Download Department of Chemistry Second Year Syllabus

Department of Chemistry
Second Year Syllabus
2004 - 2005
Contents
Page
Introduction to Second Year Chemistry.............................................................................................. 3
Inorganic II
Laboratory............................................................................................................................................... 6
Lecture synopses................................................................................................................................... 8
Organic II
Laboratory.............................................................................................................................................. 15
Lecture synopses................................................................................................................................... 17
Physical II
Laboratory............................................................................................................................................... 28
Lecture synopses................................................................................................................................... 30
Department of Chemistry Second Year Syllabus
2
Department of Chemistry – Imperial College
INTRODUCTION TO SECOND YEAR CHEMISTRY
Aims
The second year of the degree in Chemistry aims to provide the students with an expanded and
deeper understanding of the fundamental concepts required to rationalise and predict chemical
reactivity. To achieve this goal the students study the behaviour of a wide range of chemicals (both
organic and inorganic) and rationalise their behaviour using a theoretical framework (quantum
mechanics and molecular thermodynamics). Furthermore, we aim to enhance the students
understanding of important spectroscopic techniques used for characterisation of molecules (NMR,
UV/IR and X-ray crystallography). These aims can only be achieved by continuing the combined
theoretical and practical approach introduced in the first year. By the end of the year it is expected
that the students have a good understanding of the factors affecting chemical reactions, the
rationalisation of such factors and the ability to explain them within a theoretical framework based
on basic quantum mechanics, thermodynamics and kinetics.
Summary of Content
The second year consists of 160 hours of chemistry lectures, 260 hours of practical work (one
laboratory course each term) and three tutorials a week (in small groups of 4 to 6 students). In
addition there are two courses which involve lectures and practical work which are compulsory, but
cannot be pigeon holed in the traditional IOP format, Chemical Information Technology (CIT), 8
hours of lectures and 36 hours of practical, and Theoretical Methods in Chemistry, 8 hours of
lectures and 18 hours of practical. For Chemistry with a Year Abroad students only, in place of the
260 hours of practical work they are required to perform circa 180 hours, comprising half each of
the synthesis courses and all of the physical course, and all of the CIT and Mathematics courses.
In addition they have language classes of circa 63 hours plus language laboratory. The second
year is evaluated by exams (three examinations – inorganic, physical and organic – in June) and
coursework (which consists of tutorial sheets, laboratory reports, etc).
In the first two terms the coursework consists of the synthesis laboratory. The students perform a
total of eleven experiments; within these experiments are a range of tasks ranging from the
identification of an unknown compound by spectroscopy, computer assisted molecular modelling,
chromatography and a synthesis project. Additionally, in the first two terms the students also
engage in the CIT and theoretical methods practicals. In the Summer term the students are in the
physical laboratory where they are split into two groups which alternate between standard,
computer and instrumentation experiments. The physical laboratory experiments include
electrochemical processes, infrared spectroscopy, Huckel molecular orbital theory and colloid
scattering.
The inorganic courses continue to concentrate on the development of the concepts of periodicity
and inorganic reactivity through the use of specific examples for the main group elements. In
parallel to this, are courses on the characterisation of inorganic compounds (covering NMR and Xray). Transition metal chemistry is covered in depth with the use of crystal field theory, MO-theory
and the 18 electron rule. There are course introducing organometallic chemistry, bonding and
spectroscopic features, and bioinorganic chemistry, chemical elements in biology, mode of action
of inorganic based drugs.
The organic chemistry courses given during this year aim to expand the students knowledge of the
principal functional groups, their properties and reactivity. Courses deal with the strategy of organic
synthesis and C-C bond formation (electrophilic and nucleophilic carbon reagents) and functional
Department of Chemistry Second Year Syllabus
3
group interconversions (reduction of C-C multiple bonds, C-X bonds, oxidation of C-H with no
heteroatoms etc).Three courses are intrinsically involved in cyclic organic chemistry, Alicyclic
(conformation, reactivity and synthesis), heteroatomatic ( 5 – 6 membered heteroaromatic
compounds) and pericyclic reactions. There is a complimentary introductory NMR spectroscopy
course, c.f. inorganic NMR. Finally there are two courses with close overlap with physical
chemistry, physical organic (mechanism) and polymer chemistry (properties, preparation and
morphology).
The physical chemistry component of the second year further extends the links between the
atomistic and macroscopic understanding of chemistry. Thermodynamics, introduced in the
Foundation Course, is addressed in more detail, initially at a macroscopic, classical level, and
subsequently at a microscopic, molecular level. The transition from the microscopic to macroscopic
is further illustrated by the electronic properties of solids course which builds on the QM course to
rationalise the properties of metals, insulators and semiconductors. Electrochemistry and
electrochemical kinetics deals with the processes affecting current flow in electrolytic solutions
(Nernst, Butler-Volmer etc). Finally a course on Photochemistry introduces the chemistry of
molecular excited states, and shows how such chemistry can be understood in the language of
quantum mechanics.
Department of Chemistry Second Year Syllabus
4
Inorganic II
Department of Chemistry Second Year Syllabus
5
Synthesis Lab
Braddock, Chris and Hill, Mike
216 hours: 24 h per week for 9 weeks
Aims
To provide continued development of laboratory skills, interpretation of data and report writing.
Course structure
Autumn term:
• Experiment 1: Identification of an unknown compound by spectroscopy;
• Experiment 2: Preparation and addition of a Grignard reagent to isophorone;
• Experiment 3: Cr(VI) oxidation of a secondary alcohol and derivatisation with 2,4-DNPH.
• Experiment 4: An introduction to flash column chromatography;
• Experiment 5: Preparation of bis(triphenylphosphine)copper(I) tetrahydroborate and study
of its thermal decomposition products
• Experiment 6: Nitrosyl Complexes of Iron and Nickel;
• Experiment 7: Nitration of cobalt(III) acetlyacetonate;
• Experiment 8: Influence of ligand field tetragonality on the ground state spin;
• Experiment 9: [Co(dinosar)]Cl3: An encapsulation complex prepared by a template reaction;
• Experiment 10:Anomalous paramagnetism in some iron(III) chelates studied by the Evans’
NMR method.
Experiments 1-4 compulsory, three from 5-10.
Spring Term:
• Experiment 1: A three stage synthesis project including literature searching and safety
assessment;
• Experiment 2: Ferrocene and its acetylation;
• Experiment 3: Nickel(II) complexes of some Schiff base ligands;
• Experiment 4: Identification of Stereochemical Isomers of [Mo(CO)4L2] by infrared
spectroscopy;
• Experiment 5: Preparation of bis(triphenylphosphine)copper(I) tetrahydroborate and study
of its thermal decomposition products;
• Experiment 6: Nitrosyl Complexes of Iron and Nickel;
• Experiment 7: Nitration of cobalt(III) acetylacetonate;
• Experiment 8: Influence of ligand field tetragonality on the ground state spin;
• Experiment 9: [Co(dinosar)]Cl3: An encapsulation complex prepared by a template reaction;
• Experiment 10: Anomalous paramagnetism in some iron(III) chelates studied by the Evans’
NMR method.
Experiments 1 & 2 compulsory, either 3 or 4, one from 5-10.
Objectives
At the end of this course you should be able to:
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Write up and discuss / interpret their experimental results in a clear and coherent manner;
Set-up and conduct an experiment requiring heating with addition with the exclusion of
moisture;
Set-up and conduct a vacuum distillation, recording the distillation temperature and
pressure;
Set-up and perform column chromatography including tlc analysis of the fractions;
Recrystallize solids to constant m.p.;
Obtain m.p.’s, IR spectra and GC traces routinely;
Interpret IR, 1H NMR and simple ESR spectra;
Department of Chemistry Second Year Syllabus
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Calculate the magnetic moment of a compound using either a magnetic susceptibility
balance or the Evans NMR method, and comment on this value
Compare physical properties with the literature values and comment accordingly;
Identify an unknown compound by judicious interpretation of IR, NMR, MS and other
physical data and comparison with literature values on-line (Beilstein);
Obtain a suitable set of procedures given a single literature reference for a three step
synthesis of a given target molecule;
Write suitable risk assessments for the above.
Department of Chemistry Second Year Syllabus
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Main Group Chemistry
Hill, Mike
8 hours
Aims
To consider the chemistry of the s-block (groups 1 and 2) and p-block (groups 13 –18) elements
and the factors that determine the stability, structures and reactivity of selected inorganic and
organometallic compounds. To describe trends both across periods and down groups, founded
upon the principles described in the first year course ‘Periodicity and Inorganic Reactivity’.
Knowledge of material covered at that time (group oxidation states, trends in electronegativity and
ionic radii etc.) is assumed.
Structure
Lectures 1-4: Classification of the technologically-relevant organometallic compounds of groups 1,
2, 13 and 14 in terms of decreasing polarity of the M–C bond and electron deficiency; recognition
of how these factors determine the use of such compounds in synthesis and in industry. Material
includes discussion of organolithium and Grignard reagents, the use of organo-group 13
compounds in synthesis and catalysis and a discussion of polyorganosiloxanes.
Lectures 5-6: The chemistry of group 13 hydrides (boranes). Development of an electron-counting
rationale to allow structure prediction in such compounds (Wade’s Rules). A molecular orbital
rationalisation of the bonding in electron deficient cluster compounds. Isoelectronic species
including carboranes.
Lectures 7-8: Trends in the compounds of groups 15 and 16 in terms of their available oxidation
states, reactivity and structures and the factors which determine their use as ligands in transition
metal chemistry.
Objectives
• An enhanced appreciation of how periodic trends affect the observed structures, reaction
chemistry and applications of the s- and p-block elements.
• To develop a knowledge of the wide range of structures adopted by main group compounds
and also an awareness of how structures and reactivity influence their use and application
in both synthesis and industry.
Building upon
This material from this course builds upon Periodicity and Inorganic Reactivity (1st year).
Looking forward to
The material from this course will be the basis for lectures on Advanced Main Group Chemistry (3rd
year).
Department of Chemistry Second Year Syllabus
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Introduction to Organometallic Chemistry
Gibson, Vernon
8 hours
Aims
The objective of this course is to introduce students to the metal-carbon bond, ligands capable of
stabilizing metals in low oxidation states and supporting catalytically active metal centres.
Structure
Commencing with an historical introduction covering the industrial relevance of metal carbonyls,
the first part of the course examines the structural diversity of metal carbonyl complexes, the
bonding of CO to transition metal centres (the synergic bonding model) and the reactivity of metal
carbonyls towards a number of substrates. Central to the prediction of likely stability of
organometallic molecules is an understanding of the 18 electron rule and its applicability to a
variety of ligand types. Other ligands studied include: tertiary phosphines, alkenes, dinitrogen,
nitrosyls, alkyne and carbenes. A brief introduction to the use of transition metal complexes in
important catalytic transformations is given, with emphasis on the alternation of 16 and 18 electron
species, and the influence of co-ligands on catalyst activity and selectivity.
Lecture 1: Metal carbonyls - industrial significance, types, synthesis, structure & bonding, stability
(18 electron rule), reactivity.
Lecture 2: Tertiary phosphine complexes (M–PR3) - industrial significance, structure & bonding,
steric effects.
Lecture 3: Metal–alkenes - structure & bonding (Dewar, Chatt, Duncanson model).
Lecture 4: Related ligand systems - metal-dioxygen complexes, metal-alkyne, metal-dinitrogen,
metal-carbene.
Lecture 5: Metal-nitrosyls (M–NO) – synthesis, structure & bonding, reactivity.
Lecture 6: Metal-hydrides – characteristics, synthesis
Lecture 7 & 8: Applications in Catalysis - alkene hydrogenation, hydrosilylation, hydroformylation,
alkene isomerisation
Objectives
At the end of the course, students should be able to;• Determine the EAN for any given complex.
• Describe spectroscopic and bonding features to various organometallic compounds.
• Discuss the reactivity of a range or organometallic compounds.
• Discuss the important features of organometallic catalytic cycles.
Building upon
This material from this course builds upon Coordination Chemistry (1st year) and Transition Metal
Chemistry (2nd year).
Looking forward to
The material from this course will be the basis for lectures on Advanced Organometallic Chemistry
(3rd year) and Inorganic Mechanistics and Catalysis (3rd year).
Department of Chemistry Second Year Syllabus
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Bioinorganic Chemistry
Davies, Robert and Hill, Mike
8 hours
Aims
This course will examine the role of metal ions in a number of biological systems in terms of their
bioavailability, accumulation and function. A sound knowledge of previous courses on transition
metal and main group element coordination chemistry will be required to fully rationalise nature’s
‘selection’ of a particular element in terms of its electronic/magnetic structure and resultant
coordination behaviour.
Lecture 1 (MSH): Chemical elements in biology. How/why do they exist in vivo? ‘Structural’ vs.
‘Functional’ elements. Relevant principles of inorganic chemistry. Introduction
to ‘biological’ ligands. Biomimetic synthesis and useful physical techniques.
Lecture 2 (MSH): The cell’s mechanisms for the uptake of elements. The case of iron: uptake,
transport and storage of ions. Ferritin and transferrins. Comparison to the
‘labile’ alkali metals (Na, K)
Lecture 3 (MSH): Redox processes and bioinorganic chemistry. Nitrogen cycle and fixation (vs.
Haber Process). Nitrogenase enzymes and model systems.
Lecture 4 (MSH): Further Redox processes. Blue copper and iron/sulphur proteins.
Photosynthesis and Photosystems I and II.
Lectures 5,6 (RPD): Oxygen uptake, storage and transport in biological systems. Haemoglobin
and other oxygen storage proteins. Cytochrome-P450 and its synthetic mimics.
Lecture 7 (RPD): Non-redox active processes and zinc-based enzymes: carboxypeptidase and
liver alcohol dehydrogenase.
Lecture 8 (RPD): Environmental inorganic chemistry: inorganic pollutants in the environment and
their effect of biological process.
Objectives
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An appreciation of the biological function fulfilled by a variety of ‘inorganic’ elements.
An awareness of how the ‘simple’ coordination behaviour of metallic elements dictates the
behaviour of complex biological structures.
An appreciation of the importance of biomimetic species and their roles in revealing the
nature of complex biochemical processes.
Knowledge of the function of specific metal containing enzymes (nitrogenase,
carboxypeptidase and liver alcohol dehydrogenase), including a thorough appreciation of
the role played by the metal centre(s) in these proteins.
Knowledge of the function of specific metal containing proteins (Blue copper and
iron/sulphur proteins. Photosynthesis and Photosystems I and II, haemoglobin,
Cytochrome P-450), including a thorough appreciation of the role played by the metal
centre(s) in these proteins.
An appreciation of the danger posed to the environment and animal / human health by
heavy metals and other inorganic pollutants.
Building upon
This material from this course builds upon Transition Metal Chemistry (2nd year).
Looking forward to
The material from this course will be the basis for lectures on Metals in Medicine (3rd year).
Department of Chemistry Second Year Syllabus
10
NMR Methods in Inorganic Chemistry
Britovsek, George and Hii, Mimi
9 hours
Aims
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To develop a knowledge and understanding of NMR spectroscopy as applied to inorganic
and organometallic systems.
To gain familiarity with a wide range of different nuclei, both spin half and quadrupolar.
Prediction and interpretation of the appearance of multi-element NMR spectra.
To use the knowledge gained for problem solving.
Structure
Lecture 1: General principles of NMR spectroscopy. The CW versus the FT method. Glossary
of terms; ∆J, µ, I, sensitivity and relaxation. Extension of the ideas given in the earlier
organic NMR course to nuclei across the periodic table.
Lecture 2: Chemical shifts and coupling constants for common spin 1/2 nuclei 1H, 19F, 31P) in
inorganic and organometallic compounds. 13C NMR spectra. Construction of
coupling patterns for a general nucleus using Pascal's triangle.
Lecture 3: Variation of chemical shift and coupling constants for less common nuclei across the
periodic table. A more detailed examination group 14 nuclei. The choice of NMR
standards. Variation of chemical shifts with coordination number and oxidation state.
Lecture 4: Satellites, spectra and effects of low abundance spin 1/2 nuclei.
Lecture 5: NMR spectroscopy of dynamic systems, fluxionality.
Lecture 6: Quadrupolar nuclei e.g. 6Li, 11B, 14N.
Lecture 7: Solid state NMR spectroscopy.
Lecture 8: Paramagnetic compounds and the NMR method for determining magnetic
susceptibility.
Problem class: Problems involving multinuclear approaches to structure determination, satellite
spectra and quadrupolar nuclei will be handed out in advance and the answers
discussed during the problem class.
Objectives
• To understand the wide-ranging applicability of NMR spectroscopy to different elements,
structures and dynamic situations.
• To be able apply the knowledge gained to a wide range of chemical problems.
Building upon
This material from this course builds upon Characterisation on Inorganic Compounds (1st year).
Department of Chemistry Second Year Syllabus
11
Transition Metal Chemistry
Britovsek, George
8 hours
Aims
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The simple representation of transition metal complexes based on the crystal field model
will be expanded upon, using the more sophisticated molecular orbital treatment.
Using this model, the students will learn how to explain and predict various chemical and
physical properties of transition metal complexes.
Complexes containing metal-metal bonds will be discussed, and how their bond-order can
be determined.
The 18-electron rule will be introduced.
Structure
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Lecture 1: Ionic Bonding, Crystal Field Theory
Lecture 2: Covalent Bonding, MO-theory
Lecture 3: Magnetism
Lecture 4: Colour and UV-VIS spectroscopy
Lecture 5 + 6: Reactivity and stability of metal complexes
Lecture 7: Metal-Metal bonding
Lecture 8: 18 electron rule
Objectives
By the end of the course, the students should be able to:
• when presented with an unknown transition metal complex, to identify or anticipate many of
its properties, including likely geometry, electronic configuration, possible sources of colour
and magnetic properties and whether it is likely to be labile or inert.
• for bi-metallic compounds, to describe in qualitative terms the nature of the metal-metal
bonding.
• The student should have begun to develop an appreciation of where the 18-electron rule is
most useful, and how to routinely apply it.
Building upon
This material from this course builds upon Coordination Chemistry (1st year).
Looking forward to
The material from this course will be the basis for lectures on
Introduction to Organometallic Chemistry course (2nd year), Inorganic Mechanisms and Catalysis
(3 rd year) and Symmetry and Spectroscopy (3rd year).
Department of Chemistry Second Year Syllabus
12
Crystal and Molecular Architecture
Shaffer, Milo
8 hours
Aims
This course aims to introduce the students to basic elements of the structures of crystals, starting
with some fundamental crystallography and moving on to some common inorganic structural types.
The course will indicate how crystallography may be applied to structure determination, and to
understanding the behaviour of more complex systems. The students, whilst gaining 3D
visualisation skills, should realise that structure and especially defects determine properties.
Structure
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Lecture 1: What is a crystal structure? Fundamentals of lattices and unit cells
Lecture 2: Simple metals. Ionic crystals. Polymorphism. Influence of ionic ratios
Lecture 3: Lattice enthalpies, solubilities, Lattice planes & Miller indices
Lecture 4: Pointers to structure determination. Symmetry elements, lattice types,
Lecture 5: Complex oxides : symmetry changing phase transitions
Lecture 6: Molecular biological crystals, conformation
Lecture 7: Real crystals: Defects: points, dislocations, grain boundaries, polycrystals
Lecture 8: Disordered materials: Glasses
Objectives
At the end of this course the students should be able to
• Draw crystal structures, including new systems, when given lattice type and motif
• Identify symmetry and coordination features
• Label Miller planes and lattice vectors and explain the relationship between them
• Describe defect structures and how they arise
• Give examples of structure dependent properties
• Contrast glassy and crystalline phases
Department of Chemistry Second Year Syllabus
13
Organic II
Department of Chemistry Second Year Syllabus
14
Synthesis Lab
Braddock, Chris and Davies, Rob
216 hours: 24 h per week for 9 weeks
Aims
To provide continued development of laboratory skills, interpretation of data and report writing.
Course structure
Autumn term:
• Experiment 1: Identification of an unknown compound by spectroscopy;
• Experiment 2: Preparation and addition of a Grignard reagent to isophorone;
• Experiment 3: Cr(VI) oxidation of a secondary alcohol and derivatisation with 2,4-DNPH.
• Experiment 4: An introduction to flash column chromatography;
• Experiment 5: Preparation of bis(triphenylphosphine)copper(I) tetrahydroborate and study
of its thermal decomposition products
• Experiment 6: Nitrosyl Complexes of Iron and Nickel;
• Experiment 7: Nitration of cobalt(III) acetlyacetonate;
• Experiment 8: Influence of ligand field tetragonality on the ground state spin;
• Experiment 9: [Co(dinosar)]Cl3: An encapsulation complex prepared by a template reaction;
• Experiment 10:Anomalous paramagnetism in some iron(III) chelates studied by the Evans’
NMR method.
Experiments 1-4 compulsory, three from 5-10.
Spring Term:
• Experiment 1: A three stage synthesis project including literature searching and safety
assessment;
• Experiment 2: Ferrocene and its acetylation;
• Experiment 3: Nickel(II) complexes of some Schiff base ligands;
• Experiment 4: Identification of Stereochemical Isomers of [Mo(CO)4L2] by infrared
spectroscopy;
• Experiment 5: Preparation of bis(triphenylphosphine)copper(I) tetrahydroborate and study
of its thermal decomposition products;
• Experiment 6: Nitrosyl Complexes of Iron and Nickel;
• Experiment 7: Nitration of cobalt(III) acetylacetonate;
• Experiment 8: Influence of ligand field tetragonality on the ground state spin;
• Experiment 9: [Co(dinosar)]Cl3: An encapsulation complex prepared by a template reaction;
• Experiment 10: Anomalous paramagnetism in some iron(III) chelates studied by the Evans’
NMR method.
Experiments 1 & 2 compulsory, either 3 or 4, one from 5-10.
Objectives
At the end of this course you should be able to:
• Write up and discuss / interpret your experimental results in a clear and coherent manner;
• Set-up and conduct an experiment requiring heating with addition with the exclusion of
moisture;
• Set-up and conduct a vacuum distillation, recording the distillation temperature and
pressure;
• Set-up and perform column chromatography including tlc analysis of the fractions;
• Recrystallize solids to constant m.p.;
• Obtain m.p.’s, IR spectra and GC traces routinely;
• Interpret IR, 1H NMR and simple ESR spectra;
• Calculate the magnetic moment of a compound using either a magnetic susceptibility
balance or the Evans NMR method, and comment on this value
Department of Chemistry Second Year Syllabus
15
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Compare physical properties with the literature values and comment accordingly;
Identify an unknown compound by judicious interpretation of IR, NMR, MS and other
physical data and comparison with literature values on-line (Beilstein);
Obtain a suitable set of procedures given a single literature reference for a three step
synthesis of a given target molecule;
Write suitable risk assessments for the above.
Department of Chemistry Second Year Syllabus
16
Chemical Information Technology
Rzepa, Henry
8 hours
Aims
Understanding of modern computational chemistry, in particular database searching and data
manipulation.
Structure
A combination of lecture-demonstrations, supervised practical sessions on computers, online
availability, a focused student project session, and application throughout other laboratory courses
and problems tutorials.
Objectives
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Problem solving skills in coping with various software and other computer interfaces and
integrating them into an information environment
Knowledge of the various types of scientific, chemical and molecular data available in
various online archives and how to transform the data into chemical information
Knowledge in how to use modern online scientific chemical journals
Knowledge of how chemical information technology can be applied to laboratory skills and
laboratory research projects in both the molecular sciences and broader multi-disciplinary
environments such as bioinformatics etc.
Skill in identifying the appropriate information resources for a given project topic, acquiring
the information, and creating a structured project report.
Skill in applying a markup language (HTML) to presenting chemical information as part of a
project report
Department of Chemistry Second Year Syllabus
17
Organic Synthesis: Strategy and C-C Bond Formation
Craig, Donald
6 hours
Aims
To provide the students with a detailed overview of the major methods for C–C bond formation in
organic synthesis.
Structure
Lecture 1 - The disconnection approach to organic synthesis: Brief introduction to retrosynthetic
analysis; antithetical reaction; disconnection; synthons; synthetic equivalents;
functional group interconversion
Lecture 2 - Electrophilic carbon reagents: Haloalkanes; carbonyl groups in aldehydes, ketones
and carboxylic acids and derivatives; electrophilic alkenes and conjugate addition
Lecture 3 - Nucleophilic carbon reagents: Organometallic reagents: lithium, magnesium, copper;
trends and differences in regiochemistry and reactivity
Lecture 4 - Nucleophilic carbon reagents: Enolates; alkylation of enolates; C- vs. O-alkylation;
Unsymmetrical ketones – regiochemistry of deprotonation
Lecture 5 - Enolates: Control of extent of alkylation; Michael reactions; Robinson annelation
Lecture 6 - Carbanions stabilised by second-row elements: Use of sulphur- and phosphorusstabilised nucleophilic species in C–C bond formation, especially olefination (Wittig
and Julia olefinations reactions); concept and use of umpolung-type reagents
Objectives
By the end of the course the students should be able to
• identify and select key reactions for C-C bond formation
• understand the issues of regio- and stereo control relevant to them.
Building upon
All year 1 Organic chemistry courses.
Looking forward to
Organic Synthesis parts 2 and 3 (Functional Group Interconversions and Retrosynthetic Analysis);
year 3 “Advanced Stereochemistry”; year 4 “Advanced Synthesis” and “Catalytic Asymmetric
Synthesis”.
Department of Chemistry Second Year Syllabus
18
Organic Synthesis 2: Functional Group Interconversions
Armstrong, Alan
7 hours
Aims
To build on the lectures by Donald Craig and provide students with the synthetic armoury which, in
combination with the rest of the course, will allow the design and execution of simple organic
syntheses which are chemo, regio-, stereo- and (where required) enantioselective.
Course content
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Introduction to FGI's. Introduction to classes of reducing agent. Reduction of C=X bonds.
Reduction of CO2R and related functions.
Reduction of C-C multiple bonds.
Reduction of C-X bonds.
Oxidation of C-H bonds bearing no heteroatom.
Oxidation of CH-OH groups.
Oxidation of olefins.
Course objectives
At the end of this course, students should be able to:
• Select an appropriate reagent for a given transformation covered within the course, in the
context of molecules which they have not met in the course (i.e. apply their knowledge)
• Be able to explain, at the level of their colleagues, the mechanistic rationale underpinning
any issues of selectivity in the reaction (chemo, regio-, stereo- and enantioselectivity);
• Be ready to apply this knowledge with that from Donald Craig's course to tackle problems in
small molecule total synthesis.
Building upon
All year 1 Organic chemistry courses; Organic Synthesis part 1 (C-C Bond Formation)
Looking forward to
Organic Synthesis part 3 (Retrosynthetic Analysis); year 3 “Advanced Stereochemistry”; year 4
“Advanced Synthesis” and “Catalytic Asymmetric Synthesis”.
Department of Chemistry Second Year Syllabus
19
Organic Synthesis 3: Strategy and Retrosynthetic Analysis
Craig, Donald and Armstrong, Alan
7 hours
Aims
To develop the students’ skills in retrosynthetic analysis so that they can utilize the reactions they
met in the earlier parts of the course to design sensible syntheses of organic compounds.
Structure
1. Protecting groups – strategic concept. Common protecting groups for alcohols, amines,
carbonyl and carboxyl groups and the mechanistic rationale behind the choice of these.
2. Concepts of retrosynthetic analysis: synthons, synthetic equivalents, disconnections.
Simple C-X disconnections. Two-group disconnections and 1,2-difunctional compounds
3. 1,3-difunctionality: aldol and related disconnections
4. 1,4-difunctional group disconnections and umpolung
5. 1,5-difunctionality: Michael additions
6. Synthetic strategy: convergent vs. divergent syntheses and practice examples in
application of retrosynthesis
7. Comparison of synthetic strategies: critical examination of different approaches to
selected important natural product targets.
Objectives
By the end of the course the students should be able to
• devise an appropriate strategy for the synthesis of simple organic molecules, utilizing the
concepts of retrosynthesis together with the mechanistic understanding they have
developed in the course so far
• propose detailed synthetic routes to the target compounds, including an appreciation of the
key issues of selectivity governing the choice of specific reagents
Building upon
All year 1 Organic chemistry courses; Organic Synthesis parts 1 and 3 (C-C Bond Formation and
Functional Group Interconversions)
Looking forward to
Organic Synthesis part 3 (Retrosynthetic Analysis); year 3 “Advanced Stereochemistry”; year 4
“Advanced Synthesis” and “Catalytic Asymmetric Synthesis”.
Department of Chemistry Second Year Syllabus
20
Introduction to Nuclear Magnetic Resonance Spectroscopy
Law, Robert
6 hours
Aims
To provide the students with the fundamentals of NMR spectroscopy. To reinforce and consolidate
existing materials learnt in the previous year. To extend these skills to enable the student to
understand tools needed in other chemistry courses and laboratories.
Structure
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Introduction, principles of magnetic resonance
Sensitivity, quantification,
Origins of chemical shift
Spin-spin coupling, origins of spin coupling
Coupling patterns and spin systems,
More complex coupling patterns
Application of chemical shift and coupling patterns
Objectives
By the end of the course the students should be able to
a) Understand the basic theory of NMR spectroscopy
b) To solve and interpret simple NMR spectra
c) To apply the knowledge to compounds obtained in the synthetic lab course
d) To understand how this integrates to the inorganic NMR spectroscopy course
Department of Chemistry Second Year Syllabus
21
Pericyclic Reactions
Rzepa, Henry
5 hours
Further details of this course can be found at http://teaching.ch.ic.ac.uk/organic/pericyclic/
Aims
To provide an introduction to the theory and applications of pericyclic reactions.
Structure
Definitions. Types of pericyclic reaction. Theories. Electrocyclic, cycloaddition and sigmatropic
reactions.
Objectives
Students should be able to
• Recognise the main classes of pericyclic reaction
• Predict whether reactions are likely to proceed under thermal or photochemical conditions
• Predict the stereochemical outcome of these processes.
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Introduction to Stereoelectronics
Spivey, Alan
5 hours
Aims
To introduce orbital interactions and the importance of stereoelectronic effects in controlling the
conformation of molecules and the outcome of reactions.
Structure
Lecture 1: will examine the basic requirements for effective orbital interactions.
Lecture 2: will explore the importance of stereoelectronic interactions in the conformation of
hydrocarbons.
Lecture 3: will explore the importance of stereoelectronic interactions in the conformation of
selected functional groups (including e.g. anomeric and gauche effects).
Lecture 4: will look at elimination and substitution reactions, deprotonation β to carbonyls, and
Nucleophilic addition to carbonyls (Burgi-Dunitz angle).
Lecture 5: will look at stereoelectronic influences in reactions: ionic rearrangements (WagnerMeerwein) and fragmentations (Eschenmoser).
Objectives
On completion of this course you will be able to:
• Understand the factors which make good donor and acceptor orbitals
• Draw energy diagrams for a given stereoelectronic interaction
• Discuss the factors that affect orbital overlap and lead to important (stabilising) interactions
• Recognise anti-peri-planar relationships between reacting bonds in synthetic
transformations
• Appreciate the influence of orbital control in elimination and substitution reactions, and
carbonyl chemistry
• Rationalise the stereochemical outcome of synthetically important rearrangements and
fragmentations
Building upon
Year 1 “Stereochemistry”; several year 2 courses
Looking forward to
Year 3 “Advanced Stereochemistry”
Department of Chemistry Second Year Syllabus
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Heteroaromatic Compounds
Widdowson, David
6 hours
Aims
The aim of these lectures is to:—
• familiarise the student with the chemistry of the most important 5- and 6-membered
heteroaromatic compounds
• familiarise the student with the physical and spectroscopic properties of furan, pyrrole,
thiophene, indole and pyridine
• explain the commonly used heterocyclic syntheses
• illustrate their reactivities with examples of the most typical functionalisation chemistries.
Structure
•
•
•
•
•
•
Introduction: importance of heterocycles. Nomenclature.
Ring synthesis: classification and general types.
Furan: physical and spectroscopic properties; syntheses; reactivity (with electrophiles and
as a diene).
Pyrrole and thiophene: physical and spectroscopic properties; syntheses; reactivity.
Indole physical and spectroscopic properties; syntheses; reactivity.
Pyridine physical and spectroscopic properties; syntheses; reactivity.
Objectives
The student will be expected:—
• to be able to give examples for the importance of heteroaromatic compounds in natural
products, dyes, polymeric materials, and as electro-active components in device
applications.
• to summarise key physical and spectroscopic properties of furan, pyrrole, thiophene, indole
and pyridine.
• to suggest at least two synthetic routes for each of the main heteroaromatics furan, pyrrole,
thiophene, indole and pyridine and to classify each reaction into type I and II.
• to be able to explain the reactivity of furan, pyrrole, thiophene, indole and pyridine based on
their aromaticity, the effect of the heteroatom on electron distribution (s and p system
contributions and to be able to identify those reactivity patterns using valence bond theory
(Wheland intermediates, resonance stabilisation, contributions of s-complex stabilities).
• to suggest reagent(s) and conditions for the substitution of these heteroaromatics, thus
introducing sulphonic acid, nitro, halogeno, amino, acetyl, alkyl and hydroxy groups.
• to discuss on the basis of their aromaticity, the difference in stability as well as reactivity
between the different heteroaromatics presented.
Building upon
Year 1 organic chemistry, especially Chemistry of the Carbonyl Group..
Looking forward to
Year 4 “Advanced Heterocyclic Chemistry”
Department of Chemistry Second Year Syllabus
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Alicyclics and Non-Aromatic Heterocycles
Smith, Ed
10 hours
Aims
To provide an account of the conformations, reactivity and synthesis of non-aromatic heterocyclic
and alicyclic compounds.
Structure
1.
(a)
(b)
(c)
(d)
2.
(a)
(b)
3.
(a)
(b)
4.
(a)
(b)
(c)
(d)
(e)
(f)
(f)
(g)
Ring Strain
1st Lecture: Angle (Baeyer) Strain.- As tetrahedral angle is compressed p-character of ring
C-C bond increases. In cyclopropane internal bond 105o with approx. sp3.7 for C-C and sp2.3
for C-H. Thus C-C weaker and longer ( -like) shown by UV, 1H NMR; the C-H shorter and
stronger shown by IR, CH acidity, 13C NMR.
Torsional (Pitzer) Strain.- Eclipsing of groups along a -bond which cannot be relieved by
rotation. Planar and puckered cyclobutanes.
2nd Lecture: Transannular Strain.- In medium rings groups project towards one another
inside the ring.
Cycloalkenes and Cycloalkynes.- Increase in angle strain is balanced to some extent by
reduction in torsional strain. Oxirenes, 1H-azirines, 2H-azirines. Trans –cycloalkenes –
optical isomerism.
3rd Lecture: Strain measured by Ag+ complexation. Cycloalkyne-Cycloallene equilibrium.
Conformational Analysis (Alicyclic only)
Thermodynamic Aspects.- Cyclohexane chair and boat. Axial and equatorial hydrogens in
chair. Ring flipping equilibrium in monosubstituted cyclohexanes. Rigid trans –decalin and
steroid systems.
4th Lecture: Kinetic Aspects.- (i) Steric control: Base hydrolysis of esters (TS more crowded
than SM). Dichromate oxidation of alcohols (TS less crowded than SM).
(ii) Stereoelectronic control: E2 elimination. HOBr addition. Epoxide formation
(neighbouring group participation). Ring opening of epoxides. Anti-periplanar
rearrangements.
Synthesis of Three-Membered Rings (Irreversible reactions only)
5th Lecture: Additions of “X” to a double bond: carbenes, carbenoids, nitrenes, oxene
equivalents (peroxyacids). Intramolecular SN2 displacements of leaving group by
carbanions: generation of anions by deprotonation of conjugate acid to cyclopropanes
(Perkin Synthesis), oxiranes (oxyanions).
6th Lecture: Generation of anions by nucleophilic addition route to cyclopropanes, Darzen’s
condensation and modern variant, addition of H2O2 to  – enones. Aziridine synthesis
from -amino halides.
Reactivity of Cyclopropanes, Oxiranes and Aziridines
Ring Opening by Electrophilic Attack
7th Lecture: Ring Opening by Nucleophilic Attack
Electrocyclic Ring Opening: Ring Opening of Oxiranes and Aziridines and Subsequent
1,3-Dipolar Cycloaddition
Effect of Increasing Angle Strain: Electrocyclic Ring Opening of Cyclopropyl cation
Effect of Increasing Angle Strain: Electrocyclic Ring Opening of Cyclopropanones
8th Lecture: Effect of Increasing Angle Strain: Slow Ring Inversion of Aziridines
Cheletropic Reactions of Aziridines
Catalytic Hydrogenation of Cyclopropanes
Department of Chemistry Second Year Syllabus
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5.
Synthesis of Four-Membered Rings (Irreversible reactions only)
(a) Intramolecular Condensation to Oxetan-2-ones.
(b) “[2 + 2]” – Cycloadditions –
(i) h + alkene + enone
(ii) Paterno-Buchi reaction
(iii) Ketene + alkene
(iv) ketene + imine, Staudinger reaction
(v) 9th Lecture: chlorosulphonylisocyanate + alkene.
6.
(a)
(b)
(c)
(d)
(e)
Reactivity of Cyclobutanes, Cyclobutenes, Oxetanes and Azetidin-2-ones
Cyclobutyl – cyclopropyl – homoallyl cation; i-cholesterol
Cyclobutenes and oxetes – electrocyclic ring opening.
Nucleophilic attack on oxetanes and azetidin-2-ones.
10th Lecture: Nucleophilic attack on 4-acetoxy-azetidine-2-one.
Cheletropic elimination of CO2 from oxetan-2-ones.
7.
(a)
(b)
Synthesis of Medium Rings
Acyloin synthesis.
Cope rearrangement / expansion of smaller rings.
8.
(a)
(b)
Reactivity of Medium Rings
Transannular hydride shifts.
Transannular ring closures.
Objectives
Students should:
1. Understand the interrelationships between strain, conformation and hybridisation in three
and four-membered rings and between strain and conformation in medium-sized rings.
2. Appreciate the consequences of that strain on the reactivity and synthesis of those rings.
3. Recognise that the conformations of six-membered rings in rigid systems dictate the
reactivity of substituents.
4. Apply all that knowledge to unfamiliar examples.
Building upon
Conformations, Hybridisation, Nucleophilic Reaction Mechanisms and Epoxide Chemistry taught in
the first year.
Looking forward to
Reactive Intermediates and Organic Photochemistry in the third year.
Department of Chemistry Second Year Syllabus
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Physical II
Department of Chemistry Second Year Syllabus
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Physical Laboratory course
Taylor, Alan
96 hours
Aim
To provide the students with practical laboratory experience to support the lecture material in the
second year.
Structure
Over a period of fours weeks the students carry out two “standard” laboratory experiments, one
computer project and one instrumentation project.
The standard experiments relate to taught lecture material. The computational experiments show
how mathematical modelling can be used to simulate properties of matter and molecules. These
are assessed by laboratory reports The project experiments are open ended. The students are
given an introduction and encouraged to build their own instruments almost from scratch and then
use them in an investigation. They are assessed on their day to day performance in the lab and
marked for innovation and originality
Standard Experiments
• Electrode processes. Current-voltage curves
• Transport numbers of HCl
• Rotating disk electrode
• Heat Capacity of Solids
• Miscibility of three liquids
• Thin surface films - Langmuir trough
• Surface excess
• Dissociation of iodine vapour
• Infrared Spectroscopy
• Spectroscopy of Colloidal Semiconductors
Computer experiments
• Huckel Molecular Orbital Theory
• Thermal Expansion of a Metal Alloy
• Under development
Instrumentation Projects
• The Galvanostat
• Colloid Scattering
• Nanocrystalline Surface Density of States
Objectives
By the end of the course the students will be:
• More familiar and confident with the techniques of Physical Chemistry.
• Have a greater understanding of how simulation can be used to understand the properties
of matter.
• Know some of the issues involved in designing and building and experiment.
• Familiar with the concept of signal to noise issues in instrument design.
• Confident in their abilities to problem solve through experience in the instrumentation
exercise
Department of Chemistry Second Year Syllabus
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Building upon
1st Year Physical Chemistry Laboratory. Theoretical Methods 2 laboratory. Physical Chemistry
Lecture courses including in particular Electrochemical Dynamics, Interfacial Thermodynamics,
Spectroscopy and Electronic Properties of Solids
Looking forward to
3rd year lecture courses and Physical Chemistry Laboratory.
Department of Chemistry Second Year Syllabus
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Theoretical Methods in Chemistry 2
Harrison, Nic
8 hours + 2 problem classes
Aims
Provide an introduction to the theoretical methods used in physical, inorganic and organic
chemistry during the 2nd and 3rd years.
Summary
1. Series summations (e.g.: tipartition functions )
2. Convergence of bond energy sums in inorganic solids (e.g.: thermodynamics and the
quasi-harmonic approximation)
3. An introduction to matrices
4. The eigenvalue problem - diagonalisation
5. The LCAO problem for H2 – the chemical bond
6. LCAO for the H-polymer – band structure
7. Molecular symmetry (operations, groups, group properties)
8. NMR Interpretation
Assessment – the course will be examined at the beginning of the Spring term and in theoretical
methods lab reports.
Objectives
By the end of this course you should be able to:
• Sum the partition function of analytic systems
• Test series for convergence
• Perform basic matrix operations
• Solve the eigenvalue problem and describe chemical bonding
• Analyse the band structure of simple metals and semiconductors
• Identify molecular symmetries and determine molecular symmetry groups.
• Analyse NMR spectra.
Building upon
Theoretical Methods 1 and quantum mechanics lecture courses. Theoretical Methods 2 laboratory.
Physical Chemistry Lecture courses including in particular Electrochemical Dynamics, Interfacial
Thermodynamics, Spectroscopy and Electronic Properties of Solids
Looking forward to
Theoretical Methods Laboratory 2. 2nd year lecture courses in Interfacial and Statistical
Thermodynamics, Electronic Properties of Solids and Photochemistry, 3rd year lecture courses in
Quantum Chemistry and Symmetry and Spectroscopy.
Department of Chemistry Second Year Syllabus
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Theoretical Methods Laboratories 2
Harrison, Nic
24 hours
Aims
•
•
Introduce modern computer based analysis of thermodynamics, electronic structure and
molecular symmetry
Introduce the numerical and visualization tools used for the simulation and analysis of
chemical problems.
Structure
Over a period of three weeks (one in the Autumn term and two in the spring term) students carry
out three computer based projects which illustrate the concepts introduced in 2nd year lectures and
the methods taught in the theoretical methods course. The projects focus on chemical concepts
and are designed to encourage self-study, offering opportunities for students to explore theoretical
chemistry using state of the art computational tools. Each project should occupy about 12 hours in
the computer laboratory. Projects are assessed through a laboratory report for accuracy, originality
and innovation.
Laboratories are structured as supervised sessions
Projects
Vibrations, phonons and thermal expansion of MgO using DLVIz/GULP
Molecular electronic structure
Molecular Symmetry
(NMH)
(IG)
(MR/MB)
Objectives
By the end of this course students will;
• Be familiar with the Linux operating system and a number of tools for the calculation and
visualization of chemical properties...
• Have a working understanding of the self-consistent field method and its application to
chemical bonding.
• Be familiar with lattice simulation methods, vibrational states in solid state systems and the
thermodynamic basis of thermal expansion.
• A working knowledge of molecular symmetry.
Building upon
Theoretical Methods 1 and 2 and quantum mechanics lecture courses. Physical Chemistry Lecture
courses including in particular Electrochemical Dynamics, Interfacial Thermodynamics,
Spectroscopy and Electronic Properties of Solids
Looking forward to
2nd year lecture courses in Interfacial and Statistical Thermodynamics, Electronic Properties of
Solids and Photochemistry, 3rd year lecture courses in Quantum Chemistry and Symmetry and
Spectroscopy and 3rd year Physical Chemistry Laboratory.
Department of Chemistry Second Year Syllabus
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Interfacial Thermodynamics
Seddon, John
10 hours
Aims
This course first reviews the Laws of Thermodynamics, and summarises the underlying principles
governing phase stability and phase transitions, and the effects of pressure and temperature upon
them. It then goes on to introduce the concepts of partial molar quantities and chemical potential,
and to describe the behaviour of liquid mixtures. The effect of deviations from ideality are then
discussed, and the concept of activity introduced. Various forms of liquid phase diagrams are then
described, and the Phase Rule and Lever Rule explained. The concepts of surface tension and
interfacial tension are then introduced, and their roles in various interfacial phenomena described.
Finally, a brief introduction is given to the role of interfacial thermodynamics in self-assembly
processes, such as micelle and lipid membrane formation, crucial both in many industrial
processes and Biology (biomembranes).
Structure
1–2: Laws of Thermodynamics
The Second and Third Laws: entropy and the Clausius Inequality; the Gibbs and Helmholtz free
energies G and H; the fundamental equation; the variation of G with T; the variation of G with p.
3–4: Transformations and phase transitions
Stability of phases and phase boundaries; single component pressure-temperature phase
diagrams; phase transitions and chemical potential; effect of pressure on vapour pressure; effect of
temperature on vapour pressure; Clapeyron equation.
5–6: Liquid Mixtures
Partial molar quantities; fundamental equation of chemical thermodynamics; Gibbs-Duhem
equation; Gibbs free energy of mixing; ideal solutions: Raoult’s Law; ideal dilute solutions: Henry’s
Law; colligative properties and osmosis; activity of solvent and solute.
7–8: Phase diagrams
The Phase Rule; vapour pressure diagrams: the Lever Rule; distillation and azeotropes; liquidliquid temperature-composition phase diagrams; critical solution temperatures; ternary liquid phase
diagrams; liquid-solid phase diagrams: eutectics.
9–10: Interfacial tension and self assembly
Liquid interfaces: surface and interfacial tension; curved interfaces: bubbles, cavities and droplets;
nucleation: superheating, supercooling and supersaturation; wetting, spreading and contact angle;
capillary action: capillary rise and fall; adsorption at interfaces and surface excess; surface
pressure and Gibbs adsorption equation; self-assembly: micelles and membranes; supported
monolayers and Langmuir-Blodgett films.
Objectives
By the completion of the course the student should:
• understand the concepts of internal energy, heat capacity, entropy, and free energy, and be
able to manipulate these quantities;
• know what controls the stability of phases, and be able to interpret binary and ternary
phase diagrams using the Phase Rule and the Lever Rule;
• be able to analyse the effects of temperature and pressure on the vapour pressure, and the
effect of pressure on phase transitions;
• know how to use the fundamental equation of chemical thermodynamics;
• understand how to treat deviations from ideality in solutions;
Department of Chemistry Second Year Syllabus
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•
•
know how to analyse the effects of surface and interfacial tension, and their practical
importance in phenomena such as nucleation and capillary action;
understand how interfacial thermodynamics controls self-assembly processes in solution,
leading to formation of aggregates such as micelles and membranes.
Building upon
Foundation Chemical Equilibria and 1st Year Physical Chemistry Laboratory.
Looking forward to
2nd year lecture courses in Statistical Thermodynamics, Electrochemical Dynamics, Electronic
Properties of Solids and Photochemistry lecture courses and 2nd year Physical Chemistry
Laboratory.
Department of Chemistry Second Year Syllabus
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Electrochemistry and Electrochemical Kinetics
Wilde, Paul
10 hours
Aims
The aim of this course is to describe the factors that control the current that is passed at an
electrode during an electrochemical process.
Summary
There are three elements that are introduced. First, the factors that influence ion transport by
migration, convection and diffusion are presented. Then equilibrium electrochemistry is presented,
starting with an explanation of how potential differences arise and moving on to the Nernst
equation. Electrode kinetics is the next topic with the Butler-Volmer equation introduced as the
basis for understanding the relationship between current and potential. Finally the rotating disc
electrode is used to show how, as potential varies, the current can be controlled either by the
electrode kinetics or by ion transport.
Objectives
The students are expected to:
i)
Understand the concepts of activity and ionic strength and to know the factors that
affect ion-ion and ion-solvent interactions. They should be able to apply this information
to a discussion of the factors that influence ion-transport in its different forms (migration,
diffusion).
ii)
Understand how potential differences arise and how electron transfer can be driven by
application of an external voltage. Be able to apply the Nernst equation to calculate half
cell and cell potentials, free energies and equilibrium constants for cell reactions.
iii)
Be able to use the Butler Volmer equation to calculate currents passed at a particular
voltage or overpotential. Have an appreciation of the factors that affect the current
passed, such as exchange current density, and appreciate that the kinetic complexity of
reactions influences the current-voltage characteristics for an electrode reaction.
iv)
Understand that, because of the exponential nature of the Butler Volmer equation, at
potentials distant from the equilibrium potential, electron transfer can be so fast that
reactant supply can control the current that is passed.
Building upon
Foundation chemical equilibria and 1st Year Physical Chemistry Laboratory.
Looking forward to
2nd year Physical Chemistry Laboratory, Electronic Properties of Solids and Photochemistry lecture
courses. Options course in Batteries and Fuel Cells.
Department of Chemistry Second Year Syllabus
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Electronic Properties of Solids
Jones, Tim
10 hours
Aims
This course will provide a basic introduction to the electronic properties of solids. It will explain the
differences between metals, insulators and semiconductors and will introduce the theory that
rationalises the properties of each type of material.
Summary
This course provides a basic introduction to the electronic structure of the solid state and how this
is reflected in the different electrical and optical properties of these materials. The students are
expected to have a good knowledge of quantum chemistry. The students will be introduced to the
concept of energy bands, the Fermi level, the density of states, band gaps and band structures,
with simple one-dimensional models used to illustrate the important theoretical principles.
Extension to two- and three-dimensional band structures will be performed in a more qualitative
manner and the students will be expected to be able to use these band structures to explain the
key differences (primarily electrical conductivity) between metals, insulators and semiconductors.
The properties of semiconductors will are explored in greater detail since these materials play such
an important role in electronic devices. Both intrinsic and extrinsic behaviour will be introduced with
particular emphasis on the strong temperature dependence of the carrier density and conductivity.
Finally, the student will be introduced to the application of semiconductor materials in modern day
devices based on p-n junctions.
Objectives
By the end of this course, the students should be able to:
1. understand the main principles of the free electron theory of metals and its limitations in
explaining metallic properties
2. understand the importance of energy gaps and band theory
3. explain the electronic properties of solid state materials in terms of their band structure
4. explain the key differences between metals, insulators and semiconductors
5. understand the properties of semiconductor materials and the importance of doping.
Building upon
Theoretical Methods 2 and quantum mechanics lecture courses.
Looking forward to
3rd year course in The Chemistry of Solid Surfaces. Options courses including Molecular
Electronics, Nanostructured Semiconductor Materials, Optical and Electronic Properties of
Nanomaterials.
Department of Chemistry Second Year Syllabus
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Molecular Thermodynamics
Bresme, Fernando
10 hours
Aims
This course provides a basic introduction to Statistical Thermodynamics. The theoretical
framework introduced at the beginning of the course is used to explain and predict the equilibrium
macroscopic properties of atomic and molecular gases as well as chemical equilibrium.
Summary
1-2: The basis of statistical thermodynamics: Statistical definition of entropy; Microstates and
accessible energy levels; Third law and statistical thermodynamics: residual entropies; Ensembles
and ensemble averages; the ergodic hypothesis; The Boltzmann distribution.
2-3: The partition function and statistical thermodynamics: The Canonical partition function;
The partition function and thermodynamic properties; Fluctuations.
4-7: The ideal gas: The molecular partition function; The translational partition function: particle in
a box; The rotational partition function: rigid rotor; The vibrational partition function: harmonic
oscillator; The electronic partition function: degeneracy.
8: Statistical Thermodynamics and Chemical Equilibrium: The Gibbs free energy and the
partition function; Equilibrium constants from partition functions.
9-10: Statistical thermodynamics of interacting molecules: Virial coefficients: van der Waals
equation; The radial distribution function (g(r)): second virial coefficient; The liquid state: the
structure of liquids; Calculation of g(r): Monte Carlo and Molecular Dynamics methods.
Objectives
By the end of the course the students should be able to:
• State the statistical definition of entropy and calculate the entropy of simple systems in
terms of their energy levels.
• State the definition of an ensemble and express the macroscopic properties of a system in
terms of an ensemble average.
• Calculate the most probable state of a system in terms of the Boltzmann distribution.
• Relate the partition function to thermodynamic quantities, such as internal energy,
Helmholtz free energy, pressure, entropy and heat capacity at constant volume.
• Derive statistical thermodynamics expressions of the thermodynamic properties of atomic
and molecular ideal gases.
• Evaluate the thermodynamic properties of atomic and molecular gases in terms of their
partition functions.
• Express the Gibbs free energy in terms of the partition functions for the reactants and
products
• Calculate the equilibrium constant for a gas phase reaction based on the partition functions
of the chemical components
• Relate the thermodynamic properties of liquids to the radial distribution function g®.
Understand the foundations of Monte Carlo and Molecular Dynamics techniques for the
computation.
Building upon
Interfacial Thermodynamics and Quantum Mechanics lecture courses. Theoretical Methods 1 & 2.
Looking forward to
3rd year lecture course in Molecular Reaction Dynamics and options courses in Modelling of
Nanomaterials and Modelling of Complex systems.
Department of Chemistry Second Year Syllabus
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Photochemistry
Durrant, James
10 hours
Aims
•
•
Introduce the processes of photochemistry and photophysics on a molecular level
Apply this fundamental understanding to selected examples of photochemistry
Summary
Molecular Photophysics: The course will start by building upon the students understanding of
quantum mechanics to describe the fundamental process of molecular light absorption and
emission: jablonski diagram, singlet and triplet states, transition dipoles and oscillator strength,
electronic and vibronic transitions, franck condon factors, intersystem crossing, perturbation theory.
Brief consideration will be given to the Einstein coefficients, and lasers.
Molecular photochemistry: excimers and exciplexes, photoisomerisation, excitation energy transfer
and photoinduced electron transfer. Experimental studies of photochemistry: steady state and
time-resolved techniques.
The course will use a range of examples of photochemical systems, including photosynthesis,
singlet oxygen damage and PDT, photoelectrochemistry and semiconductor photocatalysis.
Objectives
By the end of the course you should be able to:
• Describe in terms of quantum mechanics and potential energy surfaces the processes of
molecular photophysics
• Extend such analyses to simple photochemical reactions, including photodissociation,
energy transfer and electron transfer
• Give examples of important photochemical processes, detailing the relationship between
molecular electronic structure and photochemical function.
Building upon
Year 1 spectroscopy and quantum mechanics lecture courses, and year two Theoretical Methods
and Electronic Properties of Solids courses.
Looking forward to
3rd year Reaction Dynamics and Symmetry and Spectroscopy Courses. Options course including
Reactive intermediates, Molecular electronics, Sensing and detection, Optical and electrical
properties of nanomaterials, Mechanistic Photochemistry.
Department of Chemistry Second Year Syllabus
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