Part II Chemistry: A Guide to the Course, Exams of Chemistry

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Department of Chemistry Part II Chemistry: A Guide to the Course Academic Year 2018/2019 Contents 1 Introduction 2 2 Introductory talk and welcome party 2 3 Careers for chemists 2 4 Outline of the course 2 5 Lecture Course Synopses 3 6 Continuously assessed work 19 6.1 Requirements 19 6.2 Special arrangements for those taking course A6 20 6.3 Arrangements for laboratory work 20 6.4 Techniques in modern synthetic chemistry 20 6.5 Joint Physical & Theoretical chemistry course 21 6.6 Chemical Informatics (Michaelmas Term) 21 6.7 Language option (Michaelmas and Lent Terms) 22 6.8 Programming option 23 6.9 Mathematical methods (Lent Term) 23 6.10 Assessment of practical work 23 7 Plagiarism 23 8 Examinations 24 8.1 Format of the papers 25 8.2 Timetable 26 8.3 Past papers 26 8.4 Pass marks 26 8.5 Disclosure of examination marks 26 9 Carrying forward marks 26 10 Admission to Part III Chemistry for the academic year 2019/20 27 11 Part II Physical Sciences: Half Subject Chemistry 27 12 Chemistry teaching website 28 13 Chemistry Consultative Committee 28 14 Library, photocopying and computing 28 15 Further details of the Department 29 16 Titles of lecture courses 31 Timetable 31 1 Dr Robert Less(4 lectures) and Dr Daniel Beauregard (3 lectures) The second half of this course examines the heavier transition metals and f-block elements, focusing on the availability (or otherwise) of valence d and f orbitals in bonding. A huge body of experimental data supports the more extensive participation of the d orbitals in the bonding of the second and third row transition metals. The more expanded nature of the 4d and 5d orbitals of the second and third row transition metals leads to significantly stronger covalency in bonding which leads to greater prevalence for metal–metal as well as metal–ligand multiple bonding for the heavier elements. These aspects will be investigated from a primarily structural view point, reinforced with bonding and thermodynamics arguments. The f-block elements comprise almost a quarter of the periodic table and we will examine their interesting properties and widespread applications. A comparison of the chemistry of the lanthanoids and actinoids reveals contrasting behaviour which is attributed to the differing extent of f-orbital availability. The effect on bonding and structures is discussed: predominantly ionic bonding in lanthanoids and signicant covalency in actinoid compounds. A good knowledge of IB coordination chemistry is desirable. Topics Metal–metal multiple bonding in the d block. Metal–ligand multiple bonding in d block chemistry. f-block atomic orbitals, and bonding: metallic, ionic and covalent. Recommended books N. N. Greenwood and A. Earnshaw, Chemistry of the Elements, Butterworth-Heinemann Ltd, 2nd Edn. [QD466.G74] F. A. Cotton and G. Wilkinson, Advanced Inorganic Chemistry, Wiley 5th Edition, 1988. [QD151.C68] J. E. Huheey, Inorganic Chemistry, Longman, 4th Edn. [QD157.H84] N. C. Norman, Periodicity in the s– and p–block Elements, Oxford Primer, 2nd Edn. [QD466.N67] N. Kaltsoyannis and P. Scott The f elements, OUP, 1999. [QD172.R2.K35] S. A. Cotton and F. A. Hart, The Heavy Transition Metals, Macmillan, 1975. [QD172.T6.C68] S. F. A. Kettle, Physical Inorganic Chemistry, Spectrum Books, 1996. [QD475.K48] Inorganic Chemistry, Housecroft and Sharpe , 4th edn., 2012. [QD151.H68] Reference only. Inorganic Chemistry, Shriver and Atkins, 4th edn. 2006. [QD151.S57] Reference only. Periodicity and the s- and p-block Elements - (OUP), N. Norman, 1997. [QD466.N6] Reference only. A2: The Foundations of organic synthesis Dr Bill Nolan This course will apply the basic organic chemistry courses, Key Organic Reactions and Shape and Reactivity taught in IB Chemistry B to organic synthesis. You will see how a molecule can be logically dissected into simple building blocks by working backwards (retrosynthetic analysis) and how using these tools you will be able to devise synthetic strategies towards new molecules. Topics Retrosynthetic Analysis and the Language of Synthesis: Target Molecules. Disconnections. Synthetic equivalents. Criteria for Good Synthetic Planning C–X Disconnections: Synthesis of halides, ethers, sulphides and amines (considered as one-group –X disconnections). Two-group disconnections illustrated by the synthesis of 1,1-, 2,2- and 1,3-difunctionalised compounds. C–C Disconnections and Synthesis using the Carbonyl Group: Carbonyl group as an a1 (acceptor) reagent. Alkene synthesis and the Wittig reaction. Carbonyl group as a d2 (donor) reagent. Enolate alkylations. The aldol condensation. Synthetic control in carbonyl condensations. α,β-unsaturated carbonyl compounds as a3 (acceptor) reagents. Synthesis of 1,5-dicarbonyl compounds. Construction of 1,4-difunctionalised compounds. Construction of 1,4-difunctionalised compounds using synthons of ‘unnatural’ polarity. 4 More Tools of the Trade: Synthesis of More Complex Systems. Control of Mixed Functionality. Use of Latent Functionality Concepts and Methods for Ring Synthesis: Heterocyclic. Carbocyclic Recommended books Warren, S., Organic Synthesis – The Disconnection Approach, Wiley 1982. [QD262.W37] Clayden J., Greeves N., Warren S. and Wothers P. Organic Chemistry, OUP, 2001. [QD251.074] Clayden J., Greeves N. and Warren S. Organic Chemistry, 2nd Edn, OUP, 2012. (either edition is fine) [QD251.074] A3: High-resolution molecular spectroscopy Dr James Keeler This course will be concerned with the high-resolution spectra of small molecules, mostly in the gas phase. We will look at rotational, vibrational and electronic spectroscopy (including the Raman effect), and the kinds of detailed structural information that can be obtained from each kind of spectrum. The course draws extensively on material previously covered in Part IB Chemistry A, showing how the concepts introduced there can be used and extended to more complex cases. Topics Electromagnetic radiation and its interaction with molecules. Transition moments and Einstein coefficients. Linewidths. Lasers. Instrumentation. Dispersive spectrometers: diffraction gratings, sources and detectors. Fourier transform instruments: advantages. Spectroscopy with lasers. Rotational spectroscopy. Classification of molecules and the resulting spectra. Intensities. Centrifugal distortion. Electric field effects (Stark effect). Vibrational spectroscopy. Classification of normal modes and vibrational wavefunctions according to symmetry. Selection rules. Overtones and combination lines. Rotational fine structure: parallel and perpendicular bands. Raman spectroscopy. Origin of the Raman effect. Practicalities. Rotational and vibrational Raman spectroscopy of linear molecules and symmetric tops. Rule of mutual exclusion. Molecular identification using IR and Raman spectra. Electronic spectroscopy. Diatomic molecules. Electronic structure and term symbols. Selection rules and the Franc–Condon principle. Vibrational and rotational fine structure. Electronic spectroscopy of larger molecules: Jablonski diagram. Fluorescence and phosphorescence. Applications. Recommended books J M Hollas, Modern Spectroscopy, 4th edit (Wiley, 2004). [QC451.H65] C N Banwell and E M McCash, Fundamentals of Molecular Spectroscopy, 4th edit, (McGraw–Hill, 1994).[QD96.M65.B36] the following texts are for reference. D A McQuarrie and J D Simon, Physical Chemistry, a Molecular Approach, (University Science Books, 1997). [QD453.M37] J M Hollas, High Resolution Spectroscopy, 2nd edit, (Wiley, 1998) [QC454.H618.H65] P F Bernath, Spectra of Atoms and Molecules, (Oxford,1995). [QC454.A8.B47] P W Atkins and R S Friedman, Molecular Quantum Mechanics, 3rd. edit, (Oxford, 1997). [QD462.A85] 5 A4: Theoretical techniques Dr Alex Thom A central goal of theoretical chemistry is the prediction and rationalization of molecular properties and reactivity. Much qualitative insight can be obtained from molecular orbital theory, which you have already encountered in the Part IB Symmetry and Bonding lectures. In this course we expand on this topic introducing some theoretical techniques and ideas, such as perturbation theory, applied to MO calculations, which enable one to extract chemical insight. For more quantitative understanding electronelectron repulsion must be taken into account and we therefore also continue the more rigorous treatment of the Part IB Quantum Mechanics course with a brief introduction of self consistent field (SCF) theory and techniques used in practical calculations of chemical systems as well as empirical techniques for larger systems. Topics Recap of Hückel theory: symmetry; linear and ring systems; population and bond-order analysis; alternant hydrocarbons; perturbation theory and heteroconjugated systems. Many-electron wavefunctions: Slater determinants; Hartree-Fock theory of two electron-systems; electron correlation and molecular dissociation; density functional theory. Empirical descriptions: intermolecular forces; molecular vibrations. Chemical Reactivity: state and orbital correlation diagrams; the Woodward–Hoffman rules. Recommended books Atkins, P.W. and Friedman, R.S., Molecular Quantum Mechanics, 3rd edit., OUP, 1997 (other editions are fine) [QD462.A85] Cotton, F.A., Chemical Applications of Group Theory, Wiley, 1990. [QD461.C68] Leach, A. R., Molecular Modelling: Principles and Applications, Prentice Hall, 2001 (Longmans edition of 1996 is acceptable). [QD480.C43] Stone, A. J., The Theory of Intermolecular Forces, OUP. [QD461.S76] A6: Concepts in physical chemistry Dr Volker Deringer and Dr Chris Truscott This course is aimed at giving you a more detailed understanding of chemical bonding than was possible in the Part IA course. This will require us to introduce some quantum mechanics, which we will do by taking an approach which is always firmly rooted in your chemical understanding and avoids excessive formality or mathematical detail. We will develop the key principles of quantum mechanics using simple model systems, which involve relatively easy mathematics, and then go on to see how these ideas can be applied in atoms and molecules. The course concludes by showing how molecular symmetry, in the form of group theory, can be used to great effect in drawing up MO diagrams of simple molecules. Topics Revision of some basic mathematics. Functions and curve sketching (polynomials and trigonometric functions). The exponential function and logarithms. Differentiation: the chain rule; differentiation of a product. Integration. Introduction to complex numbers and the complex exponential. Introducing quantum mechanics. What is quantum mechanics and why is it useful? Wavefunctions, operators and energy levels. Exemplifying these ideas for two simple systems. Atomic orbitals. Review of AOs, their shapes and energies. Multi-electron atoms: the energies of singlets and triplets. Term symbols. Molecular orbitals. The two orbital problem. Homo- and hetero-nuclear diatomics. Extended arrangements of orbitals (π systems) in rings and chains. Computational aspects. Symmetry. The description of symmetry. Symmetry elements operations. Point groups. Character tables. Representations and reduction of representations. Constructing molecular orbital diagrams using symmetry as an aid. Transition metal complexes. 6 nucleophiles and electrophiles are explored in detail, as applied to ambident systems and nucleophilic substitution reactions. Stereoelectronic effects on fundamental organic reactions are thoroughly examined, as applied to the following: cyclisation (Baldwins rules and the Thorpe–Ingold effect), elimination, fragmentation, rearrangement (migration). Electronic strain and the topic of carbene chemistry are also introduced. An introduction to pericyclic reactions is given: cycloadditions and electrocyclic reactions are examined in detail in the context of the Woodward–Hoffman Rules Recommended books Kirby, A. J., Stereoelectronic Effects, OUP 1996. [QD481.K57] Moody, C. J. and Whitham, G. H., Reactive Intermediates, OUP, 1992. [QD476.M66] Eliel, E. L., Wilen S.H. and Mander, L.N., Stereochemistry of Organic Compounds, Wiley, 2nd Edn. 1994. [QD481.E45] Fleming, I., Pericyclic Reactions, OUP, 1999. [QD281.R5.F54] Fleming, I., Frontier Orbitals and Organic Chemical Reactions, Wiley, 1996. [QD461.F54] Fleming, I., Molecular Orbitals and Organic Chemical Reactions, Wiley, 2009. [QD461.F54] Clayden, J., Greeves, N., Warren, S. and Wothers, P., Organic Chemistry, OUP, 2001.[QD251.074] Williams, D. H. and Fleming, I. Spectroscopic methods in Organic Chemistry, McGraw-Hill, 5th Edn 1995. [QD272.S6.W55] Sanders, J, K, M. and Hunter, B. K., Modern NMR Spectroscopy, OUP, 2nd Edn., 1993 [QD96.N8.S26] B3: Chemical biology I – Biological catalysis Dr Finian Leeper (6 lectures) and Prof. David Spring (6 lectures) Enzymes are the main catalysts in the cell. They catalyse an amazing array of reactions, with high chemo-, regio- and stereoselectivity and at rate enhancements of up to 1015! Consequently, about half of the drugs currently being developed in the pharmaceutical industry are targeted at enzymes. It is therefore very important for us to understand how enzymes achieve catalysis, and how to use this information to design specific inhibitors. In IB some of the basic concepts behind enzymatic catalysis were introduced. Now we will build on that foundation and explain the diversity of chemical reactions that enzymes catalyse. The examples are chosen to illustrate how enzymes are studied and to introduce concepts that you will need for subsequent biological courses in Part III. Dr Finian Leeper Topics Enzyme basics – a reprise (kinetics, free energy profiles, inhibition, isotope effects); Elimination reactions (enolase, dehydroquinase, dehydroquinate synthase, ammonia lyases); Phosphoryl transfer (phosphatases, kinases, ribonuclease, tyrosyl t-RNA synthetase); Aldol and Claisen condensations (thioesters, citrate synthase, Schiff base, aldolase); One carbon transfer reactions (THF, SAM, chiral methyl groups, thymidylate synthase); Carboxylation and decarboxylation (acetoacetate decarboxylase, biotin, rubisco, vitamin K). Prof. David Spring Topics Enzymes and Coenzymes. Vitamins; Reduction and Oxidation, NAD(P)H and Flavins; Thiamine Pyrophosphate (TPP)-Dependent Enzymes; Enzymatic Transformations of Amino Acids, PLP; Glucose Metabolism, Enzymes Work Together. Recommended books T D H Bugg, An Introduction to Enzyme and Coenzyme Chemistry Blackwell Science 2004. [QP601.B84] 9 The following texts are for reference R B Silverman, Organic Chemistry of Enzyme-Catalysed Reactions Academic Press. [QP601.S55] R B Silverman, The Organic Chemistry of Drug Design and Drug Action Academic Press. [RS403.S58] A Fersht, Structure and Mechanism in Protein Science, Freeman. [QD431.25.F47] B4: Chemistry in the atmosphere Dr Alex Archibald This course will introduce key ideas about the chemistry of the atmosphere. It will discuss the chemical processes which control the abundances of ozone, and other trace constituents in the troposphere, and the rather different chemistry of the stratospheric ozone layer. We will use examples to reinforce ideas about reaction rates, gas and solution phase kinetics and spectroscopy. Topics The physical and chemical structure of the atmosphere: composition and temperature as a function of pressure. Sources, sinks and variability. The concept of lifetimes and steady state. The role of ozone in the atmosphere. Chemistry of the stratospheric ozone layer. The Chapman reactions. Catalytic cycles for ozone destruction and the idea of ‘families’, including NOx, HOX, ClOx. Chemistry of the troposphere. Local air quality. Oxidizing and reducing smogs, photochemical oxidants. The role of nitrogen oxides and volatile organics. The global troposphere. Production and destruction of ozone. The role of OH. Sulphur compounds and acid rain Reactions of atmospheric interest. Some important gas phase atmospheric reactions will be considered in detail. Heterogeneous reactions of important gas phase compounds on atmospherically relevant aerosol particles surfaces will discussed. Sources, formation processes and chemical composition of tropospheric aerosol particles. Measurements of atmospheric composition and their applications. Remote sensing. Rovibrational spectroscopy. Ultraviolet spectroscopy. Laser studies of the atmosphere. Chemical methods: chemiluminescence, laser induced fluorescence. Electrochemical methods. Chromatographic techniques. Online and offline aerosol sampling and characterization techniques. Recommended books Chemistry of atmospheres, Wayne, R P, OUP [QC879.6.W39] Further reading/reference: Atmospheric change – an earth system perspective, Graedel, T and Crutzen, P Freeman and Co, NY [QC981.8.G73] The physics of atmospheres, Houghton, J T, OUP [QC880.H68] Chemistry of the upper and lower atmospheres, Finlayson-Pitts and Pitts, Academic Press [QC879.6.F56] Aeronomy of the middle atmosphere, Solomon and Brasseur, Reidel [QC881.2.M53.B73] Reaction kinetics, Pilling and Seakins,OUP [QD502.P55] B5: Biomaterials Dr Silvia Vignolini (6 lectures) By designing and controlling the interaction between elementary building blocks, nature is able to achieve multiple functionalities with great performances using only biomaterials. In this course, the structure-function relationship of natural polymers and their assembly into complex hierarchical architecture will be discussed, with a special focus on polysaccharides. Such biopolymers are, in fact, particularly important as sustainable source for the next-generation materials. Several examples of how the properties of polysaccharides at molecular scale directly affect their macroscopic behavior will be discussed in terms of mechanical and optical properties. 10 The course will specifically cover the following topics: 1–2 Molecular Chirality; Examples of mono-saccharides and their nomenclature; Relevant examples of Disaccharides and Polysaccharides. 3–4 Introduction to mechanical properties of materials. Cellulose as a skeletal molecule: properties, biosynthesis and function in nature. 5–6 Other relevant polysaccharides (hemicelluloses and chitin) properties and function in nature. Recommended books Basic Solid State Chemistry, A R West, John Wiley and Sons Ltd. (2nd Edition) [QD478.W47] Molecular Crystals, J D Wright, Cambridge University Press. (1st or 2nd Edition). [QD291.W75] Reactions and Characterisation of Solids, S E Dann, RSC, Tutorial Chemistry Texts. [QD478.D36] Structural Biomaterials, Julian Vincent, Princeton University Press, 1990. [QP801.B69.V56] Organic Molecular Solids: Properties and Applications, Edited by W Jones, CRC Press.[TA418.9.C7.074] Core Concepts in Supramolecular Chemistry and Nanochemistry, J. W. Steed, D. R. Turner & K. J. Wallace. Wiley, 2007. [QD878.S74] B6: Statistical mechanics Dr Aleks Reinhardt In the Part IB course ‘Molecular Energy Levels and Thermodynamics’, we saw how the thermodynamic properties of a macroscopic sample of matter can be expressed in terms of the energy levels of individual molecules. However, while we have dealt with the internal degrees of freedom, such as rotations and vibrations of molecules, we have not so far considered any interactions between molecules. In this course, we investigate how such interactions can be treated. Except in a very limited set of circumstances, approximations must be introduced to allow explicit calculations. One of the generic approximations we will study is mean-field theory, which provides a reasonable description of many systems and phenomena, such as phase transitions, magnetism and electrical double layers around membranes. This course will provide an introduction to ensemble theory, classical statistical mechanics, phase equilibria, mean-field methods and the basic theory of transport phenomena. All concepts will be illustrated by applications to physical chemistry and condensed matter science. This course is very useful preparation for a number of the theoretical courses offered in Part III. Topics Introduction: The ergodic hypothesis. Boltzmann entropy. Boltzmann distribution. Microcanonical, canonical, grand canonical and isothermal isobaric ensembles. Fluctuations. Quantum and classical statistical mechanics. Thermodynamic equivalence of ensembles. Pressure of interacting particles. Applications of elementary concepts: Ideal gas in various ensembles. Lattice paramagnet. Langmuir adsorption. Entropy of mixing. Maxwell–Boltzmann distribution. Equilibrium: Stability criteria. Maxwell constructions. Widom insertion. Second virial coefficients. Landau theory of phase transitions. Thermodynamic perturbation theory: Artificial thermodynamic integration. Gibbs–Bogoliubov inequality. Mean-field theory. Van der Waals equation of state. Ising model. Regular solutions. Flory–Huggins model. Transport : Brownian motion. Fick’s laws. Diffusion coefficient from microscopic quantities. Auto-correlation functions. Green–Kubo relations. Langevin equation. Stokes–Einstein and Einstein relations. Polymers: Freely-jointed chain model. Entropic springs. Recommended books 11 C3: NMR Dr Daniel Beauregard (6 lectures) Multinuclear NMR spectroscopy will be investigated, particularly for the characterisation of main group compounds and diamagnetic transition metal complexes. It is likely that a combination of supervisions and classes will be offered for this course. Topics NMR using nuclei other than 1H and 13C for inorganic structure determination. Pulse sequences. Structural information from relaxation rate constants. Chemical shifts: diamagnetic and paramagnetic shielding. Scalar coupling magnitudes for structure determination. Solid-state and two-dimensional NMR spectroscopy techniques for inorganic chemistry. Recommended books NMR Spectroscopy in Inorganic Chemistry J.A. Iggo, Oxford University Press, 2000. [QD96.N8.I34] C4: Chemical biology II – Proteins: structure, stability and folding Prof. Sophie Jackson This course will start with a detailed review of protein structure - covering all aspects from primary through to quaternary structure. Large macromolecular assemblies will be described in addition to ‘alternative’ structures such as amyloid fibres. The thermodynamic basis for the stability of the native structure of proteins will be illustrated and methods for studying the stability of proteins described. From this, the factors that contribute to protein stability and how they can be used to rationally increase protein stability will be presented. Case studies will be used to illustrate strategies to optimise the stability of proteins, particularly therapeutic proteins, as well as the consequences of protein structure instability. In the second part of the course, the mechanisms by which unstructured polypeptide chains spontaneously fold into their unique three-dimensional structures will be described alongside experimental and computational approaches for studying this complex reaction. In particular, the use of protein engineering techniques and φ-value analysis to determine the structure in partially structured intermediates and transition states will be presented. In addition, the factors influencing the aggregation of proteins into amorphous and highly structured (amyloid) species will be described along with the kinetics of this important process. Recommended books A. R. Fersht, Structure and Mechanism in Protein Science, Freeman. [QD431.25.F47] T. Creighton, Proteins: Structures and Molecular Properties, Freeman. [QP551.C74] S. J. Lippard and J. M. Berg, Principles of Bioinorganic Chemistry, University Science Books. [QP531.L57] T. D. H. Bugg, An introduction to Enzyme and Coenzyme Chemistry, Blackwell Science. [QP601.B84] C5: Control in organic chemistry Prof. Jonathan Goodman (6 lectures) and Prof. David Spring (6 lectures) What controls organic reactions? Is it the reagent, the functional group, the catalyst? Questions like this will be explored in the course leading to an analysis of the different types of control - chemo- regio- and stereo- (not enantio-). Reactions you have met earlier this year will be 14 examined in a new light. Building on these more familiar examples, the mechanisms of new reactions will be introduced. This course will involve a fundamental analysis of organic chemistry and have a strong mechanistic content. This analysis is vital for a mature understanding of the whole of Part II organic chemistry. Recommended books Clayden, J., Greeves, N., Warren, S. and Wothers, P., Organic Chemistry, OUP 1st Edn, 2000 or 2nd Edn, 2012. [QD251.074] C6: Diffraction methods in chemistry Dr Andrew Bond This course provides the background knowledge for one of the most powerful characterisation techniques in chemistry, namely the determination of structures by single-crystal X-ray diffraction. It illustrates the basic principles of diffraction, the fundamental relationship between a crystal structure and its X-ray diffraction pattern, and the problems that arise from the measurement of X-ray intensities rather than X-ray amplitudes. No prior knowledge is assumed and the mathematical content should be accessible to any student. The main methods of structure determination are described, ranging from relatively simple methods that can be used for structures containing heavy atoms to more general methods that are commonly used for medium-sized molecules in organic and inorganic chemistry. More advanced methods used in the determination of protein structures are also considered. The aim is to provide the underlying principles behind the techniques, with selected worked examples. The course also includes a description of powder X-ray diffraction, highlighting its complementarity to the single-crystal technique. Recommended books Clegg, W., Crystal Structure Determination, Oxford Chemistry Primer. [QD945.C54] Dunitz, J.D., X-ray Analysis and the Structure of Inorganic Solids, Cornell Univ. Press. [QD945.D86] Giacovazzo, C., Fundamentals of Crystallography, O.U.P. [QD905.2.F86] Woolfson, M.M., X-ray Crystallography, C.U.P. [QD945.W66] Stout, G.H. and Jensen, L.H., X-ray Structure Determination – A Practical Guide, John Wiley & Sons. [QD495.S76] C7: Further quantum mechanics Dr Aleks Reinhardt (6 lectures) In this course, we will continue to explore some quantum mechanics relevant to chemistry. One of the main tools that we will use is perturbation theory. Although few systems can be solved exactly, we can study the effects of a small change to the hamiltonian of a system, and using perturbation theory we can predict, for example, how a molecule responds to an applied electric field or to the presence of a neighbouring molecule. In addition to studying both stationary and time-dependent perturbation theory, we will discuss time dependence in quantum mechanics more generally, and we will look at some of the tools you are familiar with, such as operator algebra, in more detail than you have done so far. Many of the theoretical techniques introduced will be illustrated with examples from physical chemistry, and we will in particular touch upon how lasers work, what dispersion and induction forces really are, how selection rules arise in spectroscopy, and how ultrafast femtochemistry can be used to investigate reaction mechanisms at the level of individual molecules. 15 Topics Non-degenerate perturbation theory. The Hellmann–Feynman theorem. Polarisability of the hydrogen atom. Rayleigh–Schrödinger perturbation theory. Linear operators and Dirac notation. Creation and annihilation operators. Anharmonic vibrations. The helium atom: shielding and penetration. Variation perturbation theory. Degenerate and nearly degenerate perturbation theory. The linear Stark effect. Fermi resonance for CO2 and the CO2–N2 laser. Time dependence in quantum mechanics. Non-stationary states and wave packets. The Ehrenfest theorem, symmetries and conservation laws. Variation of constants and time-dependent perturbation theory. Transition probabilities. Fermi’s golden rule. Dynamic polarisabilities. The closure approximation. Dispersion and induction forces. The London formula. Recommended books P. W. Atkins and R. S. Friedman, Molecular Quantum Mechanics, Oxford University Press, 2010. [QD462.A85] for reference: C. Cohen-Tannoudji, B. Diu and F. Laloë, Quantum Mechanics, Wiley, 1977. [QC174.12.C64] N. J. B. Green, Quantum Mechanics 2: The Toolkit, Oxford Chemistry Primer 65, Oxford University Press, 1998. [QC174.12.G74] C. S. Johnson Jr and L. G. Pedersen, Problems and Solutions in Quantum Chemistry and Physics, Dover, 1986. [QD462.J64] A. J. Stone, The Theory of Intermolecular Forces, Oxford University Press, 2013. [QD461.S76] C8: Electronic structure Prof. Michiel Sprik The aim of this course is to provide an introduction to Electronic Structure theory, and in particular to go beyond the non-interacting, one-electron picture which has been implicitly assumed in the molecular orbital theory used in nearly all earlier courses. The inclusion of electron–electron repulsion is crucial for the quantitative prediction of molecular properties. Self-consistent field theory provides a way to include e–e repulsion, albeit at an approximate level maintaining a one-electron picture. Two varieties of SCF theory exist: wavefunction-based methods based on Hartree–Fock and density-functional methods. The former provides the traditional starting point to more systematic theories of electron correlation, and is the bedrock of quantum chemistry. The latter have proven a highly popular and efficient alternative to Hartree–Fock, but unlike Hartree–Fock, still account for electron correlation in an approximate way. Both topics will be covered. Topics Basis functions, hydrogenic (Slater) orbitals, atomic orbitals, Gaussian functions, and contracted functions; the secular equations from which orbitals are determined; self-consistent field theory, and its numerical implementation; beyond Hartree–Fock, electron correlation; the energy functional, the importance of electron density, Hohenberg–Kohn theorems; The Kohn–Sham equations and orbitals; comparison with Hartree–Fock theory; the exchange correlation functional; electronic structure calculations as research tool. Recommended books A. Szabo and N. S. Ostlund, Modern Quantum Chemistry, 2000, Dover publications. [QD462.S93] W. Koch and M. C. Holthausen, A Chemist’s Guide to Density Functional Theory, 2001, Wiley-VCH. [QD472.6.D45.K63] 16 6 Continuously assessed work Due to refurbishment work in the Department, the Part II Organic and Inorganic laboratory will not be available for use until the fourth week of term (the week beginning Thursday 25th October). In order to accommodate this, it will be necessary to alter somewhat the pattern of activity and, to a small extent, the requirements of the course. The changes from our normal pattern are relatively modest and we do not believe that they will detract significantly from your experience of the course You are required to complete a portfolio of continuously assessed work taken from a range of options on offer. Naturally, conventional practical work features heavily as chemistry is above all an experimentally based subject, and to describe yourself as a chemist you need to know how to design and carry out experiments. Chemists also need to develop a wider range of skills, such as how to find out and sift information, how to write, how to use computers in different contexts and how to communicate your ideas. You will have to opportunity to develop these skills as part of your portfolio of continuously assessed work. It is important to realise that even if you are not intending to carry on as a professional chemist, these skills will nevertheless be very useful to you in your future career. 6.1 Requirements The continuously assessed work you need to complete is made up in the following way (this corresponds to the ‘six units of further work’ referred to in the University Ordinance which defines the structure of Part II Chemistry): • The two core practical courses which consist of Techniques in Modern Synthetic Chemistry (organic and inorganic) and the joint Physical & Theoretical Chemistry course. • The two exercises associated with the Chemical Informatics course. • Four additional credits. The four additional credits can be made up by any combination of the following • Extended experiments offered in the Lent Term; you will be able to gain up to four credits associated with each core course • The Language Option: four credits • The Programming Option: one or two credits • The Mathematical Methods course: three credits To produce a final mark for the continuously assessed work, each component will be weighted as follows: Component % of final mark Techniques in Modern Synthetic Chemistry (core practical course) 33.5 Physical & Theoretical Chemistry (core practical course) 33.5 Informatics 7.0 Each additional credit 6.5 19 Students may complete more additional credits than the minimum, in which case the four credits with the highest marks will be used. The one exception to this is that students embarking on the Language Option cannot substitute any additional credits for the four associated with this option. The marks for the continuously assessed component contribute 25% to the overall mark for Part II. 6.2 Special arrangements for those taking course A6 If you are taking the A6 course then you will be required to complete the Techniques in Modern Synthetic Chemistry course and the following experiments 1. Experiments A, B and D from the joint Physical & Theoretical Chemistry core course; you are not expected to do any of the theoretical exercises. 2. Exercises 1, 5 and 10 from the Part IB Chemistry A course. 3. The Physical experiment Kinetics of protein folding (this may only be available in the Lent Term). 6.3 Arrangements for laboratory work The class will be divided into two equal groups. Group 1 will follow the core course Techniques in Modern Synthetic Chemistry in weeks 4–8 of the Michaelmas term, and the Physical & Theoretical Chemistry core course in weeks 1–5 of the Lent Term. Group 2 will follow the Physical & Theoretical Chemistry core course in weeks 4–8 of the Michaelmas term, and the Techniques in Modern Synthetic Chemistry core course in weeks 1–5 of the Lent Term. The core courses will build on and extend the practical skills you acquired in the second year, and you will also do experiments which illustrate the ideas and concepts presented in last year’s and this year’s lecture courses. Due to restriction on the number of computers and apparatus available, the Physical & Theoretical Chemistry core course is timetabled rigidly. You must work on the days allocated to you when you register at the start of Term. As in Part IB, your practical write-ups will be assessed in the class by one of the Senior Demonstrators. Extended experiments Extended experiments (in all areas) will be available for both Groups in weeks 6–8 of the Lent Term. Apart from those taking the Language Option, all students must complete at least one extended experiment offered in Physical or Theoretical chemistry: other than that, there are no restrictions of the extended experiments. 6.4 Techniques in modern synthetic chemistry Location East end of the Organic & Inorganic Practical Laboratory which is on the ground floor of the Department on the Union Road side of the building. Please enter the laboratory by the doors which open onto the foyer outside the BMS Lecture Theatre. Time The laboratory is open weekdays, 11:00 to 18:00; you are free to complete your work during this time. Attendance There will be an Induction Day, in the Part II Laboratory, during which safety issues will be covered, the layout of the laboratory will be explained and some techniques 20 demonstrated. For Group 1 the Induction Day will commence at 11:15 on Thursday 25th October. For Group 2 the Induction Day will commence at 14:00 on Thursday 17th January. You must attend the Induction Day assigned to your group; you will be required to attend in the laboratory from the start of the induction session to the end of the day. Personnel The technician in change of the class is Dr Rafel Cabot Mesquida and he is assisted by Maria Cascone. The members of staff responsible are Dr Rob Less, Dr Deborah Longbottom and Dr Bill Nolan. 6.5 Joint Physical & Theoretical chemistry course Physical chemistry experiments Location Part IB/II Physical Chemistry Laboratory on the first floor, Lensfield Rd side of the building. Time The laboratory is open weekdays, 11:00 to 18:00; on your allotted day you are free to complete your work during this time. Rough books As last year, you must record any measurements, as you make them, in a rough book; you need to bring your rough book with you when you have an experiment marked off. Personnel the technician in change of the class is Chris Brackstone and he is assisted by John Suberu. The member of staff responsible is Dr Peter Wothers. Theoretical chemistry exercises Location Room G30 (MCS), by the lift on the Lensfield Rd side of the building. Time Weekdays, 14:00 to 17:00; on your allotted day you are free to complete your work during this time, but it is recommended that you attend at the start of the session to be briefed about the exercise. Personnel The member of staff responsible is Dr Andreas Bender (ab454@cam.ac.uk). 6.6 Chemical Informatics (Michaelmas Term) This part of the course consists of four lectures; you will be required to complete two assessed exercises. Further details will be given out in the first lecture. Lectures 1 & 2: Chemical information Prof. Jonathan Goodman How do you write a recipe for a reaction? The answer might be in the chemistry department library which contains reports of molecular experiments performed over more than a century, or in an on-line database. The lectures will describe how this huge quantity of information can be searched and analysed, using the main databases available to us (Web of Science, SciFinder, Reaxys (Beilstein), CSD, ChemSpider, National Chemistry Database Service etc.). The problems and challenges of finding and analysing chemical information will be discussed. 21 The general university statement on plagiarism, and further general advice on plagiarism and how to avoid it, is given on the University’s plagiarism and good academic practice website www.cam.ac.uk/plagiarism. Generally the Department follows the advice and policies set out by the University. This section gives further guidance as to how these policies apply to study in the Department of Chemistry. Supervision work and Tripos questions The majority of questions set as supervision work and in Tripos examinations take the form of problems to be solved. In presenting their solutions to these problems students are not expected to quote the source or authority of the facts, theories and concepts they use to formulate their solutions. Continuously assessed work (principally practical work) Here the rules against plagiarism are especially relevant as they prohibit copying and colluding. Basing a write-up on data or answers provided by another student is an example of plagiarism (or, more simply, cheating). The following rules apply to all continuously assessed work • Unless otherwise instructed, you must work alone. Where you are permitted to work in a group, the names of those you have worked with must be stated on your practical write-up. • The write-up must be entirely your own work. In particular, you may not use spreadsheets or templates prepared by others. • It is expressly forbidden to invent, falsify or modify data, spectra or observations, or to use data, spectra or samples obtained from other persons unless authorised to do so by a Senior Demonstrator. • Where data from other sources is quoted in a write-up, the source must be identified. The following summarizes succinctly the key point: The Golden Rule: The examiners must be in no doubt as to which parts of your work are your own original work, and which are the rightful property of someone else. 8 Examinations The basic rules are • Candidates must offer four papers in total. • Candidates must offer Paper 1 and either Paper 2A or Paper 2B, Paper 3 and Paper 4. Next come the rules about which out of Papers 2A & 2B you can do. • Candidates who have taken Part IB Chemistry A and Part IB Chemistry B must take Paper 2A. • Candidates who have taken only Part IB Chemistry B may take either Paper 2A or Paper 2B. The point of these is that they allow students who have only done Chemistry B to attempt all the core courses if they wish, or to take the alternative course (A6) especially designed for them. 24 8.1 Format of the papers Note that the format of all the Papers changed in 2017/18. Paper 1 is of duration 2 hours and 40 minutes and will consist of two sections. Section A will contain 4 compulsory 5 minute questions relating to course A1 and 4 compulsory 5 minute questions relating to course A2. Section B will contain 2 compulsory 30 minute questions relating to course A1 and 2 compulsory 30 minute questions relating to course A2. Section A carries 25% of the marks and Section B carries 75% of the marks. Within a section each question has equal weight. Paper 2A is of duration 2 hours and 40 minutes and will consist of two sections. Section A will contain 4 compulsory 5 minute questions relating to course A3 and 4 compulsory 5 minute questions relating to course A4. Section B will contain 2 compulsory 30 minute questions relating to course A3 and 2 compulsory 30 minute questions relating to course A4. Section A carries 25% of the marks and Section B carries 75% of the marks. Within a section each question has equal weight. Paper 2B is of duration 2 hours and 40 minutes and will consist of two sections. Section A will contain 8 compulsory 5 minute questions relating to course A6. Section B will contain 4 compulsory 30 minute questions relating to course A6. Section A carries 25% of the marks and Section B carries 75% of the marks. Within a section each question has equal weight. Paper 3 is of duration 3 hours and will contain two 45 minute questions relating to each 12 lecture B course and one 45 minute question relating to each 6 lecture B course; candidates should answer four questions, without restriction. Each question is of equal weight. Paper 4 is of duration 3 hours and will contain two 45 minute questions relating to each 12 lecture C course and one 45 minute question relating to each 6 lecture C course; candidates should answer four questions, without restriction. Each question is of equal weight. You will be given an extra 10 minutes of reading time for all of these papers. Each of the four papers sat by a given candidate is of equal weight and together they contribute 75% of the final mark. In all of the examinations you will be provided with a Data Book which contains a simple Periodic Table, values of physical constants, certain mathematical formulae and definitions and selected character tables. You will be provided with a copy of the Data Book when you register for the course (accessible on line at www.ch.cam.ac.uk/teaching/data-book). You may take (unassembled) molecular models into the examinations. Material from the Part IB course will not be examined explicitly in the Part II examinations. However, you should be aware that a sound understanding and firm grasp of the IB material is essential for success in the Part II papers. In addition to the written papers, all candidates must submit the specified amount of continuously assessed course work as described above. Example exam entries 1. If you have taken Chemistry A and B at Part IB you should be entered for Papers 1, 2A, 3 & 4. 2. If you have only taken Chemistry A but have nevertheless decided to tackle the four core courses A1–A4 you should be entered for the papers as in 1. 25 3. If you have only taken Chemistry B and followed the course A6, then you should be entered for Papers 1, 2B, 3, & 4. 4. All candidates must be entered for the ‘six units of further work’ – this is the continuously assessed part of the course. 8.2 Timetable Although the Examination timetable will not be announced formally until early in the Easter Term, our understanding is that the papers will all be sat in the week commencing Monday 3rd June. We also expect that oral examinations, if required, will be held in the late morning of Tuesday 19th June; the names of those required for these orals will be announced by 18:00 on Monday 18th June. You must be in Cambridge and available for an oral examination on the date specified. We expect that the results will be available in CamSIS on the afternoon of Wednesday 20th June. Please note that these dates are all provisional and subject to confirmation. 8.3 Past papers Past papers are available from the relevant section of Moodle (www.vle.cam.ac.uk), and suggested answers to questions more than five years old are also available. 8.4 Pass marks The marks obtained on the written papers are combined with marks obtained from the continuously assessed work; the intention is that 75% of the final mark is for the theory and 25% for the continuously assessed work. The Examiners may, however, at their discretion alter the weight given to different papers or different parts of the continuously assessed work. The Examiners may also scale the raw marks obtained in any component of the examination e.g. the continuously assessed part. Please note that to be awarded a pass in the whole examination candidates will need to achieve: (1) a pass mark (40%) in the combined total of the theory papers, and (2) a pass mark (40%) in the total from the continuously assessed work. The Senior Examiner for Part II Chemistry is Dr James Keeler. 8.5 Disclosure of examination marks The marks which are disclosed (via CamSIS) are those for each of the papers, a total mark for the continuously assessed component of the course, and the final overall total and class. Please note that the marks from the continuously assessed component may be scaled by the Examiners. In addition you will be notified separately of your question-by-question marks. 9 Carrying forward marks Exam regulations allow the Part III examiners to take into account a candidate’s performance in Part II from the previous year. In effect, this means that marks will be ‘carried forward’ from Part II to Part III. The practice is that the Part III examiners will draw up the class list by combining the Part II and Part III marks, with a weighting of 15% for the Part II marks. However, the final allocation of a class will not simply be done by a mechanical process. Rather, the Examiners will consider each candidate’s mark profile and will give particularly careful consideration to candidates who fall on 26 www-library.ch.cam.ac.uk/committee-library-and-scholarly-communication Photocopying, printing, scanning, and computing facilities The library has 20 PCs and 2 Macs which are hosted on the MCS (Managed Cluster Service) network and print jobs can be sent from these to a multifunctional device (MFD) situated in the small room next to the Library Office. The MFD offers colour printing, as well as photocopying and free scanning. Online payment for printing and photocopying on this machine is made through the common balance scheme, there is more information at www.ucs.cam.ac.uk/desktop-services/ds-print/paying-for-ds-print There is also a traditional photocopier by the lift on the second floor of the Lensfield Road side of the Department and photocopy cards for this machine can be purchased from the Library Office. Computers and MFDs which are also attached to the MCS network are available in room G30 (by the lift on the Lensfield Rd side of the building), and in the Part IB/II Physical Chemistry Laboratory. When practicals are being run, access to the computers in G30 and the Physical Lab. may be restricted. 15 Further details of the Department In order to access areas of the Department other than the lecture theatres you will need your University card so that you can pass the turnstiles and the appropriate internal doors. You should therefore make it a point to always bring your card with you when you come to the Department. By the time of the registration process for the practical classes we should have collected sufficient information to have already programmed your University card for the appropriate access. If you find that your access rights are different to others in your year group, or access suddenly stops, please contact Mifare Admin (mifareadmin@ch.cam.ac.uk). Please note that undergraduates will not be given access to research areas. If you need to meet supervisors and so on, you will need to arrange for them to meet you in a general access area. Do make sure you know who they are and how to contact them, so that Security can help you locate them if necessary. Your card will only give you access to the building from 08:00–20:00 on weekdays, and from 08:00–13:00 on Saturdays. Outside these times you are not permitted to be in the Department unless some specific arrangement has been made. If you remain in the Department after 20:00 you risk becoming trapped by the security doors and/or the turnstiles. Should this happen use one of the emergency red telephones and contact 36330 or Central Security on 101 to let them know where you are. If you would like access to the Departmental library outside normal working hours you will need to go and see Susan Begg to arrange this (her office is on the ground floor of the Centre for Molecular Informatics building, Room UG05, next to the Unilever Lecture Theatre). She will ask you to sign the following declaration before enabling your card. I understand that my security access is being increased to allow entry to the Department of Chemistry via the main entrance, to enable me to use the library after 20:00 Monday to Friday and during weekends. I hereby confirm that I will not contravene the rules laid down in the Department Safety Handbook, and will not undertake any work in any laboratory. I will sign in and out in the book at the front entrance when I am here after 18:00 weekdays or at anytime over the weekend. I am aware that I cannot be in any part of the building after midnight. I accept that the privilege will be withdrawn if I am found to have breached this agreement. 29 Cybercafé You are most welcome to use the Departmental tea room (Cybercafé) which is located on the top floor of the Centre for Molecular Informatics Building. Service is available from 09:30 to 15:45; you may also use the room outside these hours. Hot and cold drinks, as well as a selection of snack foods are available. At busy times, please make sure that you are not occupying too much space i.e. by spreading out all your books and papers. Part II students may also use the small common room located in the centre of the Organic and Inorganic Part II Laboratory at any time that the lab. is open. The room is set out with tables and food may be eaten there. Facilities are provided for making tea and coffee. 30 16 Part II Chemistry 2018/2019: Titles of lecture courses C od e H ou rs Title Lecturer(s) A courses A1 12 Inorganic I: Structure and bonding Wheatley (5), Less (4), Beauregard (3) A2 12 The foundations of organic synthesis Nolan A3 12 High resolution molecular spectroscopy Keeler A4 12 Theoretical techniques Thom A6 12 Concepts in physical chemistry Deringer, Truscott B courses B1 12 Inorganic II: Transition metal reactivity and organometallic catalysis Bampos (6), Wood (6) B2 12 Structure and reactivity Fleming (6), Nolan (6) B3 12 Chemical biology I: Biological catalysis Leeper (6), Spring (6) B4 12 Chemistry in the atmosphere Archibald B5 6 Biomaterials Vignolini (6) B6 12 Statistical mechanics Reinhardt B7 6 Symmetry Alavi (6) B8 12 Investigating organic mechanisms Wothers C courses Inorganic III, characterisation methods: C1 6 Electrochemistry Reisner (4), Zhang (2) C2 6 Electron paramagnetic resonance (EPR) and magnetism TBC (6) C3 6 NMR Beauregard (6) C4 12 Chemical biology II: Proteins: structure, stability, and folding Jackson (12) C5 12 Control in organic chemistry Goodman (6), Spring (6) C6 12 Diffraction methods in chemistry Bond C7 6 Further quantum mechanics Reinhardt (6) C8 12 Electronic structure Sprik C9 12 Chemical biology III: Nucleic acids Bernardes (4), Chin (4), Balasubramanian (4) C10 12 Surfaces and interfaces Clarke(4), Madden (4), Jenkins (4) C11 6 Polymers: synthesis, characterisation and application Scherman (3), Bernstein (3) Other CI 6 Chemical informatics Goodman (2), Glen (2) MM 12 Mathematical Methods Vendruscolo, Jack 31