Chemistry-3H

Class Head: Dr. K.W. Muir

Course Documentation

Title: Molecular Symmetry

Lecturer(s): Dr rer nat Lutz Hecht

Aims: To demonstrate by means of worked examples how molecular symmetry arguments in the
context of the mathematical theory of groups can be exploited to deduce valuable information about
molecular properties and behaviour and how they can greatly simplify many important chemical
problems.

Objectives:

1. Define the terms symmetry element, symmetry operation and mathematical group, and
clarify their relationships.

2. Identify all the symmetry elements and symmetry operations of any given conformation of a
molecule, correctly assign it to a particular point group without any aids employing the Schoenflies
nomenclature, and sketch the correct conformation of a molecule for any given point group.

3. Construct group multiplication tables, determine matrix representations of group symmetry
operations and their characters, characterize character tables, distinguish between reducible and
irreducible representations, and indicate totally symmetric irreducible representations.

4. Reduce a general, reducible representation for any given point group using the reduction
formula and the corresponding character table, and construct appropriate sets of symmetry-adapted
basis functions from raw basis sets (such as atomic orbitals, atomic displacement coordinates or local
bond stretching coordinates) applying the projection operator method.

5. Specify the characters of direct product representations, and determine whether or not
quantum mechanical integrals will vanish identically as in the derivation of selection rules for
electronic and vibrational spectra or in molecular orbital theory.

Outline:
Symmetry arguments in the context of group theory provide a means of introducing
mathematical rigour into many important qualitative chemical problems such as the interpretation of
electronic and vibrational spectra, the simplification of quantum-mechanical calculations or the
existence of molecular properties such as permanent electric dipole moments and optical activity.

1. Definitions of molecular symmetry elements and of the associated symmetry operations they
generate.

2. Demonstration that the complete set of symmetry operations of a molecule forms a
mathematical group (a point group), Schoenflies nomenclature for molecular point groups, group
multiplication tables.

3. Representation of molecular symmetry operations by means of transformation matrices and
the associated irreducible representations and character tables, simple applications of character tables
to the determination of molecular dipole moments and optical activity.

4. Development of the general recipe for reducing representations, application to the
determination of hybridization schemes.
5. Introduction to the concept of symmetry-adapted functions, application of the projection
operator to generate sets of symmetry-adapted atomic orbitals for use as a basis in molecular orbital
calculations.

6. Formula for characters of direct product representations, vanishing integrals, applications to
molecular orbital calculations and spectroscopic selection rules.

7. Determination of the symmetry species of normal modes of vibration infrared and Raman
selection rules, stretching mode analysis to deduce the geometry of large molecules from the number
of infrared and Raman bands occuring in the appropriate stretching regions of the vibrational
spectrum.

Title: Quantum Mechanics of Atoms

Lecturer(s): Dr B C Webster

Aim: To introduce elementary concepts of quantum mechanics.

Objectives:

1. Define the concept of probability using a one-dimensional model potential and describe
tunneling.

2. Specify the use of operators and in particular, the Hamiltonian.

3. Show the energy of H(1s1) is -½ hartree and specify Eh = .

4. Define expectation value and be able to apply this in simple cases.

5. Define and illustrate hydrogenic wave functions.

6. Write down the Hamiltonian for two electron atoms.

7. Apply the variation theorem.

Outline:
A particle in a 1D potential well, with infinite walls, and with finite walls; application to solvated
electrons. Specification of requirements for a wave function, probability and normalisation worked
examples of the same, definition and use of operators, application to H (1s1) ground state,
specification of expectation values, commuting operators and observables, angular momentum
operators, H atom atomic orbitals, discussion of centrifugal term and periodic table, energy level
diagram, variation theorem.

Title: Bonding Theory

Lecturer(s): Dr B C Webster

Aims: To develop an understanding of theoretical techniques and principles applied to
contemporary chemical situations and problem-solving skills applied to material previously unseen.

Objectives:

1. Write an electronic configuration for a diatomic molecule and sketch the shape of molecular
orbitals from 1sg to 3su including 1pu and 1pg.

2. State the variation theorem and understand the origin of the secular equations and secular
determinant.

3. Determine the Hückel orbital energy level diagram for unsaturated hydrocarbons, and
calculate the molecular orbital coefficients.

4. Calculate the p-charge densities and p-bond orders and use an order/length relation.

5. Construct a set of symmetry orbitals and understand how this basis set simplified the solution
of a secular determinant.

6. Write an electronic configuration for a polyatomic molecule using symmetry labels.

7. State the Walsh rules, draw a Walsh diagram for H2O and apply these rules to predict
molecular shapes.

8. Apply your problem-solving skills to previously unseen material as, for example, to the
detection and prediction of the shape of molecules in interstellar regions.

Outline:
Molecular orbitals for diatomics; variation theorem, L.C.A.O.M.O. approximation; solution
of the Hückel secular equations; the use of symmetry orbitals; electronic configurations for polyatomic
molecules; Walsh rules.

Title: Organic Reactions

Lecturer(s): Dr E W Colvin

Aims: To introduce the mechanistic and stereochemical details of a range of synthetically useful
reactions.

Objectives:

1. Understand and discuss these reactions.

2. Give clear mechanistic explanations, using careful ‘arrow-pushing’, lone pair/bonding pair
electron involvement, and three-dimensional projection formulae.

3. Understand anti-addition of Br2 to alkenes, and appreciate its stereochemical outcome with
symmetric alkenes, and with unsymmetric alkenes.

4. Understand and apply erythro and threo diastereoisomer descriptions.

5. Interconvert Fischer and ‘sawhorse’ projection formulae.

6. Understand syn-addition of H2 (and D2), and appreciate its stereochemical outcome with
symmetric alkenes, and with unsymmetric alkenes.

7. Predict the stereochemical relationships in the products(s) from the mechanistic mode of
addition (anti or syn) and the alkene stereochemistry (E or Z).

8. Understand the regiochemistry and stereochemistry of hydroboration, and the mechanism of
oxidative cleavage of the intermediate organoborane.

9. Understand the mechanism of reaction of m-chloroperbenzoic acid with alkenes leading to
oxiranes and thence anti-1,2-diols.

10. Understand the mechanism of reaction of OsO4 with alkenes leading to syn-1,2-diols.

11. Understand the mechanism of cleavage of 1,2-diols with periodate.

12. Appreciate the stereochemical consequences of anti-elimination of the formation of alkenes.

13. Understand Wittig Olefination in terms of reagent preparation and syn-elimination.

14. Know how to prepare selenoxides, and be aware of their syn-elimination.

15. Appreciate, in both cases, their utility in regiospecific and stereoselective alkene preparation.

16. Appreciate the synthetic utility of Baeyer-Villiger oxidation, and understand its mechanism,
regiochemistry and stereochemistry.

17. Understand the preparation of phenol and acetone from cumene hydroperoxide.

18. Appreciate the synthetic utility of Hofmann and Curtius Rearrangements, and understand
their mechanism and stereochemistry.

19. Understand pinacol rearrangements, and the related rearrangement of 1,2-aminoalcohols.

20. Understand the benzil-benzilic acid arrangement.

Outline:
Mechanistic detail and stereochemistry, mainly using alkenes, with emphasis on correct and
careful arrow-pushing and lone-pair/bonding-pair electron involvement, with saw-horse projections
being used throughout.

A. Electrophilic Addition to Alkenes.

Regiochemistry - revision of Markovnikov, relative stabilities of carbonium ions; Addition of
HBr, of Br2/H2O to give bromohydrins.

1. anti-Addition

Addition of Br2 to symmetric alkenes ® ( ) or meso; intermediate bromonium ions, SN2
opening with inversion; detailed account of addition of Br2 addition to unsymmetric alkenes ® ( ) -
erythro or ( )-threo, i.e. anti addition of X2 or XY.

2. syn-Addition

(a) H2/Pd, D2/Pd.

Stereochemical conclusions - now drawn together, having been detailed in earlier individual
examples, summarised as
matched
anti-addition to a trans (E) alkene ® meso or ( )-erythro product.
syn-addition to a cis (Z) alkene ® meso or ( )-erythro product

mismatched
syn-addition to a trans (E) alkene ® ( ) or ( )-threo product.
anti addition to a cis (Z) alkene ® ( ) or ( )-threo product.
CART/TAME

Preparation of alcohols

(b) syn-Addition of BH3 and mechanism of oxidative cleavage - migration with retention to electron-
deficient oxygen.

Preparation of syn and anti 1,2-diols.

(d) OsO4 - syn-addition
(digression - Periodate cleavage of 1,2-diols, and comparison with ozonolysis).

B. Elimination Reactions to form Alkenes.

(a) anti-Elimination and E2, stereochemical consequences.

(b) syn-Elimination in Wittig Olefination - detailed.

preparation of phosphonium salts and ylids, and their reaction mechanism with carbonyl
compounds; emphasis on unambiguous alkene generation.

(c) syn-Elimination of Selenoxides - preparation, i.e., carbanion selenenylation using PhSeX and
oxirane opening by PhSe anion and utility in regiospecific and stereospecific alkene generation.

C. Rearrangement Reactions involving (formally) electron-deficient Oxygen, Nitrogen and Carbon.

All 1,2-shifts, intramolecular, retention at migrating group (carbon), all synthetically useful,
and dealt with in mechanistic detail.

To O
1. Baeyer-Villiger oxidation of ketones to esters or lactones.
2. Preparation of acetone and phenol from cumene hydroperoxide and mechanistic detail of
cumene®cumene hydroperoxide.

To N
3. Hofmann Rearrangement of primary amides to primary amines.
4. Curtius Rearrangement of acyl azides.

(Digression - isocyanates and carbamates/urethanes, insecticides, Bhopal disaster).

To C
5. Pinacol Rearrangement of 1,2-diols.
6. Rearrangement of 1,2-aminoalcohols by diazotization, ring expansion of cyclic ketones via
cyanohydrins.
7. Benzil-Benzilic Acid Rearrangement.

Title: Physical Organic Chemistry

Lecturer(s): Dr D G Morris

Aims: To achieve an understanding of the principles of organic reactivity in respect of substitution,
elimination and ester hydrolysis reactions; to enable application of the knowledge and principles
obtained in this course to be made in novel situations.

Objectives:

1. Understand the principles of order and molecularity, reaction coordinate diagrams and
kinetic and thermodynamic control.

2. Understand kinetic and steric requirements of SN2 reactions, the relationships between SN2’
and Michael reactions, what makes good nucleophiles and leaving groups and appreciate that F- is a
good nucleophile toward second row elements.

3. Understand the role of carbocations and ion-pairs in SN1 reactions, that ion-pair return
occurs with racemisation and 18O scrambling as appropriate, that Wagner-Meerwein rearrangements
can occur in SN1 reactions, that steric acceleration and anchimeric assistance can occur.

4. Describe E1, E2, E1cB, E2C+ and pyrolytic alkene forming reactions, and understand that
product regiochemistry is explicable by variable transition state theory; the relationship between E1cB
and fragmentation reactions; that presence of deuterium in a substrate normally results in a rate
retardation.

5. Understand the preferred direction of approach of a nucleophile to a carbonyl group; the acid
and base catalysed mechanisms of ester hydrolysis, also halolytic fission; the roles of nucleophilic and
general acid and base catalysis in hydrolysis of, e.g., chymotrypsin; the mechanism of the Wittig
reaction.

Outline:
Uni and bi-molecular reaction (SN1), (SN2), kinetic and stereochemical aspects, bridgehead
reactivity, Wagner-Meerwein rearrangements, SN2 reaction and Michael addition SRN 1 reaction;
E1, E2, E1cB and E2C+ eliminations; variable transition state theory, syn and anti eliminations,
pyrolytic eliminations.

Direction of attack on a carbonyl group; mechanism of acid and base-catalysed ester
hydrolysis; Wittig reaction.

Title: Organic Synthesis

Lecturer(s): Dr E Colvin/Dr J Carnduff

Aims: To review the types of mechanism of organic reactions, and factors which favour one reaction
type or one reaction site.
To introduce pericyclic reactions, their nomenclature, stereochemical rules and applications in
synthesis.
To demonstrate a number of methods of making carbon-carbon bonds, in particular next to carbonyl
groups, and to summarise briefly selectivity in reductions and oxidations.

Objectives:

1. Categorise a reaction
a) according to the overall result and
b) according to the type of electron reorganisation involved.

2. Explain how reactant structure and reaction conditions influence reaction type and reaction
site.

3. Identify factors which affect (a) equilibrium constants and (b) rate constants such as bond
energies, steric effects, electrostatics and polarity, delocalisation, intramolecularity and orbital
energies.

4. Identify types of pericyclic reactions and their stereochemical characteristics.

5. Appreciate the experimental evidence for concertedness.

6. Identify the stereochemistry of a reaction from those reactants and products.

7. Understand and use the Woodward/Hoffmann rule (toss/d).

8. Draw the shapes of pericyclic transition states.

9. Design syntheses using pericyclic processes.

10. Be able to predict approximate pKa values for a variety of compounds and apply them to
anion generation.

11. Appreciate kinetic and thermodynamic control of the relative amounts of the two enolate
anions obtained from unsymmetrically a-substituted ketones, and the factors involved.

12. Understand the use of trimethylsilyl enol ethers as enolate anion precursors for a-alkylation.

13. Know how enamines are prepared, appreciating why an unsymmetrically a-substituted ketone
gives predominantly the less substituted enamine, and understand their monoalkylation.

14. Know how aldehydes and carboxylic acids can be a-substituted via their imine and enediolate
anions, respectively.

15. Appreciate the variety of reactions involving condensation of an aldehyde or ketone with an
active methylene group and why an (E) double bond is formed on dehydration of the b-
hydroxycarbonyl compound.

16. Know that directed aldol reactions can be effected through carbanions derived from imines
and through trimethylsilyl enol ethers.

17. Appreciate the synthetic value of Robinson annulation.

18. Understand the preparation and synthetic utility of lithium dialkyl cuprates.

19. Understand metal-ammonia reductions and reductive alkylations of conjugated enones and
know that methoxybenzenes can be converted into cyclohex-2-enones.

20. Appreciate selectivity in a variety of reducing agents and oxidising agents.

21. Be able to explain the above reactions and use them in planning syntheses.

Title: Coordination Chemistry

Lecturer(s): Dr R D Peacock

Aims: To give an overview of the coordination chemistry of the transition elements; to emphasise
the differences between the chemistry of the first row elements and those of the second and third rows;
to explain the d«d spectra of transition metal ions.

Objectives:

1. Understand the basic concepts of coordination chemistry: d-orbital shapes, coordination
number and geometry, ligand substitution, chelate and macrocyclic effect, LFSE, kinetic and
thermodynamic stability, hard and soft behaviour.

2. Appreciate the type of coordination chemistry shown by the first row elements and how and
why the chemistry of the second and third row elements differs from this.

3. Understand the bonding, chemistry and spectroscopy of the metal-metal multiple bond.

4. Understand the origins of the electronic spectra of transition metal ions.

5. Be able to use Tanabe-Sugano Diagrams (for the d2 and d3 configurations) to predict spectra
or to calculate the values of D and B.

6. Be able to solve problems involving coordination chemistry.

Outline:
Revision of level 1 and 2 chemistry. Basic concepts of transition metal and coordination
chemistry. Exemplification of first row chemistry. Contrast of first row and second and third row
chemistry. The metal-metal multiple bond.
Spectroscopy of d«d transitions.

Title: Inorganic Mechanisms/Photochemistry

Lecturer(s): Dr A C Benniston

Aims: To deal in depth with inorganic mechanisms in order that students will be able to identify
and comprehend how and why reactions occur in transition metal ion complexes. Introduce students
to the area of electrochemistry and photochemistry, and in particular cyclic voltammetry and
photoinduced electron transfer.

Objectives:

1. Inorganic mechanisms (5 lectures): Understand the difference between stability and lability
and how crystal field theory can be used to explain trends in ligand substitution in metal ion
complexes. Recognise parameters associated with the kinetics at metal ion centres, and how to
interpret them. Distinguish and classify inorganic reactions; for example substitution, electron-
transfer and ligand-activated reactions. Understand the difference between associative and
dissociative reaction mechanisms and what factors influence them.

2. Cyclic voltammetry (1 lecture): Have a general understanding of reactions at an electrode
surface, and how the difference between a reversible and irreversible process. Recognise the salient
features of a cyclic voltammogram and know how to obtain physical information using the Randle-
Sevcik equation.

3. Photochemistry (2 lectures): Have a general understanding of what terms mean including
donor/acceptor, triplet/singlet state and lifetime. Understand what is photoinduced electron transfer
between donor-acceptor molecules. Be able to describe what is electron transfer and energy transfer.
Know what photoinduced electronic processes can occur in transition metal ion complexes and give
examples (e.g. Ru (bipy)3 2+).

4. Overall: Be expected to apply what has been learnt to answer problems covering relevant
aspects of the preceding topics.

Outline:
Much of this third year course will cover new material and will be as descriptive as possible.
However, for the first part of this course it is essential that students re-acquaint themselves with
first/second year work; for example, crystal field theory, stepwise stability constants, hard and soft
acids/bases and general transition metal ion chemistry.

Title: Solid State Chemistry

Lecturer(s): Dr D McComb

Aims: To advance the understanding of the structure and properties of solids.

Objectives:

1. Understand the concepts of close-packing and how this can be used to describe the structures
of common inorganic solids.

2. Have a detailed knowledge of the structures of the following inorganic solids: NaCI, ZnS
(blende and wurtzite), CsCI, CaF2, K2O, perovskites, spinels and silicates.

3. Understand the electronic properties of solids as applied to metals, semiconductors and
insulators by application of band theory and an appreciation of the factors governing the onset of
superconducting properties in some metals and alloys.

4. Appreciate the factors affecting electronic conduction (band gaps) in inorganic solids.

5. Have a knowledge of defects and ionic conductivity.

6. Have a knowledge of extended defects and their influence on material properties.

7. To be able to discuss and answer questions on the relationship between structure and
properties in inorganic solids.

Outline:
Study of inorganic solids with NaCl, ZnS (blende and wurtzite), CsCl, CaF2, K2O,
perovskite, spinel and silicate structures. Electronic properties of solids investigated using band
theory, including density of states plots, p and n type semiconductors and factors affecting conduction
in organic solids. Superconductors. Point defects and ionic conductivity. Extended defects and
material properties.

Title: Computational Chemistry

Lecturer(s): Dr C J Gilmore

Aims: To give a brief introduction to computers and their jargon, molecular mechanics, databases
and interfacing computers with equipment.

Objectives:

1. Understand the terms digital, processor, memory, disk, terminal, bit, byte, word, and how
these various components link together to give computer hardware.

2. Understand the concept of a computer program, and stored data.

3. Understand the need for molecular mechanics.

4. Understand the principles of molecular mechanics including all the force field components,
the Newton Raphson method of energy minimisation, and the source of the constants used in the force
field.

5. Understand the definition and concept of a database and the parameters which can be
obtained from X-ray crystallography; the concept of a crystallographic database, why it is useful and
what it contains.

6. Understand that the three entries for each crystal are structure-bibliographic, connectivity
and coordinate data, decide what information can be obtained from these entries.

7. Understand how some of this information can be used in molecular mechanics.

8. Describe the terms drug, receptor, receptor site, inhibitor the use of X-ray crystallography to
determine some (but not most) protein structures.

9. Understand postulate receptor site geometries from the structures of known drugs.

10. Describe how existing drugs can be improved by the use of databases and molecular
mechanics.

Outline:
The computer is having a dramatic effect on almost all aspects of modern chemistry; this
course explains why this is so and selects three aspects of computational chemistry to study in some
detail.

An introduction to computers, computer architecture and the jargon of computing science.

The computer as a “number cruncher”: designing molecules, predicting the geometries of
new or unstable molecules; molecular graphics.

The computer as a library: chemical databases.

Interfacing computers to chemical instrumentation with special reference to mass
spectrometry.
There are two experiments in the physical chemistry laboratory which give students practical
experience of these concepts.

Title: Crystallography

Lecturer(s): Dr K W Muir

Aims: To introduce students to crystallographic symmetry, crystal structure analysis by diffraction
methods, and chemical applications of diffraction techniques.

Objectives:

1. Explain and employ the concepts used to describe the internal structure of crystals, including
the following terms: net, lattice, unit cell, non-primitive unit cell, space group, screw axis, glide
plane.

2. Explain the limitation of symmetry in nets and lattices and how this leads to a limitation in
the number of possible crystallographic point groups.

3. Know how beams of monochromatic X-rays can be obtained in the laboratory.

4. Understand and explain coherent elastic scattering of X-rays.

5. Derive and apply Bragg’s Law.

6. Define and use Miller indices.

7. Explain experimental methods used in diffraction studies and the nature of the results of such
experiments including the relationship between intensity and structure amplitude.

8. Understand and explain the terms atomic scattering factor and temperature factor.

9. Understand and explain the terms structure factor, structure amplitude and phase and know
the equation relating the structure factor to the positions of atoms within the unit cell of the crystal.

10. Be able to state the Fourier series expression for electron density distribution in a crystal and
know what is required before the Fourier series expression for electron density can be applied.

11. Understand and explain the nature of the phase problem.

12. Understand and explain the properties of the Patterson function and be capable of solving
heavy atom Patterson functions in common triclinic and monoclinic and orthorhombic space groups.

13. Understand and explain the nature of heavy atom methods of solving the phase problem.

14. Be capable of stating and explaining how crystal structures are refined.

15. Understand and explain the principles and main chemical applications of neutron diffraction.

16. Be aware of the main chemical applications of single crystal diffraction experiments.

17. Solve problems on the material presented in the lecture and associated laboratory courses.

Outline:

1. The Internal Structure of Crystals: Lattices, Unit Cells, Hermann-Mauguin Notation, Bravais
Nets & Lattices, Crystallographic Point Groups, Plane & Space Groups, Role of Symmetry in
Crystallography.

2. Geometry of X-ray Diffraction: X-ray Sources, X-rays, Matter & Diffraction, Bragg’s Law,
Experimental Methods.

3. Intensity of Bragg Reflections: Addition of Coherent Waves, Atomic Scattering Factors,
Temperature Factors, Unit Cell Scattering & the Structure Factor, Fourier Series Representation of
Electron Density, Space Group Determination.

4. Structure Analysis: The Phase Problem, Heavy Atom & Direct Methods.

5. Refinement: Agreement Indices, Difference Syntheses, Least-Squares Refinement.

6. Chemical Applications of X-ray Analysis: Biological Macromolecules, Organometallics,
Databases & Published Compilations, Absolute Configuration.

7. Neutron Diffraction: Principles, Experimental Considerations, Neutron Analysis, Chemical
Applications.

8. Charge Density Studies.

Practical experience of the concepts developed in the lecture course is provided by an
experiment in the physical chemistry laboratory.

Title: Thermodynamics

Lecturer(s): Dr J H Dymond

Aims: To show how equilibrium thermodynamic properties are affected by changes in temperature,
by changes in pressure and by addition of other materials, with examples of practical importance.

Objectives:

1. Define state function and exact differential.

2. Define and use isobaric coefficient of thermal expansion a and isothermal compressibility k.

3. Use the properties of partial derivatives to relate the variation of pressure with temperature at
constant volume to a and k.

4. Describe and explain the significance of the Joule-Thomson experiment, define the Joule-
Thomson coefficient and derive relationships for it for simple equations of state; discuss its
importance in the liquefaction of gases.

5. Describe effects of change in temperature and in pressure on the Gibbs free energy and
discuss their practical significance.

6. Define chemical potential and give expressions for i) solids or liquids ii) pure gases iii)
components of an ideals gas mixture iv) components of an ideal liquid mixture and v) components of
non-ideal liquid mixture.

7. Understand and use the Gibbs-Duhem and Duhem-Margules equations.

8. Describe the composition dependence of the thermodynamic mixing properties and discuss
the deviations expected for specific real systems.

9. Describe how DmixG can be obtained from total vapour pressure curves.

10. Construct and interpret vapour pressure diagrams for mixtures of two volatile liquids and
appreciate the significance of (T-x,y) diagrams for fractional distillation.

11. Calculate the ideal solubility of a solid in a solvent.

12. Understand the physical-chemical basis for supercritical extraction.

Outline:
This course is designed to show the effects of changes in temperature and in pressure, and of
mixing, on equilibrium thermodynamic properties, with emphasis on their practical significance.
Introduction: meaning of State Functions and Exact Differentials; the isobaric coefficient of
thermal expansion; the isothermal compressibility.

The Joule-Thomson effect, evidence for molecular interactions and its importance in gas
liquefaction.
The effect of temperature on the Gibbs free energy and Ellingham diagrams; the effect of
pressure on the Gibbs free energy and its significance in geochemistry; partial molar quantities.
Chemical potential for a pure gas/liquid/solid and components in a gas/liquid mixture;
thermodynamic mixing properties for liquid mixtures.
Gibbs-Duhem and Duhem-Margules equations.
Fractional distillation; ideal solid solubility; supercritical extraction.

Title: Natural Products

Lecturer(s): Dr R A Hill

Aims: To explore the range of natural products and their biosynthetic pathways and how isotopic
labelling can be use as a tool to determine biosynthetic pathways.

Objectives:

1. Be able to identify the biosynthetic origin of a range of natural products including
polyketides, terpenoids, alkaloids and phenylpropanoids.

2. Remember the importance of structural relationships in biosynthetic studies, the use of well-
known reaction mechanisms and methods for the determination of intermediates in biosynthetic
pathways.

3. Outline the pathway from acetyl CoA to fatty acids and polyketides and how further
biosynthetic modifications can occur.

4. Apply the isoprene rule to terpenoids and outline the biosynthesis of the C5 unit and its
coupling and further modifications to give terpenoids and steroids.

5. Understand pathways to some of the important classes of alkaloids and phenylpropanoids.

6. Understand labelling studies with 2H, 3H, 13C, 14C, 15N and 18O.

Outline:
The biogenetic approach to natural product classification. Methods for determination of
biosynthetic pathways, the use of isotopic labelling including multiple labelling. Acetyl CoA in the
biosynthesis of fatty acids, prostaglandins and polyketides. Modifications of natural products
including oxidation, reduction, alkylation etc. The biosynthesis of terpenoids and steroids and the
importance of rearrangements. The alkaloids classes and the important reactions involved in their
biosynthesis. The biosynthesis of phenylpropanoids including flavonoids and lignins. Overall view of
labelling studies.

Title: Stereochemistry

Lecturer(s): Prof J D Connolly

Aims: To introduce the principles of enantioselective and diastereoselective synthesis after
establishing molecular features which lead to chirality, methods of measuring
enantio/diastereoisomeric ratios and the concept of prochirality. To introduce the ideas of
conformational analysis of monosubstituted cyclohexanes and the methods of measuring
thermodynamic parameters for the interconversion process.

Objectives:

1. Draw, using proper stereochemical conventions, molecules which owe their chirality to a
chiral centre, a chiral axis or a chiral plane.

2. Suggest analytical methods for distinguishing enantiomers (chiral solvent, chiral shift
reagent and MTPA ester in NMR spectra).

3. Understand the concept of prochirality and the significance of enantiotopic and diastereotopic
centres and faces (be able to use pro-R, pro-S, re and si).

4. Be familiar with the common Cahn Ingold Prelog rules.

5. Recognise and provide examples of enantioselective and diastereoselective reactions.

6. Rationalise stereoselectivity in terms of diastereoisomeric transition states.

7. Be familiar with the chirally modified reagents Binal-H, (IPC)2BH and the Sharpless reagent
system.

8. Apply Cram’s rule to addition to C=O groups.

9. Understand what is meant by chelation control.
10. Appreciate the factors which make conformers separable (DG#, T).
11. Appreciate the value of low temperature NMR in measuring conformational equilibria.
12. Recognise the t-Bu group as a conformational locking group for cyclohexane.
13. Be able to deal with the conformational interconversion of cyclohexane and methyl
cyclohexane.
14. Apply the Karplus relationship to cyclohexanes or carbohydrate equivalents.

15. Apply this knowledge to unseen situations.

Title: Pericycles/Photochemistry

Lecturer(s): Dr J Carnduff/Dr R A Hill

Aims: To explore the scope of pericyclic and photochemical reactions and their interpretation in
terms of frontier orbitals and excited states.

Objectives:

1. Appreciate the great variety of pericyclic processes and the site and stereoselectivities they
can show.

2. Interpret some of these pericyclic processes in terms of Frontier Molecular Orbital (FMO)
energies and coefficients.

3. Extend FMO ideas to understand soft-soft ionic reaction rates.

4. Understand the processes of excitation and decay back to the ground state and the differences
between excited singlet and triplet states.

5. Be able to give examples and propose mechanisms for photochemical reactions of ketones,
enones, dienones and alkenes.

6. Understand the production of singlet oxygen and its reactions with organic compounds.

7. Describe the photochemical reactions of other chromophores such as diazoalkanes,
diazoketones and organic nitrites.

8. Apply the principles of the course to solve unseen mechanistic problems.

Outline:

Examples of pericyclic reactions in synthesis and biosynthesis, identification of effects on
rates, on stereochemistry and on site of reaction. Frontier Molecular Orbital interactions theory
applied to cycloadditions and to soft-soft ionic reactions to interpret the Woodward-Hoffmann rule,
substituent effects on cycloaddition rates, inversion in SN2 reactions, orientation in Diels-Alder
reactions and site of reaction of enolate ions. Description of excited states and modes of decay,
fluorescence, phosphorescence, excited singlets and triplets, photosensitisation and quenching.
Photochemistry of carbonyl compounds, a-cleavage, b-cleavage, addition to double bonds, hydrogen
atom abstraction. Photochemistry of alkenes, cis/trans isomerism, addition reactions, di-p-methane
rearrangement, conjugated carbonyls. Product and reactions of singlet oxygen, organic nitrites
(Barton reaction), diazomethane, diazoketones (Wolff rearrangement).

Title: Main Group Chemistry

Lecturer(s): Prof T M Klapötke

Aims: To develop a knowledge of the main properties of s- and p-block elements and of their binary
and ternary compounds, including the physical nature of the compounds, their reactivity and their
structure and bonding.

Objectives:

1. Understand the modern VSEPR model and know about the domain version of this model;
examples to be discussed are: XeF5-, XeOF5-, HfF73-vs. NbF72-,
MoF 7 -, F4S=CH2 etc.

2. Understand the p*p* bond found in by some nonmetal molecules and ions, and know about
the molecular orbitals involved in this interaction; examples are: I42+, N2O2, N2O4,E2I42+(E =S,
Se).

3. Know the structures and properties of pseudo-aromatic inorganic ring systems (S-N and Se-N
ring systems).

4. Be familiar with the occurrence, nature and relative strength of multiple bonds between
elements (npp-npp, n ò 3).

5. Have a knowledge of the structures, properties and bonding rationalisations of inorganic
cages (e.g. C60, He@C60, E4N4n+, E = S, Se, Te; n = 0,4).

6. Understand intramolecular donor-acceptor interactions, and know about hyperconjugation,
anomeric effects and the Bohlmann effect.

7. Have a knowledge of orbital symmetry effects, and be familiar with differences between the
reaction behaviour of cis and trans N2F2.

8. Have a knowledge of molecular dynamics, and be familiar with the interplay between energy
and structure (N2H4 vs. N2H4+).

9. Have a knowledge of the construction of simple Born-Haber cycles, and be familiar with
crystal lattice energy estimations.

10. Know about preparative aspects of modern main group chemistry.

Outline:

The course covers five areas of inorganic main group chemistry: (i) structure and bonding,
(ii) rings and cages, (iii) orbital symmetry effects and kinetics, (iv) thermodynamics and (v)
preparative aspects.

It is assumed that the student has completed the relevant first and second year courses on
inorganic chemistry. Some elementary but very important topics, such as the VSEPR and increased
valence structures are included for review and emphasis.

Data from advanced experimental techniques such as NMR (14N, 19F, 77Se) and
photoelectron spectroscopy have been included where appropriate.

Structure and bonding; the VSEPR model, the electron domain model, p*-p* interactions,
pseudo-aromatic systems, intramolecular donor-acceptor interactions (hyperconjugation, anomeric
effects, Bohlmann effect).

Orbital symmetry effects and kinetics; reactions of cis and trans N2F2, reactions of N2F+,
reactions of nitrogen with hydrogen.

Thermodynamics; estimation of the heat of reaction by using a simple Born-Haber energy
cycle, estimation of the crystal lattice energy by using the Bartlett equation.

Multiple bonding; comparison of first row and heavier elements.

Title: Transition Metal Organometallic Compounds

Lecturer(s): Dr L J Farrugia

Aims: To consolidate and build on previous Level 1, 2 & 3 courses on the transition metals, to
develop ideas on their organometallic compounds with respect to type, bonding and reactivity.

Objectives:

1. Know the types of organometallic ligands found (both s-donors and p-acid ligands) and be
able to rationalise their synergic bonding to transition metals, and their formal electron donating
counts. Be familiar with the experimental evidence for p back donation in carbonyl and olefin
compounds, and basic reaction types associated with the more common ligands, i.e. oxidative
addition, hydride migration, reductive elimination.

2. Understand the metal-metal bonding in bimetallic carbonyls such as Mn2(CO)10 through the
isolobal principle. Know examples of larger carbonyl clusters with delocalised metal-metal bonds,
and how they are related to boranes via extensions of Wade’s Rules. Know about the occurrence of
multiple metal-metal bonds, and be able to rationalise the bonding in terms of s, p and d bonds.

3. Know about the occurrence of metal hydrido compounds and multiple hydrido compounds
with dihydrogen ligands. Know the experimental evidence for “non classical” hydrides, particularly
T1 NMR measurements.

4. Know a little about, and have a feel for the organometallic chemistry of all transition metals,
so they are not just symbols. In part this is achieved by the recommended readings.

Outline:

18-electron rule. Properties and synthesis of organotransition metal compounds and their
reaction types.

Title: Radiochemistry and Catalysis

Lecturer(s): Dr D Stirling/ Dr D Lennon

Aims: To introduce students to the principles of radiochemistry and catalysis.

Objectives:

1. Know the principles of the production of artificial radionuclides by particle bombardment
and nuclear fission.

2. Understand the manner of growth of activity as a function of irradiation time for irradiation
in a constant neutron flux.

3. Understand how Szilard-Chalmers processes can be used to make sources of enhanced
specific activity by n.g reaction.

4. Understand how it is possible to discriminate between components of radioactive mixtures by
measurement of the energy of radiation.

5. Understand the function of a catalyst.

6. Physical and chemical adsorption processes, BET method for determination of surface area,
derivation of Langmuir isotherm for:
a) adsorption of a single substance.
b) competitive adsorption of two gases at a solid surface. Measurements of metal surface
area of a catalyst by chemisorption.

7. Have a knowledge of how tracers can be used in mechanistic studies of catalysis.

Outline:

Production of artificial radionuclides by nuclear fission and by particle capture, concept of
specific activity. Secular equilibrium - growth back to secular equilibrium when equilibrium is
disturbed by chemical separation of some components. Neutron activation for analysis and for
producing radionuclides for tracer studies; Szilard-Chalmers processes as a means of overcoming the
disadvantage that the product is often of low specific activity because it is isotopic with the target
material. Introduction to catalysis, physical and chemical adsorption, BET method for surface area
measurement, Langmuir isotherm, chemisorption for metal surface area measurement. Applications
of tracers to the study of catalytic processes.

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