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CH3202 Methods and Mechanisms


Duration: Michaelmas and Hilary Term

Contact hours: 36 hours

Assessment: By end of year examinations

Credits: 5 ECTS

Description: This module covers topics such as physical organic chemistry, organic reaction mechanisms, and amino acid and peptide synthesis. The module currently encompasses CH3025, CH3027, CH3028.


CH3025 Physical Organic Chemistry: General introduction. Brief introduction to potential energy surfaces. Thermodynamic formulation of activated complex theory. Linear free energy relationships. Hammett equation. Separation of polar and resonance effects in aromatic systems. Application of Hammett equation in hydrolysis, elimination reactions, etc. Cross-conjugation; definition of s+, s–. Steric effects; Taft equation. Proton-transfer reactions. Iodination of acetone as example of reaction where there is specific and general acid-base catalysis. Bronsted equation. Hammond hypothesis. Kinetic isotope effects. Simple theory - assuming zero point energy only in reactants. Zero point energy contribution in activated complex. Dependence of kH/kD on transition state structure; quantum mechanical tunnelling. Brief introduction to secondary isotope effects. Solvent effects (some years only).


CH3027 Organic Reaction Mechanisms: Acid and base catalysed ester and amide hydrolysis (AAC1, AAC2, BAC2, BAL2 mechanisms etc).Enzyme-catalysedesterhydrolysis. α-Elimination (carbenes and carbenoids). β-Elimination reactions (E1, E2, E1cb). Stereochemistry and orientation (Saytzev vs Hofmannrules) in E2 reactions.γ-Eliminationreactions. Cycloaddition reactions. The Diels-Alder reaction vs the Alder ene reaction. Endo vs exo specificity. Thermally allowed [4+2], [6+4] and [8+2] processes. Photochemical [2+2] cycloadditions. 1,3-Dipolar cycloaddition reactions. Intramolecular Diels-Alder reactions. The Woodward-Hoffman rules. Frontier orbitals, HOMO, LUMO, SMO, correlation diagrams, suprafacial/antarafacial, secondary effects. Thermal [2+2] cycloadditions involving ketenes and isocyanides. Electrocyclic reactions, retrosynthetic analysis of formation of 4, 5 and 6 memberedrings. SN1, SN2 and SN2’ mechanisms. Stereoelectronic effects. Kinetic expressions. Ion pairs and internal return. The common ion effect. Salt effects. The anchimeric effect. Neighbouring group participation in substitution processes. Methods for the generation of carbonium ions. Methods for the detection and visualisation of carbonium ions. Use of “Magic Acid” NMR solvents. Methods involving kinetic measurements. Solvolysis reactions. Solvolysis in the norbornane system. Classical and non-classical ions. Evidence for the existence of non-classical carbonium ions.


CH3028 Amino Acid and Peptide Syntheses: The objectives of this course are to introduce the physical properties and synthesis of simple amino acids with special emphasis on the DNA encoded a amino acids, and their incorporation into peptides. The lectures will cover areas such as the symmetric, asymmetric and enantiospecific synthesis of amino acids. The introduction of amino, carbonyl and side group protection (groups) and the synthesis of active esters. Peptide synthesis using peptide coupling reactions. The strategy and tactics of solution and solid phase peptide synthesis, and the purification and isolation of peptides using amino acid analysis and sequencing.


CH3301 Materials, Quanta and Change


Duration: Michaelmas and Hilary Term

Contact hours: 36 hours

Assessment: By end of year examinations

Credits: 5 ECTS

Description: This module covers the basics of macromolecular and interfacial chemistry, quantum chemistry, and covers more advanced aspects of chemical kinetics. It currently encompasses CH3031, CH3033, CH3034.


CH3031 Macromolecules and Interfacial Chemistry: Interfacial Chemistry: Liquid-gas and liquid-liquid interfaces Surface tension. Interfacial tension. Surface active molecules. Gibbs' adsorption isotherm. Spreading of liquids. Langmuir trough. Monomolecular layers. Micelles. Stepwise (Condensation) Polymerisation: Brief revision of SF Material. Types of polymers, degree of polymerisation and fractional conversion, kinetics. Molecular Weight distributions, weight average and number average and number average molecular weight. Control of polymerisation. Addition Polymerisation. Types of polymerisation. Free radical methods of initiation. Kinetics. Chain transfer. Termination. Methods of radical polymerisation. Anionic, cationic and Ziegler Natta methods. Co-polymerisation. Reactivity ratios. Polymer stereochemistry. Tacticity. Polymers in Solution. Configurational entropy and Huggins-Flory theory. Sizing methods. Measurement of Molecular Weight. Review of Senior Freshman material. Colligative properties, especially osmotic pressure. Viscosity of colloids and polymers. Mark-Houwink Equation. Random coil. Solid polymers. Crystalline and amorphous polymers. Glass transition temperature. Elastomers and plastics. Methods of determining Tg.


CH3033 Quantum Chemistry: Brief review of quantum theory; wave functions, Schrodinger equations, Uncertainty Principle. Solution of the Schrodinger equation for a particle confined to a circle. Angular momentum. Schrodinger equation for chemical systems. Real and complex hydrogenic wave functions. Atomic orbitals. Variation Principle. Approximate AO wave function for He atom. Slater atomic orbital wave functions. The secular determinant and the interaction of states. Molecular orbitals. Bonding and antibonding molecular orbitals. Huckel molecular orbital theory; application to butadiene. Pi-electron charge and bond order. Incorporation of symmetries into Huckel theory; application to benzene and larger aromatic hydrocarbons. Transition moment integral; electric dipole transitions. Extended Huckel theory. Time-dependent wave functions. Quantum mechanical tunnelling. Inversion of ammonia.


CH3034 Chemical Kinetics: Introduction to potential energy surfaces. Concept of reaction coordinate and transition state. The Eyring transition state theory: thermodynamic approach and the statistical mechanical approach. Utilisation of transition state theory to calculate a bimolecular rate constant from first principles. The kinetics of solution phase reactions. Activation and diffusion control. The kinetics of ionic reactions in solution. The theory of unimolecular reactions.


CH3302 Equilibrium and Interfaces


Duration: Michaelmas and Hilary Term

Contact hours: 36 hours

Assessment: By end of year examinations

Credits: 5 ECTS

Description: This module deals with thermodynamic and interfacial electrochemistry, chemical thermodynamics, chemisorption and catalysis. It currently encompasses, CH3035, CH3036, CH3038.


CH3035 Electrochemistry: Introduction to electrochemical systems. Review of oxidation and reduction. Electrochemical reactions. Galvanic cells, electrolytic cells and corrosion as prototype electrochemical systems. Thermodynamics of Galvanic cells. Electrochemical potentials. Potentiometric measurements. Standard electrode potentials. Estimation of zero current cell potentials at equilibrium. The Nernst equation. Estimation of thermodynamic quantities such as DG, DH and DS for cell reactions. Transport processes in electrochemistry. Diffusion and migration. Steady state and transient diffusion problems with specific examples of interest in electrochemistry. Introduction to electrochemical kinetics. Derivation of the Butler-Volmer equation and examination of its various limiting forms. Examination of the interplay between diffusional mass transport and interfacial electron transfer kinetics leading to the concept of activation and diffusion control.


CH3036 Chemical Thermodynamics: Assembly of localised systems (solid). Microstates and distributions. Most probable distribution (Boltzmann). Partition function q. Thermodynamic functions U, S and F in terms of q. Assembly of non-localised systems (gas). Comparison of results for solids and gases. Molecular q expressions for translation, rotation, vibration and for electronic states. Explicit expressions for U, F, G, Cv, Cp and S (e.g., Sackur-Tetrode equation). Cv temperature dependence. Equilibrium constant K in terms of q's. Non-ideal gases, the definition, concept and evaluation of fugacity of a van der Walls' gas, the temperature and pressure coefficients of fugacity, mixtures of gases, the Lewis Randall rule. Liquid solutions, strict thermodynamic definition of activity coefficients, the Gibbs-Duhem-Migueles equation. Electrolytes, the mean ionic activity coefficient and the experimental determination of activity coefficients. Quantitative treatment of the Debye-Huckel theory, the calculation of activity coefficients and a review of the relevant experimental evidence, the extended theory, the Robinson-Stokes equation, ion association, the Debye-Falhenhagen Effect and the Wien Effects. Conduction processes in molten salts and a review of the theories used to describe the process.


CH3038 Chemisorption and Catalysis: Chemical and physical adsorption; preparation, maintenance, characterization of clean metal surfaces. Surface reactivity. Kinetics of adsorption and desorption. Langmuir and other isotherms Extensions to simple Langmuir model. Experimental isotherms and BET. ACT and heterogeneous catalysis. Catalytic reactions; NH3 decomposition; C2H4 + H2 etc; Langmuir-Hinshelwood and Eley-Rideal mechanisms. Volcano curves. Heats of adsoprtion - empirical approach to ionic & covalent adsorption; work function. Adsorption of NO, CO, O2 on d-block metals.


CH3401 Aspects of Environmental Chemistry


Duration: Michaelmas and Hilary Term

Contact hours: 36 hours

Assessment: By end of year examinations

Credits: 5 ECTS

Description: This module addresses selected basic aspects of environmental chemistry and includes atmospheric chemistry, analytical chemistry techniques and environmental inorganic chemistry. It encompasses CH3051, CH3052 and CH3053.


CH3051 Chemistry of the Atmosphere: Chemistry of stratosphere. Ozone chemistry - Chapman model. Spectroscopy of O2 and O3. Quantum yields of photochemical reactions. Determination of ozone concentration. Effect of pollutants. HOX, CIOX and NOX cycle. Role of aerosols. Tropospheric pollution. Photochemical smog formation. Role of NOx, O3, hydrocarbons, PAN, OH and NO3.Methods of monitoring pollutants. Kinetic methods for following fast reactions. Reactions involving atmospheric species. Atmospheric Microparticles. Size distribution. Methods of determining particle size and amount - filtering, light scattering.


CH3052 Analytical Methods for the Environment: Overview of the analytical method. Survey of analytical techniques. Calibration curves. Sources and types of error in analytical measurements. Simple statistical techniques and ideas applied to data analysis in analytical chemistry. Gaussian distribution. Mean, standard deviation. F test , t test , Q test. Application of statistical tests to analytical data. Least squares analysis of experimental data. Electrochemical sensors. Potentiometric measurements. The Nernst equation. Membrane potentials. pH electrodes. Ion selective electrodes. Amperometric detection. Review of interfacial electron transfer and diffusion to electrode surfaces. Batch amperometry. Electrochemical cell configurations for analysis in stagnant and flowing media. Cyclic voltammetry. Polarography .


CH3053 Inorganic Chemistry of the Environment: (Aim: to establish the principles determining the natural background of elements, particularly in the aquatic environment. References are made to the "Brent Spar" episode, and to "black smokers".) Importance of interplay of physics and geology in determining element distribution. Cosmic evolution of the " reconstituted stardust": stellar burning, the abundance curve peaks at C, N, O, Si and Fe, supernovae. Formation of Earth, outline structure, difference from large planets. Solar spectrum, vibrational and rotational selection rules determining atmospheric absorption. Significance of "greenhouse effect" in determining liquid nature of most of terrestrial water, enhancement by anthropogenic CO2 and methane. Distribution diagrams for solar system, whole earth, crust and sea. Physical and chemical reasons for the differences. Redox competition for O, native elements and those found as sulfides. Effect of "pollution by life (O2)" on Fe and other elements. Effects on water solubility. Ionic charge/radius and ion hydration/ hydroxide / oxyanion chemistry. Metallic element solubilities in presence of carbonate, phosphate and sulfate. Interplay with oxidation state, esp. Fe and Mn, composition of sea water, major changes from crust. Al: effect of pH; P: interaction with Ca. Element distribution in human body, differences from sea. Possible reasons for the differences. Redox systems and biology involving C, N, S: methane, nitrifying/denitrifying bacteria , possibility of life in low oxygen potential, natural S deposits. Element cycling for P and S.


CH3402 Cross-Disciplinary Techniques


Duration: Michaelmas and Hilary Term

Contact hours: 36 hours

Assessment: By end of year examinations

Credits: 5 ECTS

Description: This module deals with both the fundamental principles and application of spectroscopic and other characterization techniques and includes material such as the fundamental basis of, structural characterization techniques in inorganic chemistry, organic spectroscopy, and molecular spectroscopy. It currently encompasses CH3015, CH3024, CH3032.


CH3015 Structural Methods in Inorganic Chemistry: A survey of the techniques employed by synthetic inorganic chemists to elucidate structure. Emphasis is given to a multi-spectroscopic approach. Fluxionality and time-scales. Infrared, Raman and Resonance Raman spectroscopy. Selection rules. Rule of mutual exclusion. Case studies into changes of ligand vibrations on coordination, CO, CN, modes of bonding. Isotopic substitution. IR vs. X-ray crystallography. NMR spectroscopy of less commonly encountered nuclei. 31P, 19F, 11B and 195Pt. Coupling between non-equivalent spin systems. Fluxionality. Derivation of multiplicity and intensity, satellites and abundance. Specific examples. Decoupling and isotopic substitution experiments. Magnetochemistry. Curie/Weiss law. Magnetically dilute and concentrated systems. Antiferro- and ferro- magnetism. Methods of measurement. Derivation of m. Paramagnetism. Zeeman effect. A and E ground levels. Spin-only formula and deviations from it. T ground levels. Orbital contributions. Temperature dependence of ground states.


CH3024 Organic Spectroscopy: Principles of spectroscopy. Mass spectroscopy. Instrumentation, fragmentation and spectra interpretation. Nuclear Magnetic Resonance (NMR). Introduction, basic theory (recap), magnetic fields and nuclear spin energy levels, the concept of resonance, continuous wave (CW) NMR spectroscopy Basic FT NMR theory. Concept of chemical shift, the d-scale, major factors influencing d: inductive electron withdrawal (-I), magnetic anisotropy of double bonds, diamagnetic ring current, resonance effects (+M, -M), solvents. 1H NMR: Chemical equivalence, homotopic, enantiotopic and diastereotopic protons, magnetic equivalence/non-equivalence and its effect on NMR spectra. 13C NMR spectroscopy – effect of carbon hybridisation on chemical shift, -I effects, +M and –M effects 13C-1H spin coupling, broadband decoupling, off resonance decoupling, the nuclear Overhauser effect (NOE) and its implications for 13C NMR sensitivity, relaxation of 13C nuclei as a function of the No. of attached protons, identification of quaternary 13C nuclei in broadband decoupled 13C spectra. The concept of polarisation transfer, DEPT 135 and DEPT 90 experiments – theory and application to structure elucidation. 1-D NOE experiments – principle and application. 2-Dimensional NMR spectroscopy – 1H-1H COSY, 1H-13C COSY (HETCOR), NOESY and INADEQUATE. Other useful NMR acronyms.

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