molecules.
Be able to carry out conformational analysis of
simple acyclic and cyclic molecules using
appropriate diagrams (Newman projections, chair /
boat structures).
Explain the effect of ring size on energy and
conformation of small and medium sized rings.
Lectures, computer aided workshop, tutorials
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Explain in mechanistic terms how conformation in
cyclic systems directly affects reactions such as
base catalysed (E2) eliminations in cyclic systems.
Appreciate importance of enantio- and
diastereotopism.
Lectures, computer aided workshop and tutorials.
Understanding of the mechanistic concept to
describe chemical reactions and awareness of
some of the tools to derive mechanistic insight
Construction of a reaction profile based on kinetic
and thermochemical properties of a chemical
reaction.
Confident design of labelling experiments to obtain
mechanistic insight into the reaction.
Lectures and tutorial.
Lectures, tutorials, workshops..
Lectures, computer aided workshop and tutorials.
Lectures, computer aided workshop and tutorials.
Lectures, tutorials, workshops.
Lectures, tutorials, workshops.
Lectures, tutorials, workshops.
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
5
Module proposal
Understanding of the concept of kinetic isotope
effects and its use to determine energetic and
geometrical changes.
Differentiate the ring substituents on benzene into
activating and deactivating, and ortho/para or meta
directing.
Lectures, tutorials, workshops.
Understand the role hetero atoms play in the
chemistry of heteroaromatic systems.
Lectures, tutorials, workshops
Describe the synthesis and chemistry of aliphatic
heterocyclic compounds.
Lectures, tutorials, workshops
Understand how & when to use organopalladium
chemistry in heterocyclic synthesis
Lectures, tutorials, workshops
Lectures, tutorials, workshops
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
Formative assessment by set and marked work for
tutorials and examples classes
summative assessment by examination
6
Module proposal
10.
Syllabus:
Give an outline of the syllabus for the module.
Chirality
Chirality in systems lacking a stereogenic carbon atom. Point chirality: tertiary amines,
sulfoxides, phosphines. Axial chirality: allenes and hindered biphenyls. Assignment of
stereochemistry in these systems. Helical structures: helicenes, other examples. Prochirality
and facial chirality Si, Re.
Conformational analysis
Revision ethane and butane. Newman projections and energy -  plots. Terms used include
staggered, eclipsed, gauche, anti-conformations. Heats of combustion – comparison of cyclic
and acyclic systems leading to concepts of strain (torsion and syn-pentane). Strain in acyclic
molecules: 1 consequences on conformations e.g. 1,5-pentane interactions.
6-Membered rings (how to draw). Axial and equatorial hydrogens. Chair (GS), half chair (TS),
twist chair (GS), boat (TS). 6-Rings. A-values - gauche and syn-pentane interactions (1,3diaxial); experimental evidence and linkage to computation (see also workshop on using PC
Model).
Ring size strain for cyclopropane, cyclobutane, cyclopentane. Medium rings and transannular
strain. Stabilising electronic effects upon conformation. Simple orbital view of organic
molecules and orbital overlap. Look at consequences of best donor – best acceptor
interactions upon conformation e.g. FCH2CH2F ‘gauche effect’. Sugars and the anomeric
effect. Esters and amides; peptide bond; phosphodiesters in DNA.
Introduction to reactivity
Rate determining steps and reaction profiles. Exothermic and endothermic reactions. Early
and late transition states. Stereoselectivity and stereospecificity definitions Kinetic and
thermodynamic control.
Elimination reactions. Basicity and nucleophilicity: hard and soft; E2 vs SN2. 4pKa vs.
nucleophilicity. alpha effect E1 and E2 elimination reactions: mechanism. a) kinetics and
stereochem 4-tBu-cychex-OTs cis eliminates with EtO- in EtOH , trans does not react. b)
orbital alignment c) reaction profiles. Single step reaction. Enthalpy and entropy of activation
d) solvent dependence of selectivity.
Syn vs anti-eliminations. E1cb reactions: mechanisms a) kinetics and stereochem b) electron
withdrawing groups and acidity c) Two step reaction RDS vs slow step (two extreme cases).
Changes in rate determining step.Reactions in six-membered rings.
More reactions in 6 membered rings.Rates of ring closure.Ring contractions and
fragmentations
Anchimeric assistance.
Carbonyl reactions
Carbonyl reactions. Additions and additions/eliminations. General trends in reactivity. Sterics
and electronics. Kinetics of hydrolysis and esters and amides: data analysis and mechanistic
elucidation. Imine formation and hydrolysis. Rates and mechanistic interpretation. A Ac1
isotopic labelling.
Acid and base catalysis
From rate data to a inferring a mechanistic hypothesis. Mechanisms and catalysis – looking at
ester hydrolysis and inferring mechanism. Specific acid catalysis, General acid catalysis.
Specific base catalysis, General base catalysis. Precise meanings of each term arising from
rate data. Enzymatic catalysis – chymotrypsin. Termolecular base amide hydrolysis
Linear free energy relationships
Mechanistic investigations. Substituent effects. Hammett equation. Sigma (substituents), Rho
(reactions). Similarity parameters. Swain-Scott nucleophilicity scales. Brønsted plots.General
base catalysed eliminations. general acid catalysed reactions.
7
Module proposal
Diastereoselective reactions.
Definitions; measuring diastereoselection. Examples for carbonyl additions. Development of
models for understanding experimental results: Felkin-Anh model. Aldol reaction and cyclic 6membered transition states.
Isotope Effects in Elucidation of Mechanism
Primary kinetic isotope effects. Secondary isotope effects. Equilibrium isotope effects. What
they tell us about the reaction mechanisms.
Applying stereoelectronic principles.
Non-classical carbocations. Examples of stereoelectronic effects in synthesis.
Stereoelectronics of non-first row elements.
Revision lectures on aromaticity
Aromaticity, aromatic ions and annulenes, orbital explanation of aromaticity, cyclobutadiene
(distortion). Electrophilic substitution, o, m, and para, directing, activating and deactivating
groups in benzene.
Further chemistry of benzene derivatives
Halogenation, Freidel Crafts acylation and alkylation, sulfonation, formylation, ipso
substitution. Sulfonation of napthalene (kinetic verses thermodynamic), polyaromatics, C60
Electrophilic substitution reactions of disubstituted aromatics. Nucleophilic aromatic
substitution, aryne formation
Birch reduction, directed ortho lithiation, reduction of nitroaromatics, azo and diazonium
compounds and transformations.
 Deficient heterocycles
Pyridine, electrophilic substitution, nucleophilic substitution, pyridine-N-oxides, Chichibabin
reaction. Electrophilic and Nucleophilic substitution of pyrimidines, quinolines and
isoquinolines, pyrones. Synthesis of pyridines, pyrimidines, quinolines, isoquinolines
 Excessive heterocycles
Pyrrole, substitution at N and C, furan, thiophene and reactions with electrophiles,
cycloadditions. Imidazole, Indole, benzofuran, benzothiophene, reations with electrophiles.
Synthesis of pyrrole, furan, thiophenes, imidazoles, indoles, benzofurans.
Saturated heterocycles and carbohydrates
Synthesis of 3-6 membered oxygen and nitrogen saturated heterocycles (lactones and
lactams). Effect on rate of cyclisation of ring size (entropy and enthalpy). Macrocyclisations
reactions to give medium ring and large ring lactones, metathesis reactions.
Synthesis of epoxides, aziridines and thiiranes, the bonding orbitals that form the ring
How ring strain dominates the reactivity of small rings (ring opening epoxides/penicillin
Acetonides/acetals as protective groups (synthesis and hydrolysis).
Organopalladium chemistry
Advantages/disadvantages compared to electrophilic aromatic substitution.
Pd(0) (electron rich) oxidative insertion into “electron poor” bonds via pi complex.
Generation of the Pd(0) catalyst from Pd(OAc)2.
Displacement of halide from complex by other organometallic coupling partner (Grignard
organo zinc/tin/borate and how to make them.
Reductive elimination to make C-C bond (or C-N with nitrogen nucleophiles).
Electrophilic aromatic substitution of aryl silanes.
11.
Illustrative Bibliography:
List the core texts only. The illustrative bibliography should provide an
indication of the focus and level of the reading required by this module, rather
than the full range (this should not be more than half a page):
8
Module proposal
1.
2.
3.
4.
5.
6.
7.
Organic Chemistry J. Clayden, N. Greeves, S. Warren, P. Wothers OUP, 2001
[CGWW].
Modern Physical Organic Chemistry E. V. Anslyn, D. A. Dougherty University Science
Books, 2005
Stereochemistry David G. Morris, RSC Books, 2001.
Stereoelectronic Effects A. J. Kirby, Oxford Chemistry Primers, 1996.
A Guidebook to Mechanism in Organic Chemistry, P. Sykes, 6th Edn., Longman.
Molecules in Four Dimensions, http://www.cmbi.kun.nl/wetche/organic/
Chemtube3D.com
Further Reading
1.
Mechanism in Organic Chemistry R. W. Alder, R. Baker, J. M. Brown Wiley, 1971.
QD 1722.A5.
2.
The search for organic reaction pathways P. Sykes Longman, 1972.
3.
Stereochemistry at a Glance J. Eames and J. M. Peach, Blackwell, 2003.
4.
Guide to Organic Stereochemistry S. R. Buxton, S. M. Roberts, Longman, 1996,
QD1858.B8.
5.
Mechanism and Theory in Organic Chemistry, T.H. Lowry, K. S. Richardson, 2nd
Edn., Harper & Row, 1981, QD 1722.L6.
6.
Advanced Organic Chemistry, J. March, 4th Edn., Wiley, 1992, QD 1722.M2.
7.
Alicyclic Chemistry, F. J. McQuillan, 2nd Edn., Cambridge, 1983, QD 2310.M2.
8.
Physical Organic Chemistry N. S. Isaacs, 2nd Edn., Longman, 1995, QD 1611.I8.
9.
Stereochemistry of Organic Compounds E. L. Eliel, S. H. Wilen, L. N. Mander Wiley,
1994, QD1858.E5.
10.
Heterocyclic Chemistry, T. L. Gilchrist, Longman.
11.
Heterocyclic Chemistry, J. A. Joule, G. F. Smith, Reinhold.
12.
Aromatic Chemistry, M. Sainsbury, Oxford University Press.
12.
Teaching:
Give the number of each type of teaching event per week and the length of
each session in hours.
(10 weeks)
Lectures
Workshops
Tutorials
Private / self study
Total contact hours
Module duration (weeks, if applicable)
13.
Assessment Methods:
Type of assessment
Examinations 15 CATS
Assessed essays/ coursework
Other type of formal assessment
14.
3 hrs a week (30hrs in total)
3 hrs in total
5 hrs in total
112 hrs in total
150 hours
10 weeks
Length
3 hour
paper
N/A
N/A
% weighting
100%
N/A
N/A
Resources:
Are any resources required for this module which are not already available
from the Department’s own baseline resources (e.g. staff costs,
accommodation, equipment, minor works, library costs, audio visual and
computing facilities, vacation study requirements)? Is the module likely to
require high usage of centrally timetabled teaching rooms or specific slots
(e.g. for a module on a part time postgraduate course)?
Any additional requirements should be discussed with the appropriate Officer
(see list below) before submitting the proposal.
9
Module proposal
List any additional requirements and indicate the outcome of any discussions.
None
Signature of Module Leader:
Date
Signature of Chair of Department:
Date
10
Exams Office
Assessment Details (information required by the Exams Office)
This form should be completed only for modules to be assessed by an exam organised by the Exams Office
The form does not have to be submitted for approval but should be sent to Andrea Humber in the Exams
Office. If this information is not provided the module cannot be set up on the Student Record System
and students will therefore be unable to register for the module and exam. If you have any queries about
this form please contact Andrea Humber in the Examination Office (ext 74160)
Module Title
Department
Module Leader
Name of Examiner
Organic Chemistry II
Chemistry
Dr Andrew Clark
Indicate all available methods of assessment in the table below
% Examined
% Assessed by other methods
100%
Length of examination paper
3hr (15 CATS)
Examination Details
Will this module be examined together with any other module (sectioned paper)? If so please give
details.
No
Is the module to be examined by 1 paper
[ X]
or 2 papers
[ ]
When will the exam take place (e.g. Jan, April, Summer)? Summer . . . . . . . . . . . . . . . . . . .
Is reading time required?
Yes [ ]
No [ ]
Give any special exam timetable arrangements
Stationery Requirements
No. of Answer Books
Graph Paper
Calculator
List any other special stationery requirements (e.g. Data books, tables etc):
Type of Paper
Seen:
Yes [ ] No [ ]
Open Book : Yes [ ] No [ ]
Restricted:
Yes [ ] No [ ]
Where restricted please provide list of texts permitted here:
8