FIRST YEAR CLASS SYLLABI

DETAILS OF FIRST YEAR COMPULSORY CLASSES

All of the courses in the following list have a number of key and transferable skills associated with them. Please consult Appendix 2 at the end of this handbook for information about which skills are embedded in particular courses. These skills will be examined in the assessments associated with each particular class.

MM 116 MATHEMATICS

Lectures: Mondays, Tuesdays and Fridays 12-1, first and second semester

Tutorials: Thursdays 12-1, first and second semester

20 credits (ECTS 10): There are 4 multiple choice class tests (2 in Semester 2 and 2 in Semester 2) and averaging 60% and above in these tests exempts from final examination. The final examination is a 3 hour written exam in May with resit in August. Lecturers: Dr P Davidson and Dr M Grinfeld

SHE Level: 1

Aims

To give a basic understanding of mathematical functions, differentiation, integration, complex numbers, matrices and vectors.

Learning Outcomes

On completion of this class, the student should

• understand the concept of a mathematical function; • be familiar with commonly occurring functions and their properties, and be able to manipulate and solve equations and inequalities involving them;

• know the factorial and binomial coefficient notation, and be able to use the binomial theorem;

• be able to differentiate functions, via combinations of the various differentiation rules;

• be able to locate and classify stationary points of a function of one variable;

• be able to integrate simple functions;

• be able to use integration to calculate the area between two curves;

• be able to manipulate complex numbers in Cartesian, polar and exponential form;

• be able to find definite and indefinite integrals using substitutions, partial fractions and integration by parts;

• be able to carry out standard matrix operations; • be able to express systems of linear equations in matrix form, and to apply elementary row operations on the associated augmented matrix to find the solution of a given system; • be familiar with the concept of a vector and the fundamental operations with vectors: addition, multiplication by a scalar, and scalar and vector products;

• be able to solve first-order separable differential equations;

• be able to fit a straight line to data (including in a log plot), to verify experimental laws and determine suitable values for the parameters of such laws.Syllabus

Syllabus

Mathematical Foundations:

Algebra – mathematical notation, number sets and inequalities, basic operations (+,–,×,÷), modulus, factorial, indices, rules of precedence, use of brackets, expanding brackets, binomial expansion, simplifying algebraic expressions, factorisation, common denominators, cancelling common factors, proportionality, mathematical formulae and transposition, partial fractions. Functions – basic concepts and notation, graphs, continuity and limits; composition of functions; inverses; linear and quadratic functions, completing the square; other commonly occurring functions (including polynomials, rational functions, exponentials, logarithms, hyperbolic functions, modulus); odd and even functions; periodic functions. Solving equations – linear equations, quadratic equations, polynomial equations; simultaneous equations in two unknowns. Trigonometry – definitions and graphs of sine, cosine and tangent; periodicity; radian measure; definitions of sec, cosec and cot, and of inverse trigonometric functions; important trigonometric identities; solving simple trigonometric equations. Verification of experimental laws – linear or log plots to fit straight lines to data.

Introduction to Calculus:

Differentiation – definition of a derivative; notation; simple examples from first principles; graphical interpretation; stationary points; higher derivatives. Standard derivatives – including x^a and trigonometric, exponential and natural log functions. Rules of differentiation – linearity; product rule; quotient rule; chain rule. Indefinite integration – reversing differentiation; standard integrals; linearity. Definite integration – motivation: area under a curve; definition; the Fundamental Theorem of Calculus.

Complex Numbers:

Algebra of complex numbers – motivation and definition of i; real and imaginary parts; arithmetic of complex numbers. Polar and exponential forms – the Argand diagram; modulus and argument; polar form; Euler's formula; exponential form; products and quotients in exponential form; De Moivre's Theorem.

Matrices and Systems of Linear Equations:

Matrix algebra – definitions, notation, and some special matrices; multiplication by a constant; addition of matrices; matrix multiplication. Matrix inverse – definition of the inverse of a square matrix; the inverse of a 2 × 2 matrix; singular and non- singular matrices. Linear equations – representation of a system of linear equations in matrix form. Solution of systems of linear equations – augmented matrix for n equations in n unknowns; reduction to triangular form using elementary row operations; unique solution, non-uniqueness and inconsistency.

Vectors:

Motivation as quantities having magnitude and direction, e.g. force, displacement, velocity, etc; vectors as directed line segments; vector algebra; orthogonal unit vectors; representation of vectors as number triples; scalar and vector products; triple products.

Further Calculus:

Applications of differentiation – simple graph sketching; optimisation problems; related rates of change; linear approximation and error analysis. Methods of integration – integration by substitution; integration by parts; integration of rational functions; integrals of some trigonometric functions. Applications – area between curves; first-order separable ODEs.

PH 151 MECHANICS, OPTICS AND WAVES

Lectures: Mondays, Tuesdays, Thursdays and Fridays 9-10, first semester

Laboratory/tutorials: One afternoon per week, first semester

10 credits (ECTS 5): Written examination (1 hour 30 min) in January with resit in August.

Lecturers: Dr N Langford

SHE Level: 1

Learning Outcomes

By the end of the course a student shall show: • Ability to analysis the motion of a particle in two dimensions. • Ability to apply Newton’s three laws to analysis bodies in different conditions. • Ability to explain difference between elastic and inelastic collisions. • Ability to address problems on conservation of linear momentum. • To understand circular motion • State and apply Newton’s Law of Gravity, determine gravitational field strength at a given point. • Know the difference between conservative and dissipative forces, work and power. • Ability to apply kinematic equations to angular motion and associated rotational forces. • To describe conditions necessary for a body to execute simple harmonic motion and determine displacement, velocity and acceleration of body. • Define a wave, differentiate between wave types . • Identify key parameters associated with harmonic / periodic waves and use different notations to describe wave. • Differentiate between travelling and standing waves and write down equations for each type of wave – identify conditions necessary for node and anti-nodes. • Understand difference between particle and wave velocity. • Explain reflection and transmission of mechanical waves at a boundary. • State and apply principle of linear superposition to waves – beats and interference. • Understand effect of relative motion between wave source and detector- Doppler effect. • Understand and apply Huygen’s Principle to reflection, refraction and diffraction. • Explain the concepts of critical angle and total internal reflection.

Mechanics • Motion in 1 dimension: Definitions of velocity and acceleration, equations of motion for constant acceleration. • Vectors: Addition of vectors, resolution into components, use of unit vectors. Vector multiplication, scalar and vector products. • Motion in 2 dimensions: Motion in a plane, projectiles. • Newton’s Laws: Statements of Newton’s three laws, equilibrium, statics and dynamics, friction forces. • Linear momentum: Centre of mass, conservation of linear momentum. Impulse and momentum, elastic and inelastic collisions. • Uniform circular motion: Angular speed, centripetal acceleration, examples of uniform circular motion. • Work and Energy: Mechanical work, kinetic and potential energy. Conservative and dissipative forces. Gravitational and Elastic Potential Energy functions. Conservation of mechanical energy. Energy and Power. • Gravitation: Newton’s law of gravitation, gravitational field strength (g) and variation with altitude. Motion of satellites. • Simple Harmonic Motion: Defining equation and its solution. Meaning of amplitude, angular frequency and phase constant. Forces producing simple harmonic motion. • Rotational Mechanics: Angular velocity and angular acceleration. Kinematic equations for rotation with constant angular acceleration. Moment (Torque) of a force about a point and relationship to angular acceleration. Moment of inertia of systems of particles and rigid bodies. Rotational kinetic energy. Angular Momentum. Waves • Wave fundamentals: Definition of a wave. Types of wave Frames of reference, wave function y(x,t) = f(x- vt), speed of wave, phase of wave. • Periodic Waves. Definition of wavelength and period. Harmonic waves and w-k notation, initial phase f and phase differences. Difference between wave speed and particle speed. Particle velocity and acceleration. Wave speed on a string. Energy transport by a wave on a string. • Principle of linear superposition. Reflection at free and fixed ends, reflections at interfaces. Resonant waves on strings and in open and closed pipes. Standing waves. Beats. Interference and coherence • Waves in more than one dimension, circular and spherical waves, energy conservation in spherical waves. Huygens’ Principle. Optics • Idea of electromagnetic (em) waves. Speed of light in vacuum. Huygens' principle applied to reflection, refraction and diffraction. Laws of reflection. Diffuse and specular reflections. • Images: Introduction to real and imaginary images and objects. Deviation introduced by reflection. Image formation in plane mirrors. • Refraction in materials. Speed of light in a material. Snell’s law. Deviation induced by refraction. Critical angle and total internal reflection. Optical fibres. Refraction in prisms. Minimum deviation in a prism.

BM102 BIOSCIENCE CLASS

BM 102 Molecular Bioscience (20 credits, ECTS 10)

Lectures: Mondays and Fridays 9-11, first semester

SHE Level: 1

This class covers cellular structure and function and is concerned with the chemical basis of life and the fundamentals of cell biochemistry. Microscopy, cell theory, cell types, cell size, organelles, membrane structure and function and the structure and function of cell organelles are considered, as well as the chemical constituents. The molecular basis of inheritance, human genetics, genes and the environment: chemical structure of the gene; DNA replication; genes and enzymes; protein synthesis; regulation of gene expression; genetic engineering and genetic diseases are also covered.

You will note that Bisocience students also taking this class have a personal response receiver. That Department provides these to each of their students but Chemistry has not adopted this policy. You will still be able to test yourself by attempting to answer the questions posed in class.

CH 106 CHEMISTRY: PRINCIPLES AND PRACTICE 1

First semester Credits 20 (ECTS 10) Lectures 46 Revision classes 14

Multiple choice examination (2 hours) in January with resit in August.

Lecturers: Dr EJ Cussen, Prof D Graham, Prof JA Murphy, Dr AR Kennedy, Prof PJ Halling

SHE Level: 1

Analytical Chemistry

Lectures: 4

Revision Classes : 2

Lecturer : Prof D Graham (Room TC632D)

Aims and Objectives

To provide the students with the knowledge and accomplishments needed to appreciate the calculations and importance of the volumetric analysis illustrated in the first year laboratory

Learning Outcomes - On completion of this course the student should be able to:

• Describe the precautions needed to obtain a good titration and to decide if a chemical reaction would be a suitable basis for a titration. • Calculate from the titrant volume consumed in a titration: • the molarity and concentration of the titrand solution • the percentage of the analyte in a known weight of sample • Balance Redox equations • Choose a suitable indicator and a suitable primary standard for acid/base, redox, and complexometric titrations.

Content

1 Introduction to Volumetric Analysis - requirements for good titration - speed of reaction, completeness of reaction, alternative reactions.

2 Indicators, Titrant concentrations, Primary Standards, Titration Calculations, Stoichiometry.

3 Molarity and Concentration, Weights and percentages, Acid-Base titrations. Concept of pH, pH titrations. Complexometric titrations - EDTA titrations.

4 Redox reactions - Redox couples - Balancing Redox equations.

Redox titrations - permanganate titrations, iodine titrations.

Structure and Bonding Lectures : 12

Revision classes : 3

Lecturer: Dr E Cussen (Room TG506)

Aims and Objectives

To provide an understanding of the basic theory of atomic structure and bonding in molecules. The specific objectives are an understanding of Bohr theory of the atom, of the modern quantum mechanical approach to atomic structure, of the valence bond and molecular orbital approaches to bonding in molecules and the use of bonding theory to predict structure of specific molecules as examples.

Learning Outcomes - On completion of this course the student should be able to:

• Describe the structure of atoms in terms of Bohr theory and modern atomic theory. • Relate the above to emission spectra and to the position of atoms in the periodic table. • Understand the concept of quantum number and describe specific atoms in terms of the appropriate quantum number set. • Be able to draw and interpret the angular functions for s, p and d orbitals. • Understand the concepts of valence bond and molecule orbital theory. • Use the concept of hybridisation to describe the bonding in simple organic and inorganic molecules • Describe the molecular structure of simple diatomic molecules using molecular orbital correlation diagrams • know about the key experiments which led to Bohr theory; • describe the Bohr theory of the atom; • describe the extensions of Bohr theory and the introduction of quantum numbers; • detail the advantages and disadvantages of Bohr theory; • calculate the energy levels in atoms; • describe the quantum numbers and their relationships; • state the Pauli principle and the Aufbau principle; • use the Pauli principle and Aufbau principle to build up atomic structure; • explain the relationship between atomic structure and the arrangement of the elements I the periodic table; • explain why modern atomic theory was necessary; • describe the approach of modern atomic theory; • explain the use of the DeBroglie relationship and the wave/particle nature of electrons; • explain what a wave function is; • describe radial and angular functions; • define and plot radial distribution functions; • plot s, p and d angular functions; • define and explain the terms ionisation potential, electron affinity and electronegativity. Show how the values of ionisation potentials are related to atomic structure; • define the repulsive and attractive forces in a simple molecule; • plot a diagram to describe the effect on energy of forming a bond; • define the basic concepts of the valence bond and molecular orbital approaches; • indicate how the strength of a bond is measured in valence bond theory; • explain what is meant by hybridisation; • draw an Sp hybrid and be able to indicate the directions in space of Sp2 and Sp3 hybrids; • explain how hybridisation can be used to describe the bonding in simple molecules such as BeF2, BF3, CH4, NH3, C2H4 and C2H2;

• know about hybridisation of molecules such as PF5; • describe a dipole of a molecule; - • describe the concept of resonance and apply it to NO3 and benzene; • describe the main concepts of molecular orbital theory; • explain how molecular orbitals are usually constructed;

• draw a correlation diagram for H2, label it and explain the terms;

• draw correlation diagrams for O2, N2, CO, NO; • explain how correlation diagrams can be used to understand the chemical and physical properties of a molecule;

• explain the use of these diagrams to describe the reactivity of O2, N2, CO, NO with metal ions.

Content

1 Introduction to the atom-fundamental particles. Rutherford and Bohr atom-line emission spectrum, quantum numbers.

2/3 Photoelectric experiment - dual nature of light and electrons. De Broglie equation - lead up to wave equation. Solutions of Schroedinger's equation.

3/5 Atomic orbitals - shapes, sizes, and nature - Heisenberg Uncertainty Principle.

5/6 Quantum numbers - electron spin - Pauli principle - Hund's rule - electronic energy levels - Aufbau principle - Periodic Table construction. Ionisation potential, electron affinity, electronegativity.

7/8 Simple valence bond theory - forces in molecules, overlap of orbitals, bonding of unpaired

electrons and shape of molecules, e.g. H2, HF, F2, H2O, NH3.

3 2 8/10 Introduction to hybridisation. sp hybridisation CH4; sp hybridisation C2H4; benzene; sp 3 3 2 hybridisation C2H2. sp d hybrids in phosphorus compounds, sp d hybrids in sulphur compounds. Concept of resonance.

10/12 Molecular theory for diatomic molecules - H2, He2, N2, O2, F2. Concept of stabilisation energy.

Unpaired electrons in O2. Reactivity vs. antibonding electrons. Heteropolar molecules, e.g. CO, NO.

Physical Chemistry

Lectures : 10 Revision classes : 3

Lecturer: Prof PJ Halling (Room TG103)

Aims and Objectives

The aim is to demonstrate how physical chemistry can make accurate and often quantitative predictions about the behaviour of chemical systems, with an initial focus on chemical equilibria. The general philosophy is to promote understanding rather than memory, as this will offer more lasting benefit. Calculations are a significant element, with a focus on understanding the principles involved rather than attempting to memorise formulae.

Learning Outcomes - On completion of this section of the class the student should be able to:

• Explain the concept of dynamic chemical equilibrium • Write down equilibrium constant expressions for homogeneous and heterogeneous reactions • Calculate equilibrium constants given sufficient information about equilibrium and/or initial concentrations

• Calculate equilibrium concentrations for a reaction given initial values and Kc • Explain Le Chatelier’s principle and be able to apply it in predicting the effect on equilibria of changes in temperature, concentrations and pressure • Know and use Hess’s Law in calculations of various ΔH values • Understand the concept of a function of state, as exemplified by H • Appreciate how the First Law of thermodynamics leads to relationships between work done, heat, ΔU and ΔH for simple changes • Understand in outline how the Second Law of Thermodynamics tells us the spontaneous direction of change • Explain what is meant by water auto-ionisation, Kw, pKw and pH • Define and identify Bronsted-Lowry acids and bases

• Explain how acid and base strengths are measured, write and use expressions for Ka, Kb, pKa and pKb

• Calculate the pH of an acidic or basic solution given initial concentrations and pKa values • Describe the components, applications and mode of action of a pH buffer • Use the Henderson-Hasselbalch equation to calculate the pH of buffer solutions

Content

1. Nature and importance of physical chemistry. Reversible reactions and dynamic chemical equilibrium. 2. Equilibrium constant expressions, reverse and multiple reactions 3. Heterogeneous equilibria, combining equilibria, calculating Kc from yields 4. Calculation of equilibrium concentrations 5. Le Chatelier's principle - effects of concentration, pressure and temperature on equilibria 6. Enthalpies of reaction, Hess’s Law, state functions 7. First Law of Thermodynamics. Work of expansion, internal energy and enthalpy. Outline of 2nd Law. 8. Acids and bases, Bronsted Lowry definition. Ionic product of water, pH scale. Strengths of acids and bases, Ka. 9. Kb, pKa and pKb. Calculations of extent of dissociation. 10. Principles of buffer action, calculation of pH or required compositions.

Inorganic Chemistry

Lectures : 10

Revision Classes : 3

Lecturer: Dr AR Kennedy (room R617)

Aims and Objectives

To provide knowledge of the fundamental chemistry of hydrogen and the Main Group elements (Groups IA - VIIIA) by giving an account of their descriptive chemistry and by introducing concepts such as oxidation state and VSEPR theory through worked examples, which once mastered can be applied to a vast number of compounds.

Learning Outcomes - On completion of this part of the course the student should be able to:

• Define atomic radii, ionisation energy, electron affinity and electronegativity, and describe how these properties vary throughout the Periodic Table. • Predict and explain the molecular shapes of a large number of covalent molecules by consideration of VSEPR theory. • Describe the structures of ionic solids and indicate how radius ratio rules can be used to predict these structures. • Calculate lattice energies from the Born equation. • Work out oxidation states of elements from the molecular formulae of a given compound. • Define what is meant by Lewis acidity and Lewis basicity, and differentiate between normal covalent - and dative- bonding • Discuss the natural occurrence, physical properties and principal preparative methods of these elements. • Describe basic aspects of the chemistry of Hydrogen and the Main Group family of elements (Groups IA - VIIIA). • Classify oxides as being acidic, basic or amphoteric. • Classify elements as being metallic, non-metallic or metalloidal.

Content

1 Chemical periodicity and the Periodic Table. Shapes of covalent molecules based on VSEPR method.

2 Chemistry of hydrogen. Chemical properties of water.

3 Solid state packing of spheres, metallic structures, ionic bonding and ionic structures, close packing of spheres, radius ratio, energetics of ionic interaction, lattice energy.

4 Group 1 and 2 elements - properties and reactions

5 Group 3 elements - properties and reactions

6 Group 4 elements - properties and reactions

7 Group 5 elements - properties and reactions 8 Group 6 elements - properties and reactions

9 Group 7 elements - properties and reactions

Organic Chemistry

Lectures: 10

Revision Classes : 3

Lecturer: Prof JA Murphy (room TG606)

Aims and Objectives

To instil a familiarity with the mainstream concepts of elementary organic chemistry and ensure that the student can use these effectively.

Learning Outcomes - On completion of the course the student should, in the following specific subject areas:

Formulae: be able to convert any structure from full, condensed or line structures into either if the others. Be able to determine the molecular formula (CaHbNcOd) from any of the above.

Nomenclature: be able to name alkanes, alkenes, alkynes, cycloalkanes, cycloalkenes with longest chains or largest rings up to C8. Be able to draw correct structures, given these names.

Functional groups: be able to recognise and name all the functional groups listed in the handout table. Be able to draw structures containing any of these functional groups.

Stereochemistry: be able to determine whether geometric isomers involving double bonds or rings are cis or trans or E or Z. Be able to recognise all stereogenic centres in a molecule.

Acidity: be able to recognise which functional groups are acidic, basic or neutral. Be able to convert between Ka and pKa; and give definitions of both.

Mechanisms: be able to explain the meanings of the terms “starting materials”, “reactive intermediates” and “products”. Be able to recognise functional groups as being electrophilic or nucleophilic in character; and compounds as polar or non-polar. Reactivity: be able to recognise a series of common reactions of organic functional group types and apply this typical reactivity within previously unseen molecules.

N.B. These are genuine learning outcomes, but they do not cover the whole syllabus, which must remain as a description of the course content.

Content

1 The Nature of Organic Chemistry: How to draw organic molecules. Organic reactions as multi-stage processes. Reactive intermediates. Reaction mechanisms. Aids to learning.

2 Alkanes and Free Radical Intermediates: Reminder of structure and bonding σ-bonds and chain reactions. Combustion and explosions. Fire Retardants.

3 Alkenes, Alkynes Cationic Intermediates: Reminder of structure and bonding, π-bonds. Addition of halogens and hydrogen halides and nucleophiles. Hydrogenation. Demonstrations of reactivity.

4 Molecular Motion, Isomerism, Stereochemistry: Isomers in alkanes compared with alkenes. Conformation in alkanes - free rotation. Configuration in alkenes - breaking π-bonds. Ring compounds - faces. Nomenclature of alkene isomers, cis and trans and E and Z. Polymers, radical polymerisation.

5 Benzene & Aromatic Compounds: Structure and bonding in benzene, delocalisation. Reactivity of aromatic compounds compared with alkenes. Electrophilic substitution.

6 Alkyl Halides: Bonding in C-X compared with C-H; polarised single bonds. Substitution reactions, making bonds to carbon. Elimination reaction; competing reaction pathways. Organometallic compounds; reversal of reactivity. Applications and uses of alkyl halides.

7 Carbonyl Groups & Tetrahedral Intermediates: Bonding compared with alkenes, polarised multiple bonds. Compounds containing carbonyl groups, nucleophilic addition, making bonds to carbon, tetrahedral intermediates. Selective reduction of alkenes and carbonyl groups, selectivity in modern organic chemistry. Condensation. Imine formation (vision), oximes etc.

8 Acids and Bases: Bronsted acids and bases, definition of pKa. Aciditiy of carboxylic acids, phenols and alcohols (ketones and alkynes). Rationalisation: charge delocalisation. Basicity of amines. Very weak basicity of amides. Practical applications. Solvent extraction (cf. laboratory). Indicators.

9 Isomerism: Revision of types of isomerism so far. Characterisation of compounds by physical methods. Symmetry and chirality in objects and molecules, optical isomers and their significance: flavours and drugs. Enantiomers and their representation. Diastereoisomers, Resolution of racemic mixtures.

CH 107 CHEMISTRY: PRINCIPLES AND PRACTICE 2

Second semester Credits 20 (ECTS 10) Lectures 48 Revision Classes 8

Multiple choice examinations (2 x 1 hour) in May with resits in August.

Lecturers: Dr EJ Cussen, Dr CM Davidson, Dr DJ Nelson, Dr MD Spicer, Dr D Willison

SHE Level: 1

Physical Chemistry

Lectures: 10

Revision classes : 2

Lecturer: Dr EJ Cussen (TG506)

Aims and Objectives

The general philosophy is adopted of reducing reliance upon memory and increasing understanding of the various topics This allows the student to rapidly check the validity of equations on the various topics. It is intended that this should instil a body of knowledge in elementary physical chemistry which will be of more lasting benefit than the memory approach allows.

Learning Outcomes - On completion of the course the student should be able to:

• Understand the ideal gas laws, justify their form qualitatively and use them to calculate gas properties. • Calculate relative and absolute pressures. • Understand the concepts of the Mole, Partial Pressure and Effusion. • Calculate and convert between equilibrium constants in terms of partial pressures and concentrations

• Calculate equilibrium pressures for a reaction given initial values and KP. • Understand the simpler aspects of real gas behaviour as exemplified by the Van der Waals equation, and use it to discuss intermolecular forces and calculate gas properties. • Kinetic theory of gases. Root mean square velocity of molecules in a gas. Diffusion in gases - relation to RMS velocity. Graham's law of diffusion. • Understand the behaviour of gases in equilibrium with liquids, vapour pressure, Raoult’s Law, its deviations and Henry’s Law. • Calculate molecular weights from ideal gas, effusion experiment and colligative property data. • Justify the form of Colligative Property relationships and deal with association and dissociation in these. • Write down solubility constant expressions

• Calculate saturated salt concentrations from KSP values and vice versa • Explain what is meant by the common ion effect, and calculate saturated salt concentrations in the presence of common ions • Understand how conductivity measurements can determine the extent of ionisation in solution • Explain what is meant by electrolysis • Relate the current passed to molar yields in electrolysis reactions

Content

1. Properties of gases; Avogadro’s number; ideal gas equation of state; measurement of pressure; liquid/air manometers; Victor-Meyer experiment.

2. Gas mixtures; Dalton’s Law of partial pressures; vapour pressure of immiscible liquids. 3. Reaction in gases; calculation of equilibrium concentrations; relationship between KP and KC. 4. Kinetic theory of gases; RMS speed of a gas; Graham’s Law of Effusion. 5. Deviations from ideality in real gases; derivation of Van der Waals equation. 6. Gases in equilibrium with liquids; Henry’s Law; Raoult’s Law; temperature-composition diagram for distillation.

7. Colligative properties; freezing point depression and boiling point elevation; ebullioscopy and cryoscopic constants; molarity and molality; osmotic pressure.

8. Solubility constant; ion product and common ion effect. 9. Electrolyte conductivity; ionic migration and Kolrausch’s Law; Ostwald’s dilution Law for weak electrolytes.

10. Electrolysis; anodes and cathodes in galvanic and driven cells; electrochemical series.

Organic Chemistry

Lectures: 12

Revision classes : 2

Lecturer: Dr DJ Nelson (room TG404)

Aims and Objectives

This course aims to get you thinking in detail about, and explaining the outcomes of, organic reactions by looking at the fundamental mechanisms of the reactions. It also introduces some new chemical reactions, including the chemistry of carboxylic acids and their derivatives. The main points of emphasis of the course will arise from the need to:

1. Describe elementary reaction mechanisms in detail.

2. Introduce the concept of selectivity and multiple reaction pathways in organic chemistry. 3. Use a combination of basic theories to explain more complex phenomena. 4. Introduce concepts of stereochemical courses of reactions.

Learning Outcomes

On completion of this course you should be able to: • describe the meaning of electrophile, nucleophile and radical, and to classify molecular species as electrophiles or nucleophiles. • classify double bonds as conjugated or isolated and identify aromatic compounds. • predict the site of electrophilic addition to unsymmetrical alkenes and explain it in terms of relative carbocation stabilities. • describe the molecular structure of conjugated dienes. • explain why 1,2- and 1,4-addition can occur upon the addition of an electrophile to a conjugated diene. • use curly arrows to show resonance structures, especially for allylic and benzylic systems. • give the reagents necessary for the generation of trans-dibromides, cis- and trans-diols, epoxides, ketones (or aldehydes) and carboxylic acids from cyclic alkenes. • explain the stereochemistry of additions to alkenes (cis- and trans-addition reactions). • explain mechanistically the influence of substituents on the reactivity of mono-substituted benzenes towards electrophilic aromatic substitution. • name simple benzene derivatives. • describe the reasons for the stability of allylic, benzylic and related carbanions, carbocations and radicals, and be able to differentiate these from aryl and vinyl systems. • understand the reactivity of allylic and benzylic systems with chlorine in the presence of light (radical reactions). • describe the oxidation of side-chains of alkyl benzenes.

• describe the stereochemistry, kinetics and dependence on structure of SN1 and SN2 reactions. • use curly arrows to show the mechanism of a reaction. • describe the mechanism of E1 and E2 reactions • describe the factors which influence the competition between substitution and elimination reactions. • understand the synthesis and reactions of carboxylic acids, acid halides, acid anhydrides, esters and amides. Content

1 Addition to unsymmetrical alkenes. Stability of carbocations. Markovnikov's Rule.

2 Stereochemical course of addition reactions to alkenes.

3-4 Nucleophilic aliphatic substitution reactions. Kinetics and mechanism of nucleophilic aliphatic substitution, stereochemistry, leaving groups.

5-6 Elimination reactions. Experimental conditions of elimination reactions, regioselectivity and stereochemical course of reaction.

7-8 Molecules with >1 Double Bond. 1,2- and 1,4-additions, resonance in allylic cations.

9-11 Aromatic compounds. Orientation effects in aromatic substitution. Side chain reactivity. Benzylic and allylic halides, aryl and vinyl halides.

12 Carboxylic acid derivatives. Interconversion of acids, acid chlorides, acid anhydrides, esters, amides and nitriles.

Inorganic Chemistry

Lectures: 11

Revision classes : 2 Lecturer: Dr M D Spicer (room R617)

Aims:

A systematic study of the principles of transition metal chemistry.

It includes:

Electronic structure, Electronic configurations, orbitals, oxidation states, atomic sizes, effect of d- block contraction.

Bonding. Ionic, covalent, valence bond, crystal field, molecular orbital.

Ligands and Geometries. Definitions of monodentate, bidentate, polydentate, chelate, Octahedral, square planar, trigonal bipyramid, other.

Magnetism and Colour. Unpaired electrons, energies of electronic arrangements, high spin, low spin.

Chemical properties. Extraction, reactions, compounds, with emphasis on Ti, Cr, Fe, Cu; rusting of Fe; Mo, Pt.

Uses in Industry, Biology, Medicine. Includes Fe Cu metals; Ti, Pt Pd catalysts; Fe haemoglobin, enzymes; Pt, Cu Zn drugs.

Learning Outcomes - at the end of the course the student should be able to:

• understand the implications of electron configuration and electronic structure on atomic size, oxidation states, shapes of complexes, coordination geometry isomerism, and bonding in transition metal complexes. • understand the influence of the geometry of ligands on energies of d-orbitals in octahedral, tetrahedral and square planar complexes, and hence the origin and nature of magnetic properties (high spin and low spin) and colour through the crystal field approach. Should have a factual understanding of the chemical properties of the transition metals (d-block), lanthanides and actinides (f-block) with particular emphasis on Ti, Cr, Fe and Cu. • understand some of the important industrial applications of transition metals and their compounds including Ziegler-Natta catalysis, and rusting of Fe. Should understand redox processes and standard potentials with particular reference to laboratory reagents including dichromate, permanganate and in applications to batteries. appreciate of the biological importance and processes involving transition metals, including Fe (iron storage and transport - haemoglobin, myoglobin, cytochromes and other enzymes), Zn (carboxypeptidase etc); Cu (ceruloplasmin etc), Co (vitamin B-12), Mo (bacterial N-fixation), W (bacterial enzymes), V (marine organisms); metal drugs (Cu, Au - arthritis, Pt - cancer).

Content

1 Periodic table, definitions of transition metals, lanthanides and actinides; Electronic structure, electronic configurations, orbitals and radial functions, oxidation states.

2 Atomic radii, d-block and f-block contractions; angular functions and shapes of d-orbitals; definitions of complexes, ligands. Types of ligand. Geometries.

3 Coordination geometry and isomerism; structural isomers, geometric isomers, cis-& trans- square planar, and octahedral; optical isomers. 4 Magnetism and colour; valence bond and crystal field theories; paramagnetism, high-spin and low-spin, octahedral splitting of d-orbitals; electronic transitions for d1 and d9.

5 Chemistry - Scandium and Titanium. TiCl4, rutile, redox Ti(IV) 5 Ti(III), Ziegler-Natta catalysis.

6 Vanadium - Oxidation states V and II, redox, complexes including acetylacetonato-, vanadyl.

7 Chromium and Manganese. Cr(VI), Cr(III), colour, complexes, redox. Mn(VII), Mn(II), (also III, IV). Chromate, permanganate, charge transfer, redox, acid and alkali, dry battery.

8 Iron. Blast furnace reactions, chemical properties, oxidation states VI, II, III, redox, rusting of 2+/3+ 4-/3- 3 iron, complexes [Fe(H2O)6] , [Fe(CN)6] , [Fe(SCN)6] -. Demonstration of thiocyanate/Fe3+, Prussian blue.

9 Iron. Redox, crystal structure of halides and oxides; paramagnetism, ferromagnetism, antiferro- magnetism; hydrolysis of aquo salts. Cobalt - Oxidation states II, III; aquo and ammino-complexes; redox.

2- 10 Co(II) and Co(III) high spin and low spin complexes (octahedral). [Co(II) Cl4] high spin tetrahedral. Nickel. d8 octahedral, tetrahedral and square planar. Cu(I) and Cu(II). Zn(II).

11 4d and 5d elements. Effects of lanthanide contraction. Higher oxidation states; Ti, Zr, Hf; Cr, Mo, W; Ni, Pd, Pt; Cu, Ag, Au.

12 Lanthanides and actinides 4f and 5f. Oxidation states; radioactivity ; coordination numbers.

Spectroscopy

Lectures: 11

Revision classes : 2

Lecturers: Dr C M Davidson (room R673) and Dr D Willison (room TG210b)

Aims and Objectives

The First Year Spectroscopy course introduces to the student the spectrum of electromagnetic radiation and the interaction of radiation with matter.

Learning Outcomes

At the end of the course the student should be able to:

• Describe the fundamental principles of spectrometry, including the interactions of electromagnetic radiation of different wavelengths with matter • State Beers Law and perform calculations based upon it. • Describe the basic components of a uv/visible spectrometer • Describe the practice of uv/visible spectrometry, including methods to improve sensitivity and selectivity and spectrophotometric titrations. • Understand the schematics of IR, UV/Vis and NMR instruments. • Have the ability to use IR spectra for identification of functional group. • Understand the concept of nuclei as bar magnets. • Have the ability to use 13C spectra for the elucidation of structural formulae.

Content

1. Introduction: the electromagnetic spectrum and the nature of light; interaction of electromagnetic

radiation with matter; absorption and emission.

2. UV/visible spectrophotometry, chromophores, Beer’s Law.

3. Direct spectrophotometry; instrumentation for uv/vis spectrometry.

4. Methods to improve sensitivity and selectivity in uv/vis spectrometry.

5-6. Spectrophotometric titration.

7 Interaction of infrared radiation with covalent bonds. Stretching and bending vibrations of simple molecules. Interpretation of useful regions of the infrared spectrum. Salient features of infrared spectra of simple organic molecules.

8 Brief description of techniques for obtaining spectra of solids, liquids and gases. Brief description of how an infrared instrument operates.

9 Use of infrared spectra to identify functional groups and applications, i.e. follow reaction paths.

10 Introduction to NMR Spectroscopy. Nuclei as mini magnets absorbing radio frequency energy in a magnetic field. Isotopomers. Identification of different types of carbon atom and hence expected number of 13C signals.

11 Interpretation of simple 13C NMR spectra and application to lead to elucidation of structural features.

SECOND YEAR CLASS SYLLABI

CH 202 INORGANIC CHEMISTRY

Both semesters Credits 20 Lectures 44 Tutorials 8 SHE level 2

Lecturers: Dr E Hevia, Professor RE Mulvey, Dr J Reglinski, Dr MD Spicer and Dr A Wark

Written examination (1.5 hours) in January and class test and continuous assessment in second semester with resit in August.

Aims

• to provide a broad knowledge of the important concepts in inorganic chemistry from which more specialist topics can be tackled. • to investigate systematically the chemistry of the main group and transition metals. • to introduce topics at the forefront of inorganic and materials chemistry.

This class builds on the first year inorganic chemistry classes. The second year class provides a broad knowledge of important concepts in inorganic chemistry from which the more specialist third and final year topics can be tackled. Direct entry students are encouraged to refer to the syllabuses of the first year classes to ensure that they are familiar with the content of these courses before the commencement of this second year class.

Learning Outcomes

Upon the completion of the class the student will be able to:

• differentiate between ionic and covalent bonding, and predict the nature of bonding in complex molecules; • understand the principles governing the periodic trends of the main group elements; • discern between the terms co-ordination number and oxidation number; • understand the consequences of the d- and f-block contractions on the p-block elements; • relate the physical properties of the elements to their electronic configuration; • understand acidity from the Lewis definition; • predict the gas phase structures of molecules using VSEPR theory and rationalise the limitations of this method; • understand the why crown and cryptand metal complexes impart covalent character on ionic metal salts; • have a detailed understanding of the relationship between the available oxidation states of the elements and their electronic configuration; • understand the principles giving rise to the inert pair effect; • relate the structures, bonding and physical properties of the allotropes of the elements; • understand electron deficient bonding in compounds; • describe the preparation, bonding and structures of organometallic compounds of the main group elements; • understand the principles of band gap theory and relate this to conductivity variations across the periodic table; • understand the concepts of orbital availability and promotional energy, and relate this to the maximum co-ordination and oxidation numbers of the elements; • comprehend the influence of low lying d-orbitals on the chemistry of period three and below; • understand the relationship between catenation and homonuclear bond energy; • understand the principles of multiple bonding, including partial multiple bonds; • rationalise the structures, reactivity, and key properties of transition metal complexes on the basis of crystal field theory; • understand the concepts of paramagnetism and diamagnetism in transition metal chemistry; • describe how cooperative magnetic effects can lead to ferromagnetism or antiferromagnetism; • understand the concept of the trans effect and how it relates to stereospecific reactions; • define the delta bond and how it contributes to metal-metal bonding; • comprehend the basics of transition metal organometallic chemistry, metal carbonyl complexes; back-bonding, electron-counting and the significance of the 18-electron rule; • have a thorough grasp of the common reaction types found in organotransition metal chemistry, which will be necessary as a precursor to understanding catalytic processes. • understand the role of inorganic chemistry in biological systems • comprehend the basics of catalytic processes. • have a knowledge of the use of inorganic materials in a variety of applications

Content

A: Main Group Chemistry

1-2 Important concepts in main group chemistry: general trends in effective nuclear charge, atomic radii, ionisation energies (IE), electronegativities (χ) etc.. Covalent vs ionic bonding: use of χ, IE and lattice energies. Introduction to orbital and electron promotion energies.

3-4 Oxidation and valence states within the main group: octet rule, disproportionation reactions, inert pair effect, hypervalency, variable oxidation states.

5 Second row anomalies: no d-orbitals available, contracted orbitals – effects on element- element and multiple bonding, coordination numbers and reactivity.

6-7 Allotropy in the main group: relationship between structure, physical properties and bonding.

8-9 Conductivity: introduction to band theory, n- and p-type doped semiconductors, trends in main group allotropes, superconductivity, ionic conductivity.

10-12 Bonding in compounds: electron deficient bonding (B2H6, structures of methyl- organometallics of groups 1-17), coordinate (dative) bonds, bridge bonding, multiple π- bonding (stabilities), partial π-bonds.

13 Trends in homo- and heteronuclear bond energies: catenation, anomalies due to lone pair repulsions, binding energies in allotropes. Origin of colour: molecular, charge transfer and flame tests.

14 Fluorides of the main group: relationship between bonding, structure and physical properties, interhalogens. Macrocycles: crowns and cryptands, porphyrins.

15 Introduction to the reaction chemistry of the main group elements: reactions of the elements with water and oxygen. Organometallics: syntheses, transmetallations and reactions with protic substrates.

16 Introduction to Organometallic chemistry of groups 1 and group 2: Organolithium and Grignard reagents: synthesis, structure and synthetic applications. The importance of the metallation reaction.

B: Transition Metal Chemistry

17-18 A revision of the basic principles: Shape and position of the d-orbitals, radial functions, Hunds rule, Pauli principal, electron configuration(s), relative energies of the 4s and 3d orbitals. Exchange energies. Screening and effective nuclear charge as a basis for understanding oxidation states and simple chemistry. Patterns in oxidation states.

19 Coordination chemistry: classification of ligands, chelate effect; porphyrin in haemoglobin and vitamin B-12.

20-22 Ligand field Theory: Ligand effects on the d-orbital degeneracy (octahedral, tetrahedral, square planar fields) of the metal in a complex. Low spin and high spin complexes, the spectrochemical series and their effects on the magnetic behaviour. Cooperative magnetic effects.

23-24 Brief introduction to 4d and 5d chemistry: rationalisation of size and oxidation state effects; effects on crystal field splitting parameters; metal-metal bonding; the delta bond.

25-26 The trans effect: stereospecific substitution reactions in d8-complexes; platinum anticancer agents; cisplatin and carboplatin; associative and dissociative mechanisms.

27-29 Introduction to transition metal organometallic chemistry: backbonding through metal carbonyls (phosphines, NO CN-); structures and physical properties of metal carbonyls; the 18-electron rule; photochemical reactions; π-systems; Zeiss’s salt, ferrocene, and benzene- molydenum complexes.

30-32 Survey of fundamental organotransition metal reactions: oxidative addition and reductive elimination; sigma-bond metathesis; insertion reactions; beta-hydride elimination; cyclometallation reactions.

C: Frontiers in Inorganic Chemistry

Bio-inorganic Chemistry

33 The potassium and sodium balance: Valinomycin & Gramicidin Antibiotics.

34 Platinum anticancer drugs and their action.

35 Iron haem proteins.

36 Energy harvesting. Photosystem I and II (Mg and Mn Chem) How do plants make oxygen and how do we propose to do it (Ru photochemistry).

Catalysis

37 Introduction: what is a catalyst. Homogeneous vs heterogeneous catalysts. Thermodynamics and kinetics. Turnover number and turnover frequency. Selectivity.

38 Polymerisation Catalysts. Ziegler – Natta olefin polymerisation. Metallocene catalysed polymerisation. Green polymers – lanthanide based catalysts for lactide polymerisation.

39 Steam reforming and water-gas shift reaction.

40 Alkene and alkyne metathesis. Palladium catalysed coupling reactions. Asymmetric Catalysis.

Functional Materials

41-42 Introduction to metallic, magnetic, semi-conducting, silicaceous and carbonaceous nano- materials

43 Superconductors and metal oxides

44 Applications of the f-block elements.

45-48 Workshops and consolidation exercises

Recommended Reading:

“Shriver and Atkins’Inorganic Chemistry”, 5th Edition, Oxford University Press, 2009

Shriver and Atkins is recommended as a text which will cover both second and third year courses. If this text is found to be too advanced initially, attention is drawn to the following series of books published by Oxford

Science Publications which offer a cheap and simple introduction to a number of the key areas:

DMP Mingos Essential Inorganic Chemistry I

NC Norman Periodicity and the p-block

MT Weller Inorganic Materials

MJ Winter Chemical Bonding

MJ Winter d-Block Chemistry

CH 205 PRACTICAL PHYSICAL AND APPLIED CHEMISTRY

First or Second semester Credits 20 Hours 96 SHE level 2

Physical Chemistry

Aims

• to give experience at making accurate physical measurements on chemical systems, • to develop practical skills using sensitive instrumentation, with assessment of its errors and limitations, • to give practice at writing up a set of physical measurements in a professional manner, • to give practice at communicating verbally about chemistry, both one-to-one and in a seminar, and • to underpin the theoretical work covered in lectures.

Students will attend the Physical and Applied Chemistry Laboratory and the Analytical Laboratory for six weeks, and must satisfy the requirements of each laboratory separately for the award of these practical credits. During the course, students will be allocated experiments from the following lists.

Physical and Applied Chemistry - Head of Laboratory: Dr LEA Berlouis

1 Viscosity of liquids

2 pH titration of acetic acid using an autoburette

3 Volume changes on mixing via liquid density determinations

4 Elevation of boiling point

5 Enthalpy of vaporisation of water

6 Determination of the vapour pressure of a liquid

7 Calorific value using a bomb calorimeter

8 Hydrolysis of ethyl ethanoate

9 Acid-catalysed iodination of propanone

10 Kinetics of the oxidation of iodine to iodide by persulfate

11 Potentiometric titrations

12 Corrosion and protection of metals 13 Characteristics of the proton exchange membrane hydrogen-air fuel cell

14 Atomic spectrum of atomic hydrogen

Assessment of the Class

Practical work is an essential part of the preparation of a professional chemist, and the Royal Society of Chemistry places great emphasis on the practical content of a qualifying course. The requirements of each laboratory are based on continuous assessment, and students who do not attend or do not submit laboratory work will find their situation difficult to rectify. Students are responsible for measuring their own performance against laboratory requirements, but where possible they will be warned in advance if their performance appears to be of a lower standard than that required.

The laboratory requirements are summarised below, but the full details will be found in the appropriate Laboratory Manual.

A student whose performance falls marginally short of the standard required may exceptionally be permitted to carry out a short exercise designed to demonstrate sufficient practical competence for the award of the credit; this exercise may be held at the conclusion of a diet of examinations, at the discretion of the Head of the Laboratory concerned.

When absence from the Laboratory has been caused by medical or compassionate reasons, or when failure of a practical class is the only impediment to a student’s progress to third year, it may exceptionally be possible to arrange for practical experience to be gained (and the laboratory credits awarded) by work in the laboratory between the end of the term and the August diet of examinations. Students should note, however, that summer vacation experience can realistically be gained in only one laboratory area.

Laboratory Requirements

Attendance is expected on 4 afternoons each week, and students attending for less than 80% of the available afternoons will automatically fail the laboratory.

Experiments are assessed and a mark awarded by written report. The laboratory requirement will be explained fully at the Introductory Session, which students attend before embarking on practical work.

Further Applied Chemistry - Forensic and Analytical Chemistry Lab Co-ordinator: Dr P Allan

Aims

• To conduct experiments in analytical chemistry and forensic science • To gain practical experience of theoretic aspects of analytical chemistry and forensic science covered in lecture courses • To develop skills in analytical observation, use of basic statistics in the evaluation of data, and report writing.

Learning Outcomes

At the end of the course the student should:

• Have developed improved practical skills, especially in techniques and procedures relevant to analytical and forensic science • Be able to interpret analytical data and apply simple statistics • Be able to write both laboratory and court reports

Students will conduct a selection of experiments from the following list:

I1 Use of a pH meter for an Acid-base Titration

I2 Use of a pH meter for a Potentiometric Titration

I3 Determination of Ethanol in Alcoholic Drinks by the Method of

Internal Standard Calibration

I4 Determination of Caffeine in Cola by High Performance Liquid Chromatography

I5 Determination of Ammonia in Water by Automated Direct

Spectrophotometry

I6 Calibration of Volumetric Apparatus I7 Determination of the Formation Constant of a Metal Complex

by the Molar Ratio Method

18 Alleged Assault: Analysis of Fibre Dyes and Shoe Polish

I9 Alleged Abduction and Assault: Search and Recovery and Fibre Comparison

I10 Fibre Analysis using Polarized Light Microscopy

CH 208 FUNDAMENTAL ORGANIC CHEMISTRY

Both semesters Credits 20 Lectures 48 Tutorials 12 SHE level 2

Written examinations (2 hours) in January and May with resit in August. This class also has three compulsory class tests in Semester 1 (in weeks 1, 4 and 10), and two compulsory class tests in Semester 2 (in weeks 4 and 10) which count as 4% each towards your degree examination mark.

Lecturers: Professor J M Percy (JMP) Dr C Jamieson (CJ) and Dr A Watson (AW)

Aims

• impart knowledge of the fundamental principles of infra-red, ultra-violet, nuclear magnetic resonance and mass spectroscopy, • promote competence in the interpretation of spectra, • develop awareness of the role of spectroscopic techniques in structure determination, the study of bonding characteristics, the progression of chemical reactions and the analysis of products, • develop students’ knowledge of reactions, understanding of mechanisms and appreciation of the role of reactivity in organic chemistry • inculcate the ability to predict reaction mechanisms and outcomes from a reading of the substrate structure and reaction conditions • begin to develop skills in synthetic planning and analysis • develop problem solving ability across a wide range of organic chemical and spectroscopic problem types via self-study and guided sessions.

Learning Outcomes

Upon the completion of the class the student will be able to:

• understand the fundamental principles of IR, UV, NMR and mass spectroscopy; • be competent in the interpretation of spectra; • understand the importance of spectroscopy in elucidation of structure; • be aware of which part of the electromagnetic spectrum each type of spectroscopy originates from; • understand the interaction of infrared radiation with covalent bonds; • be aware of the connection between bonds and force constants; • be at least familiar with the concept of Raman spectroscopy; • utilise IR spectroscopy for following reactions in organic chemistry; • identify different types of proton in 1H NMR by their chemical shift. • use integration to identify how many protons are within a particular signal; • understand the origin of line multiplicity, including the (n + 1) rule, and be able to measure coupling constants; • interpret 13C NMR and understanding the term decoupling; • interpret spectra containing other nuclei, e.g. 19F, 31P etc; • understand the concept of electronic transitions from a pictorial viewpoint; • understand the Beer Lambert Law and the significance of ε and λ; • understand the effect of conjugation; • be aware of the analytical applications of UV; • be aware of how M+ ions are generated and how a mass spectrum is produced; • be aware of isotope peaks and how they can be used in the calculation of molecular formulae; • understand how structures can be elucidated using fragmentation patterns; • describe the relationship between the structure of carbonyl derivatives and their bond order/reactivity; • predict the outcomes of reactions of carbonyl derivatives and relate outcomes to structures; • identify and use the principles that control tetrahedral intermediate formation and breakdown; • rationalise and predict the outcomes of carbonyl derivatives with a range of nucleophiles including σ-organometallic reagents, hydride transfer reagents, ylides, alcohols and amines; • exploit the Wittig reaction for the synthesis of terminal alkenes, and sulfur ylide chemistry for the preparation of epoxides; • explain the formation of ring expansion products in diazomethane reactions of cyclic ketones; • propose syntheses for a wide range of alcohols, aldehydes, ketones, acids, amides, acetals and amines; • describe acetal formation and hydrolysis mechanisms with arrow-pushing explanations; • deploy acetal protecting groups for hydroxyl and carbonyl groups in synthesis; • propose syntheses of amides from acid chlorides/anhydrides and amines; • deploy the reductive amination reaction for the synthesis of secondary and tertiary amines; • identify sites at which aldehydes and ketones can be deprotonated to form enolates; • deploy enolates in C-C bond forming reactions (the aldol reaction); • identify aromatic molecules based on the usual criteria (electron count, planarity, full cyclic conjugation); • use Frost’s circle to locate the orbitals available to the aromatic system, and populate those orbitals accurately with the p-electron complement;

• understand why electrophilic aromatic substitution (SEAr) and not addition is the mode of reaction of aromatic compounds; • describe the two-step energy profile of the reaction identifying the Wheland intermediate explain how the energy of the Wheland intermediate affects the rate of reaction;

• and extend that idea to show how a substituent controls the rate and regiochemistry of subsequent electrophilic aromatic substitutions of a substituted benzene; • use the ideas of activation or deactivation, and ortho/para, or meta direction to rationalise and predict reaction outcomes; • rank substituents in terms of the nature and power of the effects they exert; • understand how the basicity of the amino group can complicate nitration reactions of aminobenzenes (or other aminoarenes), and apply a protecting group strategy to avoid the problem; • deal with situations where two substituents compete for control of, or have reinforcing effects on the addition of a further group; • define the limits of the common electrophilic aromatic substitution reactions for substituted benzenes (for example, Friedel-Crafts reactions require a substrate as reactive as benzene, nitration works on almost any substrate) ; • provide reaction mechanisms for electrophile generation for Vilsmeier-Haack, nitration, Friedel- Crafts acylation ; • explain why direct alkylation of benzenes is an extremely difficult reaction to control, and show why acylation and subsequent reduction is a more effective strategy; • use the synthetic relationship between nitro- and amino- groups (reduction), and diazonium cations to introduce a wide range of substituents (halides, hydroxyl, cyano) onto benzenes; • describe why the development of aromaticity provides a driving force for a reaction (eg. Ionisation to form an aromatic carbenium ion); • identify when a benzyne reactive intermediate would be expected to form • understand how a benzyne is formed exclusively in the s-plane of an arene and provide arrow- pushing for the formation and subsequent reaction with nucleophiles • describe substituent effects on nucleophilic addition to benzynes • relate the high reactivity of benzyne to the ease with which it adds to alkenes and dienes

• assess the likelihood of a nucleophilic aromatic substitution (SNAr) occurring • show how the presence of one or more strong electron-withdrawing groups, and a leaving group is essential, by carrying out accurate arrow pushing

• identify the usual rate-determining step in the in the SNAr reaction • compare and contrast the different substitution mechanisms available for aromatic molecules

• predict the outcome of a proposed aliphatic nucleophilic substitution or elimination reaction (SN1 or SN2, E1 or E2 mechanism) • with precise arrow-pushing • writing accurate line formulae for the reaction products • accounting for stereochemical changes • rationalise the success or failure of proposed substitutions (by either mechanism) in terms of substrate, nucleophile and/or leaving group structure and reaction conditions • rank potential substrates, nucleophiles and/or leaving groups in reactivity order • select between potential routes for ether synthesis • identify and deploy effective nucleophiles for C-C bond formation • reaction conditions for the accurate inversion of configuration of alcohols • reagents and reaction conditions for the conversion of alkyl halides or sulfonates to amines (azide, Staudinger reaction but not the mechanism) • understand the relationship between substrate structure, reaction conditions and mechanism for the reactions of secondary halides and sulfonates

• identify and account for similarities and differences between the main (SN1 and SN2, E1 and E2, SN2 and E2) mechanisms • understand how mechanism can change as substrate structure varies; for example, substituents on an aromatic ring can modulate carbenium ion stability at a benzylic position very strongly • show how to distinguish between the unimolecular and bimolecular mechanisms experimentally • show why cyanide ion is a valuable tool for C-C bond formation • show why ethyne ion is a valuable tool for C-C bond formation (link with Lindlar reduction to Z- alkenes) • show how steric hindrance affects the rate of bimolecular substitution • identify functional groups which accelerate bimolecular substitution and locate them correctly • account for the accurate inversion of configuration which occurs in bimolecular substitution (in terms of transition state geometry and involvement of the s* orbital) • describe how carbenium ions are stabilised and indicate the relative effectiveness of each type of stabilisation

• understand how SN1/E1 reaction rate is geared to carbenium ion stability • illustrate the consequences of carbenium ion partitioning between nucleophiles • progress elimination substrates through the E2 reaction mechanism understanding and explaining the relationship between configuration, conformation and the antiperiplanar stereoelectronic requirement • In alicyclic chemistry (the chemistry of rings) • draw the chair conformer and other species on the energy surface for cyclohexane, identifying maxima and minima • distinguish clearly between axial and equatorial environments on the chair conformer • understand the nature and origin of substituent preferences for equatorial locations • identify substituents with small and large A-values • describe the relationship between substituent size and equatorial preference • interconvert accurately between line formulae and conformational drawings • detect antiperiplanar relationships on cyclohexane templates and understand how reaction outcomes can be controlled by stereoelectronic relationships • make clear conformational drawings for cyclohexene and cyclohexene oxide half-chair and locate substituents as pseudo-axial or pseudo-equatorial • represent trans-decalins and locate substituents, accurately • identify important conformations for other ring systems (3-8 membered) • describe the nature of strain and break it down into the three component types (angle, torsion, transannular) • identify the dominant strain contribution for the different ring systems • understand how the development of strain can retard reactions • explain how the relief of strain can accelerate reactions • recognise and explain the term I-strain • detect changes in strain arising from common reaction types (elimination, substitution, addition) and their consequences for comparative reaction rates • carry out arrow-pushing for cyclopropane ring opening reactions and understand the origin of this reactivity in strain relief • explain how the avoidance of strain may channel reactions towards a single regiochemical outcome • explain the relationship between the high chemical reactivity of epoxides and strain relief • deduce the outcomes of trans-diaxial ring-opening reactions of unsymmetrical epoxides

Content

Introduction to Spectroscopic Methods (CJ, Semester 1, 12 lectures) The spectrum of electromagnetic radiation. Pictorial description of the interaction of different types of radiation with matter, types of transition, energy states, absorption spectra, units etc.. Vibrational Spectroscopy Interaction of infrared radiation with covalent bonds. Stretching and bending vibrations of simple molecules. Bonds and force constants (in simple terms). Useful regions of the infrared spectrum. Salient features of infrared spectra of simple organic molecules. The variation of ν(CO) with structure in different types of carbonyl compound. Mention of Raman spectroscopy. Brief descriptions of techniques for obtaining spectra of solids, liquids and gases. Use of infrared spectroscopy for following organic reactions. Nuclear Magnetic Resonance Spectroscopy Nuclei as mini-magnets absorbing RF energy in a magnetic field. Sensitive nuclei for I = ½. Technique used for determination of NMR spectra, solvents, use of computers etc. 1H NMR: Identification of different types of 1H atoms in a molecule leading to different chemical shifts in the NMRspectrum. The δ scale of 1H chemical shifts. Measurement of peak areas and use of integrals. The origin of line multiplicity and the (n + 1) rule. Measurement of coupling constants (J values). Simulation of 1H NMR spectra using tree diagrams. How to analyse an nmr spectrum, H-H decoupling; COSY spectra. All the above to be illustrated with simple examples. 13C NMR: Isotopomers. Identification of different types of carbon atom and hence expected number of 13C signals. Decoupling of 1H-13C signals. Use of correlation tables. Simple examples. 19F NMR: Spectra of simple fluorine-containing molecules. Measurement of J(F-F), J(F-H), J(P-F). Other nuclei with I = ½ e.g, 31P. Electronic Spectroscopy Pictorial representation of electronic transitions. Bonding and antibonding energy levels. σ → σ*, π → π*, n → π* terminology with examples. The Beer-Lambert law and significance of ε and λmax. λmax for simple ketones, the effect of conjugation and substitution.

Electronic spectra of acids and bases in neutral, alkaline and acid solution. Determination of pKa values. Analytical applications. Mass Spectrometry Generation of ions. The mass spectrum. The mass spectrometer. High resolution mass measurement and determination of best fit for a given molecular ion. Peaks due to isotopes. Simple fragmentation patterns, M+ → daughter ions. Use in determination of structure. Advanced Chemistry of the Carbonyl Group (JMP, Semester 1, 12 lectures); revison of basic ideas on same basis as Year 1 (hybridisation theory, bonding model, arrow-pushing); C-C and C-H bond formation based upon aldehydes and ketones; the addition/elimination mechanism and control of reaction through selective reagents for C-C bond formation and reduction; addition of phosphorus, sulfur and nitrogen ylides to C=O for alkene (contrasting N versus P behaviour), epoxide and migratory product synthesis respectively; deprotonation of aldehydes and ketones – enols and enolates revisited; C-C bond forming reactions using enolates; acetal formation and hydrolysis (and why this is important); concept of protecting groups and simple examples; imine formation and role in reductive amination; supporting functional group transformationscumulative and synoptic examples of syntheses using these reactions and everything developed previously. Substitution and Elimination reactions (JMP, Semester 2, 8 lectures); mechanisms, competition and shifts between mechanisms as substrate, nucleophile/base, leaving group vary; why it matters (applications of substitution reactions in pharma synthesis); basis of inversion (in orbital terms) or racemisation (planar carbenium ions); idea of stereoelectronic control of elimination reactions (revision and extension of conformation); nucleophilicity versus basicity; scope and limitations of substitution and elimination reactions in synthesis; cumulative and synoptic examples of syntheses using these reactions and everything developed previously. Aromatic Chemistry (JMP, Semester 2, 8 lectures); wider definition of aromaticity, Hückel, electron counting, Frost’s circles; IR and NMR characteristics of arenes; cyclopropenium ions, cyclopentadiene, cycloheptatriene and ideas of reactions assisted/driven by developing aromaticity (deprotonation, protonation, hydride transfer); electrophilic aromatic substitution – additional reactions, Vilsmeier- Haack, limitations of alkylation as a strategy; competitive substitutent effects; diazonium salts and their applications; applications of reactions in pharma synthesis; benzyne formation and chemistry (used to illustrate idea of cycloaddition) including mild methods of generation and reactions of unsymmetrical benzynes; SNAr reactions –requirements for and examples of; applications of reactions in pharma synthesis; cumulative and synoptic examples of syntheses using these reactions and everything developed previously. Introduction to Alicyclic Chemistry (AW, Semester 2, 8 lectures); conformational behaviour of cyclic molecules (cyclohexane, cyclopentane, cis- and trans-decalin, cyclohexene, cycloheptane); conformational searching and screening; concept and components of ring strain; ring strain as an opponent of cyclisation and an assistant to ring-expansion or contraction; ring size effects on substitution and elimination reactions, and on additions to the carbonyl group; substituted cyclohexanes, A-values and conformational locking; stereoelectronic control on conformationally- locked systems; carbocycle synthesis based on simple carbonyl group reactions; cumulative and synoptic examples of syntheses using these reactions and everything developed previously.

Booklist

‘Spectroscopic Methods in Organic Chemistry’ McGraw Hill 6th Edition (2008) D. H. Williams and I. Fleming. ‘Organic Chemistry’, Pearson International 5th Edition (2007) by P. Y. Bruice, ISBN: 0-13-199631-2 Highly valuable and readily available Supplementary Resources for Organic Chemistry include: i) the web-based program ACE Organic, ii) the OneKey Student Access Kit, and iii) the “Molecular Modelling Workbook”, by W. J. Hehre, A. J. Shusterman and J. E. Nelson (2006), Pearson Prentice Hall, ISBN: 0-13-236731-9. The latter includes SpartanView™ and SpartanBuild™. ‘Alicyclic Chemistry’, Oxford University Press (1997) by M. Grossel, ISBN: 0-19-850104-8. ‘Stereoelectronic Effects’, Oxford University Press (1996) by A. J. Kirby, ISBN: 0-19-855893-7. ‘Chemical Structure and Reactivity: an Integrated Approach’, Oxford University Press (2008) by J. Keeler and P. Wothers, ISBN: 978-0-19-928930-1.

CH 212 PHYSICAL CHEMISTRY 1

Both semesters Credits 20 Lectures 40 Tutorials 12 SHE level 2

Written examinations (1.5 hours) in January (Thermodynamics & Kinetics) and May (Electrochemistry & Energy), each contributing 50% to the final mark, with resit in August (2 hours). There will also be at lest two online quizzes, designed to give students feedback on their learning. Students failing to complete the quizzes may be declared not qualified to sit the examinations.

Lecturers Dr LEA Berlouis, Professor PJ Halling and Dr AW Wark

Aims

• To provide a broad knowledge of the important concepts in Thermodynamics from which more specialist topics can be tackled.

• To investigate systematically the major features of basic Thermodynamics as applied to chemical systems.

• To provide a broad knowledge of the importance of reaction rates in chemical systems.

• To understand how to set out the rate equation for any given system and evaluate the rate constant and so predict the reaction rate. • To explain the concepts of the electrode/solution interface, equilibirum and electron transfer kinetics and mass transport; to apply these concepts to real systems – batteries, fuel cells and corrosion,

• To provide an understanding of the composition and utilisation of fossil fuels (oil, coal and gas) using basic concepts in organic and physical chemistry.

• To provide an overview of environmental pollutants from fossil fuels and methods for their capture and storage.

• To address nuclear and renewable energy sources including solar and the hydrogen economy.

Learning Outcomes

Upon the completion of the class the student will be able to:

• Understand the concept of the system and surroundings in thermodynamics

• Show how the first law of thermodynamics sets the relationship between the change in internal energy of a chemical system and the heat added to the system and the work done on the system.

• Understand the relationship between internal energy and enthalpy and interconvert values for changes in them. Relate this to use of the bomb calorimeter.

• Show some appreciation of the concept of entropy, and of the second law of thermodynamics

• Appreciate how Gibbs energy changes in the system reflect entropy changes in the universe. Know the relationship between changes in the system of Gibbs energy, enthalpy and entropy.

• Understand the concept of functions of state and thermodynamic cycles. Know how they can be used to calculate changes in enthalpy (Hess’s Law), Gibbs energy and entropy, for example by combining different reactions.

• Be familiar with the use of standard enthalpies and Gibbs energies of formation, and standard entropies

• Understand the meaning of “spontaneous” referring to a chemical reaction, and how Gibbs energy shows the spontaneous direction

• Know and be able to use the relationships between the actual and standard Gibbs energy changes and the reaction quotient and equilibrium constant

• Be conversant with electrochemical cell notation, and the meaning of “half cell” and “cell reaction”

• Understand what is meant by “standard electrode potential”, and be able to interconvert with cell potentials

• Interconvert cell potentials and Gibbs energy changes • Relate actual cell potentials to the reaction quotient (i.e. the Nernst equation)

• Understand the concept of thermodynamic activities as used in the expressions for equilibrium constant or reaction quotient

• Appreciate the concept of a thermodynamically reversible process

• State the third law of Thermodynamics and be able to calculate the absolute entropy of a substance at any temperature.

• Use a thermodynamic cycle to estimate the effects of temperature on changes in enthalpy, entropy and Gibbs energy for a reaction, using heat capacities of reactants and products

• Apply the relationship between temperature and equilibrium constant or vapour pressure (simple case where enthalpy and entropy change are temperature independent)

• Use techniques to determine changes in reactant concentration during the course of a reaction.

• Differentiate between zero order, first order and second order reactions.

• Understand and apply the Arrhenius equation to determine the activation energy for a reaction.

• Understand the significance of the Arrhenius parameters in terms of Transition State theory.

• Apply the steady state approximation to enzyme-catalysed reactions.

• Use techniques to determine changes in reactant concentration during the course of a reaction.

• Differentiate between zero order, first order and second order reactions.

• Understand and apply the Arrhenius equation to determine the activation energy for a reaction.

• Understand the significance of the Arrhenius parameters in terms of Transition State theory.

• Apply the steady state approximation to enzyme-catalysed reactions.

• Understand how a potential difference arises at interfaces (solid /solution, liquid /liquid);

• Be fully conversant with and the application of the Nernst equation;

• Have a sound knowledge of the kinetics of electron transfer through the use of the Butler-Volmer and Tafel equations;

• Understand the workings of batteries and of the PEM fuel cell;

• Understand the corrosion process and the usefulness of Pourbaix diagrams;

• Calculate energy densities and apply it when comparing different chemical fuels. • Application of bomb calorimetry for characterising chemical fuels and calculate the gross and net values for

the heat of combustion.

• Know and describe strategies for the capture and storage of various pollutants emitted during the combustion of fossil fuels.

• Describe the basic principles of a nuclear reactor.

• Understand the principles of solar energy and photovoltaic cells.

• Be conversant with the key concepts associated with the development of H2 as a fuel including preparation, storage and chemical-energy conversion.

Content

Why thermodynamics is so useful in chemistry. Combining reactions, equilibrium constants and ΔG° values. . Thermodynamic cycles for ΔG° and ΔH°. ΔG away from standard conditions. The ultimate driving force entropy (ΔS), relationships with ΔG and ΔH. Redox reactions and electrochemical cells –

Ecell and the direct link to ΔrG. Standard electrode potentials. Cells away from standard conditions, thermodynamic activities. Reversibility. Internal energy and enthalpy, calorimetry. Temperature effects on enthalpy and entropy, the Third Law. Gibbs energy and equilibria, effects of temperature and mixing.

Introduction: simple techniques for measuring reaction rates, spectroscope HPLC etc. Defining rates of reaction and the form of rate equations. Relationship between rate equations and mechanisms. Determining reaction orders from experimental data. Integrated rate expressions: Derivation of first- order. Half lives, Pseudo first-order. Derivation of second order rate expressions: Class 1, Class 2. Zero-order reactions. Elementary reactions and molecularity. Choosing between plausible reaction mechanisms. More complex reaction schemes: parallel reactions, series reactions. Effect of temperature on reaction rates: Arrhenius behaviour. Transition state theory and derivation of Eyring Equation. Potential Energy Diagrams: illustration with reaction of H with hydrogen molecule. Steady state approximation. Introduction to enzyme kinetics. Michaelis-Menton constant. Lineweaver-Burke plots. The metal-electrolyte interface; electrochemical equilibrium; the Nernst equation. Electrochemical cells; electromotive force; liquid junction potential. Electrode kinetics; overpotential, the Butler-Volmer equation. Tafel equation, exchange current density and mass transfer effects. Batteries: battery characteristics; voltage, current, capacity, storage density and cycle life. Current- voltage discharge curves. Examples: lead-acid, Ni-Cd, Ni-MH, Leclanché cells. Introduction to Fuel Cells: reactions and cell design; source of H2 fuel; applications and future prospects. Pourbaix diagrams: Features: vertical, horizontal and sloping lines; relevant chemical and electrochemical equilibria. Examples: Fe, Ni, Cu. Regions of active dissolution, immunity and passivity. Applications of Pourbaix diagrams. The corrosion cell. Evaluation of the free energy change in the corrosion reaction. Corrosion prevention and control; anodic and cathodic protection. Chemical Reactors. Unit Operations. Flow sheets and flow diagrams. Overview of different fuels and relative energy densities. Combustion of fossil fuels; bomb-calorimetry; gross and net heats of combustion. Chemical composition of fossil fuels; syn gas and methanol production; cracking/reforming. Pollutants capture and storage. Nuclear energy. Solar energy; biomass and photovoltaic cells. The Hydrogen Economy.

Textbook: You are strongly recommended to purchase a copy of Atkins & De Paula, “Physical Chemistry”, OUP, which will serve as a textbook not only for this class - but will also help you with aspects of spectroscopy in other classes this year. It is also a recommended purchase for core 3rd year physical chemistry, and helps with other topics like polymer physical chemistry. Finally it is good background for final year classes in topics like photochemistry, catalysis, and nanochemistry.

CH 213 FORENSIC TRACE ANALYSIS AND ANALYTICAL CHEMISTRY

Both semesters Credits 20 Lectures 40 Tutorials 12 SHE level 2

Written examination (1.5 hours) in January and continuous assessment through second semester with resit in August.

Lecturers: Dr LT Gibson, Dr P Haddrill, Dr A Nordon

Aims

• to explain the need for separation science in analytical chemistry. § to impart knowledge of the fundamental principles of analytical separations. § to provide introductory knowledge of separation techniques such as solvent extraction, solid phase extraction and thin layer chromatography. • to describe the basic instrumental components of a packed or capillary column gas chromatograph (GC) • to discuss GC applications with packed and capillary columns. • to explain solute migration in gas liquid chromatography. • to describe the basic instrumental components, and applications of liquid chromatography (LC). • to enable students to make informed choices when developing chromatographic methods in analytical science. • to develop an understanding of chromatographic efficiency through theoretical plates and resolution calculations. • to understand what trace evidence is and the search and recovery methods used for materials such as glass, hair, fibres and paints. • to gain knowledge of microscopy techniques and other analytical techniques used to examine hair, fibres, glass and paint.

This course provides students with fundamental concepts of separation science and outlines its importance in obtaining qualitative and quantitative information about analytes in a sample. It also provides students with the fundamental concepts of recovery of trace evidence and treatment of materials to provide identification.

The handling chemical data part of the course will provide students with the basis and fundamental concepts of assessing chemical data. The students will be taught how to handle, examine and assess errors in chemical measurements. Basic statistical calculations will be introduced, and used, to assess the accuracy and precision of analytical data, and to examine the source of errors in chemical experiments.

The last part of the course will focus on mathematical manipulation of chemical data. The students will be taught how to use and apply algebraic and calculus methods to investigate chemical relationships and assess chemical data.

Learning Outcomes

Upon the completion of the class the student will be able to:

• be familiar with the concept of separation science in chemistry. • use their knowledge and understanding to explain the concept of solvent (liquid-liquid) and solid phase extraction methods. • describe the basis and procedural aspects of thin layer chromatography. • discuss capillary and packed chromatography columns and understand the advantages and disadvantages of each. • alter gas chromatographic parameters in order to improve the overall chromatographic process. • be familiar with some typical gas chromatography applications. • Be able to discuss and apply methods of quantification of unknowns in a sample. • describe the basic components of a liquid chromatograph (LC). • discuss reversed phase and normal phase LC (columns and eluent compositions). • be able to discuss the chromatographic parameters which affect separation of analytes in normal phase LC and reversed phase LC. • be familiar with some typical LC applications. • characterise chromatographic peaks. • Discuss the meaning of terms such as distribution constant, the selectivity factor, efficiency, resolution and peak symmetry. • Apply basic equations to calculate theoretical plates and resolution from a given chromatogram. • be aware of the importance of trace evidence and how search, recovery and analyses of paint, glass, hairs and fibres are performed. • understand the composition and physical properties of different glasses and how these properties influence the breaking of glass structures. • understand the different analytical techniques used in the investigation of glass fragments including refractive index measurement and elemental analysis. • use their knowledge, understanding and skills to critically evaluate chemical data, • have a familiarity with errors in chemical data (both random and systematic errors), • identify which statistical tests are required to interrogate chemical problems of a routine nature, • understand the essential theories behind hypothesis testing, Normal distributions and confidence intervals, • effectively deploy tests to understand results obtained from analytical experiments, • explain and communicate the results of the statistical tests applied, • identify and address areas of data handling which can be applied across all areas of chemistry, • apply their subject-related and transferable skills in contexts where the scope of the task and the criteria for decisions are generally well defined, but where some initiative is required, and • use excel spreadsheets for the application of hypothesis tests and unweighted regression analysis. • understand the nature of the scientific method, particularly the testing of hypotheses by fitting straight lines to data. • communicate the results of chemical calculations according to accepted conventions. • building on prior mathematical knowledge, understand logarithmic and exponential transformations, and calculus in a chemical context. • use and apply logarithmic and exponential transformations, and calculus in the analysis of chemical data. • use Excel to manipulate and analyse chemical data using algebraic and calculus methods.

Content

Introduction to solvent and solid phase methods of extraction. The partition coefficient and solution equilibria are described for solvent extraction, as is the method of extraction using solid phase cartridges. The advantages and disadvantages of both methods are discussed. Introduction to chromatography. Explanation of terms such as the stationary phase, mobile phase, the distribution coefficient and elution. Discuss the characterisation of different chromatographic methods according to their separation procedures and the nature of the mobile phase. Introduce the concept of planar and column chromatography. Thin layer chromatography (TLC). Describe silica and modified silica stationary phases. Discuss the use of solvents to prepare mobile phases of different composition. Describe TLC development procedures, and the methods used to detect and identify spots on TLC plates. Gas Chromatography (GC). Describe the basic instrumental components in a gas chromatograph. Outline the main differences between packed and capillary columns in gas-liquid chromatography (GLC). Explain the order of elution of solutes in GLC with respect to the analyte's boiling point and polarity. GLC sample introduction. Discuss different sample introduction methods such as headspace sampling, pyrolysis and direct injection of liquids. Explain the need for, and principles of operation of, a split/splitless valve for injection of samples onto capillary columns. Detectors for GC. Briefly describe the principles of operation of the flame ionisation detector, the thermal conductivity detector and the electron capture detector. Discuss the use of temperature programming and derivatisation to improve the separation and detection of analytes, respectively, in GC. Qualitative and quantitative analysis. Measure chromatographic parameters such as retention time and peak width. Use quantitative methods of analysis such as; area normalisation, area normalisation with response factors, external standards, internal standards and standard additions to determine the concentration of unknowns in a sample. High performance liquid chromatography (HPLC). Discuss the basic components of the instrument. Revisit Beer's law and absorbance. Describe the use of single wavelength UV absorbance detectors, and the advantage of using diode array detectors. Stationary phases in HPLC. Describe the use of silica particles in adsorption chromatography (normal phase HPLC), and the use of modified silica particles for reversed phase HPLC applications. Explain the order of elution of analytes in normal phase, and reversed phase, HPLC. Introduce the concepts of gradient elution and derivatisation to improve the separation and detection of analytes, respectively, in LC. Assessing quality in column chromatography. How to measure peak retention times and the widths of chromatographic peaks. Explanation, and calculation, of terms such as: the selectivity factor, resolution, chromatographic efficiency and peak symmetry. Introduce the simple form of the van Deemter equation to describe band broadening. Search and recovery of trace materials. How to recover and preserve microtrace evidence occurring in a variety of settings, alternative methods are considered and compared. The microscope. Fundamentals of optics, fibre optics, search fluorescent, comparison and polarising light microscopy. Hair. Morphology, surface texture and structure, the examination of hair and the evaluation of hair as evidence. Morphology of synthetic and natural fibres. A review of the appearance of natural fibres as seen by high poer microscopy and a consideration of special difficulties in identifying the generic class of synthetic fibres. Fibre transfer and persistence. A review of the factors that affect the numbers of fibres transferred and the findings of exercises to study the persistence of fibres on clothing after a contact, primary & secondary contact considered. Presumptive test for trace materials. A review of the presumptive tests used to determine the possible presence of drugs, explosives and gun shot residues. Glass. A review of the composition and manufacture of glass, its physical examination and the forensic context in which it might be found as well as looking at chemical methods to determine its composition. Paint. A review of the composition of paint, its uses and the physical examinations undertaken on both single and multi-layered paints. The forensic context in which it might be found is considered as well as looking at the various chemical methods to determine both its colour and its composition.

Understanding data: the mean and standard deviation, types of error in chemical analyses and maximum possible errors in the laboratory, accuracy and precision. Reporting data: rounding, significant figures and propagation of errors. Sample v's Population. Understand the concept of data samples, and how to represent data using probability distribution functions. Introduce the concept of Normal distribution curves and confidence intervals for small, and large, samples. Standardising the Normal probability distribution function. Use of z-tables to determine the proportion of results that lie between two limits of a data set. Interpretation of z-tables. Significance Tests. Use of the t- test and the z-test to compare the results of a chemical experiment with a known, standard, value. Use of the F-test to compare the variance of two sets of data. Use of t-tables, z-tables and F-tables. Hypothesis tests (z-test and t-test) to compare two sets of experimental data. One-sided and two- sided tests. Linear Regression. To apply linear least squares regression to calibration data to obtain the 'best fit' model for the experimental data. Calculation and interpretation of values such as the scatter error, slope error and intercept error. Validation of linear models using residual plots (homoscedastic v's heteroscedastic data). Use of weighted regression lines for heteroscedastic data. Understanding the correlation coefficient. Reporting data: IUPAC convention, converting between different units. Calculating concentrations and dilution factors. Logarithms and exponentials: definitions and properties, significant figures, base 10 with application to pH and Beer’s Law, base e with application to kinetics, Boltzmann equation and Arrhenius equation, conversion between different bases, linearising equations. Differentiation: definitions and properties, calculating rates of change via slopes, tangents and differential calculus, use of rates of change to identify the equivalence point in a titration, identifying turning points, removal of baseline offsets and sloping baselines in spectroscopy. Integration: definitions and properties, calculating areas using numerical integration methods, using integral calculus to calculate the inverse of differentiation, integration of first and second order rate equations, assessing reactions via concentration and instrument response data. Fourier transforms: use of the Fourier transform to convert from the time to the frequency domain, application in spectroscopy.

Draft Booklist

Mute Witnesses : Trace Evidence Analysis / edited by Max M. Houck.

Trace Evidence Analysis : More Cases in Mute Witnesses / edited by Max Houck and Color Atlas and Manual of Microscopy for Criminalists, Chemists, and Conservators / Nicholas Petraco, Thomas Kubic

CH 214 PRACTICAL ORGANIC AND INORGANIC CHEMISTRY

First or Second semester Credits 20 Hours 96 SHE level 2

Aims

• to develop basic laboratory skills, particularly in preparative chemistry and in analysis • to give experience in the applications of spectroscopy and of common instrumental techniques • to provide a practical demonstration of topics contained in the lectures. • to instruct students in a wide range of transferable skills which will add to their chemical knowledge and ensure that they are marketable graduates.

Students will attend the Preparative Laboratory for six weeks, and must satisfy the requirements of both Organic and Inorganic separately for the award of these practical credits. They will also participate in the transferable skills activities listed below. During the course, students will be allocated experiments from the following lists.

Organic Chemistry – Head of Laboratory: Dr J Haddow

Preparations:

1 Preparation of an alkyl halide, 2-chloro-2-methylpropane

2 Thin-layer chromatography - dye mixtures and the identification of unknowns

3 Reduction of 4-nitrobenzaldehyde with sodium borohydride

4 Separation of an unknown mixture

5 Preparation of an alkanoic acid via a Grignard reagent

6 Nitration of an aromatic compound.

7 Preparation of hexan-1,6-dioic acid

Inorganic Chemistry - Head of Laboratory: Dr C Dodds

One Day Experiments:

D1 Qualitative analysis D2 Redox titrations

D3 Preparation of a salt of iron in a less common oxidation state

D4 Gravimetric and titrimetric analysis of red lead

Analytical Chemistry:

A1 Determination of hydrazine in hydrazine sulphate by titrimetric analysis

A2 Determination of chromium in potassium chromium(III) sulphate by titrimetry

A3 Determination of molybdenum by gravimetric analysis - formation of an oxine complex

A4 Determination of cobalt by gravimetric analysis - cobalt(II) tetrathiocyanatomercurate(II) complex

Instrumental Techniques:

I1 Use of a pH meter to determine the equivalence point of an acid-base titration

I2 Use of a pH Meter for a potentiometric titration

I3 Analysis of xylene isomers by gas liquid chromatography (GLC)

I4 Determination of caffeine in cola by high pressure liquid chromatography (HPLC)

I5 Determination of ammonia in waters by automatic colorimetry

I6 Calibration of volumetric apparatus

I7 Analytical techniques for the identification of shoe polish

I8 Thin layer chromatographic analysis of fibre dyes

Spectroscopic Experiments:

S1 Spectra of transition-metal ions

S2 Determination of the formation constant of a metal complex by the molar ratio method

S3 Infrared spectroscopy

S4 Spectrophotometric determination of iron

Synthetic Chemistry: P1 Preparation of vanadyl acetylacetonate

P2 Preparation of a chelate complex of an alkali metal salt

P3 Preparation of nitrogen (group V) and sulphur (group VI) compounds

P4 Preparation of halide salts of group IV elements

P5 Preparation of a complex oxalate of iron(III)

Assessment of the Class

Practical work is an essential part of the preparation of a professional chemist, and the Royal Society of Chemistry places great emphasis on the practical content of a qualifying course. The requirements of each laboratory are based on continuous assessment, and students who do not attend or do not submit laboratory work will find their situation difficult to rectify. Students are responsible for measuring their own performance against laboratory requirements, but where possible they will be warned in advance if their performance appears to be of a lower standard than that required.

The laboratory requirements are summarised below, but the full details will be found in the appropriate Laboratory Manual.

A student whose performance falls marginally short of the standard required may exceptionally be permitted to carry out further experiments designed to demonstrate sufficient practical competence for the award of the credit; this exercise may be held at the conclusion of a diet of examinations, at the discretion of the Head of the Laboratory concerned.

When absence from the Laboratory has been caused by medical or compassionate reasons, or when failure of a practical class is the only impediment to a student’s progress to third year, it may exceptionally be possible to arrange for practical experience to be gained (and the laboratory credits awarded) by work in the laboratory between the end of the term and the August diet of examinations. Students should note, however, that summer vacation experience can realistically be gained in only one laboratory area.

Laboratory Requirements

Attendance is expected on 4 afternoons each week, and students attending for less than 80% of the available afternoons will automatically fail the laboratory.

Experiments are assessed and a mark awarded by written report. The laboratory requirement will be explained fully at the Introductory Session, which students attend before embarking on practical work.

Transferable Skills Dr LA Thomson

Aims

• To make students aware of how often scientists must rely on the written word to make themselves understood, and improve their written communication skills. • To provide training in the chemical drawing package ChemBioDraw, to allow them to produce chemical drawings by computer. • To apply a range of scientific and transferable skills to a case study working as part of a small group. This includes making a group presentation.

Scientific Skills Learning Outcomes:

• Scientific knowledge: matching analytical techniques to the application. • Handling information: Manipulating and evaluating information and data to make realistic decisions on the evidence available. • Problem Solving: Tackling unfamiliar problems, using judgement, evaluating information, formulating hypotheses, analytical and critical thinking.

Transferable Skills Learning Outcomes:

• Communication skills: Discussion of case within group and oral presentation of conclusions to other students and course tutors. • Planning and organisation: Managing an investigation, individual judgement, taking responsibility for decision making and time management. • Information Technology: Preparing material for presentation. Use of chemical drawing software. • Improving learning & performance: Using feedback to reflect upon group and individual performance • Working with others: Brainstorming, discussion, division of tasks and feeding back to the group.

Content

1. Scientific Writing Skills This lecture/workshop is designed to prepare the student for a range of scientific writing tasks which they will encounter both as students and ultimately as professional chemists. Topics covered will include grammar, style (correct use of language), conventions (such as keeping a good laboratory notebook, figures, tables and referencing) and formatting (such as report writing.) A plagiarism exercise will also be undertaken. A written assignment will be given at the end of the workshop, which will be assessed by the course tutors.

2. Group working Within teams of 4/5 students, the problem solving case study provides a framework for a wide range of team-working and problem solving skills in a general chemistry related context. This will involve the students contributing to the planning of the overall strategy for their team and making a broad range of decisions under tight time deadlines. The students will be assessed by the course tutors throughout the duration of the unit. To pass this section of transferable skills, each student must contribute to a group presentation, which will be assessed by the course tutors.

3. Chemical Drawing Skills Following initial tutorial sessions, the students will be required to independently complete a series of individual chemical drawing tasks using ChemBioDraw. They must also learn how to use the NMR prediction facilities of this software. They will be assessed by completion of an assignment, marked by the course tutors.

Assessment of Transferable Skills

The requirements of these classes are based on attendance, participation and continuous assessment. There are formal assignments associated with scientific writing and chemical drawing, both with a pass mark of 40%. The outputs from the group working activity, including a group presentation are also assessed. The whole transferable skills part of CH 214 will be assessed on a pass/fail basis.

THE NEXT CLASS IS COMPULSORY FOR STUDENTS ON THE MChem/BSc Honours CHEMISTRY WITH DRUG DISCOVERY DEGREES

MP 217 PHARMACEUTICS

First semester Credits 20 Lectures 20 Tutorials 6 SHE level 2

Written examination: 1 hour MCQ class test contributes 30%. The MCQ class test will focus on basic numeracy, numerical manipulations and core pharmacy concepts (dilutions, concentrations etc). A 2 hour degree examination contributes 70%. The degree examination will focus on the material covered in lectures and consists of short answer questions. A resit exam (2 hours) will take place in August.

Lecturer Dr I Oswald

Aims

• This module provides an introduction to: • Thermodynamics, and its application to pharmaceutical systems. • Chemical kinetics, and the stability of drug molecules. • The solid state, where a knowledge of crystal structure often explains drug properties. • Dissolution and solubility, and their importance to drug absorption. • Surface chemistry, and the role of surface-active compounds in formulation in the solubilisation of drug molecules.

Learning Outcomes

On successful completion of this class, students should be able to do the following:

• Define and interconvert the terms associated with concentration • Distinguish differences in equilibria • Understand the principles of chemical kinetics • Define various solid state terms • Define various solute and solubility terms • Have an overview of surface chemistry

Topics

Concentrations 1. (a) molarity (b) molality (c) %(w/v) (d) %(w/w) (e) mole fraction Equilibria 2. Open systems, closed systems and isolated systems. 3. Potential energy and kinetic energy. 4. Enthalpy, H, entropy, S, and Gibbs free energy, G. 5. The relationship between equilibrium constant, K, and temperature, T. 6. The relationship between K and ΔGo. 7. The relationship between ΔGo, ΔHo and ΔSo. Chemical kinetics 8. Stoichiometric and reaction rate equations. 9. The effect of change of concentration of reactants on reaction rate. 10. Define the following terms: (a) order (b) molecularity (c) rate-determining step (d) rate constant, k 11. The relationship between concentration and time for zero order and first order chemical reactions. 12. The Arrhenius equation and its use to predict a value of k at a given T. Solid state 13. (a) molecular crystal (b) unit cell (c) polymorph 14. Why polymorphic solid forms of the same chemical compound can have different physical properties. 15. Analytical techniques to distinguish different physical forms of an organic compound. Solutions and solubility 16. (a) dissolution (b) equilibrium saturation solubility 17. The Noyes-Whitney equation to predict the effect of solution pH on the rate of dissolution of a solid drug. 18. The effect of ionisation on the solubility of an organic compound. 19. The pH-partition hypothesis. Surface chemistry and Micelles 20. Surface tension. 21. Formal definition of surface tension. 22. The relationship between surface tension and surface free energy, ΔG*. 23. Identify the hydrophobic and hydrophilic portions of a molecule, and explain the mechanism by which surfactants decrease surface tension. 24. Gaseous and condensed surfactant monolayers. 25. Hydrophilic and hydrophobic coarse and colloidal dispersions. 26. The conditions under which water-soluble surfactants associate to form micelles. 27. The structure of the electrical double layer surrounding an ionic micelle. 28. (a) surface potential (b) zeta potential 29. The mechanism of solubilisation of poorly water-soluble ‘guest’ molecules by surfactants.

THIRD YEAR CLASS SYLLABI

CH 309 PHYSICAL CHEMISTRY 2

Both semesters Credits 20 Lectures 40 Tutorials 12 SHE level 3

The main assessment will be a 3 hour examination in the May diet, covering the whole class. In this, students will have to answer one question out of two on Intermolecular Forces and Non-ideality, one question out of two on statistical mechanics, and two questions out of four on Bonding and Symmetry. In addition, two elements of continuous assessment will each count for 10% of the overall mark:

• An open book test in semester 1, week 8 or 9 • A series of class assignments in semester 2 The resit will be a 3 hour examination in August, with the same format as the May examination. The marks from the continuous assessment component of the class will not count towards the mark for the resit.

Lecturers Dr EJ Cussen, Professor PJ Halling, Dr D Palmer

Aims

• To provide core knowledge and skill in physical chemistry, as an essential basis for a competent graduate in chemistry. • To provide an understanding of intermolecular forces and their importance in defining key aspects of chemical behaviour and molecular organization. • To provide an introduction to the current understanding of the knowledge of the electronic structure of atoms and molecules through the prism of quantum chemistry. • To establish the principles of bonding in molecules as described by valence bond and molecular orbital theories. • To provide an introduction to group theory and how it can be applied to the determination of the symmetry of molecules and their properties.

Outcomes Upon the completion of the class the student will be able to:

• Understand how intermolecular forces underlie all types of non-ideal behaviour • Appreciate the nature and applications of supercritical fluids • Understand the principle of corresponding states, and how the van der Waals equation can be recast in terms of critical constants • Estimate pressures in non-ideal systems using van der Waals equation, virial equations or compression factor plots • Understand the concept of fugacities, and estimate by simple integration of equations of state with pressure or from reduced variable plots • Understand the origin of intermolecular forces in terms of molecular dipoles and polarisabilities • Recognise and use the equations for interaction energies, including simple models incorporating repulsion • Calculate molecular dipole moments from partial charges, and estimate by vector sum • Understand how dielectric or refractive index measurements can be used to calculate dipole moments and polarisabilities • Appreciate how boiling points give evidence for the strength of intermolecular interactions, and for hydrogen bonds • Appreciate the difference between ideal and ideal-dilute behaviour in liquid mixtures, and the links to standard states for activities • Calculate mean activity coefficients using the Debye-Huckel limiting law and appreciate its limitations • discuss Schroedinger’s equation of the hydrogen atom and be able to write down and interpret the solutions to the equation; • explain the variational theorem; • rationalise the electronic structure of many-electron atoms; • explain the concepts of quantum numbers and electron spin; • write down the form and energy of (i) the simple product wave-function and (ii) the Heitler-London wave- function for the valence bond treatment of H ; 2 • explain the basis of the molecular orbital theory; • construct the molecular orbital correlation energy diagrams for the diatomic molecules from H to 2 F , and use the diagrams to rationalise the variation of bond lengths, bond dissociation energies, 2 and magnetic properties; • detail the approximations present in the Hückel theory and explain how they are used to simplify the secular equations/determinant; • use the results of a Hückel calculation to obtain the π-bonding energy, π-delocalisation energy, π- electron densities and π-bond orders; • use molecular orbital theory to help to rationalise electrophilic aromatic substitution and to explain aromaticity; • identify the symmetry operations/elements of a molecule and hence identify the point group of the molecule; • describe the 1:1 relationship between operations and matrices, and use the character of the matrices to reduce a reducible matrix; • evaluate the number and type of the normal modes of vibration for any molecule and identify their activity in the infra-red and Raman; • use the orthogonality theorem to predict the intensity of spectroscopic transitions; • determine the symmetry labels of π-molecular orbitals and work out the possible π-excited states of molecules; and • evaluate the symmetry labels of a “central atom” and the corresponding.

Syllabus

A: Intermolecular forces and non-ideality Types of intermolecular interaction: Discussion of key features (origin, strength, range and directionality) of the main types of interaction, introduced through examination of specific example molecules: Permanent and induced dipoles, dipole moments and polarisability; ion-dipole interactions, dispersion forces; hydrogen bonding; π-π interactions. Lennard-Jones potentials. Dielectric properties: Polarisation, dielectric constant, effect of frequency, Clausius-Mossotti and Debye equations. Intermolecular forces and non-ideality: Revision of the van der Waals equation. The Boyle temperature. Real gas isotherms and the critical region, supercritical fluids and their applications. Solutions: solubility and solvation. Ionic strength, activity, Debye-Huckel limiting law. B: tbc The second block in this class will cover statistical mechanics and related topics. Full details were still being developed when this handbook went to press but will be provided at the start of the class. C: Bonding and Symmetry Schrödinger's equation. I: Introduction and simple examples. De Broglie's relation. One dimensional Schrödinger equation. Particle in box. Energy levels and wavefunctions. Schrödinger's equation II: The variational principle. Example. Schrödinger's equation in three dimensions. The Hamiltonian operator. Setting up Schrödinger's equation for atoms and molecules. Atoms I: Solutions for the H-atom. The atomic orbitals and quantum numbers. Atoms II: Many electron atoms. Structure of periodic table. Spin: Electron spin. The anti symmetrization principle and Pauli's principle. Ground and excited state wavefunctions of the He atom. Singlets and triplets. Valence Bond Theory (VB): Heitler-London wavefunctions for H2. Extensions to hetero-polar systems. Molecular Orbital Theory (MO): General philosophy of the method. Correlation diagrams, bonding and antibonding orbitals. Illustrated for 2nd period diatomics. Comparison of VB and MO methods. Hückel Molecular Orbital Theory I: π-orbitals, secular determinants. MO energies and coefficients. Approximations of Huckel Theory. Electron density, bond order, delocalization energy. Hückel Molecular Orbital Theory II: Alternant hydrocarbons, hyperconjugation, aromaticity. electrophilic aromatic substituents, Heteroatoms. Symmetry Groups: Symmetry operations. Point groups. Molecular symmetry Matrices: Matrices and symmetry operations. Character of a matrix. Irreducible matrices. Direct sum rule. Normal Modes of Vibration: Finding number of normal modes of vibration for any molecule. Normal Modes of Vibration: Identifying infra-red and Raman active. Symmetry around a Central Atom: Symmetry of combinations of ligand orbitals, construction of correlation diagrams. π-molecular orbitals: Symmetry of π-orbitals and excited states. Transition probabilities. Vibronic Coupling. Ring Closure Reactions: Principle of conservation of symmetry in ring closure reactions. Application to appropriate reactions.

Booklist Atkins’ Physical Chemistry (8th Edition), OUP.

Molecular Quantum Mechanics (4th Edition) – P. Atkins and R. Friedman: Chapters 0 - 8.

CH 313 PRACTICAL PHYSICAL, APPLIED, FORENSIC AND ANALYTICAL CHEMISTRY

First or Second semester Credits 20 Hours 100 SHE level 3

Staff in charge of Laboratories: Dr LEA Berlouis (Physical and Applied) and Dr P Allan (Analytical)

Aims

• To conduct experiments in physical, applied and analytical chemistry and in forensic science • To gain practical experience of theoretic aspects of physical, applied and analytical chemistry, and in forensic science, covered in lecture courses • To develop skills in - physical chemistry, forensic and analytical observation,

- use of statistical methods in the evaluation of data

- demonstration of physical chemical principles, using analytical data

- interpretation of forensic and analytical data, and

- writing of laboratory and court reports.

Outcomes

Upon the completion of the class the student will:

• Have developed improved practical skills, especially in techniques and procedures relevant to physical, applied and analytical chemistry, and in forensic science • Be able to interpret analytical data arising from physical and applied practical chemistry experiments and in terms of physical and applied chemistry principles • Be able to interpret analytical and forensic data and apply statistics where appropriate • Be able to write both laboratory and court reports

Content

Students will conduct the following experiments:

A: Physical and Applied Chemistry

Group N – Mass and heat transfer

N2: Diffusion of gases

N3: The rotating disk electrode (RDE) and the reduction of oxygen

N4: Redox potentiometry and the oxidation of ferrous ions in two different acidic media

Group P – Polymers

P1: Molecular weight determination from viscosity measurements

Group Q – Atomic and molecular properties

Q1: x-ray diffraction from solids, the powder method

Q2: Activity coefficients from cell measurements

Q3: Polarimetry

Q4: Crystals under the microscope and kinetics of crystal grwoth

Q5: Determination of the dipole moment of nitrobenzene

Group R – Kinetics R1: Determination of the level of quinine in tonic water using fluorimetry

R2: A kinetic study of the catalytic decomposition of hydrogen peroxide

R3: Study of the kinetics of the rapid reduction of methylene blue by ascorbic acid using a stopped- flow technique

R4: Colorimetric determination of iron (as Fe3+) in Irn Bru

R5: Raman spectroscopy and the detection of alcohol

Group S – Surface properties

S1: Adsorption isotherm of oxalic acid on charcoal

B: Forensic and Analytical Chemistry

FA 1 Flame Atomic Absorption Spectrometry: Optimisation of Flame Conditions and Control of Chemical Interference Effects

FA 2 Ion Chromatography: Determination of Chloride, Nitrate and Sulfate in Rainwater

FA 3 Radioanalytical Chemistry: Interpretation of Alpha Particle and Gamma Ray Spectra

FA 4 Electroanalytical Chemistry: Use of an Ion Selective Electrode to Determine the Concentration of Fluoride in a Waste Effluent

FA 5 Electrophoresis: Estimation of the Molecular Weight of a Protein by Polyacrylamide Gel Electrophoresis

FA 6 Drugs of Abuse 1: Presumptive Tests and High Performance Liquid Chromatography

FA 7 Drugs of Abuse II: Fourier Transform Infra-red Spectrometry

FA 8 Analysis of Ignitable Liquids and Other Items Associated with Incendiary Devices

FA 9 Analysis of Footwear Marks

FA 10 Document Examination

FA 11 DNA Profile Interpretation

FA 12 Solid Phase Extraction of Caffeine from Urine

Assessment of the Class Practical work is an essential part of the preparation of a professional chemist, and the Royal Society of Chemistry places great emphasis on the practical content of a qualifying course. The requirements of each laboratory are based on continuous assessment, and students who do not attend or do not submit laboratory work will find their situation difficult to rectify. Students are responsible for measuring their own performance against laboratory requirements, but where possible they will be warned in advance if their performance appears to be of a lower standard than that required. A student whose performance falls marginally short of the standard required may exceptionally be permitted to carry out further experiments designed to demonstrate sufficient practical competence for the award of the credit; this exercise may be held at the conclusion of a diet of examinations, at the discretion of the Head of the Laboratory concerned.

When absence from the Laboratory has been caused by medical or compassionate reasons, or when failure of a practical class is the only impediment to a student's progress to fourth year, it may exceptionally be possible to arrange for practical experience to be gained (and the laboratory credits awarded) by work in the laboratory during the later part of the second semester, or (for students not going on placement) during the early part of the third term. Students should note, however, that these additional opportunities can realistically be taken in only one laboratory area.

CH 314 PRACTICAL PYHSICAL, APPLIED AND DRUG DISCOVERY CHEMISTRY

First or Second semester Credits 20 Hours 100 SHE level 3

Staff in charge of Laboratories: Dr LEA Berlouis (Physical and Applied) and Dr J Haddow (Drug Discovery)

Aims • To conduct experiments in physical and applied chemistry and in chemistry relating to drug discovery • To gain practical experience of theoretic aspects of physical, applied and synthetic medicinal chemistry covered in lecture courses • To develop basic laboratory skills in - physical chemistry and analytical observation,

- use of statistical methods in the evaluation of data

- demonstration of physical chemical principles, using analytical data

- synthetic medicinal chemistry and analysis

- applications of spectroscopy and of common instrumental techniques

- writing of laboratory and court reports.

Learning Outcomes

Upon the completion of the class the student will be able to: • Have developed improved practical skills, especially in techniques and procedures relevant to physical, applied and synthetic medicinal chemistry • Interpret analytical data arising from physical and applied practical chemistry experiments and in terms of physical and applied chemistry principles • Write laboratory reports • Understand the need for good laboratory practice • Confidently handle chemicals in a safe and confident manner • Realize the COSHH and safety issues associated with handling chemicals and pharmaceuticals • Time manage practical work • Carry out multi-step syntheses • Safely handle pyrophoric reagents • Handle microscale laboratory glassware in a confident manner • Carry out manipulations using microlitre syringes. • Carry out microscale experiments and be able to purify products on a microscale • Undertake solid-phase syntheses • Carry out experiments under a dry atmosphere • Carry out a fractional vacuum distillation • Carry out recrystallizations using single and mixed solvents • Purify products by column chromatography • Measure optical rotations and determine ees and enantiomeric compositions • Run infra red spectra using liquid cells • Assign nmr and ir spectra of their products and starting materials • Use in silico methods to design novel enzyme inhibitors

Content Students will conduct the following experiments:

A: Physical and Applied Chemistry

Group N – Mass and heat transfer

N2: Diffusion of gases

N3: The rotating disk electrode (RDE) and the reduction of oxygen

N4: Redox potentiometry and the oxidation of ferrous ions in two different acidic media

Group P – Polymers

P1: Molecular weight determination from viscosity measurements

Group Q – Atomic and molecular properties

Q1: x-ray diffraction from solids, the powder method Q2: Activity coefficients from cell measurements

Q3: Polarimetry

Q4: Crystals under the microscope and kinetics of crystal grwoth

Q5: Determination of the dipole moment of nitrobenzene

Group R – Kinetics

R1: Determination of the level of quinine in tonic water using fluorimetry

R2: A kinetic study of the catalytic decomposition of hydrogen peroxide

R3: Study of the kinetics of the rapid reduction of methylene blue by ascorbic acid using a stopped- flow technique

R4: Colorimetric determination of iron (as Fe3+) in Irn Bru

R5: Raman spectroscopy and the detection of alcohol

Group S – Surface properties

S1: Adsorption isotherm of oxalic acid on charcoal

B: Synthetic Medicinal Chemistry

The students carry out one multi-step synthesis involving the isolation of ibuprofen from tablets and then the formation of diasteromeric amides. The ibuprofen is also used to prepare lactate esters that are subsequently hydrolysed.

The students also have to carry out one solid-phase synthesis experiment from a choice of two (preparation of a diketopiperazine or preparation of a tertiary amine).

The preparation of a chiral intermediate is undertaken using Baker’s yeast and the ee of the product is assessed by polarimetry after vacuum distillation of the product.

Finally, molecular modelling software is used to design novel enzyme inhibitors.

Assessment of the Class Practical work is an essential part of the preparation of a professional chemist, and the Royal Society of Chemistry places great emphasis on the practical content of a qualifying course. The requirements of each laboratory are based on continuous assessment, and students who do not attend or do not submit laboratory work will find their situation difficult to rectify. Students are responsible for measuring their own performance against laboratory requirements, but where possible they will be warned in advance if their performance appears to be of a lower standard than that required. A student whose performance falls marginally short of the standard required may exceptionally be permitted to carry out further experiments designed to demonstrate sufficient practical competence for the award of the credit; this exercise may be held at the conclusion of a diet of examinations, at the discretion of the Head of the Laboratory concerned.

When absence from the Laboratory has been caused by medical or compassionate reasons, or when failure of a practical class is the only impediment to a student's progress to fourth year, it may exceptionally be possible to arrange for practical experience to be gained (and the laboratory credits awarded) by work in the laboratory during the later part of the second semester, or (for students not going on placement) during the early part of the third term. Students should note, however, that these additional opportunities can realistically be taken in only one laboratory area.

CH 315 PRACTICAL ORGANIC AND INORGANIC CHEMISTRY

First or Second semester Credits 20 Hours 100 SHE level 3

Staff in charge of Laboratories: Dr J Haddow (Organic) and Dr C Dodds (Inorganic)

Transferable Skills staff: Dr LA Thomson

Aims • to develop basic laboratory skills, particularly in preparative chemistry and in analysis • to give experience in the applications of spectroscopy and of common instrumental techniques • to provide a practical demonstration of topics contained in the lectures • To instruct the student in a wide range of transferable skills which will add to their chemical knowledge and ensure they are marketable graduates.

Learning Outcomes Upon the completion of the class the student will be able to:

• Time manage practical work • Carry out multi-step syntheses • Safely handle pyrophoric reagents • Handle microscale laboratory glassware in a confident manner • Carry out manipulations using microlitre syringes. • Carry out microscale experiments and be able to purify products on a microscale • Carry out experiments under a dry atmosphere • Carry out a fractional vacuum distillation • Carry out recrystallizations using single and mixed solvents • Conduct electrochemical synthesis and investigation of inorganic compounds • Purify products by column chromatography • Run infra red spectra using liquid cells • Assign nmr and ir spectra of their products and starting materials • Assign Mass Spectra of their compounds • Give oral presentations • Work as part of a group

Content

A: Organic Chemistry The students carry out one compulsory multi-step synthesis involving the Wittig reaction and bromination of the resulting alkene.

They then have to carry out two macroscale experiments chosen from: • Diels-Alder Reaction. • Acylation of Ferrocene. • Fenbufen Preparation. • Crossed Aldol Reaction. • Enantioselective Reduction of a Ketone.

The students must carry out two microscale experiments chosen from: • Diels-Alder Reaction. • Beckmann Rearrangement. • Preparation of an Enol Acetate. • Oxidation of an Alcohol.

B: Inorganic Chemistry The students will carry out four experiments as directed by the demonstrators from the following list:

• The Stabilisation of an Oxidation State of a Transition Metal which is unknown as a Simple Ion • Inorganic Reactions of Sodium Borohydride • Nickel Triphenylphosphine Complexes • Preparation and Characterisation of a Substituted Cyclotriphosphazene

• Preparation and Characterisation of Organotin Compounds, (PhCH2)4-xSnBrx • Deduction of a Spectrochemical Series from Octahedral Chromium(III) Complexes • Isomerism and Coordination Geometries Explored by Spectroscopic and Magnetic Measurements • Electrochemical Methods in Inorganic Chemistry • Preparation of π-Arene Ruthenium Complexes • Preparation of a Macrocyclic Ligand and its Complexes

Transferable Skills Dr LA Thomson

Aims • To improve presentation skills • To improve data retrieval skills • To encourage group work • To raise students awareness of quality issues.

Learning Outcomes

By the end of the course the students should be able to:

• Research a given topic • Present their findings in a clear and structured manner • Consider quality issues in an industrial setting • Present chemical details in a clear and concise manner.

Content

1. Poster Presentation Skills The poster presentation exercise provides the opportunity for students to develop written and graphic presentations skills and to extend and utilise their team abilities in a new, and chemically related, context. Within teams of 4/5 students, this will involve the group producing a poster describing an important area of science. Each team will have an academic member of staff as their supervisor for this task and each poster will be prepared within a given time period. The students will be assessed by the teaching associates and the academic supervisor throughout this task. This assessment will be based on the individual and team performance of each student. At the end of the academic year, all posters will be judged and prizes will be awarded to the best ones. 2. Data Retrieval Skill This will involve the student in gaining experience in the use of the library and electronic databases, an include an exercise where the student will demonstrate skills in the use of data retrieval.

3. Oral Presentation Skills fter a brief introductory session o After a brief introductory session outlining good practice in oral presentations, each student will prepare and deliver an oral presentation. Each presentation will be carried out in a small group and assessed by the teaching associate. Feedback will be given.

4. Quality Systems Workshop This interactive workshop addresses the controls required to achieve quality products and how this may be achieved within a quality system. Many of the issues covered in this exercise will be encountered by students in their industrial placement year and this is an important introduction. During the course of the exercise each student will complete a workbook.

CH 316 ANALYTICAL CHEMISTRY AND DRUGS OF ABUSE

Both semesters Credits 20 Lectures 40 Tutorials 8 SHE level 3 Continuous assessment through first semester and written examinations (1.5 hours) in May. Continuous assessment and written examination (1 hour) in August.

Lecturers Dr CM Davidson, Dr LT Gibson and Dr L Dennany.

Aims

• to impart declarative knowledge of fundamental analytical methods, • to familiarise students with advanced theories in chromatography, mass spectrometry and electroseparations. • to permit a deeper understanding of the principles of operation of the chosen methods, • to introduce the concept of experimental design and its application in analytical, forensic and preparative chemistry, • to give students the ability to perform analytical calculations and interpret the data in scenarios they would face in the chemical industries and research. • to provide students with a knowledge of the analytical procedures used to identify substances controlled under the Misuse of Drugs Act 1971, Misuse of Drugs Regulations 2001, the Medicines Act 1968 and the World Anti-Doping Agency. It will introduce students to methods of clandestine synthesis and how drug profiling can identify the synthetic route used. • The concept of a drug c.f. a drug of abuse will be introduced, their bioavailable routes and actions. • The course will cover classification, administration routes, mechanisms of action, medical uses and side effects of opiods, stimulants (e.g. MDMA), cannabis, benzodiazepines. • Drug screening will be discussed as will drug abuse in sport.

Learning Outcomes

Upon the completion of the class the student will be able to:

• communicate the results of their studies accurately and reliably • discuss the main context of the subject areas using the information provided, • show familiarity and a detailed knowledge of mass spectrometry (MS), selected chromatographic separations and electroseparations; giving an overview of the main components of various instrument systems, • have a critical understanding of the fundamental principles of band broading (including discussing of van Deemter, Golay and van Deemter plots), • have a detailed understanding of ANOVA for the evaluation of chemical data (both one-way and two-way tests) • have a reasonable understanding of the essential theories and concepts behind experimental design, and ways in which it can be applied in analytical, forensic and preparative chemistry. • understand the current UK legislation controlling drugs of abuse and related compounds • be familiar with the physical and chemical characteristics of different controlled substances • understand the process of analyzing a controlled substance including: Physical description, sampling, presumptive testing, thin later chromatography, immunoassay, instrumental techniques (GC-FID, GC-MS, HPLC, FTIR & UV) and quantification techniques • understand some of the synthetic processes involved in the manufacture of drugs of abuse and how these can be exploited for drug profiling • understand the pharmacodynamics of drugs of abuse • understand the various matrices used to screen for the presence of drugs of abuse in the body

Content

A: Analytical Chemistry (semester one) – examined by continuous assessment.

Mass Spectrometry

Introduction: basic principles, characteristics and instrument systems. Sample introduction. Ion production: gas phase ionisation methods (electron impact ionisation, chemical ionisation, the electrospray); desorption methods (thermal ionisation, ion bombardment, laser ablation / desorption, matrixassisted laser desorption ionisation (MALDI)). Mass separation: magnetic sector analyser, electrostatic analyser, time-of-flight/reflectron analysers, quadrupole analyser; MS-MS. Ion detection: Faraday cup and electron multiplier.

Advanced Separation Science

Kinetic theory of band broading processes. Detailed discussion about the original van- Deemter equation for packed columns, the Golay equation for capillary columns. Interpretation of van Deemter plots. Explanation of solution migration in gas liquid chromatography. Describe the factors that influence solute migration. Understand how solutes with the same polarities, or boiling points, can separate. Use of Kovat's retention indices and McReynolds constants to characterise solute migration. Special liquid chromatographic processes: molecular exclusion chromatography, ion-pair chromatography and ion-exchange chromatography. Coupling considerations when interfacing chromatographic instruments to mass spectrometers.

Electroseparations

Introduction and basic principles: electrophoretic mobility, Joule heating, role of buffers. Gel electrophoresis: gel types, gel preparation, apparatus and procedures. Capillary electrophoresis: electroosmosis, apparatus and procedures Methods and applications: SDS-PAGE, iso-electric focussing, cross-over electrophoresis with immunoprecipitation, capillary gel electrophoresis (CGE). Electrochromatography: micellar electrokinetic chromatography (MEKC), capillary electrochromatography (CEC).

Handling Chemical Data

Revisit hypothesis tests: Concepts introduced in Handling Chemical Data will be revised and used to evaluate chemical data. Explain the statistical theory behind analysis of variance (ANOVA) calculations for the determination of within-run and between-run errors. Use one-way ANOVA to determine whether differences between experimental results are significant (systematic) or random. Use one-way ANOVA of residuals to validate linear regression models. Extend the use of ANOVA to consider two variables at one time. Introduce the concept of experimental design. How to evaluate chemical experiments and identify which parameters (main effects and interactions) influence the result of the experiment. Optimisation of experiments. Use of surface response models, or sequential optimisation designs (e.g, simplex) to obtain optimise the parameters which affect the response of an experiment.

B: Drugs of Abuse (semester two) – assessed by written examination.

UK Legislation (MDA 1971, MDR 2001); terms/definitions; physical descriptions and trafficking Sampling of drug seizures – the hypergeometric distribution and simple colour change presumptive tests Thin layer chromatography – extraction, choice of phases and visualization agents HPLC, GC & GC-MS – separation techniques, phase choices and detectors Quantification processes UV and FTIR methods for analysing controlled substances Drug profiling – cannabis, opiates, cocaine and amphetamine Drugs in sport including legislation, description of drug types used in sport and their reasons for use The pharmacology of drugs of abuse including opioids, benzodiazepines, cannabinoids and stimulants An introduction to drug screening and biological sample types Immunoassay

Booklist

It is not expected that students will require to purchase a textbook for the analytical chemistry segment. However, it may be useful to consult the following reference texts for different aspects:

Analytical Chemistry, D Kealey and P J Haines, BIOS Scientific Publishers, Oxford, 2002.

Contemporary Instrumental Analysis, K A Rubinson and J F Rubinson, Prentice Hall, New Jersey, 2000.

Instrumental Methods of Analysis, H W Willard, L L Merritt, J A Dean and F A Settle, Wadsworth publishing, California, 1988.

Quantitative Chemical Analysis, D C Harris, W H Freeman, New York, 2002.

Statistics and Chemometrics for Analytical Chemistry, 4 th edition, J. N. Miller and J. C. Miller, Prentice Education Limited, Harlow, 2000.

For the Drugs of Abuse segment, the following are recommended

Analysis of Drugs of Abuse: Instruction Manual, M. D. Cole & B. Caddy, Ellis Horwood, 1995

Handbook of Forensic Drug Analysis, Frederick P Smith, Elsevier, 2005.

CH 323 CHEMICAL BIOLOGY

Both semesters Credits 20 Lectures 40 Tutorials 8 SHE level 3

Assessment: Two class tests in semester 1 with a resit examination in August. Written examination in semester 2 for topics C – E, continuous assessment for topic F. Resit examination in August, combined with semester 1 resit.

Lecturers: Dr G Burley, Dr MJ Dufton, Dr CL Gibson, Professor PJ Halling, and Dr BF Johnston

Aims

This course will provide a detailed overview on the structure, function and chemistry of biological macromolecules such as proteins, nucleic acids, lipids and carbohydrates. Topics include protein and nucleic acid folding, energetics of macromolecular interactions (kinetics and thermodynamics) and mechanistic enzymology. The overarching theme in this course will be that structure and function are intimately linked.

Outcomes Upon the completion of the class the student will be able to:

• Describe the structural features of biopolymers and explain the relationship between chemical structure, conformational variety and biological function in nucleic acids, proteins and carbohydrates • Know the structure of key sugars, particularly glucose, and including the pyranose ring and anomers • Appreciate the nature of glycoside bonds and their nomenclature • Understand the importance of configuration and conformation for the physical properties and biological function of polysaccharides • Know the structure of the 4 most common biogenic fatty acids, and their linkage in oils, fats and waxes • Understand the basic parts of phospholipid structure – fatty acids, glycerol, phosphate, alcohol • Understand how phospholipids form bilayers and vesicles • Understand the concept of the cell as the basic element/unit of life, bounded by its cell membrane • Appreciate the nature of biological membranes, and transport across them • Know about organelles in eukaryotic cells, with nucleus and mitochondrion as examples • Recognise terpene and polyketide carbon skeletons, and outline how they are biosynthesised. • Understand how proteins achieve selective recognition and catalytic action • Use direct experimental evidence to diagnose enzyme properties • Understand the concept of selective binding of molecules by non-covalent interactions, and the terms used to describe it (molecular recognition, host, guest, ligand, receptor) • Know the types of intermolecular forces that can contribute to binding, and how they can combine to give strong binding (including chelate and macrocyclic effects). Entropy and enthalpy contributions, and an outline of the effects of molecular structure and medium. • Have an appreciation of the nature, causes and importance of the hydrophobic effect • Understand how binding can be characterized by association or dissociation constants, how they can be measured • Be able to illustrate these ideas with appropriate examples • Understand the concept of self-assembly, in both biological systems and purely chemical alternatives • Appreciate why non-biological self-assembly does not yet come close in complexity to biomolecules • Know and understand the roles of key constituents of biological membranes: phospholipids, integral membrane proteins, cholesterol • Understand the key features of membrane behaviour: vesicle formation, permeability, fluidity, curvature • The connection between organic chemical mechanisms and the mode of action of some drugs • The nature of chemical bonding between a drug and its biological target • Understanding the processes involved in molecular modeling and virtual screening in relation to drug discovery.

Syllabus

Semester 1 A: Biological Macromolecules (MJD (8 lectures))

Nucleic acids: Cellular location. Biopolymer structure, nucleotide variation, contrasts between DNA and RNA. Importance of hydrogen bonding in determining conformation. How structural organisation of DNA facilitates duplication, transcription into RNA and translation into proteins. Genetic code, gene expression and regulation.

Proteins. Overview of activities. Biopolymer structure, amino acid variety, evolution of primary structure. Characteristics of secondary, tertiary and quaternary structures and their dynamic behaviour. Types of protein and functional capabilities. Importance of enzymes, their role in metabolism, and the use of cofactors such as NAD, ATP.

B: Carbohydrates, lipids, phospholipids, membranes, cell structure and function (CLG (8 lectures))

1. Monosaccharides 2. Glycosides, polysaccharides 3. Fatty acids and simple esters 4. Phospholipids, bilayers and vesicles 5. Biological membranes and transport. The cell as the basic unit of life. 6. Prokaryotes, eukaryotes and organelles 7. Terpenes, steroids and other natural products 8. Problem/tutorial session

Semester 2

C: Enzyme structure and kinetics (MJD (6 lectures),

1. Nature of enzyme molecules and active sites. 2. Theories of catalysis. 3. Enzyme kinetics. 4. Examples of enzyme mechanisms (serine proteinase).

D: Supramolecular Chemistry: Molecular Recognition, Self Assembly and Membranes (PJH (7 lectures))

1. Molecular recognition: Binding interactions of natural biomolecules and synthetic host-guest systems.

2. Intermolecular forces, and their effects on structures and thermodynamics of binding. Key role of the

hydrophobic effect.

3. Selectivity, chelate and macrocyclic effects. Measurement of binding. Host synthesis.

4. Introduction to self-assembly.

5. Bilayers and vesicles.

6. Biological membranes.

7. Tutorial, question and answer session.

E: GB (7 lectures)

1. Principles of small molecule-biomolecule interactions

2. Drug-Nucleic acid interactions

3. Drug-Protein interactions

Drug interactions with lipids

5. Tutorial, question and answer session.

F: Molecular Modelling and Electronic databases (Blair Johnson, 4 Lectures)

This section will provide you with an introduction to molecular modelling and virtual screening through the use of a variety of cutting-edge drug discovery related software packages including: Accelerys’ Discovery Studio, Pipeline Pilot: and CCDC’s GOLD.

Recommended Reading:

Carbohydrates, lipids, phospholipids, membranes, cell structure and function

Further explanations of the material in this part of the course may be found in a wide variety of textbooks on biological sciences. Look particularly for those with “Biochemistry”, “Molecular Biology” or “Cell Biology” in the title, but these topics will now almost always be covered to some extent in general biology books. It should be quite easy to find the relevant parts using the index and the key biological terms highlighted in my notes. The chemistry of carbohydrates, fatty acids and their esters, and terpenes is well covered in textbooks of organic chemistry.

One textbook says it is particularly designed for those who have little or no previous study of biology: W J Mitchell & J C Slaughter, Biology and biochemistry for chemists and chemical engineers, 1989, Ellis Horwood, D574.192MIT.

Supramolecular Chemistry

P D Beer, P A Gale, D K Smith Supramolecular chemistry. 1999. OUP. D547.7 BEE. (In short loan). Gives good coverage of much of the topic, especially on molecular recognition, as well as more advanced material.

J W Steel, J L Atwood Supramolecular chemistry. 2008, 2nd ed, Wiley. D547.7 STE. The first chapter on concepts is a good introduction, but there is much more detail later on.

H J Schneider, A Yatsimirsky. 1999. Principles and methods in supramolecular chemistry. Wiley. D547.7 SCH. Covers the principles well, then detail well beyond level of this class.

P.J.Cragg, 2010. Supramolecular chemistry: from biological inspiration to biomedical applications. Springer. E-book available via library site. Good on examples of molecules involved, some errors discussing intermolecular forces.

For biological membranes, it is useful to consult general textbooks on biochemistry, cell biology or molecular biology – there are a large selection in the library with these terms in the titles.

Medicinal Chemistry

An Introduction to Medicinal Chemistry Fourth Edition, Graham L Patrick, Oxford University Press ISBN: 978

0-19-923447-9

CH 325 INTERMEDIATE ORGANIC CHEMISTRY AND SPECTROSCOPY

Both semesters Credits 20 Lectures 36 Tutorials 10 Workshops 3 x 3 hours SHE level 3

A written examination (2.5 hours) covering the Organic Chemistry and NMR Spectroscopy components of this class will take place in May. This examination will account for 2/3 of the final marks for this class, with the additional 1/3 being provided via Class Tests (see below). The Computational Chemistry component of this class will be assessed on a Pass/Fail basis via workshop exercises (see below).

The Organic Chemistry component of this class will be delivered through Semester 1 (one lecture per week) and Semester 2 (one lecture per week). The NMR Spectroscopy component of this class will be delivered in Weeks 7-12, inclusive, of Semester 1 (one lecture per week), and Weeks 1-6, inclusive, of Semester 2 (one lecture per week). The Computational Chemistry component of this class will be delivered in Weeks 10-12, inclusive, of Semester 2 via three 3 h workshops.

Based on that stated above, the written examinations covering the Organic Chemistry and NMR Spectroscopy components of this class will provide 100 marks (2/3 of the total available marks). In addition, the Class Tests will provide 50 marks (1/3 of the total available marks). The Class Test schedule will be:

Organic Chemistry: Semester 1, Week 7/8, accounting for 10 marks towards the overall assessment;

Organic Chemistry and NMR Spectroscopy: End of Semester 1 (January), accounting for 30 marks towards the overall assessment; and

Organic Chemistry: Semester 2, Week 7/8, accounting for 10 marks towards the overall assessment.

For the Computational Chemistry exercises and lectures, the students will receive an exercise handbook, which details the various computational experiments that need to be completed during the lab sessions. Assessment of this part of the course will be based on the students satisfactorily completing all exercises and answering the accompanying questions in the handbook. This part of the course will be graded as pass (all exercises completed with satisfactory answers to the questions) or fail (incomplete exercises). If this part of the course is passed then the final mark for the course overall will be based on the student’s performance in the Class Tests and final exam, as described above. If the student fails this part of the course, they will not be eligible to sit the end of year final exam and will fail the course.

Resit Examination: Since Faculty of Science regulations state that no element of assessment can contribute towards more than one recorded result, the August resit examination will cover Organic Chemistry, NMR Spectroscopy, and Computational Chemistry.

Lecturers: Professor WJ Kerr, Dr JA Parkinson, Professor NCO Tomkinson and Dr T Tuttle

Aims • to teach modern NMR spectroscopy as it is applied to chemistry • to equip with skills for handling and interpreting NMR data for the purposes of chemical structure elucidation • to teach the theoretical basis of the NMR experiment using the vector formalism • to develop further an understanding of the reactivities of organic molecules • to elucidate the strategies, planning and execution of organic syntheses using the disconnection approach • to develop an understanding of the synthesis and reactivities of electron-poor and electron-rich heterocyclic molecules • to introduce and elucidate the properties and reactivities of a series of organoelemental compounds (including those of B, Si, P and S), and • to introduce and elucidate the mechanistic features of basic palladium-catalysed reactions for use in organic chemistry. • To introduce students to practical aspects of computational quantum chemistry. • To introduce the concept of a potential energy surface and provide an understanding of how this can be calculated. • To provide an insight into the role of computational chemistry – its abilities and limitations – in modern chemical research. • To provide first hand training in the use of modern computational chemistry software. Outcomes At the end of the course the student should be able to:

NMR Spectroscopy

• recognise and interpret one-dimensional 13C NMR data for simple organic molecules • understand the effects of scalar coupling upon the appearance of one-dimensional 1H and 13C NMR data of simple organic molecules • understand and use the concept of scalar correlation in the context of homo- and hetero-nuclear two-dimensional NMR spectroscopy • use nuclear Overhauser effect data in the context of determining simple molecular structures from NMR data • understand the meaning of the term spin-system • understand and use the relationship between scalar coupling and torsion angle • explain the basic principles of the pulsed NMR experiment in terms of vector and energy level descriptors • recognise and use the terms scalar coupling, J-coupling, Karplus, chemical shift, δ, coupling constant, J, nOe, spin-system, COSY, TOCSY, HSQC, HMBC, DEPT, JMOD, magnetisation vector, resonance, Larmor precession, rotating frame of reference, free induction decay, FID, integral, relaxation, spin • use sets of one- and two-dimensional NMR data to enable informed decisions to be made concerning potential molecular structures that may be represented by the data. Organic Chemistry

• understand the transferable principles of organic chemistry, in particular with regards synthetic strategies involving polyfunctional molecules, • manipulate a variety of organic structural formulae with elevated levels of proficiency and with an emphasis on polyfunctional organic compounds and heterocyclic compounds, • understand the mechanism and reactivity principles involved in the use of organoelemental reagents (including organoboron, -silicon, -phophorus, and -sulfur compounds) and the employment of palladium-mediated processes, • understand the chief characteristics (including structure, reactivity, and synthesis) of polyfunctional molecules, heterocyclic compounds, and such organoelemental species that overlays the knowledge base obtained from second level organic courses, • understand the reaction mechanisms that account for the chemical properties of the subjects of the course, and • apply the acquired knowledge and understanding to the solution of problems and to the prediction of chemical properties of previously unseen compounds or reactions. Computational Chemistry

• Obtain a sense of what a “good” method is and what method should be applied to what problem. • Obtain a “user” level knowledge in building and running calculations with Gaussian. • Demonstrate an understanding and provide a rationale for the computational costs associated with different methods. • Be able to calculate a potential energy surface for a simple reaction. • Be able to relate the calculated energetics of a reaction to the experimental conditions required for a reaction to proceed. • Be able to visualize the Natural Bond Orbitals of a molecule. • Be able to calculate the IR/Raman spectrum of a molecule.

Content NMR Spectroscopy – Nuclear Magnetic Resonance (NMR) for Organic Molecules

NMR data in one dimension: 13C and 13C-{1H} NMR spectra, JMOD, DEPT, chemical shift, signal counting & identification, spin quantum number, spin state population, magnetization vector, resonance frequency.

Scalar coupling patterns, coupling constant, integration, effects of structural symmetry, digital resolution.

The pulsed NMR experiment, vector description, spin population description, frame of reference, the free induction decay.

Correlation through the chemical bond: introduction to two-dimensional NMR data, relationship between coupling patterns in 1D and correlation data in 2D NMR.

Correlation in a homonuclear context: reading COrrelation SpectroscopY (COSY) data.

Spin-systems and reading TOtal Correlation SpectroscopY (TOCSY) data.

Torsion angle/coupling constant relationships and the Karplus equation.

Correlation through the chemical bond: reading one-bond heteronuclear two-dimensional NMR data.

Correlation through the chemical bond: reading multiple bond heteronuclear two-dimensional NMR data.

Correlation through space – the nuclear Overhauser effect.

Classes will run interactively using a ‘lecture/problem solving’ model style of delivery and will be supplemented with a number of large group tutorial sessions.

Organic Chemistry

Synthon, Disconnection, Functional Group Interconversion, Target Material. Aliphatic C-X Disconnections. 1,2-Difunctionalised Compounds. β-Aminoalcohols; the use of epoxides; a summary of synthetic strategy. Aromatic C-C Disconnections.

GroupDisconnections C-X, X-C-X, X-C-C-X, X-C-C-C-Xwhere X is a heteroatom, O, N, S, Halogen.

One group C-C disconnections. Additions to carbonyl groups and epoxides; Michael additions. Enolates as nucleophiles. Regioselectivity of enolate formation; regioselectivity in additions to α,,β- unsaturated carbonyl compounds. Two group C-C disconnections.

1,2- Dicarbonyl Disconnections using dithianes as acyl anion equivalents

1,3-Dicarbonyl Disconnnections. Examples using aldol, Claisen, Reformatsky, and Mannich reactions.

1,4-Dicarbonyl Disconnection. Enamines, Activation of enolates with a second carbonyl group. The Darzens reaction. 1,5-Dicarbonyl Disconnnections exemplified by Michael Addition, Robinson Annulation.

1,6- Dicarbonyl Disconnection featuring ozonolysis.

The Diels Alder reaction. Frontier Orbital approach to rationalise why electron-deficient dienophiles react well. Frontier orbitals and stereochemistry: secondary orbital overlap. Frontier Orbitals and Regiochemistry.

Disconnections featuring alkynes and alkenes. Strategy in Synthesis.

Heterocyclic chemistry. π-Excessive and π-deficient systems: pyridine, quinoline, isoquinoline, pyrrole, furan, thiophen, and indole.

An introduction to Organoboron Chemistry: Hydroboration of alkenes and regioselectivity in hydroboration reactions using a range of alkylboranes. Reactivity of organoboranes. An introduction to Organosilicon Chemistry: Fundamental properties of organosilicon compounds. Preparation and uses of organosilicon compounds. An introduction to Organophosphorus Chemistry: Use of organophosphorus compounds in the Wittig and the Horner-Wadsworth-Emmons olefination reactions. An introduction to Organosulfur Chemistry: Formation and reactivity of α-thioanions.

Introduction to Palladium-Catalysed Reactions: The important mechanistic aspects of the chemistry in this area will be discussed; this will include oxidative addition, reductive elimination, β-hydride elimination, as well as the general catalytic cycles involved in Pd-mediated coupling.

Computational Chemistry

A series of workshops will explore the use of Gaussian to determine chemical reactivity and properties, including: relative energies of conformers; reaction energy profiles; infrared spectroscopy; and molecular orbitals.

Booklist

Organic Structure Analysis, P. Crews, J. Rodríguez and M. Jaspars, Oxford University Press [Andersonian Library: D 547.122 CRE]

Introduction to Organic Spectroscopy, L. M. Harwood and T. D. W. Claridge, Oxford University Press [Andersonian Library: D 547.3085 HAR]

Spectroscopic Methods in Organic Chemistry (5th Edition). D. H. Williams and I. Fleming, McGraw-Hill, London [Andersonian Library: D 547.3085 WIL] High Resolution NMR Techniques in Organic Chemistry (2nd Edition), T. W. D. Claridge, Elsevier ISBN- 13 978-0-08-054818-0 (Paperback) 383 pages

Nuclear Magnetic Resonance, P. J. Hore, Oxford Chemistry Primers Series, No. 32, Oxford University Press ISBN 0-19-855682-9 (Paperback) 90 pages

S. Warren, "Organic Synthesis - The Disconnection Approach", John Wiley & Sons, Chichester, 1982 or 2nd edition S. G. Warren and P. Wyatt, John Wiley & Sons, Chichester, 2008

S. Warren, "Workbook for Organic Synthesis - The Disconnection Approach", John Wiley & Sons, Chichester, 1982 or 2nd edition S. G. Warren and P. Wyatt, "Workbook for Organic Synthesis –

The Disconnection Approach", John Wiley & Sons, Chichester, 2009

J.A. Joule and K. Mills, "Heterocyclic Chemistry", 4th Edition, Blackwell Science, Oxford, 2000.

T.L. Gilchrist, “Heterocyclic Chemistry”, 3rd Edition, Longman, Harlow, 1997.

W. Carruthers and I. Coldham, "Modern Methods of Organic Synthesis", 4th Edition, Cambridge, 2004.

M.B. Smith and J. March, "March’s Advanced Organic Chemistry; Reaction, Mechanism and Structure", 6th Edition, Wiley-Interscience, 2007.

J. Clayden, N. Greeves, S. Warren and P. Wothers, “Organic Chemistry”, Oxford University Press, Oxford, 2001.

G. H. Grant, W. G. Richards, “Computational Chemistry”, Oxford University Primers, Vol. 29, OUP, Oxford, 1995.

J. B. Foresman, A. Frisch, “Exploring Chemistry with Electronic Structure Methods”, 2nd Edition, Gaussian Inc. Pittsburgh, 1996.

CH 326 INORGANIC CHEMISTRY, STRUCTURES AND SPECTROSCOPY

Both semesters Credits 20 Lectures 40 Tutorials 8 SHE level 3

Semester 1 covers transition metal and main group chemistry (24 lectures COH/AW) and will be examined by a “class test” in January which is worth 50% of the overall mark. Tutorials throughout the semester.

Semester 2 starts with 6-8 lecture slots on single crystal XRD (ARK) and will be examined by assignment Worth 20% of the overall mark. The course then finishes with Vibrational and Electronic Spectroscopy (14 lectures KF) and NMR spectroscopy (4 lectures COH) which will be examined by a class test in May, worth 30% of overall mark.

Lecturers: Dr K Faulds, Dr AR Kennedy, Dr CT O’Hara and Dr AW Wark

Aims • To give a more advanced view of main group and transition metal coordination and organometallic chemistry. Themes to be covered include ligands and their influence on complexes, trends in structure and bonding, stereochemistry, reactivity, and the application of spectroscopic and other methods of identification. • To teach modern spectroscopy as it is applied in chemistry

Outcomes Upon the completion of the class the student will be able to:

• have a detailed knowledge of coordination chemistry and discuss how steric and electronic effects can influence the chemistry of transition metal complexes; • discuss transition metal reaction mechanisms; • understand key organometallic concepts; • give examples of the use of important ligands in organometallic chemistry; • detail the use of organometallic reagents in several key industrially important processes; • have detailed knowledge of the synthesis, structures and bonding characteristics of homoatomic and heteroatomic cyclic main group compounds; • be familiar with the various types of main group element cage compound; • have an understanding of the fundamental principles of silicate mineral chemistry, including an appreciation of representative silicate minerals, and be able to rationalise complex morphologies in terms of the fusing together of simple tetrahedral SiO4 units; • relate the chemistry of main group fluoride compounds with the position of the elements in the periodic table; • obtain the number and type of the normal modes of vibration for any molecule and comment on the infra-red and Raman activity of these modes; • use the principle of the conservation of orbital symmetry in electrocyclic ring closure reactions to determine the mode of ring closure; • understand the basic concepts of vibrational and rotational spectroscopy; • use the Boltzman equation; • apply the selection rules for vibrational spectroscopy of diatomics; • understand the harmonic oscillator model and the effect of deviations from it; • understand the nature of Raman scattering; • apply the basic selection rules for infrared absorption and Raman scattering; • use the mutual exclusion rule; • apply the basic concepts of atomic spectroscopy; • explain the Frank Condon principle; • interpret fluorescence and resonance Raman scattering spectra; • understand the advantages of FT methods in vibrational spectroscopy; • what single X-ray diffraction does and how it does it; • understand unit cells, defining points & planes and equivalent positions within unit cells; • discuss Braggs Law and intensity, structural amplitude, scattering and structure factors; • be familiar with electron density calculations; • discuss phase problems; • understand refinement.

Content A: Inorganic Chemistry

The Transition Metals 1-3 Ligands in transition metal chemistry. Steric effects - ligand substituents, backbone and geometry. Examples - Schiff's bases, tripodal ligands, macrocycles. Mono vs polydentate ligands.

4 Electronic effects. Metal ligand bonding modes, base strength, hard/soft acids and bases. Examples in synthesis of metal complexes.

5-6 Reactions at metal centres; Substitution reactions. General mechanisms. Square planar complexes, trans-effect. Ground state and transition state effects. Octahedral complexes. Rates of reaction - inert, labile complexes. Influence on reaction rates. Trans-effect

7-8 Redox reactions. Outer sphere mechanism. Activation energy, electron transfer. Inner sphere mechanism. Bridging ligands, resonance vs. chemical transfer.

Organometallics

9 Organometallic chemistry. Basic concepts - Electron counting, 18 electron rule, hapticity, nomenclature.

10-12 Survey of ligands in organometallic chemistry: alkyls, aryls, π-alkenyls, π-alkynyls, carbenes, carbynes, π-alkenes, π-alkynes, π-allyl, cyclopentadienes and π-arenes. Includes: preparations, structure and bonding.

13-14 Reactions of organometallic species: substitution, oxidative addition/reduction elimination, CO insertion/alkyl migration, olefin insertion, π-hydride transfer.

15 Use of s and p block organometallics. Synthesis structure and solution phase behaviour.

Main Group Chemistry

16-18 Inorganic rings which are devoid of carbon. An overview of homoatomic and heteroatomic ring systems across the Main Group, with special emphasis on the synthesis, structure and bonding of sulphur and silicon homoatomic rings along with B-N, P-N, and S-N heterosystemssystems.

19-20 Synthesis, bonding and structure of the main group fluoride compounds. Building upon concepts already learned in second year will be emphasised.

21-22 Examination of main group oxides – particularly the important silicon oxides and aluminosilicates.

23-24 Tutorial/consolidation sessions interspersed through the above lectures at appropriate points.

B: Interpretative Spectroscopy

Vibrational Spectroscopy

1 Rotational, vibrational and electronic energy levels. Review of rotational states and transitions. Population of rotational levels from the Boltzman Law.

2 Vibrations of diatomics. Review of the harmonic oscillator model, anharmonicity, overtones, p and r branches.

3 Principles of infrared adsorption and Raman scattering. Basic selection rules.

4 Vibrations in more complex molecules. Group vibrations and assignments. Normal modes, mutual exclusion rule to determine cis and trans isomers.

5 Fourier Transform methods in modem vibrational spectroscopy. FTIR and FT Raman.

6 Resonance Raman scattering. Basic concept, use of Raman spectroscopy to obtain electronic as well as vibrational information, advantages of enhanced sensitivity, applications in solutions and on surfaces.

7 Advanced methods. Applications on surfaces - ATR and SERS. Modem assignment methods, OFT calculations versus previous assignments (visualisation software available).

Electronic Spectroscopy

8 Atomic adsorption spectroscopy. The concept of states, Laporte and spin selection rules.

9 Molecular adsorption spectroscopy. Separation of rotational, vibrational and electronic states. Born Oppenheimer Principle.

10 Frank Condon transitions. Charge transfer, spin allowed and spin forbidden bands.

11 Band shapes, vibrational electronic coupling, examples of chromophores and oxochromes, explanation of the colour from selected dyes.

12 Quantitative electronic spectroscopy. Beer Lambert Law, single and double beam spectrometer ranges.

13-14 Ligand field spectra. Contribution of atomic states and the interaction with the ligand field, splitting diagrams, spin allowed and spin forbidden bands. Prediction of colour and geometry in complexes.

NMR Spectroscopy

15-16 Use of multinuclear NMR spectroscopy in inorganic/organometallic chemistry. Worked examples. Dynamic exchange processes. Variable temperature NMR spectroscopy.

C: Single-Crystal X-Ray Diffraction.

1 Overview – what SXD does and how it does it. Unit cells, defining points & planes and equivalent positions.

2 Braggs Law. Intensity, Structural Amplitude, Scattering factors.

3 Structure Factors. Electron Density Calculations.

4 Phase Problem. Direct Methods, Patterson Methods.

5 Refinement. How good is the model? R and S. Example of structure solution and refinement.

6-8 Workshop covering full class.

Booklist

• F. A. Cotton, C. A. Murillo, M. Bochmann, “Advanced Inorganic Chemistry”, 6th Edition, Wiley, 1999. • R.A. Henderson, "The Mechanisms of Reactions at Transition Metal Sites", Oxford Chemistry Primers, Oxford University Press, 1994. • N.N. Greenwood and A. Earnshaw, "Chemistry of the Elements", Pergamon, 1984. • M. Bochmann, "Organometallics I" and "Organometallics II", Oxford Chemistry Primers, Oxford University Press, 1994. • Modern Raman Spectroscopy – A Practical Approach (mainly ch.3) by W.E. Smith and G. Dent (it is not recommended you buy this book) • Physical Chemistry by P. W. Atkins • W. Clegg. “Crystal Structure Determination”, Oxford Chemistry Primers, Oxford University Press, 1998.

FINAL YEAR CLASS SYLLABI

CORE CHEMISTRY CURRICULUM (CH 412 or CH 552)

Lectures: 96 (6 blocks of 12 lectures and 1 block of 24 lectures):

CH 403/CH 503 Organic Chemistry 24 lectures CH 404/CH 504 Cage and Cluster Molecules 12 lectures CH 406/CH 506 Environmental Chemistry 12 lectures CH 407/CH 507 Interpretative Spectroscopy 12 lectures CH 432/CH 514 Transition Metal Chemistry 12 lectures CH 453/CH 572 Nanochemistry 12 lectures CH 459/CH 574 Understanding Molecules and Materials 12 lectures

Tutorials: as required. ECTS Credits: 20

CORE MChem CHEMISTRY WITH DRUG DISCOVERY CURRICULUM (CH 541)

Lectures: 96 (4 blocks of 12 lectures and 2 blocks of 24 lectures):

CH 503 Organic Chemistry 24 lectures CH 506 Environmental Chemistry 12 lectures CH 507 Interpretative Spectroscopy 12 lectures CH 514 Transition Metal Chemistry 12 lectures CH 574 Understanding Molecules and Materials 12 lectures CH 577 Chemical Biology II 24 lectures

Tutorials: as required. ECTS Credits: 20

CH 403/CH 503 ORGANIC CHEMISTRY (Professor JM Percy and Dr AJB Watson) SHE Level 4 and 5 ECTS Credits 5.0

Aims: • To survey some of a series of contemporary organoelemental techniques that has been developed for use in organic synthesis. • To highlight a further selection of developing methods and strategies in organic chemistry and to link the new synthetic methods to both mechanistic understanding and the practical processes employed. • To reinforce the use of retrosynthetic analysis as a method by which organic synthesis can be planned and, in so doing, show how the use of the delineated techniques can be embedded within synthetic pathways. • To examine the use of these techniques and strategies, where they have been applied, in target molecule synthesis. • To apply the techniques being covered within chemical problem solving sessions. • To discuss prostereoisomerism and outline the nomenclature protocols. • To exemplify prostereoisomerism in enzymatic processes. • To detail stereoselective and stereospecific processes. • Briefly overview thermodynamic principles of selectivity. • Briefly overview methods of measuring chirality.

Learning Outcomes:

Level 4

To develop an understanding of the mechanism and reactivity principles involved in the use of more advanced organoelemental reagents (including organoboron, -silicon, -phophorus, –sulfur, and –selenium compounds). To develop an understanding of the regio- and stereoselectivity that can be achieved in organic synthesis by the use of such organoelemental methods. To establish an understanding and awareness of the continually evolving nature of organic chemistry by the introduction of new and developing methods in organic chemistry (e.g. mild and selective oxidations and reductions, emerging olefination techniques, and hypervalent-iodide derived methods). To build a knowledge base of the chief characteristics of such organoelemental species and other contemporary reagents that overlays the knowledge base obtained from earlier stages of the chemistry course and, in particular, that covered in Year 3 (and 4). To develop an understanding of the mechanism and reactivity principles involved in the use of the new and developing methods and to establish the levels of selectivity that can be achieved by the use of such techniques. To develop problem solving abilities in a range of synthetic contexts by applying the advanced preparative techniques delineated as part of this programme. To further extend and develop an understanding of the transferable principles of organic chemistry, in particular with regards synthetic strategies involving polyfunctional molecules. To further develop the application of knowledge and understanding to the solution of problems and to the prediction of chemical properties of previously unseen compounds or reactions. • Be able to assign prostereoisomeric groups and faces using stereochemical nomenclature. • Be aware of the methods of controlling stereoselective and stereospecific processes and be able to apply these to synthetic transformations. • Understand the thermodynamic principles of selectivity. • Be aware of the methods of measuring chirality with an appreciation of the advantages/disadvantages of each method.

Level 5

• To develop abilities to establish an appreciation of a range of distinct reagents and techniques that have the abilities to perform similar synthetic transformations and, by taking an overview, to develop the abilities to discern the comparative advantages and disadvantages of the individual reagents and techniques. • For a given synthetic transformation or series of transformations, to develop the abilities to reason whether a given reagent/technique or reagents/techniques would be used over alternative reagents or methods. • To develop a proficiency in manipulating a variety of organic structural formulae with an emphasis on polyfunctional organic compounds. • To further develop the application of knowledge and understanding to the solution of problems and to the prediction of chemical properties of previously unseen compounds or reactions.

Topics 1-8 Use of Organoelemental Reagents in Synthesis

This will expand on the introduction to this general area as covered in the 3rd Year and will include more advanced aspects of organoboron chemistry (e.g. carbonylation reactions and use of alkynes), organosilicon chemistry (e.g. further use of allyl and vinyl silane [including aspects of regio-and stereoselectivity], organophosphorus chemistry (e.g. E- and Z-selective olefinations, conversion of aldehydes to alkynes), orgnosufur chemistry (e.g. selectivity in use of sulfonium ylides and Shapiro- type processes), and organoselenium chemistry. Within this area and as part of the problem solving sessions, aspects of retrosynthetic analysis using these and other (previously covered) reagents will be embedded within the lectures.

9-12 Contemporary Reagents for Use in Synthesis.

Alternative contemporary alkene forming processed and a range of selective oxidation and reduction processes will be delineated. The synthetic methods will be linked to mechanistic understanding and the practical techniques used. Again, problem solving sessions will illustrate how these (and previously covered) techniques can be used in synthetic organic sequences.

12-17 Scope of content, definitions, historical perspectives, identification of areas of interest, methodologies. Topics will be selected from: The Diels-Alder reaction; revision (from Year 3) of FMO model, role of HOMO and LUMO orbitals and stereoselectivity, kinetic and thermodynamic control; inverse electron demand Diels-Alder (enol ethers, pyrones); heteroatom-containing dienes (furan inter alia); catalysis by Lewis acids. Other useful cycloadditions. Topics will be selected from: cyclopropanation, dipolar cycloadditions (nitrile oxides, azomethine ylides); higher order cycloadditions. Sigmatropic rearrangements. Topics will be selected from: classification, FMO patterns and constraints; group shifts (H-atom and other species); [3,3] rearrangements as C-C bond forming reactions including Claisen, (Cope), oxy- and aza-Cope rearrangements, located in synthetic context and discussed with mechanistic evidence and characterisation; potential for complex skeletal reorganisation and stereoselective synthesis.

Re-introduction of chirality and prostereoisomerism discussed in terms of hydride addition to prochiral and chiral carbonyl compounds and some basic definitions (ee, dr, de, kinetic resolution). Selectivity & Specificity: Steric & co-ordination control, mechanistic control, stereoelectronic control (Felkin Ahn and chelation models, relative topicity) thermodynamic/kinetic control. Thermodynamic principles of selectivity. Measurement of chirality, polarimetry NMR shift reagents and chromatography.

CH 404/CH 504 CAGE AND CLUSTER MOLECULES (Professor RE Mulvey) SHE Level 4 and 5 ECTS Credits 2.5

18-20 Aims: 18-21 To introduce students to the fundamental importance of cage and cluster molecules in chemistry. To gain an appreciation of the widespread importance of organolithium compounds as indispensable reagents for synthesis. To gain an understanding of the preparation, structural principles and general reaction chemistry of key cage and cluster molecules.

18-22 Learning Outcomes: At the end of the course the student should be able to: 18-23 • have an appreciation of the complexity and breadth of the structural chemistry of organolithium compounds, both in the solid state and solution • relate the reactivity and selectivity of organolithium reagents to their structures and bonding types 18-24 • understand the difference between cage and cluster compounds • differentiate between electron-rich, electron-precise, and electron-deficient molecules • rationalise and predict the structures of boron hydride and related clusters by applying Wade’s rules 18-25 • be familiar with the terms isoelectronic, isolobal, and frontier orbitals in relation to cluster compounds 18-26 • adjust Wade’s rules for electron counting in transition metal carbonyl and Zintl cluster compounds 18-27 • describe the preparation, structures, physical properties and reactivity of fullerene clusters

18-28 Topics 18-29 1-2 Basics of organolithium chemistry: general preparative methods; synthetic applications of and selectivity patterns of lithium alkyls, lithium amides, and mixed-metal superbases.

3-4 Principles of aggregation and solvation in organolithium compounds. Electron-deficient bonding, tetrameric and hexameric cages, polymers and other oligomers. Ring-stacking and ring-laddering.

5 Dynamic structures in solution. Structural rearrangements. The role of the metal in synthetic applications – a case study of the aldol reaction.

6-7 Cluster molecules. Common geometries. Electron -precise, -deficient and -rich clusters. Boron hydride clusters. Electron-counting and Wade’s rules. Carborane and metallocarborane clusters.

8-9 Transition metal clusters. Osmium carbonyl species, high-nuclearity clusters, electron-counting rules, 4- 4- capping rule, clusters with encapsulated heteroatoms. Zintl clusters: group 14 and 15 anions (Ge9 , Sn9 , 2- 2- Sn8 , Pb5 ).

10 Buckminsterfullerene and fullerene chemistry. General properties. Reactivity. Organometallic derivatives. Endohedra clusters.

CH 406/CH 506 ENVIRONMENTAL CHEMISTRY (Dr CM Davidson) SHE Level 4 and 5 ECTS Credits 2.5

Aims: To provide students with knowledge about • the chemistry of the natural environmental and • the influence of Man on the environment.

Background expected The course builds on various aspects of the chemistry undergraduate degree program and so reasonable familiarity with material covered in previous years is expected. An important feature of the course is its “inter- disciplinary” nature, covering relevant aspects of analytical, inorganic, organic, and physical chemistry.

Learning outcomes (CH 406): At the end of the course the student should be able to: • describe the principles of biogeochemical cycling and provide outline examples of elemental cycles • discuss the fundamental chemistry of the geosphere, hydrosphere and atmosphere, especially in relation to current environmental problems such as global climate change • discuss the factors that mean some chemicals are designated as priority pollutants, and provide outline examples • demonstrate the ability to link concepts from different parts of the course.

Learning outcomes (CH 506): At the end of the course the student should be able to: • describe the principles of biogeochemical cycling and provide detailed examples of elemental cycles • discuss the chemistry of the geosphere, hydrosphere and atmosphere, especially in relation to current environmental problems such as global climate change • discuss the factors that mean some chemicals are designated as priority pollutants, and provide specific examples • demonstrate the ability to link concepts from different parts of the course and to apply the principles learned in new situations.

Topics

1 Introduction; The spheres of the environment; Biogeochemical cycling. 2 Geochemistry and mineralogy. 3 Chemistry of soil: Essential element supply, Deficiency disease in plants, animals and Man. 4 Chemistry of natural waters I: composition, pH, alkalinity, redox considerations. 5 Chemistry of natural waters II: oxygen depletion and BOD, nutrient loading and eutrophication. 6 Chemistry of the atmosphere I: stratospheric ozone production, cycling and depletion. 7 Chemistry of the atmosphere II: the greenhouse effect and global climate change. 8 Introduction to pollution: the pollutant pathway concept, properties of priority pollutants (e.g. toxicity, cancer / genetic effects, bioaccumulation, persistence, chemical speciation). 9 Organochlorine insecticides: DDT, Lindane, Cyclodienes. 10 Organophosphate insecticides; Triazine and chlorophenoxy acid herbicides. 11 Dioxins, polychlorinated biphenyls and furans. 12 Heavy metals: cadmium; mercury and tin (chemical speciation and importance of organometallic forms).

Textbooks Purchase of a textbook is not required. However, the following texts (available in the University Library) are recommended for background reading on various aspects of the course: P O’Neill, Environmental Chemistry, Chapman and Hall, London, 1993 S E Manahan, Environmental Chemistry, CRC Press, Florida, 1994 C Baird, Environmental Chemistry, Freeman, New York, 1995 G W van Loon and S J Duffy, Environmental Chemistry: a global perspective, OUP, Oxford, 2005.

CH 407/CH 507 INTERPRETATIVE SPECTROSCOPY (Dr MD Spicer) SHE Level 4 and 5 ECTS Credits 2.5

Aims: To review, using appropriate case histories, the use of a variety of spectroscopic and physical techniques for the elucidation of structural information from chemical compounds. The extent of available information and the limitations of each technique will be highlighted.

Learning Outcomes:

• appreciate applications of NMR nuclei other than 1H and 13C. • understand factors affecting ease of observation of NMR nuclei • know the main differences between I = ½ and quadrupolar nuclei • have an understanding of factors affecting linewidths in quadrupolar nuclei • be aware of factors influencing chemical shifts • be able to interpret NMR spectra with respect to chemical shifts, coupling patterns and linewidths • Understand the underlying principles of ESR • Know the significance of g-values, hyperfine coupling constants and anisotropy. • Be able to interpret the form of ESR spectra • Understand the basic magnetic phenomena and how temperature dependence arises • Knowledge of deviation from spin only formula • Be able to deduce ground terms from magnetic behaviour • Have a basic understanding of diffraction. • Be able to derive Bragg’s law. • Understand crystals, lattices, space groups. • Have a basic understanding of the experimental aspects of crystallography • Be able to understand the physical basis of X-ray absorption Spectroscopy (XAS) • Be aware of the strengths and weaknesses of XAS as a technique

Topics

1 Multinuclear NMR spectroscopy. Revision of fundamentals of multi-pulse operation. Relaxation times. Spin-spin coupling. Satellite Spectra. 2nd Order Spectra.

2 Quadrupolar nuclei. Receptivity; line-width factor; quadrupolar relaxation time. Effects of symmetry and physical conditions on linewidths.

3 Chemical Shifts – diamagnetic and paramagnetic shielding parameters. NMR of transition metal nuclei. NMR of paramagnetic species. Examples from a range of less common nuclei.

4 ESR Spectroscopy. Basics, electron spin in a magnetic field, selection rules, g-values and hyperfine coupling constants. Experimental considerations. Anisotropy. Examples from inorganic and organic chemistry.

5 Magnetic properties of materials. Deviations from spin only behaviour: orbital contributions; 2nd order spin-orbit coupling.

6 Temperature dependence. Spin cross-over. Magnetic materials.

7 X-ray crystallography. Basics of diffraction. Bragg’s law. Unit cell; crystal system; Miller indices; Space groups.

8 The structure factor. Electron density. The Phase problem.

9 Structure solution. Direct methods. The Patterson function. Data refinement. Assessment of data quality. Practicalities – crystal growth, quality and mounting. Data collection.

10 XAS. The X-ray absorption spectrum. Electron wave propagation: the equation. Backscattering: amplitude, phase shift, atomic motion. Obtaining structural information from the absorption spectrum. Limitations of that information.

CH 432/CH 514 TRANSITION METAL CHEMISTRY (Dr SD Robertson) SHE Level 4 and 5 ECTS Credits 2.5

Aims: • To discuss advanced topics in the coordination and organometallic chemistry of the transition metals, including metal-metal bonding, cluster formation, ligand effects and small molecule activation, with particular reference to the 4d, 5d and 4f elements. • To discuss the influences of ligand properties.

Learning Outcomes: At the end of the course the student should:

• have an appreciation of the similarities and the differences between the 3d and the 4d/5d elements and an understanding of the reasons behind them; • have knowledge of the effect of physical differences on the chemical properties of these elements; • be able to understand why metal-metal bonding occurs; • be able to describe the main structural types of metal-metal bonded species, in terms of structures and bonding; • be able to calculate bond orders of metal-metal bonds and to understand the factors which can cause the bond order to change; • have an understanding of steric and electronic influences in ligand chemistry; • have an appreciation of activation or stabilisation of organic and organic fragments and metal centres; • be able to give examples from N2-fixation, sublogical O2-transport and C+H activation.

Topics 1 Comparison of the 3d and 4d/5d elements. Thermodynamic aspects, lanthanide contraction. Effect on their chemistry; oxidation states, coordination numbers, bonding, and magnetic properties.

2-4 Metal-metal bonding. Orbital interactions leading to M-M bonding, M2 dimer. MO diagram, electron counting. Review of structural types. Bond orders. Review of species containing single to quadruple bonds. Interchange of bond orders.

5 Ligands, Bonding modes. Influence of steric and electronic properties. Exemplified by Phosphines (Tolmans cone angles, substituents effects, chirality) and cyclopentadienyls (Substituents and rates of reaction).

6 Dioxygen as a ligand. MO diagram. Bonding Modes. Co, Rh, Ir systems. Reactivity versus reversibility, exemplified by M(PPh3)2(O2), (M = Ni, Pd, Pt). Relation to biological oxygen transport, an example of ligand design.

7 Dinitrogen and its complexes. Towards N2 fixation. Bonding (comparison with CO) structural types. Preparation and reactivity (activation). Ti, V, Zr, Mo, W, Ru, Os complexes.

8-9 C-H activation. Hydrogen migration, orthometallation, insertion reactions.

Draft Booklist

FA Cotton and G Wilkinson, "Advanced Inorganic Chemistry", 5th Edition, John Wiley.

CH 453/CH 572 NANOCHEMISTRY (Professor D Graham and Professor PJ Skabara) SHE Levels 4 and 5 ECTS Credits 2.5

Aims:

• To provide an understanding in the concept of nanochemistry and its application in a diverse range of subjects.

Learning Outcomes At the end of the course the student should be able to: • Understand the definition of nanochemistry through a range of examples and applications. • Recognise the importance of nanostructures and how new properties arise which are different from those of the parent bulk materials or individual atoms, ions or molecules. • Give an account of the various synthetic routes available towards the synthesis of nanostructures using bottom up methodologies. • Describe the techniques available for the preparation of nanostructures from bulk materials. • Discuss a range of techniques available for the characterisation of nanostructures. • Understand how to synthesise metallic nanoparticles and their unique optical properties. • Explain the significance and application of nanotechnology in the biosciences.

Topics

1 Introduction to nanotechnology: synthesis, bottom-up and top-down approaches. Basic concepts and trends in miniaturisation – strategies and advantages. 2-3 Fullerenes, carbon nanotubes. Inorganic compound semiconductors: quantum dots based on II-VI and III- V structures. 4-5 Organic nanomaterials: convergent and divergent synthetic approaches, self-assembly, electronic and optical properties. 6 Applications of semiconductor nanostructures: photonics, solar cells. 7-8 Definition and examples of metallic nanoparticles, common routes of synthesis, characterisation and optical properties. 9-10 Functionalisation of metallic nanoparticles for sensing applications. Localised surface plasmon resonance based assays for DNA and proteins, surface enhanced raman scattering based assays using nanoparticles. 11 Nanoparticles for nanomedical applications such as cancer imaging and treatment. Photothermal therapy, energy applications. 12 Chemical nanopatterning of surfaces and dip pen nanolithography.

Recommended text: Nanochemistry, A Chemical Approach to Nanomaterials, Ozin, Geoffrey A., Arsenault, André C., Cademartiri, Ludovico, 2nd ed., 2009, ISBN: 978-1-84755-895-4.

CH 459/CH 574 UNDERSTANDING MOLECULES AND MATERIALS (Dr EJ Cussen) SHE Level 4 and 5 ECTS Credits 2.5

Aims: The design and application of new materials is becoming more and more feasible in the laboratory. Pivotal to this development is an understanding of the underlying models that are employed to predict, guide and modify the observable properties of these systems. In this course students will develop an understanding of the models used in predicting the properties of new materials. These models will be introduced in the context of real life applications, such as the development of oxide ion electrolytes, battery materials, ferroelectrics and molecular adsorption into porous materials.

Learning Outcomes: At the end of the course the student should be able to; - explain the concept of a molecular model - write a z-matrix input for a simple molecule - define a potential energy surface - relate the meaning of a potential energy surface to the concept of chemical reactivity - describe the terms comprising a simple molecular force field - describe the processes of minimisation and outline various approaches to minimisation. - describe the process of molecular dynamics - describe the problems of both length- and time-scale involved in simulating solids - explain the approximations made in applying interatomic potentials to solids - apply the bond valence approach to evaluate the energy of different defect types in a structure - explain the process of testing a simple interatomic potential against experimental data - explain different mechanisms for ion transport in solids and the significance of activation energy - describe the key features that allow Li+ and O2- transport in solid electrolytes - describe the causes of structural distortions in simple perovskites - describe the impact of structural distortion on ferroelectric behaviour - explain how the stabilisation of different perovskite distortions can be evaluated - describe how pore structure can influence gas sorption and movement

Topics: 1. Molecular Models and Modelling 2. Molecular Mechanics 3. The special problems of calculations of solids and periodic arrays 4. Calculation of Lattice Energies using bond valence sums and interatomic potentials 5. Potential Energy Surfaces 6. Principles and Methods of Molecular Dynamics 7. Applying Molecular Dynamics to Crystalline Solids and selection of interatomic potentials 8. Interpreting dynamic processes in solids; ion hopping and cooperative mechanisms 9. Li+ conduction in battery materials 10. Oxide ion movement in fuel cell materials 11. Octahedral tilting and distortion in ferroelectric perovskites 12. Modelling of gas storage and diffusion in porous materials

Recommended Texts: - A. R. Leach, Molecular Modelling: Principles and Applications, 2 ed., Pearson Education, Harlow, 2001. - G. H. Grant, W. G. Richards, Computational Chemistry, Oxford Chemistry Primers, Vol. 29, OUP, Oxford, 1995. - F. Jensen, Introduction to Computational Chemistry, 2nd ed., Wiley, Chichester, 2007. - C. J. Cramer, Essentials of Computational Chemistry, 2nd ed., Wiley, Chichester, 2004. - C. R. A. Catlow, R. G. Bell and J. D. Gale, Computer Modelling as a Technique in Materials Chemistry, Journal of Materials Chemistry, 1994, 4(6), 781-792 - M. W. Lufaso, P. W. Barnes and P. M. Woodward , Structure prediction of ordered and disordered multiple octahedral cation perovskites using SPuDS, Acta Crystallographica B, 2006, 62, 397.

CH 577 CHEMICAL BIOLOGY II ( Professor NCO Tomkinson and Dr GA Burley) SHE Level 5 ECTS Credits 5.0

Aims This advanced course will cover chemical biology techniques and strategies of relevance to the drug discovery process. The course will be delivered in two parts. Part 1 will cover DNA damage and repair (10 lectures). Part 2 will cover post translational modification and the chemical and genetic validation of drug targets (10 lectures).

Learning Outcomes

• To introduce how our genome is damaged by both extracellular (e.g. radiation and UV light) and metabolic processes (oxidative respiration). • To introduce how these DNA damages are repaired by DNA damage repair pathways. • To introduce how DNA damage, if left unrepaired can lead to ageing and cancer. • To introduce the concept of post translational modification through covalent • To present how phosphorylation, glycosylation, alkylation and acylation can alter/define the structure, function and localisation of a protein. • To introduce how understanding of these modifications through the development of chemical tools can facilitate intervention in disease pathways. Syllabus DNA damage and repair (10 lectures) 1. UV and radiation damage of DNA 2. Oxidative damage of DNA 3. Formation of DNA bulky adducts 4. Reactive nitrogen species and DNA damage 5. Introduction to DNA damage repair pathways 6. Base excision repair 7. Nucleotide excision repair 8. DNA repair in plants 9. 6-Methylguanosine repair Post translational modification and target validation (10 lectures) 1. Post translational modification and the introduction of complexity 2. Effect on activity, location and function of a protein 3. Protein phosphorylation 4. Protein glycosylation 5. Protein alkylation 6. Protein acylation 7. Effects of post translational modification in disease pathways 8. Use of chemical tools to identify, understand and validate disease pathways Recommended reading An Introduction to Medicinal Chemistry Fourth Edition, Graham L Patrick, Oxford University Press. ISBN: 978- 0-19-923447-9.

CHEMISTRY AND CHEMISTRY WITH TEACHING SPECIALISATION CURRICULUM (CH 413 or CH 553 CHEMISTRY)

CH 413 (BSc Honours) Lectures: 48 (4 blocks of 12 lectures each):

CH 508 Advanced and Modern Methods in Organic Synthesis 12 lectures CH 511 Synthesis of Polymers 12 lectures CH 538 Molecular Catalysis 12 lectures CH 578 Molecular Driving Forces in Bionanotechnology 12 lectures

Tutorials: as required. ECTS Credits: 10

CH 553 (MChem) Lectures: 96 (2 blocks of 24 lectures and 4 blocks of 12 lectures):

CH 509 Advanced and Modern Methods in Organic Synthesis 24 lectures CH 510 Polymers: Synthesis and Chemical Properties 24 lectures CH 513 Solid State Chemistry 12 lectures CH 538 Molecular Catalysis 12 lectures CH 559 Advanced Electrochemistry 12 lectures CH 578 Molecular Driving Forces in Bionanotechnology 12 lectures

Tutorials: as required. ECTS Credits: 20

CH 508/CH 509 ADVANCED AND MODERN METHODS IN ORGANIC SYNTHESIS ( Professor JA Murphy and Dr AJB Watson) SHE Level 5 ECTS Credits 2.5 AND 5.0

Aims: • To outline some of the currently available methods used in asymmetric synthesis including chiral auxiliaries, reagents and catalysts. • To discuss the mechanisms of these processes, where appropriate. • To relate these methods of asymmetric synthesis to selected industrial and research syntheses of simple biologically active molecules. • To survey some of the most contemporary metal-mediated techniques that have been developed for use in organic synthesis. • To examine the use of these organometallic strategies, where they have been applied, in target molecule synthesis. • To examine the mechanistic aspects of the metal-mediated processes and to explore how the proposed reaction pathways have led to the discovery of the optimum reaction techniques. • To apply the techniques being covered within chemical problem solving sessions.

Learning Outcomes:

• To appreciate the various methods of asymmetric synthesis and be able to give appropriate examples • To be aware of the structure of the key chiral reagents in all synthesis processes • To understand the mechanism of selected reactions and be able to discuss and outline them • To apply the knowledge gained to propose asymmetric syntheses of chiral compounds • To develop an understanding of the important mechanistic aspects of palladium-catalysed coupling reactions, to develop a familiarity with the important reactions in this area, and to develop an ability to employ these palladium-based strategies in synthetic organic sequences. • To develop an understanding of copper-mediated cross-coupling processes and conjugate addition reactions for the construction of a variety of carbon-carbon and carbon-heteroatom bonds. • To create a familiarization with organocatalysis in terms of iminium and enamine activation and their use in stereoselective formation of a variety of carbon-carbon and carbon-heteroatom bonds.

• To develop an understanding of the synthesis, reactivity, and mechanism of action of selected metal carbene complexes and to create the ability to recognise and employ the described techniques in synthetic organic sequences. • To develop an understanding of the mechanism and efficiency of selected metal-mediated cycloaddition processes for the synthesis of a range of carbo- and heterocycles

Topics 1-7 Asymmetric Organic Synthesis.

The emphasis will be on how we can use modern asymmetric synthesis as a tool in the synthesis of biologically active compounds. Also, in the use of enzymatic and microbial methods in synthesis. General Introduction (Enantioselective synthesis, thermodynamic principles). Very briefly, first generation methods. Second generation methods (chiral enolates/azaenolates, aldol, (Li & B chemistry) conjugate addition (Cu & Mg), Diels-Alder (A1, Ti). Third/Fourth Generation methods. Definitions (reagent/catalyst control). Carbon-carbon bond formation (Addition to C=O (An, Li) conjugate addition (P, Cu), Diels-Alder (Ti-B)). Chiral bases. Enantioselective oxidation (Sharpless (Ti), asymmetric dihydroxylation (Os), aminohyroxylation, Jacobsen epoxidation (Mn (III), Shi epoxidation). Enantioselective reduction (catalytic hydrogenation (C=O, double bond isomerisations (Rh, Ru), CBS). Enzymatic and microbial methods (biocatalytic oxidation and reduction, esterases/lipases).

8-9 Palladium Catalysed Processes

The important mechanistic aspects of the use of palladium-catalysed transformations in organic synthesis will be discussed to build the concepts for the general catalytic cycles involved in this area. The common reagents and ligands used in this field will be detailed. More specifically, in terms of synthesis, the commonly used and important Pd-catalysed reactions will be discussed in detail and examples given. This will include the Suzuki, Stille, Kumada, Sonogashira, Heck and carbonylation reactions as well as similar and related processes. Applications of the Pd-based processes in total synthesis will be given throughout.

10-11 Key Radical Reactions in Synthesis

Show how radical chemistry extends and complements polar chemistry for the synthetic chemist. Organotin methods for radical generation, benefits and problems; activation by thermal and photochemical means; catalytic methods.

End of lectures for BSc students.

12-15 Advanced Radical Processes

Silanes as radical generators. Cobalt complexes as radical precursors. Atom transfer and group transfer strategies. Barton esters and the Zard strategy. The versatility of samarium diiodide. Manganese (III) complexes and tetrathiafulvalene as radical-polar crossover reagents. Polar effects and polarity reversal catalysis. Control and selectivity in applications to synthesis.

16-20 Advanced Organic Synthesis.

Useful and widely applicable organometallic and organocatalytic transformations in organic synthesis will be detailed: further methods of Pd-based cross-coupling processes will be discussed which lead on to the use of analogous copper-based methods. Copper-based conjugate addition processes will be explored which will lead on to the use of organocatalytic methods for stereoselective 1,4-addition via iminium catalysis and then to the orthogonal method of enamine catalysis. Metal carbene-mediated metathesis processes will be described and the scope and limitations of this important technology will be explored. Lastly, metal-mediated cycloaddition processes will be introduced and a variety of these methods discussed. Throughout the focus will be on economical and bond-forming processes which display high degrees of regio- and stereoselectivity. The mechanistic details of each process will be described, in turn, showing how this influences the reaction conditions employed. Applications of all these processes will be given throughout in order to illustrate their wide utility.

CH 510 POLYMERS: SYNTHESIS AND CHEMICAL PROPERTIES (Professor PAG Cormackk, Dr JJ Liggat) SHE Level 5 ECTS Credits 5.0 CH 511 SYNTHESIS OF POLYMERS (Professor PAG Cormack) SHE Level 5 ECTS Credits 2.5

Part One (students taking CH 511 attend this part ONLY) Aims: The use of polymers as materials, adhesives, additives etc. is now so widespread that it is certain, no matter what branch of chemistry you enter, you will encounter these materials. The number of graduates from UK universities with a specialised knowledge of the subject is, nonetheless, surprisingly low and industry is constantly advertising for people with expertise in the subject. The aims of the class are therefore: • to develop a detailed understanding of the chemistry of addition polymerisation processes and polycondensation processes. • to introduce and develop the concept of co-polymerisation • to explain the important stereochemical aspects of polymerisation processes

Learning Outcomes: At the end of the course the student should: • be able to understand the basic concepts of addition polymerisation applied to vinyl, diene and cyclic monomers; • be fully knowledgeable of the kinetics and mechanism of free radical polymerisation; and solution, bulk, suspension and emulsion polymerisation systems; • have a sound grasp of free radical co-polymerisation mechanism and kinetics; • be able to understand the extension of addition polymerisation to include anionic and cationic polymerisations, and particularly Ziegler-Natta catalyst systems; • be able to understand the basic concepts of step-growth polymerisation, including kinetic and statistical treatments; • be familiar with the basis of polymer structure and stereochemistry and be aware of methods by which polymer structure can be controlled;

Topics 1. Introduction Simple concepts, terminology, nomenclature, reference to third year course

2. Addition Polymerisation Vinyl, alkene (olefin) and diene monomers. Cyclic monomers. Addition polymerisation processes. Mechanism of free radical polymerisation of vinyl and related monomers. Kinetics of free radical polymerisations. Molecular weights and free radical chain transfer. Solution and bulk polymerisations. Gel or Trommsdorf effect. Suspension and emulsion polymerisations. Examples and applications. Free radical co-polymerisations. Kinetics and instantaneous copolymer composition as a function of comonomer feed. Ionic polymerisations of vinyl and cyclic monomers. Cationic and anionic polymerisation mechanisms – vinyl monomers. Living polymerisations and block copolymers. Susceptibility of different monomers to polymerisation by different mechanisms. Ionic copolymerisation. Ionic polymerisation of cyclic monomers – cyclic ethers, sulphides and amines, butyrolactone and caprolactam. Ziegler-Natta polymerisation of ethylene and propylene. Mechanistic considerations. Recent novel metallocene catalysts.

3. Step-growth Polymerisation – Polycondensation Important examples of polycondensation species. Polyesters, polyamides (nylons), polyurethanes, epoxides, phenol-formaldehyde. “Thermoset” versus “thermoplastic”. Kinetics of step-growth polymerisations. Catalysed and “non-catalysed” reactions. Statistics of step- growth polymerisation – evolution of molecular weight with time. Molecular weight control. Uses of step-growth polymers.

4. Polymer Structure and Stereochemistry Linear head-to-tail vinyl polymers, head-to-head links, branching in low density polyethylene. High density and linear low density polyethylene. Iso-, syndio- and heterotactic (atactic) vinyl polymers. Internal symmetry and stereo-blocks leading to zero optical activity. General criteria required for tactic polymerisations. Synthesis of syndiotactic vinyl polymers. Stereocontrol in Ziegler-Natta polymerisations. Stereochemistry of diene polymers – 1,2 and 1,4 polymers. Stereochemical control in diene polymers. Booklist General FW Billmeyer, “Textbook of Polymer Science”, John Wiley MP Stevens, “Polymer Chemistry”, 3rd Edition JMG Cowie, “Polymers: Chemistry and Physics of Modern Materials”, Blackie RJ Young, “Introduction to Polymers”, Chapman and Hall Advanced KJ Saunders, “Organic Polymer Chemistry”, Chapman and Hall AD Jenkins and A Ledwith, “Reactivity, Mechanism and Structure in Polymer Chemistry”, John Wiley G Moad and DH Solomon, “The Chemistry of Free Radical Polymerisation”, Pergamon

Part Two

Aims: • to develop an understanding of the way in which molecular weight of chemical and sequence structure of macromolecules influence their physical properties • to indicate the way in which theoretical models can be developed to the mechanism and kinetics of crystal growth • to introduce the principles of small molecule permeation through polymers with a particular emphasis on practical applications.

Learning Outcomes: At the end of the course the BSc students have an understanding of:

• the importance of chemical structure in determining the shape and properties of polymeric materials both in solution and in a solid phase; • the difference between amorphous and crystalline states in the polymeric phase of materials and the influence which this difference has on the mechanical properties; • the glass transition phenomena and its implications; • the influence of microstructure on the polymeric phase; • the factors influencing the generation of a crystalline phase within polymeric materials and the influence of molar mass and temperature on the nature of that phase structure; • differences between different types of crystalline structure related to the organisation at a molecular level; • the influence of crosslink structure and chain mobility on the elastomeric rubbery state; • the principles of permeation; • practical applications of permeation theories.

At the end of the course the MChem students should in addition have an understanding of:

• how manipulating osmotic pressure, viscosity and related data can allow you to obtain the molecular weight for a polymer; • how to calculate the changes in properties arising when polymers are blended, placiticized or synthesisied in the form of copolymers.

Topics 1-2 The characteristic feature of macromolecules is their chain-like nature. A theoretical model of polymer chains will be presented which will lead to more detailed models that can predict polymer properties with great accuracy. This is particularly true of the rotational isomeric state models developed by Volkenstein and Flory. 3-4 Methods of molecular mass determination will be discussed, with particular reference to osmotic pressure measurements and the application of the Virial equation.

5-6 In the solid state where most polymers are employed, macromolecules have two forms; completely amorphous or partially crystalline. The amorphous state is characterised by a glass transition temperature, Tg, where the strength of the polymer decreases drastically. This Tg is an example of a relaxation process which results from motion of the molecule or part of the molecule. All these will be illustrated and theories of the glass transition presented in conjunction with the rheology of polymer melts.

7-9 In semi-crystalline polymers there is a large degree of organisation over a range of length scales. The mechanism and kinetics of crystal growth at a molecular level lead to a consideration of the organisation of molecules in crystalline polymers. In addition to the crystalline unit cell, semi- crystalline polymers are organised into lamellar structures which have an important role in determining properties.

10-12 Permeation is a two-stage process best described by the “solution-diffusion” model. The diffusion process is governed by the size and shape of the permeating mollecule and the dynamics and morphology of the polymers. The relationship between permeation properties and practical applications such as packaging will be discussed.

Suggested Reading

JMG Cowie, "Polymeric Chemistry and Physics of Modern Materials", Blackie, 2nd Edn. (1991) DI Bower, “An Introduction to Polymer Physics,” Cambridge University Press, (2002)

CH 513 SOLID STATE CHEMISTRY (Dr AR Kennedy) SHE Level 5 ECTS Credits 2.5

Aims: To introduce the concepts of modern solid state chemistry. These will include:

• the dependence of physical properties on solid-state structure • supramolecular chemistry • modern applications and materials

Learning Outcomes At the end of the course the student should be able to:

• describe the nature of amorphous and crystalline phases • understand the common intermolecular interactions found • understand the connection between solid-state structure and physical properties • appreciate solid-state aspects of pharmaceutical formulation • relate structural properties to the usefulness of materials such as pigments, electronic devices and zeolites • appreciate the methods used to probe the solid-state

Topics 1 Introduction. Amorphous vs crystalline phases. Order, disorder and molecular motion. Structure’s effect on bulk physicochemical properties. 2 Polymorphic materials and the implications for their industrial exploitation. Examples from pharmaceutical and other chemical industries. Solubility, melting point, stability, hardness, hydration, colour. 3 Non-covalent Intermolecular Interactions. Ions and dipoles, hydrogen-bonding, cation to π and π-π interactions. Organic and organometallic supramolecular stucture. 4 Nucleation and Crystal Growth. Mechanism of Dissolution Process. 5 Measuring the solid state. DSC, TGA, Diffraction, Solid-State Spectroscopy (IR, nmr). 6 Predicting the Solid-State Structure. Potential Packing Energy Calculations and Crystal Engineering. 7 Reactions in channels and pores (zeolites, clathrates, intercalates). 8 Electronic and magnetic materials. Spinels, fast-ion conductors, 1-D conductors.

In addition two tutorial/consolidation sessions will be held, one halfway through and one at the end. Suggested reading: “Supramolecular Chemistry,” JW Steed and JL Atwood

CH 538 MOLECULAR CATALYSIS (Dr M.D. Spicer) SHE Level 5 ECTS Credits 2.5

Catalysis has been a major focus of organometallic chemistry over the past 40 years, with applications from heavy industry to fine chemicals. This course is designed to cover the fundamental concepts of organometallic compounds as used in catalysis and to use case studies to illustrate aspects of catalyst design and control of activity and selectivity.

Learning Outcomes: At the end of the course the student should:

• Understand the basic concepts of catalysis • Know the factors which influence catalyst activity and selectivity • Be able to construct catalytic cycles • Have a grasp of the application of different techniques to elucidation of mechanism of catalyst action • Appreciate the advantages and disadvantages of immobilised catalysts • Have some knowledge of metallo-enzyme mediated catalysis • Have an appreciation of organocatalysis; advantages, catalyst classes, reaction mechanisms, chiral organocatalysis.

Topics

1 Introduction to catalysis. Definitions. Thermodynamic and kinetic background. Homogeneous vs heterogeneous catalysis. Historical perspective.

2 Tolman’s rules, organometallics reactions and catalytic cycles.

3 - 6 Case Studies: hydroformulation – Co and Rh catalysed reactions, effect of phosphine, activitiy and selectivity, deducing mechanisms: Wacker Process – isotopic substitution for probing mechanism; Alkene Hydrogeneation – Rh catalysed, mechanistic studies.

7 - 8 Immobilisation of catalysts – organic and inorganic polymer supports; biphasic catalysis (aqueous and fluorous phases).

9 Organocatalysis; advantages. Lewis Base catalysts (iminium, enamine and carbine catalysed reactions).

10. Proline catalysed reactions – chiral organocatalysis. Relation to enzyme and metallo-enzyme catalysis (examples: aldolase; liver alcohol dehydrogenase; sulfite oxidase).

CH 559 APPLIED ELECTROCHEMISTRY (Dr LEA Berlouis) SHE Level 5 ECTS Credits 2.5

Aims and Objectives: To examine two very important applications of electrochemistry in industry. These are (i) corrosion protection and prevention and (ii) design and analysis of electrochemical reactors used in electrosynthesis (e.g. chlor-alkali process), in effluent treatment for heavy metal removal as well as precious metal recovery.

Content

Electrochemistry of corrosion; thermodynamics of corrosion, Pourbaix Diagrams. Kinetics of corrosion; corrosion currents, corrosion potential, Evans Diagram. Measuring and monitoring corrosion; electrochemical methods, physical methods. Analysis of corrosion products. Corrosion problems in practice; types of corrosion, localised corrosion, stress and corrosion. Corrosion prevention and control; materials selection and design, inhibition, coatings. Nature of electrochemical reactions: spontaneous or driven cells. Fundamentals and general concepts of electrochemical engineering. Performance and figures of merit for electrochemical cells. Fractional conversion, yield, current efficiency, energy consumption, cell voltage, energy efficiency, mass transfer coefficient, space time yield. Principles of cell design - batch reactor, plug flow reactor, CFSTR. Improving electrochemical reactor performance.

Recommended Reading:

Industrial Electrochemistry (2nd Edition) Derek Pletcher and Frank C Walsh, Blackie Academic and Professional (1990).

CH 578 MOLECULAR DRIVING FORCES IN BIONANOTECHNOLOGY (Drs KHA Lau, Dr D Palmer, Dr CT Tuttle) SHE Level 5 ECTS Credits 2.5

Class Aims Bionanotechnology refers to the development and application of biochemical based systems that are present on the nanoscale. In order to design and utilize these systems for different technological applications it is necessary to understand the various factors (driving forces) that result in the structure and function of the system. This class is intended to give you an understanding of what these driving forces are and how their relative importance can be measured and understood. In order to do this you will necessarily gain an understanding of the different computational and experimental techniques to interrogate the driving forces.

Learning Outcomes – at the completion of the course students should be able to: • Describe the relative merits and drawbacks of different methods for modeling solvents in computational chemistry. • Discuss how solvent influences conformational degrees of freedom in biomolecular systems. • Define solvation free energy, enthalpy and entropy. • Explain how to compute solvation free energy using molecular dynamics simulations or implicit continuum models. • Discuss the role that solvation free energy plays in computing other physico-chemical properties. • Describe how solvation free energy is measured experimentally. • Describe the different interactions that contribute to the stability of biomolecular systems. • Discuss the role of time, length, and force scales with respect to the structure and function of biomolecular systems. • Differentiate between static and dynamic techniques. • Define the different interactions that are driving forces in molecular recognition. • Describe a computational approach for calculating binding free energy. • Discuss experimental methods that can be used to determine binding free energy. • Describe an experimental design for assessing the strength of an intermolecular interaction. • Compare and contrast the information available from experimental and computational approaches to calculating binding free energy. • Define what a non-equilibrium method is. • Describe a computational approach for calculating protein stability. • Discuss experimental methods that can be used to determine protein stability. • Describe an experimental design for assessing protein stability. • Compare and contrast the information available from experimental and computational approaches for studying protein unfolding. Teaching and Learning Methods Molecular Driving Forces in Bionanotechnology (DFB) uses a variety of teaching and learning approaches including practical sessions, individual readings, lectures, discussions and case studies. Student participation and interaction is essential to this class and students are expected to participate fully in all sessions.

Indicative Structure of Class Programme The class is organized such that the three main themes (the environment; the stability of biomolecular systems; and molecular recognition) are addressed through an integrated teaching and learning approach. The students will receive an introductory lecture (lectures 1, 5, and 9) on the background of the subject. The second lecture (lectures 2, 6, and 10) will provide details of the specific theories that are required to investigate the particular theme. Students will then be required to read up on the corresponding computational methods that allow them to utilize these theories to compute the corresponding properties. The third lecture (lectures 3, 7, and 11) will be run as a computational workshop whereby the pre-reading will be put into practice by the students through the application of the theories to a real-world problem. The fourth lecture (lectures 4, 8, and 12) will use a case study to discuss how the results calculated in the third lecture by the students can be directly compared to results obtained through the corresponding experimental techniques.

Lecture Topics (topics in italics will be carried out as computational workshops following student pre-reading). 1. The Role of Solvent in Biomolecular Systems 2. The Theory of Solvation Thermodynamics 3. Computing Solvation Free Energy from Molecular Dynamics Simulations 4. Practical Applications of Liquid State Simulations 5. The Role of Molecular Recognition in Nanoscale Systems 6. Driving Forces that Control Single Molecule Recognition 7. Computing Binding Free Energies of Single Molecules 8. Experimental Approaches to Measure the Binding Free Energy 9. Interrogating the stability of Nanoscale Biomolecular Systems 10. Equilibrium Properties from Non-Equilibrium Simulations 11. Computing the Free Energy for Protein Unfolding from Molecular Dynamics Simulations. 12. Equilibrium Properties from Non-Equilibrium Experiments

Reading List The reading list will involve several case-studies and excerpts from the articles literature that will be announced at the start of the course. In addition, background reading on established techniques will be based on the following recommended texts: • A. R. Leach, Molecular Modelling: Principles and Applications, 2 ed., Pearson Education, Harlow, 2001. • G. H. Grant, W. G. Richards, Computational Chemistry, Oxford Chemistry Primers, Vol. 29, OUP, Oxford, 1995. • F. Jensen, Introduction to Computational Chemistry, 2nd ed., Wiley, Chichester, 2007. • C. J. Cramer, Essentials of Computational Chemistry, 2nd ed., Wiley, Chichester, 2004.

CHEMISTRY WITH DRUG DISCOVERY SPECIALISATION CURRICULUM (CH 442 or CH 542 CHEMISTRY WITH DRUG DISCOVERY)

CH 442 (BSc Honours) Lectures: 48 (2 blocks of 24 lectures each):

CH 526 Advanced Medicinal Chemistry 24 lectures CH 527 Metals, Co-factors and Biosynthesis 24 lectures

Tutorials: as required. ECTS Credits: 10

CH 542 (MChem) Lectures: 96 (4 blocks of 24 lectures each):

CH 509 Advanced and Modern Methods in Organic Chemistry 24 lectures CH 525 Biomolecule Analysis 24 lectures CH 526 Advanced Medicinal Chemistry 24 lectures CH 527 Metals, Co-factors and Biosynthesis 24 lectures

Tutorials: as required. ECTS Credits: 20

CH 508/CH 509 ADVANCED AND MODERN METHODS IN ORGANIC SYNTHESIS (Professor JA Murphy and Dr ABJ Watson) SHE Level 5 ECTS Credits 2.5 AND 5.0

Aims: • To outline some of the currently available methods used in asymmetric synthesis including chiral auxiliaries, reagents and catalysts. • To discuss the mechanisms of these processes, where appropriate. • To relate these methods of asymmetric synthesis to selected industrial and research syntheses of simple biologically active molecules. • To survey some of the most contemporary metal-mediated techniques that have been developed for use in organic synthesis. • To examine the use of these organometallic strategies, where they have been applied, in target molecule synthesis. • To examine the mechanistic aspects of the metal-mediated processes and to explore how the proposed reaction pathways have led to the discovery of the optimum reaction techniques. • To apply the techniques being covered within chemical problem solving sessions.

Learning Outcomes:

• To appreciate the various methods of asymmetric synthesis and be able to give appropriate examples • To be aware of the structure of the key chiral reagents in all synthesis processes • To understand the mechanism of selected reactions and be able to discuss and outline them • To apply the knowledge gained to propose asymmetric syntheses of chiral compounds • To develop an understanding of the important mechanistic aspects of palladium-catalysed coupling reactions, to develop a familiarity with the important reactions in this area, and to develop an ability to employ these palladium-based strategies in synthetic organic sequences. • To develop an understanding of copper-mediated cross-coupling processes and conjugate addition reactions for the construction of a variety of carbon-carbon and carbon-heteroatom bonds. • To create a familiarization with organocatalysis in terms of iminium and enamine activation and their use in stereoselective formation of a variety of carbon-carbon and carbon-heteroatom bonds. • To develop an understanding of the synthesis, reactivity, and mechanism of action of selected metal carbene complexes and to create the ability to recognise and employ the described techniques in synthetic organic sequences.

• To develop an understanding of the mechanism and efficiency of selected metal-mediated cycloaddition processes for the synthesis of a range of carbo- and heterocycles

Topics 1-8 Asymmetric Organic Synthesis.

The emphasis will be on how we can use modern asymmetric synthesis as a tool in the synthesis of biologically active compounds. Also, in the use of enzymatic and microbial methods in synthesis. General Introduction (Enantioselective synthesis, thermodynamic principles). Very briefly, first generation methods. Second generation methods (chiral enolates/azaenolates, aldol, (Li & B chemistry) conjugate addition (Cu & Mg), Diels-Alder (A1, Ti). Third/Fourth Generation methods. Definitions (reagent/catalyst control). Carbon-carbon bond formation (Addition to C=O (An, Li) conjugate addition (P, Cu), Diels-Alder (Ti-B)). Chiral bases. Enantioselective oxidation (Sharpless (Ti), asymmetric dihydroxylation (Os), aminohyroxylation, Jacobsen epoxidation (Mn (III), Shi epoxidation). Enantioselective reduction (catalytic hydrogenation (C=O, double bond isomerisations (Rh, Ru), CBS). Enzymatic and microbial methods (biocatalytic oxidation and reduction, esterases/lipases).

8-10 Palladium Catalysed Processes

The important mechanistic aspects of the use of palladium-catalysed transformations in organic synthesis will be discussed to build the concepts for the general catalytic cycles involved in this area. The common reagents and ligands used in this field will be detailed. More specifically, in terms of synthesis, the commonly used and important Pd-catalysed reactions will be discussed in detail and examples given. This will include the Suzuki, Stille, Kumada, Sonogashira, Heck and carbonylation reactions as well as similar and related processes. Applications of the Pd-based processes in total synthesis will be given throughout.

10-12 Key Radical Reactions in Synthesis

Show how radical chemistry extends and complements polar chemistry for the synthetic chemist. Organotin methods for radical generation, benefits and problems; activation by thermal and photochemical means; catalytic methods.

End of lectures for BSc students.

12-16 Advanced Radical Processes

Silanes as radical generators. Cobalt complexes as radical precursors. Atom transfer and group transfer strategies. Barton esters and the Zard strategy. The versatility of samarium diiodide. Manganese (III) complexes and tetrathiafulvalene as radical-polar crossover reagents. Polar effects and polarity reversal catalysis. Control and selectivity in applications to synthesis.

16-21 Advanced Organic Synthesis.

Useful and widely applicable organometallic and organocatalytic transformations in organic synthesis will be detailed: further methods of Pd-based cross-coupling processes will be discussed which lead on to the use of analogous copper-based methods. Copper-based conjugate addition processes will be explored which will lead on to the use of organocatalytic methods for stereoselective 1,4-addition via iminium catalysis and then to the orthogonal method of enamine catalysis. Metal carbene-mediated metathesis processes will be described and the scope and limitations of this important technology will be explored. Lastly, metal-mediated cycloaddition processes will be introduced and a variety of these methods discussed. Throughout the focus will be on economical and bond-forming processes which display high degrees of regio- and stereoselectivity. The mechanistic details of each process will be described, in turn, showing how this influences the reaction conditions employed. Applications of all these processes will be given throughout in order to illustrate their wide utility.

CH 525 BIOMOLECULE ANALYSIS (Dr R de la Rica, Dr MJ Dufton and Dr JA Parkinson) SHE Level 5 ECTS Credits 5.0

Aims:

This course aims to introduce students to modern methods of analysing biomolecules by concentrating on the use and outcomes of the various techniques. This will cover a broad range of techniques, which will be taught in context with examples from real life problems and using, where possible, modern software.

Learning Outcomes:

By the end of the course the students will know the following:

• The biology behind the identification of the target biomolecules.

• Utilization of sensors, biosensors and nanosensors for analysing biomolecules and biomolecule interactions

• What a lab-on-a-chip is and how it is used for biomolecular analysis.

• The molecular biological concepts behind the identification of specific sequence variations within DNA.

• The different chemistries commonly used for quantitative PCR identification of DNA defects or specific target sequences.

• The use of real time and reverse transcriptase PCR for identification of DNA sequence variations.

• Techniques for high-throughput detection of biomolecule interactions: ELISA, DNA and protein microarrays

• What aptamers and molecularly imprinted polymers (MIPS) are and how they can be generated from the use of synthetic chemistry.

• The types of targets that aptamers and MIPS combine to and how they are used in practice.

• The principles behind 2D gel electrophoresis and how it is used for identification of biomolecules.

• The chemistry behind the sequencing of DNA by fluorescence methods.

• The chemistry behind the sequencing of proteins.

• Alternative chemical methodologies for the sequencing of DNA and proteins.

• The significance of molecular dynamics in the context of enzyme mechanism.

• How NMR can be used to study biomolecule motional characteristics.

• familiar with the concepts behind NMR data assignment strategies for biomolecule analysis.

• A simplified spin system and interpret a simplified NMR data set.

• The approaches used to determine biomolecular structures in solution.

• Understand and explain the significance of the terms: heteronuclear correlation, isotope editing, T1 and T2 relaxation and Nuclear Overhauser Effect (NOE).

Topics 1-4 Identification of biomolecules of interest

Sensors, biosensors, nanosensors, lab-on-chip Microarrays-Protein and DNA Arrays 2D Electrophoresis Aptamers-SELEX (in vitro selection followed by cloning and sequencing) and molecularly imprinted polymers

5-8 Determination of covalent structure (primary sequence information)

Sequencing of DNA, peptides proteins and carbohydrates. Identification of sequence variations by: QPCR RT PCR

9-15 The manner by which enzymes enable chemistry to occur under their control is dependent not only on the three-dimensional structure of the enzyme and the fit between enzyme and ligand structures but also and crucially upon the motional.characteristics of the enzyme itself. This part of the class takes a look at one specific example of enzyme motion with respect to the chemistry it performs and discusses in a wider context the manner by which such motion may be measured on the basis of modern NMR methods.

Dynamics and Enzyme Mechanism: Enzymes and their chemistry, Dihydrofolate Reductase (DHFR); structure, motion, chemistry, inhibitors and cofactors; an introduction to the Order Parameter, S2.

Biomolecular NMR Methods A: Revision of NMR background; relaxation and its relationship to motion; isotope enrichment, the heteronuclear NOE (Nuclear Overhauser Effect) and its relationship to motion.

Biomolecular NMR Methods B: Tools and tricks to understand NMR data from proteins; dispersion, magnetic field strength, 2D and 3D NMR, interpretative methods.

Protein structure determination from NMR: Parameters and methods; structure prediction methods; chemical shift indexing; family of structures; average structure; rmsd; how well does a ‘family’ of structures represent a protein’s true motional properties?

16-20 Bioinformatics International Nucleic Acid & Protein databases Data volume and limitations on direct experiment Classification and association techniques Techniques for prediction of structure and function Application to biomolecular engineering

CH 526 ADVANCED MEDICINAL CHEMISTRY (Dr C Jamieson, Dr I Simpson (AstraZeneca Ltd)) SHE Level 5 ECTS Credits 5.0

Aims: • to introduce some of the more modern concepts and problems in the medicinal chemistry field, including modern synthetic and screening strategies • modern approaches to disease states with reference to cell signalling cascades, drug metabolism and developability. • To understand the role of physicochemical properties in the context of modern drug discovery and metabolism.

Learning Outcomes: At the end of the course the student should have:

• An appreciation of the major influences on current scientific practice in the pharmaceutical industry. • Knowledge and understanding of the uses of instrumentation and advanced technology in the drug discovery and development process. • An understanding and appreciation of the interface between chemistry and biology in the context of drug discovery, for example the impact of genome projects. • Knowledge and understanding of the problems synthetic chemistry posed by drug discovery and of the solutions of those problems. • Knowledge and understanding of case studies that illustrate and illuminate the above. These may include the following: diseases of lipid metabolism; modern approaches to cancer chemotherapy; neurological disorders. Other case studies may be selected to take account of recent developments in the field. • An ability to apply all of the above to problems in drug discovery, including the interpretation of biological data, the selection of lead compounds, the synthesis of lead compounds, and routes to optimisation (all with an appropriate level of length and difficulty).

Topics 1 An overview of the modern pharmaceuticals industry.

2 Recent trends in research strategy for drug discovery.

3 Cell signalling as a target for drug action.

4 Nuclear hormone receptors, 7TM receptors, tyrosine kinase receptors, Ion Channels..

5 7TM receptors and Ion Channels – structural work and impact on drug discovery.

6 Cholesterol imbalance. Potential sites of intervention. Role of LXR.

7 Bile acid sequestrants, the statins, ACAT inhibitors, Ezetimibe. Tissue selective activity.

8 Modern cancer chemotherapy: protein tyrosine kinases. Structure and mechanism of action.

9 Pharmacophores associated with inhibition of enzymes and anticancer activity (Iressa and Gleevec). Cyclin dependent systems.

10 Central Nervous System Disorders: Challenges and treatment units.

11 Structure-property relationships - the physicochemical partner to SAR. Lipinski’s rule and developability parameters.

12 Synthesis in medicinal chemistry. Features of discovery synthesis: libraries, technology, parallelisation, the building block approach. Features of development and process chemistry: environmental factors, yield and work up problems.

13 Recent contributions of fragment screening to hit finding efforts. Relationships with physicochemical properties.

14 Design, synthesis and application of PET ligands in translational medicine.

15 Role of non-Lipinski species in modern target validation and drug discovery.

CH 527 METALS, CO-FACTORS AND BIOSYNTHESIS (Dr CL Gibson and Dr J Reglinski) SHE Level 5 ECTS Credits 5.0

Aims: • To provide a detailed insight into how specific metals and metalloids are employed in biology. • To demonstrate that inorganic chemistry is relevant to medicinal chemistry, toxicology and environmental science. • To demonstrate how the concepts which underpin inorganic chemistry are integrated in real situations with the context of biology. • To provide an overview of how key natural products are biosynthesised and the techniques used to establish biosynthetic pathways.

Learning Outcomes: At the end of the course the student should be able to:

• Show an appreciation of how biological systems work, viz the source and use of chemical energy. • Understand the role that inorganic chemistry plays in biology. • Understand how biology adopts and fine tunes chemical principles to achieve function. • Show that many targets in medicinal chemistry can be metal based or metal regulated. • Recognise the biosynthetic pathways leading to fatty acid and polyketide biosynthesis. • Outline the methods used to establish biosynthetic pathways. • Describe biosynthetic routes to terpenoids and steroids • Be able to delineate the biosynthesis of natural products obtained via shikimic acid. • Be capable of outlining the biosynthesis of simple alkaloids.

Topics

Section 1 Inorganic Biochemistry

As a vibrant and expanding area only the introductory lectures remain the same each year. The following four 2 hour lectures (selected from the list) service two intertwined themes – the role of metals in biology and their interaction with the major biological sites/regions (viz. membranes, proteins, lipids, sugars).

1-2 Introduction – Essential elements, position in the periodic table, bio-availability, concentrations, redox properties. The main axioms (e.g. chelate effect, hard and soft acid/bases, coordination chemistry) of inorganic chemistry are revised.

Topic 1 Medical imaging. Explanation of SPET (single photon emission Tomography). Design of imaging agents (Tc, Gd) and specific uses (blood flow, thyroid function, cardiac function, neuroscience and tumour location).

Topic 2 Importance of the alkali metals and alkali earth metals (Na, K, Mg and Ca). Discussion of magnesium dependent Na/K/ATPase and membrane proteins. Comparisons are made with the antibiotics valinomycin and gramicidin.

Topic 3 Environmental organometallic chemistry chemistry of arsenic. Uptake and metabolism. Biomethylation via S-adensoyl methionine and cobalamins. Possible extension into bismuth chemistry and anti-ulcer treatment.

Topic 4 Oxygen management: Cytochrome-oxidase. The terminus of the respiratory chain. Electron transfer mechanisms and high oxidation state metals. Failure of the system and the generation .- of toxic oxygen species (O2 ) and H2O2) and their removal (superoxide dismutase, glutathione peroxidases and Catalase).

Section 2 Cofactors

9 Introduction to metal controlled DNA function; zinc fingers, structure, function, metal implications. Interaction of DNA with platinum metal. Cis-platin; mode of action, advanced analogues. Effect of chromium on DNA.

10 Importance of magnesium interaction with phosphate backbone of DNA. ATP structure and reactivity. Cofactors definition: ATP as a cofactor and basic unit of energy, role of magnesium and ATP/ADP in myosin mode of action.

11 H-transfer cofactors for oxidation of fuel molecules; nicotinamide adenine diphosphate with zinc flavin adenine dinucleotide.

12 Acyl transfer cofactor; Coenzyme A, Methyl transfer cofactor; S-Adenosylmethionine Carboxy transfer cofactor; biotin.

13 Carbanion stabilising cofactors involved in metabolism: thiamine pyrophsphate.

14-15 Pyridoxal phosphate; reactions to degrade or transform amino acids.

Section 3 Biosynthesis of Natural Products

16 Primary & Secondary Metabolism. Fatty acid biosynthesis (Biosynthesis, Chain assembly, Saturated fatty acids, Unsaturated fatty acids).

17 Polyketide biosynthesis (Cyclisation of linear polyketides). Elucidation of biosynthetic pathways (isolation of intermediates, radioactive and stable isotopes).

18 Terpenoid and Steroid biosynthesis (Acetate to mevalonate, mevalonate to C-5 pyrophosphates, terpene pyrophosphates, cyclisation and rearrangement, Triterpenoids and steroids).

19 Biosynthesis of aromatic amino acids (Biosynthesis of shikimic acid, shikimate to chorismate, amino benzoates, phenylpropanoids).

20 Alkaloid biosynthesis (pyrrolidine and piperidine alkaloids, introduction to opiate alkaloids).

FORENSIC AND ANALYTICAL CHEMISTRY SPECIALISATION CURRICULUM (CH 554 FORENSIC AND ANALYTICAL CHEMISTRY) ANALYTICAL CHEMISTRY SPECIALISATION CURRICULUM (CH 417 ANALYTICAL CHEMISTRY) FORENSIC CHEMISTRY SPECIALISATION (CH 414 FORENSIC CHEMISTRY)

CH 417 (BSc Honours Chemistry with Analytical Chemistry) Lectures: 48 (4 blocks of 12 lectures each, students do CH 519, CH 579, CH 580 and any class from the four remaining classes):

CH 519 Surface Analysis and X-ray Techniques 12 lectures CH 579 Atomic Nuclear Spectroscopy 12 lectures CH 580 Multivariate Analysis 12 lectures

CH 520 Process Analytical Chemistry CH 521 Toxicology and Alcohol 12 lectures CH 523 The Chemistry of DNA Profiling 12 lectures CH 524 Fires and Explosives 12 lectures

Tutorials: as required. ECTS Credits: 10

CH 414 (BSc Honours Forensic Chemistry) Lectures: 48 (3 blocks of 12 lectures and 1 block of 24 lectures, students do CH 560 and any two from the remaining three classes):

CH 521 Toxicology and Alcohol 12 lectures CH 523 The Chemistry of DNA Profiling 12 lectures CH 524 Fires and Explosives 12 lectures CH 560 Forensic Science: Principles and Practice Parts 1 and 2 24 lectures

Tutorials: as required. ECTS Credits: 10

CH 554 (MChem) Lectures: 96 (6 blocks of 12 lectures and 1 block of 24 lectures):

CH 519 Surface Analysis and X-ray Techniques 12 lectures CH 521 Toxicology and Alcohol 12 lectures CH 523 The Chemistry of DNA Profiling 12 lectures CH 524 Fires and Explosives 12 lectures CH 560 Forensic Science: Principles and Practice Parts 1 and 2 24 lectures CH 579 Atomic Nuclear Spectroscopy 12 lectures CH 580 Multivariate Analysis 12 lectures

Tutorials: as required. ECTS Credits: 20

CH 519 SURFACE ANALYSIS AND X-RAY TECHNIQUES (Professor D Littlejohn and Dr KHA Lau) SHE Level 5 ECTS Credits 2.5

Analysis of surfaces is important in studies of catalysis, corrosion, adhesion, biomaterials and electronic fabrication.

Aims: • To impart knowledge of the fundamental principles of techniques which use electron probes to examine topography or atomic and molecular structure of surfaces; • To develop understanding of the chemical information that can be obtained with different techniques; • To provide an introduction to the phenomena which result from the interaction of X-rays with matter; • To develop awareness of the instrumental and sample-related features of X-ray fluorescence analysis

Learning Outcomes: At the end of the course students should be able to:

• understand the origin of X-ray photons emitted from samples in a scanning electron microscope and their use in element analysis; • understand the Auger process and its use in element analysis; • understand the surface sensitivity of analytical techniques; • understand the photoelectron process and its use in element analysis; • know methods of depth profiling; • explain the phenomena which occur when X-rays interact with matter; • discuss the relative merits of SEM and STEM analysis coupled with EDAX; • understand factors which affect optimisation of instrument operation in wavelength dispersive XRFS; • use knowledge of absorption edge wavelengths to estimate optimum excitation conditions; • appreciate the causes of spectral and matrix interference effects in wavelength dispersive XRF; • select appropriate procedures for sample preparation and prevention/reduction of interference effects. • calculate the escape depth for X-ray photo electrons; • be able to interpret a set of XPS data in terms of their molecular significance; • be able to discuss how a particular surface analytical problem might be addressed using a combination of EDAX, XPS and SIMS.

Topics 1 Definition of surfaces, depth profiling, vacuum, Scanning Electron Microscopy-EDAX.

2 Transmission Electron Microscopy-EELS, Auger spectroscopy

3 Photoelectron spectroscopy, work function, Binding Energies, photon sources, electron analysers

4 Core level signals, BE shifts

5 Escape depths, peak widths, small spot XPS, synchrotrons

6 Scanning Tunnelling Microscopy. AFM.

7 Introduction to X-ray fluorescence; Instrumentation for wavelength dispersion and energy dispersion systems

8 Absorption edge and line spectra

9 Optimisation of instrumental parameters

10-11 Interaction of x-rays with water; absorption, scatter, Auger effect, fluorescent yield.

12 Matrix interferences (physical and absorption/enhancement chemical effects); applications

CH 520 PROCESS ANALYTICAL CHEMISTRY (Dr A Nordon) SHE Level 5 ECTS Credits 2.5

This class is part of the distance learning assignment MChem students complete in their fourth year. It is offered to honours students in the same mode, i.e. there will be no formal lectures for this class but you will be supplied with a set of notes and given a set of supporting tutorials.

Until recently, only a few simple measurements such as temperature and pressure have been available to monitor chemical processes. However, process analytical chemistry is now receiving increasing attention as the limitations of physical measurement instruments are realised. Industries as diverse as petroleum refining and food processing share a common reliance upon chemical processes to convert raw materials into finished products. During manufacturing operations engineers need to ensure the chemical composition of materials in order to adequately adjust product quality and lower production costs. There is, therefore, a need for greater sophistication in real-time monitoring and control of processes, and correspondingly, a greater demand for analytical chemists and technologists who are able to provide and implement systems that can supply the necessary chemical information. The goal of Process Analytics is therefore to supply quantitative and qualitative information about a chemical process which will allow safe, efficient and environmentally responsible operation of the plant.

Aims: To introduce and to review the principles and applications of Process Analysis and Control.

Learning Outcomes: • To appreciate the challenges of on-line process analysis versus laboratory-based analysis. • To understand the instrumental and procedural requirements for successful use of different techniques in on-line process monitoring. • To be able to select appropriate techniques for different process monitoring requirements. • To be able to relate process control needs to process analysis.

Topics 1,2 Benefits of improved process monitoring and control; differences in requirements of laboratory and plant based instruments; off-line, on-line, at-line, in-line and non-invasive analysis; sampling and sample conditioning.

3 Aspects of on-line mass spectrometry for process monitoring.

4 Aspects of on-line Raman spectrometry for process monitoring.

5,6 Process monitoring by UV-visible spectrometry and the use of flow-injection analysis methodologies; examples of industrial applications.

7 Use of mid infra-red spectrometry for on-line process monitoring; industrial examples.

8,9 Use of near infra-red spectrometry for on-line process monitoring; industrial examples.

10 Process gas chromatography.

11,12 Process control requirements; combination of control and process monitoring; examples from an ethylene production plant - safety, product quality, environmental factors (will feature different techniques including gas chromatography).

CH 521 TOXICOLOGY AND ALCOHOL (Dr MJ Baker) SHE Level 5 ECTS Credits 2.5

Aims: An understanding of the analytical procedures used for identifying drugs (including alcohol) in body fluids and tissues and the evaluation of results. An understanding of mathematical modelling procedures for assessing the physiological condition and assessment methods used in conjunction with current UK road traffic legislation.

Learning Outcomes: At the end of the course the student should:

• know the current UK legislation governing drink driving; • be able to interpret the results of the analysis of blood, urine or breath samples for alcohol (ethanol); • be able to prepare suitable reports in connection with defences under the drink driving legislation; • be able to understand the duties of the forensic toxicologist, the problems experienced in identifying unknown poisons and the importance of preparing a case history; • know which extraction techniques should be used to isolate poisons from toxicological samples and calculate extraction efficiencies; • be able to determine the distribution of drugs in body fluids from knowledge gained on pharmacokinetics.

Topics 1 Forensic Toxicology in Context – Definition(s) of a poison. Types of poison. The roles of the Procurator Fiscal, Pathologist and Toxicologist in the medico-legal investigation. Chain of custody. Overview of other contexts: drugs and driving, workplace testing, clinical toxicology, drugs in sport. If possible, arrange a session for the class to watch a video of an autopsy (about 1 hour 30 minutes total).

2 Systematic Toxicological Analysis (STA) (1) – What substances to look for and where to look. Distribution of drugs and poisons in different tissues, pharmacokinetics. Tissue sample selection for different types of analyte. Pre-treatment to adjust pH, protein precipitation, homogenisation, dialysis, digestion, etc. Hydrolysis of conjugates. Extraction by LLE, SPE, SPME. Headspace analysis. Theory and examples.

3 Systematic Toxicological Analysis (STA) (2) – Screening and confirmatory methods. Analytical methodology used in toxicology: chromatographic and immunoassay methods – their practical application to drug classes in STA with examples of analyses e.g. basic drug screen, drugs of abuse, etc. Derivatisation procedures.

4 Systematic Toxicological Analysis (3) – Quality assurance. Method selection, development and validation.

5 Interpretation of toxicology reports – sources of information. Factors affecting the dose-response curve. Tolerance. Case examples.

6 Problems of interpretation – difficult analyses. Post-mortem redistribution of drugs and other artefacts. Use of alternative specimens such as hair. Case examples.

Blood Alcohol 7 This describes current UK legislation governing the enforcement of drink-driving laws and describes the involvement of forensic scientists.

8-9 The analyses of samples of blood, urine and breath using gas chromatography, fixed wavelength IR detectors and solid state sensors.

10-11 The metabolism of alcohol within the body including its absorption, distribution and elimination.

12 The statutory defences to drink-driving charges and the application of the features described in lectures 10 and 11.

CH 523 THE CHEMISTRY OF DNA PROFILING (Dr P Haddrill) SHE Level 5 ECTS Credits 2.5

Human identification by DNA testing has been the most significant single advance in forensic science in the last twenty five years. While clearly related to the biological sciences the means of testing involves much chemistry and biochemistry. The science is used far beyond forensic applications in a diverse range of disciplines such as archaeology and clinical screening for genetic disease. Moreover the interpretation of the results has served as a bench mark for the interpretation of all sorts of forensic evidence.

Aims: • To introduce the principles upon which DNA analytical techniques are currently applied to human identification. • To demonstrate how these techniques have been applied to problems of human identification. • To describe the chemistry used for selected alternative technologies for DNA profiling that have been introduced or may be used in future.

Learning Outcomes: At the end of the course the student should:

• Be familiar with aspects of the chemistry of DNA that are exploited in the tests. • Know how the polymerase chain reaction is used in conventional DNA testing and know the artefacts that the analyst has to recognise. • Know how the results of DNA testing are assessed for use in court reports. • Be familiar with alternative types of DNA such as mitochondrial DNA and Y chromosome DNA that are also profiled by DNA testing. • Be able to describe emerging technologies such as microarray testing and the role these alternative approaches play in profiling forensic science. • Be able to see the wider context of the applications of DNA profiling in all its forms.

Topics 1 Using case examples, different forms of human identification by DNA profiling will be shown. 2 Specific aspects of the chemistry of DNA that are exploited in testing will be considered. 3 A description of the conventional method of human identification by DNA profiling. 4 A description of the advantages of capillary electrophoresis as a means of bio molecule separation and analysis in DNA analysis. 5 A review of different chemistries used in DNA testing world wide. 6 A description and explanation of anomalies and artefacts that occur in DNA profiling and how the DNA profile is interpreted. 7 Profiling single nucleotide polymorphisms, an alternative approach. 8 The chemistry of DNA sequencing and SNP analysis. 9 DNA profiling of mitochondrial DNA. 10 DNA profiling of Y chromosome DNA. 11 High throughput DNA profiling technologies. Suggested reading;

These books need not be purchased s they are available in the library. Other references, mostly available electronically, will be given in lectures and the list will be posted on SPIDER.

“The Analysis of Body Fluids” by Nigel Watson, in “Crime Scene to Court : The Essentials of Forensic Science”, second edition, editor P.C. White, The Royal Society of Chemistry, 2004

“Forensic DNA Typing: Biology, Technology and Genetics of STR Markers” by John M Butler, Elsevier, 2005

“Introduction to Statistics for Forensic Scientists” by David Lucy, Wiley, 2005

CH 524 FIRES AND EXPLOSIVES (Dr MJ Baker) SHE Level 5 ECTS Credits 2.5

Aims:

To explain the role of the forensic scientist in the investigation of scenes of fires and explosions. The course will also provide information on the chemical analysis of fire debris, post blast residue and explosives.

Learning Outcomes: At the end of the course the student should:

• Be able to give an account of the process of combustion, fire development, flashover and similar phenomena • Have a clear understanding of the chemical techniques and methods for the analysis of fire debris and explosive residue • Understand the process of fire scene investigation and issues arrising from such investigations regarding contamination • Have a clear understanding of the different nature of explosions and the chemical analysis of explosives including issues relating to contamination.

Topics 1 Introduction to fire scene investigation 2 Different ignition sources, combustion, heat transfer mechanisms 3 Introduction to fire dynamics, fire growth and flashover, heat flux and heat release rates, thermal inertia 4 Response of materials in fire scenes, introduction to electricity 5 Fire scene investigation including case studies 6 Sampling and analysis of fire debris 7 Interpretation of the results of fire debris analysis 8 Investigation of explosions and improvised explosive devices 9 Chemistry of explosive materials 1 10 Chemistry of explosive materials 2 11 Improvised explosive devices 12 Chemical analysis of explosives

CH560 FORENSIC SCIENCE: PRINCIPLES AND PRACTICE PARTS 1 AND 2 (Professor JG Fraser, Dr L Dennany, Dr P Haddrill, Ms L Shaw) SHE Level 5 ECTS Credits 5

Aims: • To provide an understanding of forensic strategies, the investigative process and procedure and crime scene management • To provide an understanding of court report writing and giving expert evidence • To provide an understanding of the context in which statistical tests and probabilistic reasoning are used in the evaluation of scientific evidence • To provide an understanding of the court and legal process including the process pertaining to expert witnesses

Learning Outcomes:

Upon completion of the course the students • will gain an understanding of the full crime scene to court process • will gain and understanding into the basis of forensic and investigative strategy • will understand the different statistical methodologies used in a forensic science context • will gain an understanding of the use of Bayes theorem for trace evidence and the evaluation of DNA evidence • will gain an understanding of the use of quality assurance methods in forensic science

Topics – PART 1

1. Purpose of court proceedings and how courts operate 2. Investigative process 3. Crime scene management 4. Forensic strategies and case management 5. Law, process and procedure 6. Expert witness law

Topics – PART 2 1. Evaluation of evidence – concepts and theory 2. Bayes theorem, statistics, databases and intelligence linkage tools 3. Quality assurance and forensic science 4. Evaluation of trace and chemical evidence 5. Evaluation of DNA and other biological evidence 6. Report writing and presentation of evidence in court

CH 579 ATOMIC NUCLEAR SPECTROSCOPY (Dr CM Davidson) SHE Level 5 ECTS Credits 2.5

Aims • to establish detailed knowledge of the principles and operation of various atomic spectrometry techniques • to review principles and types of radioactive decay, and the interaction of ionising radiation with matter. • to establish detailed knowledge of the principles and operation of various radiometric techniques.

Learning Outcomes

At the end of the course the student should be able to: • describe the processes of atomic absorption, atomic emission and atomic fluorescence • describe the instrumentation required for atomic absorption, atomic emission and elemental mass spectrometry and understand the importance of each component • outline the chemical processes involved in atom formation in atomic spectrometry, some key interference effects, and means by which these can be overcome • explain excitation and ionisation processed in the inductively coupled plasma • suggest a suitable atomic spectrometry technique for a specific type of analysis • describe types of radioactive decay (including specific examples) and write balanced decay equations, • predict the likely decay mode of a radionuclide, based on its atomic number and mass number, • discuss ways in which each type of radiation interacts with matter, • describe the principles and operation of various types of instrumentation for measuring nuclear radiation, • suggest a suitable detector for different types of nuclear radiation, • carry out calculations relating to radionuclide mass, activity, and count rate

Topics

Atomic spectrometry 1. Introduction. Atomic absorption, atomic emission and atomic fluorescence (processes and outline instrument systems). General procedure for analysis. 2. Flame atomic absorption spectrometry: instrument system; atomisation processes; optimisation; interference; application(s). 3. Electrothermal atomic absorption spectrometry: instrument system; atomisation processes; optimisation; interference; application(s). 4. Atomic emission spectrometry: Importance of temperature: thermal equilibrium and local thermal equilibrium. Excitation processes. 5. Inductively-coupled plasma atomic emission spectrometry: instrument system; atomisation processes; optimisation; interference; application(s). 6. Inductively-coupled plasma mass spectrometry: instrument system; atomisation processes; optimisation; interference; application(s).

Nuclear spectroscopy 1&2. Basic radioactivity: kinetics of radioactive decay; decay processes (α, β, γ). The interaction of radiation with matter. Typical α, β and γ spectra. 3. Overview of radioanalytical instrumentation. Gas-filled detectors: principle of operation; ionisation chamber, proportional counter and Geiger-Muller counter. 4. Semiconductor-based detectors: principle of operation; high purity germanium detector; silicon surface- barrier detector. Scintillation detectors: principle of operation; liquid scintillation counting; Cherenkov counting; solid scintillation counting with the Nal(TI) detector. 5. Background radiation: sources and methods by which it may be overcome (background subtraction, shielding, coincidence and anti-coincidence counting). Sample preparation: example procedures for α, β and γ-emitting radionuclides. Summary of detectors and types of radiation detected. 6. Selected applications: the civil UK nuclear industry; radiocarbon dating.

CH 580 MULTIVARIATE ANALYSIS (Dr A Nordon) SHE Level 5 ECTS Credits 2.5 Aims - to determine the covariance and correlation in data sets. - to introduce principal component analysis (PCA) for the examination of correlation between analytes and samples in complex data sets. - to examine the results of PCA. - to introduce the concept of multivariate curve resolution. - to introduce the concept of multivariate regression. - to provide an overview of the main features, advantages and limitations of different multivariate regression methods. - to determine main effects and interactions in Design of Experiments using multivariate regression. - to introduce the concepts of classification and cluster analysis of data.

Learning Outcomes At the end of the course the student should: - be able to perform calculations on data sets to statistically determine covariance and correlation coefficients. - understand the need for multivariate analysis techniques for the examination of complex data sets. - understand the basic principles behind PCA, and be able to deduce significant correlations from the loading and scores plots generated by PCA. - understand the basic principles behind multivariate curve resolution and its relationship to PCA. - understand the basic principles behind multiple linear regression methods, principal component regression and partial least squares regression. - be able to identify which multivariate regression techniques are best suited to examine complex data sets arising from chemical experiments. - understand how multivariate regression can be used to determine the coefficients relating to main effects and interactions in Design of Experiments. - understand the basic principles behind classification and cluster analysis methods.

Topics 1 Determination of covariance in data sets; use of the product-moment correlation coefficient. The use of t-tests to assess the significance of correlation coefficient values. 2-3 Principal Component Analysis (PCA). Decomposition of chemical data sets; determination of scores and loadings matrices; geometrical interpretation of PCA; interpretation of scores, loading and eigenvalue data plots. 4-5 PCA of spectral data. Use of multivariate curve resolution (MCR) for analysis of spectral data. Comparison of PCA and MCR. 6-9 Review of univariate calibration. Introduction to multivariate regression: multiple linear regression methods (classical least squares (CLS) and inverse least squares (ILS)); principal component regression (PCR); partial least squares (PLS). Determination of regression coefficients and prediction of concentration in unknown samples using spectral data. Comparison of multivariate regression methods: key features, advantages and disadvantages. 10 Review of Design of Experiments. Use of multivariate regression for determination of coefficients relating to main effects and interactions. 11-12 Introduction to classification and cluster analysis of multivariate data. Comparison of methods.