Module Information For Visiting and Erasmus Students
2014/15
School*
Module Code*
Chemistry
CH3103
ORGANOMETALLICS & COORDINATION CHEMISTRY
Module Name*
ECTS Weighting*
5
Semester/term Semester 1
taught*
Contact Hours*
33 Hours
Module Prof. Bob Baker, Prof. Sylvia Draper, Prof. Yurri Gu’nko
Personnel
Learning
Outcomes
Understand the basics of organometallic chemistry
• Understand the structure-reactivity relationships for selected metals in each
group of ligands
• Understand the differences in ligand structures and how these influence the
reactivity of the transition metal
The subject of this course is the electronic spectroscopy of transition metal complexes, as
observed by UV-visible spectroscopy. The aim of the course is to develop an understanding
of:
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

The absorption of light and the mechanism by which this leads to electronic
rearrangement in a transition metal complex
The implications that this has for the origin of the wide-ranging and characteristic
colours of coordination complexes.
The importance of both the wavelength and intensity of the light absorbed in
determining the nature of the transitions between electronic energy levels.
The influence of the metal oxidation state, the nature of the ligand and the
coordination number and geometry of the complex on its electronic properties.
The application of UV-visible absorption spectroscopy and the effective interpretation
of spectra.
It also develops skills in the manipulation of data and in analysing spectra
Students will learn main principles of homogeneous catalysis by TM complexes,
mechanisms and catalytic cycles.
Module Learning
Aims
To learn main principles of homogeneous catalysis by TM complexes, mechanisms
and catalytic cycles.
Organometallics (Prof. Y.K. Gun’ko):
Module Content/
Description* 9 lectures and 2 tutorials covering:
Introduction, Main definitions, Importance of Organometallic Chemistry: Industrial
Applications.
Organometallic Chemistry of the Main Group Elements
General Synthetic Approaches in Main Group Organometallics.
Chemistry of Alkali Metals
Chemistry of Alkali Earth Metals
Chemistry of 12th Group of the Periodic Table
Chemistry of 13th Group of the Periodic Table
Chemistry of 14th Group of the Periodic Table
E-E multiple bonding (E = main group element)
Organometallic Chemistry of the Transition Metals
Definition and classification of TM Organometallic compounds.
Organometallic Chemistry of 1-ligands (alkyl, aryl and carbonyl)
Organometallic Chemistry of 2-ligands (alkenyl)
Organometallic Chemistry of 3-ligands (allyl)
Organometallic Chemistry of 4-ligands (di-ene and cyclobutadiene)
Organometallic Chemistry of 5-ligands (Cp)
Organometallic Chemistry of 6-ligands (Arenes)
Each species is examined in turn, detailing their synthesis, properties characteristic
reactions and applications
Transition metal compounds and complexes (Prof. Sylvia Draper):
9 lectures and 2 tutorials covering:
Lecture 1
Definitions and concepts; What is electronic spectroscopy? Absorption of light by transition
Metal Complexes; Limits of Ligand Field Theory – interelectron repulsion; Microstates;
Russell-Saunders Coupling
Lecture 2
Tutorial; Revision of quantum numbers and Pauli Principle; Formation of microstates in
metal ions; Generation of term symbols; Assignment of Ground state term symbols
Lecture 3
Cystal Field Splitting on Free ion terms; Orgel Diagrams for weak field ligand complexes
d1, d4, d6, d9 d2, d3, d7, d8
Lecture 4
Orgel Diagrams continued and Interpretation of weak field spectra
Quantum mixing; Calculation of quantum mixing term x and Racah parameter
Lecture 5
Nephelauxetic effect; d5 – orgel diagram and spectra; Spin and Lapporte Selection Rules;
Spectrochemical Series
Lecture 6 Overview and Consequence of Selection Rules; Understanding and reasons for
the broadening of electronic Transitions; Molecular Vibrations, spin-orbit coupling, JahnTeller distortion
Lecture 7
Problem-base exercises combing electronic and magnetic data; Using Orgel Diagrams
Lecture 8 and 9
Tanube-Sugano Diagrams; High-spin/Low spin transition
Calculation of octahedral splitting, E and B
d0 and d10 ions –charge transfer transitions; Continuation of problem based exercises using
Tanube Sugano Diagrams
Inorganic reactions mechanism and homogenous catalysis (Prof. Robert
Baker):
9 lectures and 2 tutorials covering:
1. Comparison of Homogeneous and Heterogeneous catalysts, Features of Transition Metal
Catalysts: Bonding ability; Ligand variety; Ligand effects.
2. Features of Transition Metal Catalysts: Variability of oxidation state, Variability of
coordination number, The eighteen electron rule, Solutions to tutorial on the 18 e- rule.
3. Stage 1: Assembly: Transmetallation; Substitution/Addition reactions; substitution of a 2 edonor; addition of a 2 e- donor; Oxidative Addition
4. 2 e- oxidative addition continued; Modification; Migratory Insertion Reactions; 1,1migratory insertion; 1,2-migratory insertion; Nucleophilic attack on alkenes.
5. Stage 3: Expulsion: 1,1-reductive elimination; Hydride elimination; beta-hydride
elimination; alpha-hydride elimination; Catalytic Cycles: Hydrogenation with Wilkinson's
catalyst.
6. C-C bond formation: Pd-catalysed cross coupling, Hydroformylation by the Oxo-process.
7. Hydroformylation, Wacker Process, BP(Monsanto) acetic acid process.
8.Tennessee-Eastman acetic anhydride process, Shell Higher Olefin Process.
9.Ziegler-Natta ethylene oligomerisation, Kaminsky catalyst, Asymmetric hydrogenation:
catalyst and mechanism for asymmetric synthesis of L-dopa.
Recommended
Reading List
Organometallics – A Concise Introduction – Ch. Elschenbroich, A. Salzer, 1st
edition, VCH, Weinheim, 1989.
Cotton, Wilkinson, Murillo, Bochmann, Advanced Inorganic Chemistry, 6th Ed
R. Whyman, Applied Organometallic Chemistry and Catalysis, Oxford Chemistry
Primers
Module Pre N/A
Requisite
Module Co N/A
Requisite
Assessment Annual examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH3104
SOLID STATE MATERIALS
5
Semester/term Semester 2
taught*
Contact Hours*
33 Hours of Lectures
Module Prof. Yurri Gun’ko, Prof. Graeme Watson, Prof. Wolfgang Schmitt
Personnel
Learning
Outcomes
Module Learning
Aims
After this course students will be able describe types, synthesis, properties,
structures and applications of main inorganic polymers including boron and
aluminium containing polymers: borates, borides, B-N systems, carboranes,
aluminoxanes. Silicon-containing polymers: silicates and alumosilicates (zeolites),
polysilanes, polisiloxanes, polisilazanes and polysilazoxanes. N,-P- and Scontaining polymers: phosphates, P-N systems, polymeric sulphur, S-N
compounds and polymers. Organometallic and coordination polymers
To learn types, synthesis, properties, structures and applications of main inorganic
polymers
Inorganic Polymers (Prof. Yurii Gun'Ko)
Module Content/
Description* 9 lectures and 2 tutorials covering:
Main definitions and comparison of organic and inorganic polymers. Homo- and heterocatenation; survey of catenation in the Periodic Table. Characterisation and evaluation of
inorganic polymers.
Boron and aluminium containing polymers: borates, borides, B-N systems, carboranes,
aluminoxanes. Silicon-containing polymers: silicates and alumosilicates (zeolites),
polysilanes, polisiloxanes, polisilazanes and polysilazoxanes. N,-P- and S- containing
polymers: phosphates, P-N systems, polymeric sulphur, S-N compounds and polymers.
Organometallic and coordination polymers. Inorganic-organic hybrid polymeric materials.
Structural Inorganic Chemistry (Prof. Wolfgang Schmitt)
9 lectures and 2 tutorials covering:
- Description of chemical structures. Solid state structures seen as arrays of linked polyhedra
and as sphere packings with occupied interstices;
- Structure of the metals; element structures of the non-metals (halogens; chalcogens,
carbon, boron).
- Polymorphism and phase transitions;
- The interplay of chemical bonding/energy and structure; Factors governing the structure of
ionic compounds, molecules and metals; Chemical bonding in solids: band theory; Peierls
distortion;
- Structural chemistry of the major solid state families: diamond-type structures (diamondtype structures under pressure); spinells; perovskites; oxides; halides; silicates and zeolites;
NiAs and NaCl structure; rutile structure; SiO2 structures;
- Structure and properties of semiconductor materials;
- Structural principles of polyanionic, polycationic and cluster compounds; Wade rules,
PSEPT rules; EAN rule; Klemm-Zintel-Bussmann; Isolobal principle; metal clusters and their
applications;
- Zintl and Chevrel phases; intermetallic phases
- Properties of solids (e.g. Introduction to electronic, magnetic, piezoelectric and ferroelectric
properties);
- Symmetry as an ordering principle of crystal structures.
- Metal-organic frameworks and reticular synthesis concepts;
Synthetic methodologies and characterisation techniques of solid state materials:
Synthesis:
-Solid State Reactions (Area of contact between reacting solids, diffusion processes, the rate
of nucleation of the product phase)
-Steps in Conventional Solid State Synthesis
- Solid state preparative methods, including chimie douce, sol-gel and vapour phase
deposition.
- Examples of syntheses of advanced materials with novel properties and potential
applications including: Solid Electrolytes, Mixed Ionic/Electronic Conductors, Intercalation
Materials and their applications (eg. Solid State Batteries, Fuel Cells and Gas Sensors);
-Crystal defects, eg. interstitials, vacancies, dislocations, shear structures and solid-state
solution doping mechanisms.
Characterization:
- Diffraction methods: crystal systems and Bravais Lattices - space group notation and space
group diagrams. Bragg's Law in reciprocal space . Space group extinctions. Indexation of
reflections. Scattering factors. Fourier Synthesis. The phase problem. The Patterson function
and the direct method- structure refinement. Synchrotron Sources. Instrumentation.
- The principles of EXAFS and its use as a structural technique - the interpretation of an
EXAFS spectrum.
-Introduction into electron microscopy (SEM and TEM) characterization techniques; possibly
AFM and STM techniques; Solid state NMR and Raman spectroscopy (if not discussed in
CH3015)
Possibly if time permits or if not subject in SS):
- Relationship between crystal structure, defect structure, composition and properties - as
applied to a wide range of materials, with useful magnetic, electrical and optical properties
(extends concepts discussed in Structural Inorganic Chemistry), lasers and smart windows.
Recommended
Reading List
N. N. Greenwood and A.E. Earnshaw, Chemistry of the Elements, 1st or 2nd
edition.
J.E. Huheey, Inorganic Chemistry, 3rd and later editions.
Inorganic and Organometallic Polymers, 1988, ACS, Washington, editors: M.
Zeldin, K.J. Wynne, H.R. Allcock
Inorganic Materials, 2nd edition, 1996, J. Wiley &Sons, edited by D.W. Bruce and
D. O’Hare.
Inorganic and Organometallic polymers, 2005, Springer Berlin Heidelberg New
York, By Vadapalli Chandrasekhar
Module Pre N/A
Requisite
Module Co
N/A
Requisite
Assessment Annual Examination
Details*
Module Code*
CH3203
Module Name*
SYNTHETIC ORGANIC CHEMISTRY I
ECTS Weighting*
5
Semester/term Semester 1
taught*
33 Hours
Contact Hours*
Module
Personnel
Learning
Outcomes
Module Learning
Aims
Prof. Mike Southern, Prof. Stephen Connon
To understand the basic mechanisms and uses of metal-catalyzed reactions in
synthetic chemistry
Being able to analyze pericyclic reactions based on orbital considerations
Understanding the basic reaction mechanisms of transition metal catalyzed
reactions.
Being able to apply a repertoire of organometallic reactions to synthetic problems.
nic materials (coordination compounds).
Organometallic C-C couplings
Module Content/
Description* 9 lectures and 2 tutorials covering:
Pd: Heck-, Suzuki-, Stille-, NEgishi-, Kumada- and Hiyma-couplings; Sonogashira
and Trost-Tsuji reaction
Ni: variations of the Pd(0) coupling; [4+4] cycloaddition
Zn: Reformatsky reaction; Simmons-Smith cyclopropanation
Cu: Gilman reagents and other organocuprates; Ullman coupling; Huisgen Cu(I)
click chemistry
Ru/Mo: Olefin metathesis; Grubbs catalysts; Schrock catalysts
Co: Pauson-Khand reaction; Nicholas reaction
Rh: Rhodium carbenoid insertion reactions
Pericyclic Reactions and FMO Theory (Prof. Mike Southern)
15 lectures and 2 tutorials covering:
Recap basic orbital theory
FMO theory: simple MO theory, quantum chemistry of HOMO and LUMO. Orbital
coefficients
Suprafacial-suprafacial interactions: simple cases, comparison thermal and
photochemical reactions, Woodward-Hoffman rules.
Examples: [2+2], [3+2], [4+2] cycloadditions,
Cheleotropic reactions
Electrocyclic reactions: ring-closing reactions, con- and disrotatory reactions
Sigmatropic rearrangements:
[3,3]-sigmatropic rearrangements: Cope, Claisen, diazaCope, Johnson
[2,3]-sigmatropic rearrangements: Wittig-Still, Stevens
[1,3]- and [1,5]-alkyl/hydride shifts
Stereoelectronic effects:
FMO explanation of basic organic reactions
Baldwin's rules
Thorpe-Ingold effect
Non-benzoid aromatic systems
Physical Organic Chemistry (Prof. Stephen Connon)
9 lectures and 2 tutorials covering:
Potential energy surfaces
Thermodynamics of activated complex formation
Hammett equation and its application
Steric effects and Taft equation
Proton-transfer reactions
Hammond postulate
Isotope effects
Recommended
Reading List
C. Elschenbroich, Organometallics, Wiley-VCH
G. Spessard, G. L. Miessler, Organometallic Chemistry, Oxofrd University Press,
2009
R. B. Woodward, R. Hoffman, The Conservation of Orbital Symmetry, Academic
Press, 1970.
I. Fleming, Molecular Orbitals and Organic Chemistry, Wiley, 2010.
E. V. Anslyn, D. A. Dougherty, Modern Physical Organic Chemistry, University
Science, 2005.
Module Pre N/A
Requisite
Module Co N/A
Requisite
Assessment
Details*
Annual Examination
CH3204
Module Code*
SYNTHETIC ORGANIC CHEMISTRY II
Module Name*
ECTS Weighting* 5
Semester/term
taught*
Contact Hours*
Semester 2
33 Hours
Module Prof. Thorri Gunnlaugsson,
Personnel
Understanding the different reactivities of organoheteroatom compounds
Learning • Being able to use organoheteroatom compouonds in complex syntheses
Outcomes • Understanding the mechanistis aspects of rearrangement reactions
• Understanding the reactivity of basic platonic hydrocarbon systems
• Being able to use induced rearrangement reactions in total synthesis
Module Learning
Aims
Introduction to heteroatom organic chemistry.
Understanding the reactivity of organo-P, -S, -Si, -B, -SN systems.
Carbocation structure and reactivity and use in chemical synthesis. Appreciating
scientific discourse in chemistry.
Heterocyclic Chemistry (Prof. Thorri Gunnlaugsson)
Module Content/
Description* 9 lectures and 2 tutorials covering:
Five-membered rings:
Pyrrole: natural systems, Paal-Knorr synthesis, SEAr, C2 versus C3 substitution,
basic reactions (Vilsmeier, Mannich, Michael)
Furan: natural systems, Knorr synthesis, reactivity
Thiophene:
Indole: natural systems, Fischer indole synthesis
Systems with more than one heteroatom
Imidazole:
Thiazole: Stetter reaction
Six-membered ring systems
Biological systems
Pyridine syntheses
Pyridine reactions
Quinolines and isoquinolines
Organoheteroatom Chemistry (Prof. Matthias Senge)
15 lectures and 2 tutorials covering:
Organoheteroatom systems:
P: Organophosphorous compounds. Scope and mechanism of Wittig reaction,
ylides, Horner-Wadsworth Emmons reaction, Mitsonobu reaction, Staudinger
reaction. Natural products and chemical warfare agents.
Si: Organosilicon compounds. Electronic, structural and energetic aspects of the
Si–C bond. Silyl ether as protecting groups. -Silyl effect. Chemistry of silanes,
alkynyl and vinyl silanes. Peterson olefination reaction.
S: Organosulfur compounds. Thiol chemistry and reactivity. Sulfides. 1,3-Dithianes
in Umpolung reactions. Sulfoxides and sulfones; extrusion reactions. Julia
olefination.
B: Organoboranes. Hydroboration and reagents. Allylboranes.
Sn: Organostannanes. Comparison C-Si and C-Sn chemistry. Use of R3SnH in
synthesis.
Carbocations and rearrangements
Carbocation structure and electronic effects. Wagner-Meerwein rearrangement.
Carbocations and regioselectivity: Zaitsev dn Bredt's rule.
Classical and nonclassical carbenium ions, history of Winstein-Brown debate.
Superacids.
Nametkin, pinacol, and semipinacol rearrangement reactions. Tiffenau-Demjanov
reaction.
Hydride shifts.
Anion-induced rearrangements: Favorskii, Ramberg-Bäcklund, benzylic acid.
Carbene-induced rearrangements: Wolff, Arndt-Eistert, Curtius, Lossen, Schmidt,
Hofmann, Beckmann, Neber, Stieglitz.
Baeyer-Villiger reaction; Dakin reaction.
Cascade reactions in organic synthesis
Retrosynthesis and Functional Group Interconversion (FGI) (Prof. Stephen
Connon)
9 lectures and 2 tutorials covering:
Functional group interconversions
Oxidation of alcohols
Alkene oxidation
Reduction of carbonyl compounds
Other reduction reactions
Retrosynthetic Analysis
Definition and basic principles.
Retrosynthetic analysis, synthons, disconnections, examples
Recommended
Reading List
T. L. Gilchrist, Heterocyclic Chemistry, Prentice Hall, 1997
R. Brückner, Advanced Organic Chemistry: Reaction Mechanism, Academic Press.
M. B. Smith, J. March, March's Advanced Organic Chemistry: Reactions,
Mechanisms, and Structure, Wiley Interscience, 6th Ed., 2007.
C. Elschenbroich, Organometallic, Wiley-VCH
G. Spessard, G. L. Miessler, Organometallic Chemistry, Oxofrd University Press,
2009
R. W. Hoffmann, Elements of Synthesis Planning, Springer, 2009.
E. J. Corey, X.-M. Cheng, The Logic of Chemical Synthesis, Wiley-Interscience.
1995.
Module Pre N/A
Requisite
Module Co N/A
Requisite
Assessment Annual Examination
Details*
CH3303
Module Code*
QUANTUM MECHANICAL CONCEPTS IN PHYSICAL CHEMISTRY
Module Name*
ECTS Weighting*
Semester/term
taught*
Contact Hours*
5
Semester 1
33 Hours of Lectures
Module Prof. Tony Morton-Blake, Prof Dónall MacDónaill, Prof. Rachel Evans
Personnel
Learning
Outcomes
Module Learning
Aims
Quantum Chemistry (Prof. Tony Morton-Blake)
Module Content/
Description* 9 lectures and 2 tutorials covering:
Brief review of quantum theory; wave functions, Schrödinger equations, Uncertainty
Principle.
Solution of the Schrödinger equation for a particle confined to a circle. Angular momentum.
Schrödinger equation for chemical systems. Real and complex hydrogenic wave functions.
Atomic orbitals. Variation Principle.
The secular determinant and the interaction of states. Molecular orbitals. Bonding and
antibonding molecular orbitals. Hückel molecular orbital theory; application to butadiene. pelectron charge and bond order. Incorporation of symmetries into Hückel theory; Application
to benzene and larger aromatic hydrocarbons.
Transition moment integral; electric dipole transitions.
Spectroscopy (Prof. Rachel Evans)
8 lectures and 1 tutorial covering:
Semiclassical treatment of light-matter interaction, Einstein’s coefficients and lasing
Time-dependent perturbation theory (basics), Fermi’s golden rule
Born-Oppenheimer approximation, Vibrational-rotational spectroscopy: Infrared
spectroscopy, Selection rules for infrared spectroscopy, Rotational spectroscopy, Selection
rules for rotational spectroscopy
Fundamentals of electronic spectroscopy, Vibronic structures, Franck-Condon’s factors
Orbital and spin rules and Fermi’s golden rule
Group Theory (Prof. Dónall MacDonaill)
8 lectures and 1 tutorial covering:
1.2.1 Basics:




Symmetry elements and operations. (1 lecture)
Point Groups: symmetry classification of molecules. (1 lecture)
Representations: introduction of numbers. (1 lecture)
Reducing Representations (1 lecture)
1.2.2 Applications



Simple applications in chemical bonding (2 lecture)
Applications in molecular rotational and vibrational spectroscopy (1 lecture)
Applications in Molecular Orbital calculations, projection operators - relates to the
quantum chemistry course (2 lectures)
Recommended
Reading List
Module Pre N/A
Requisite
Module Co
Requisite
Assessment
Details*
Annual Examination
CH3304
Module Code*
MOLECULAR THERMODYNAMICS AND KINETICS
Module Name*
ECTS Weighting*
Semester/term
taught*
Contact Hours*
5
Semester 2
33 Hours
Module Prof. Michael Lyons, Prof. Michael Bridge
Personnel
Learning
Outcomes
Module Learning
Aims
Module Content/
Description*







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


Thermodynamics, quantum mechanics and statistical thermodynamics
States, configurations, distributions
Boltzmann distribution (1 Lecture)
Molecular partition function (q) (2 Lectures)
Thermodynamic functions in terms of q (1 Lecture)
Determination of q for molecular translation, rotation, vibration and electronic states
(1 Lecture)
q, Q: molecular and canonical ensemble (1 Lecture)
Explicit expressions for U, H, A, G, S, Cv etc (2 Lectures)
Entropy and 3rd Law; residual entropy; Cv for solids; Cv for diatomic gases (2
Lectures)
Equilibrium, Kc and q (1 Lecture)
q and reaction rates – calculating rate constants and testing mechanisms (1











Lecture)
Electrochemical Thermodynamics Electro ystems: fuel cell thermodynamic;
Electrochemical potential; conditions for electrochemical equilibrium; potentiometric
sensors (2 Lectures)
Ionic Systems - Ion/solvent interactions; ion/ion interactions; conductivity in
electrolyte solutions (2 Lectures)
Interfacial Electrochemistry - Models of interface region ; Transport processes in
electrochemistry; Electrode kinetics, Butler Volmer and Marcus-Hush approaches;
Kinetics ofmultistep electron transfer processes; electrocatalysis (5 Lectures)
Molecular collisions - Review of simple collision theory and its limitations. Potential
energy curves and classical motion over a surface. Reaction cross sections and
their link to rate constants (1 Lecture)
The transition state – the derivations - The Eyring transition state theory:
thermodynamic approach and the statistical mechanical approach (1 Lecture)
Transition state theory – applications. Comparison with simple collision theory.
Calculations of rate constants. Bimolecular rate constant from first principles.
Temperature dependence of rate constants. Kinetic isotope effects. Entropies of
activation (1 Lecture)
Kinetics in the liquid phase - Comparison of liquid and gas phase reactions, radical
scavenging, (1 Lecture)
Diffusion controlled reactions - Stokes-Einstein relation, influence of solvent
viscosity and temperature, electrostatic forces between ions. The theory of
unimolecular reactions. (1 Lecture)
Activation controlled reactions - Effect of electrostatic interactions, influence of
solvent dielectric constant, entropy and volume of activation, influence of pressure,
influence of ionic strength, kinetic salt effect. (1 Lecture)
Experimental methods in gas and solution phases (1 Lecture)
Modern Gas phase kinetics (1 Lecture)
Recommended
Reading List
Module Pre N/A
Requisite
Module Co N/A
Requisite
Assessment Annual Examination
Details*
Module Code* CH3403
ANALYTICAL METHODS
Module Name*
ECTS Weighting*
Semester/term
taught*
Contact Hours*
5
Semester 1
33 Hours of Lectures
Prof. Wolfgang Schmitt, Prof. Paula Colavita, Prof. Michael Lyons, Prof. Thorri
Module
Gunnlaugsson
Personnel
Learning
Outcomes
Module Learning
Aims
Understanding and application of analytical techniques (may be applied in the JS
Inorganic Chemistry laboratory course)
To learn types, applications and theoretical background of spectroscopy
techniques relevant to organic synthesis
Module Content/ Analytical Methods in Inorganic Chemistry (Prof. Wolfgang Schmitt)
Description* 9 lectures and 2 tutorials covering:
Lecture 1 – Lecture 3: IR spectroscopy in Inorganic Chemistry: Theoretical concepts;
Instrumentation; Characteristic group vibrations of common organic ligands; IR spectra of
important coordination complexes; Tendencies of related complexes; IR spectra of amino
acid-stabilised complexes, IR spectra of polynuclear complexes; IR spectra of bioinorganic
model compounds; IR spectroscopy of carbonyl complexes and derivatives; Quantitative
methods in IR spectroscopy; Raman spectroscopy: Theoretical concepts and examples of
inorganic compounds;
Lecture 3 – Lecture 7: NMR spectroscopy in Inorganic Chemistry; Theoretical concepts;
Instrumentation; 1H-NMR spectra of representative complexes and tendencies; carbonyl
complexes and related cluster compounds; phosphine complexes; 13C-NMR spectra of
representative complexes and tendencies, 11B-NMR;195Pt-NMR; multinuclear NMR; NMR
of paramagnetic systems; Fluxional NMR, Solid state NMR; Solid state NMR spectra of
representative complexes and tendencies; EPR in Inorganic Chemistry; Theoretical
concepts and EPR spectra of selected coordination complexes (depending on the time
available);
Lecture 8 – Lecture 9: Molecular Magnetism: Types of magnetism; Spin-spin coupling, Spinorbit coupling, Zeemann effect, case study: analysis of simple dinuclear copper(II), cobalt
and nickel(II) complexes; Instrumentation;
Analytical Methods in Physical Chemistry (Prof. Paula Colavita, Prof. Michael
Lyons)
9 lectures and 2 tutorials covering:
Statistics (4 Lectures)
• Analytical Method development
• Distributions, Samples and Estimators
• Reporting values: errors, CI, Significant Figures
• Two sample tests
• Chi-square and fits
• Figures of merit
Analytical Spectroscopy (4 Lectures)
• Fundamentals of spectroscopic instrumentation
• Quantitative Determinations using Absorption/Emission
• Analytical Atomic Spectroscopy: AAS, AES (XRF)
Analytical Electrochemistry (3 lectures)
• Capacitive vs. Faradaic currents
• Limit of Detection
• Voltammetry: sweep & pulse methods (CV, DPV, SV)
• Analysis of heavy metals and organics
• Electrochemical instrumentation (electronics, Op-Amp, etc.)
Organic spectroscopy (Prof. Thorri Gunnlaugsson)
9 lectures and 2 tutorials covering:
Mass spectrometry:
EI-MS
FAB
ESI
Maldi
Tandem MS/MS
Fragmentation pattern; McLafferty rearrangement
Mass spectra by functional group
Recommended
Reading List
Structural Methods in Inorganic Chemistry, 2nd Ed., E.A.V. Ebsworth, D.W.H
Rankin, S. Cradock Blackwell Scientific Publications, 1991; Inorganic Spectroscopic
Methods, A.K. Brisdon Oxford University Press, 1998; Inorganic Chemistry, D.F.
Shriver, P.W. Atkins and C.H. Langford, 2nd Ed., Oxford University Press, 1990;
Inorganic Chemistry C.E. Housecroft and A.G. Sharpe 2nd Ed, Prentice-Hall, 2005..
M. Hesse, H. Meier, B. Zeeh, Spectroscopic Methods in Organic Chemistry,
Thieme, 2nd Edition, 2007
Module Pre N/A
Requisite
Module Co N/A
Requisite
Assessment
Details*
Annual Examination
Module Code* CH3404
Module Name*
ECTS Weighting*
Semester/term
taught*
Contact Hours*
BIOMATERIALS & MACROMOLECULES
5
Semester 2
33 Hours of Lectures
Module Prof. Rachel Evans, Prof. Aidan McDonald, Prof. Thorri Gunnlaugsson, Prof. Eoin Scanlan
Personnel
Understand the role of metal and peptide for biological processes
Understand metabolic processes of certain substrates
Understand catalytic cycles for enzymes
Learning •
Outcomes •
•
Appreciate the importance and difficulties of model studies
Introduction to bioinorganic chemistry and the natural roles metals play in biology.
Module Learning The student is provided with a brief introduction to the coordination chemistry of
Aims metals in biology, and to the spectroscopic techniques employed to study metals in
biology. A variety of metalloenzymes and their Chemistry are discussed in detail.
One experiment in the practical course is directly linked to metalloenzyme
chemistry and thus the Bioinorganic section of this module.
Learning outcomes: identify biological ligands; identify techniques to probe
metals in biology; be able to predict catalytic cycles of metalloenzymes; have a
deep understanding of Mn, Fe, Cu redox chemistry and be able to relate that to
biological transformations.
Soft Matter (Prof. Rachel Evans)
Module Content/ 9 lectures and 2 tutorials covering:
Description*
Surface and interfacial tension (1 lecture)
Langmuir adsorption isotherm, insoluble monolayers, physical states (1 lecture)
Surfactants: properties, structure, thermodynamics of micelle formation, aggregation
number, structure (1 lecture)
Lyotropic liquid crystal phases, biological membranes (1 lecture)
Colloidal dispersions – stability, preparation, Hamaker theory, DVLO theory, applications (3
lectures)
Polymers: morphology-property relationships, solvation thermodynamics, molecular weight
determination, viscoelasticity, glass transition temperature
Bioinorganic Chemistry (Prof. Aidan McDonald)
9 Lectures and 2 Tutorials
The course will provide students with an introduction to the natural roles metals
play in Biology. The course will consist of 9 lectures, and 2 tutorials. The topics to
be covered during the course are listed below:
Lecture 1: Introduction to Bioinorganic Chemistry
Lecture 2: Spectroscopic Techniques in Bioinoragnic Chemistry
Lecture 3: Photosynthesis - Photosystem II - manganese, iron, magnesium
Lecture 4: Dioxygen Transport - iron and copper
Lecture 5: Dioxygen Activation - iron and copper
Lecture 6: Electron Transfer - iron/sulfur clusters, blue copper
Lecture 7: Nitrogen Fixation - nitrogenase
Lecture 8: Hydrogenases - iron, nickel
Lecture 9: Metals and Reactive Oxygen Species - Neurodegeneration
Bioorganic Chemistry (Prof. Thorri Gunnlaugsson, Prof. Eoin Scanlan)
9 Lectures and 2 Tutorials
DNA: Basic structure and components, single- and double stranded DNA, A-, Band Z-forms; cell cycles, natural DNA synthesis; chemical DNA synthesis;
polymerase chain reaction; automated synthesis.
Amino acids and peptides: Basic structure and properties; protein structure,
chemical peptide synthesis and coupling agents (DCC, DIC, EDCI, HATU), protecting
groups; Merrifield synthesis; automated processes, in vivo protein biosynthesis.
Carbohydrates: Recap SF chemistry, configuration of natural sugars, glycosyl
donors and acceptors, coupling methods and protecting group chemistry.
Glycoconjugate synthesis.
Porphyrins: nomenclature, biological examples, heme, chlorophyll; applications in
PDT, NLO.
Recommended
Reading List
G. Barnes and I. Gentle, Interfacial Science: An Introduction, Oxford University
Press, 2nd Edition
- Bioinorganic Chemistry: Inorganic Elements in the Chemistry of Life - An
Introduction and Guide [Paperback], Wolfgang Kaim, Brigitte Schwederski, WileyBlackwell
- The Biological Chemistry of the Elements: The Inorganic Chemistry of Life
[Paperback]
- Bioinorganic Chemistry; Bertini, Gray, Lippard, Valentine; University Science
Books
- Principles of Bioinorganic Chemistry; Lippard, Berg; University Science Books
J. J. R. Frausto da Silva, R. J. P. Williams, OUP Oxford
Module Pre N/A
Requisite
Module Co N/A
Requisite
Assessment
Details*
Annual Examination
CH3080
Module Code*
PRACTICAL CHEMISTRY
Module Name*
ECTS Weighting*
15
Semester 1
Semester/term
Semester 2
taught*
Contact Hours*
33 Hours of Lectures
Module
Personnel
Learning
Outcomes
Module Learning
Aims
Module Content/
Description*
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Practical in-course assessment through laboratory reports
Assessment
Details*
CH3441
Module Code*
MEDICINAL CHEMISTRY
Module Name*
ECTS Weighting*
5
Semester 1
Semester/term
Semester 2
taught*
Contact Hours*
33 Hours of Lectures
Module
Personnel
Learning
Outcomes
Module Learning
Aims
This module covers material dealing with fundamental medicinal chemistry. It encompasses
Module Content/ CH3041, CH3042 and CH3043
Description*
CH3041 - Introduction to Medicinal Chemistry - 15 Lectures - M. Southern
Principles of drug action; drug properties; drug targets and modes of action.
Molecular components of cells: lipids, proteins, nucleic acids. Control through non-covalent
interactions: electrostatic, hydrogen bonding, hydrophobic. Conformations of biological
macromolecules, organisation of cell, basic biochemical machinery. Sites for drug action:
DNA/RNA (alkylation, intercalation etc.), enzymes (inhibition), receptors (agonism,
antagonism).Enzyme substrates/transition states, receptor ligands (hormones and
neurotransmitters) as lead compounds for drug development. Drug development, e.g. from a
biologically active natural product: identification of pharmacophore, application of QSAR.
Alternative sources of lead compounds (random screening, combinatorial chemistry, protein
crystallography/molecular modelling).Pharmacodynamics: drug transport, stability,
metabolism. Use of pro-drugs.
CH3042 - Antiviral and Anticancer Chemistry - 9 Lectures - E. M. Scanlan
Antimetabolites-antifolates, pyrimidine and pruine antagonists; Alkylating agents;
Microtubule active agents.
CH3043 - QSAR Methods - 9 Lectures - I. Rozas
Hansch Model
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment
Details*
Annual Examination
CH3446
Module Code*
MICROBIOLOGY & PHARMACOLOGY
Module Name*
Medicinal Chemistry II - Microbiology and Medicinal Chemistry
ECTS Weighting*
5
Semester/term Semester 2
taught*
Contact Hours*
33 Hours of Lectures
Module
Personnel
Learning
Outcomes
Module Learning
Aims
This module covers antimicrobial agents, antiinfective agents, antimalarial chemistry and
Module Content/
aspects of industrial chemistry.
Description*
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment
Details*
Annual Examination and partial assessment by essay
CH3447
Module Code*
BIOCHEMISTRY & PHARMACEUTICAL CHEMISTRY
Module Name*
Medicinal Chemistry III
ECTS Weighting*
5
Semester/term Semester 2
taught*
Contact Hours*
33 Hours of Lectures
Module
Personnel
Learning
Outcomes
Module Learning
Aims
Module Content/
Description*



Protein Structure, Function, Activity and Regulation (15L)
Receptors, Drugs and the Autonomic Nervous System (9L)
Steroids (9L)
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
CH3601
Module Code*
COMPUTATIONAL CHEMISTRY
Module Name*
ECTS Weighting*
5
Semester/term Semester 2
taught*
Contact Hours*
30 Hours of Lectures
Module
Personnel
Learning
Outcomes
Module Learning
Aims
Module Content/
Description*
This module covers a range of topics on offer from computational numerical
optimization methods, molecular quantum chemistry and an introduction to static
and dynamic atomistic simulation. It encompasses:



CH3062
CH3063
CH3067
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
CH3602
Module Code*
COMPUTATIONAL CHEMISTRY II
Module Name*
ECTS Weighting*
5
Semester 1
Semester/term
Semester 2
taught*
Contact Hours*
54 Hours of Lectures
Module
Personnel
Learning
Outcomes
Module Learning
Aims
Module Content/
Description*
This module covers programming and related skills, with course on Unix, Fortran
77 and Fortran 90(+). This material is assessed during the year through practicals
and assignments.
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment In-course assessment
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4102
ADVANCED ORGANIC CHEMISTRY I
5
Semester/term Semester 2
taught*
Contact Hours*
Module
Personnel
Learning
11 Hours of Lectures; 1 Hour of Tutorials
Outcomes
Module Learning
Aims
These modules involves core lectures in comptemporary organic synthetic methods
Module Content/ and heterocyclics and drugs.
Description*
CH4001
Principles and historical development of synthetic methods.
Fischer, Perkin, Woodward, Corey and modern approaches towards synthesis.
Retrosynthetic analysis: disconnections, synthons, retrons, latent polarities.
Linear versus convergent syntheses.
Protecting group strategies.
Chemo-, regio-, stereo- and enantioselective methods.
Synthesis of heterocycles.
Examples from the literature: e.g. terpinol, cage compounds, steroids, longifolen, vitamins,
drugs, artesiminin, brevetoxin or others
CH4033
Detailed chemistry of selected classes of heterocyclic drugs, including the quinolone
antibiotics, histamine H2 antagonists, etc.
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4103
ADVANCED ORGANIC CHEMISTRY II
5
Semester/term Semester 2
taught*
Contact Hours*
9 Hours of Lectures; 2 Hours of Tutorials
Module
Personnel
Learning
Outcomes
Module Learning
Aims
The following topics will be covered in this lecture course:
Module Content/
Description* Radical Chemistry: Generations of radicals, physical properties of radicals, their stability
and structure, simple radical reactions on hydrocarbons, the radical chain reactions,
persistent radicals, ways of generating radicals using photolysis, thermolysis and redox
reactions, exploring the mechanism for various named radical reactions which will be
followed by in-depth discussion of large numbers of reactions which will involve: coupling,
addition, substitution, reduction, fragmentation and rearrangement reactions.
Protection Chemistry: Introduction to the concept of protection chemistry most of the
lectures will focus on the strategy and the methods used for the protection and deprotection
of amines and carbocyclic acid s, alcohols (and diols) and carbonyl functional groups.
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4104
ADVANCED INORGANIC CHEMISTRY I
5
Semester/term Semester 2
taught*
Contact Hours*
9 Hours of Lectures; 2 Hours of Tutorials
Module
Personnel
Learning
Outcomes
Module Learning
Aims
CH4005 - Advanced Organometallic Chemistry
Module Content/ Main synthetic approaches in modern Organometallic Chemistry. Types and properties of MDescription* C bonds. Main reactions and mechanisms. New ligands in Organometallic Chemistry. Role
of the metal nature. Stabilisation of unusual oxidation states. Organometallic Chemistry of
water. Bio-Organometallic Chemistry. Supramolecular Organometallic Chemistry.
CH4014 - Main Group Organometallics
This course deals with the organometallic chemistry of Groups 1, 2, 13, 14 and 15. The
relationship between structure and reactivity is explored, with particular reference to alkyl
lithiums, grignards, dialkyl zinc and trialky aluminium compounds (6-7 Lectures).
Finally selected aspects of contemporary main group chemistry are explored (1-2 lectures).
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4105
ADVANCED INORGANIC II
5
Semester/term Semester 2
taught*
Contact Hours*
18 Hours of Lectures; 5 Hours of Tutorials
Module
Personnel
Learning
Outcomes
Module Learning
Aims
CH4004 – Heavy Transition Metals
Module Content/
Description* Lecture 1: The course begins with a revision of concepts reapplying them to the Heavy
Metals e.g. definitions of transition metal and lanthanide and actinide, nature of d and forbitals, radial distribution functions and lanthanide contraction
Lecture 2: Gives an overview of the electronic spectra of the 2nd and 3rd row transition
metal and f-block metal elements
Lecture 3: Details the common geometries and coordination numbers of compounds and
complexes, particularly focussing on coordination number 7 and 8, variations in the stability
of oxidation states
Lecture 4: Looks at the Magnetic Properties of TM and f-block metals, Russell Saunders
coupling and the spin-only formula
Lecture 5: The prevalence of M-M bonding in the heavier TM series and detailed examples
from the oxide and halide chemistry of Mo, W, Nb and Ta.
Lecture 6: Re chemistry: the fluorides, chlorides and oxo compounds. Uses simple MO
theory and electron counting to examine the formation of M-M bonds
Lecture 7: Ru and Os oxo compounds giving consideration to MO interactions
General Properties of the Lanthanides: History, extractions, separation and general
chemistry
Lecture 8: uses of the Lanthanides, luminescent applications, catalysis, MRI, NMR shift
reagents, organometallic compounds of the lanthanides
Lecture 9: brief overview of the chemistry and organometallic chemistry of the actinides
CH4011 - Advanced Coordination Chemistry
Spin-crossover (SCO) phenomena and how to generate this condition, functional aspects of
SCO, potential use of SCO, supramolecular chemistry, metallo-supramolecular chemistry,
coordination chemistry, metallo-helicate chemistry design and synthesis, catenane and
rotaxane design and synthesis, kinetic vs. thermodynamic templates, self-assembly, Hbonding, p-p interactions, charge-transfer, metal-templation, metallo-polyhedra syntheis and
design, experimental aspects of synthesis and characterisation, Metal-organic frameworks
and coordination polymers, design strategies and synthesis, potential uses.
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4106
ADVANCED PHYSICAL CHEMISTRY I
5
Semester/term Semester 2
taught*
Contact Hours*
14 Hours of Lectures; 3 Hours of Tutorials
Module
Personnel
Learning
Outcomes
Module Learning
Aims
CH4006 - Photochemistry
Module Content/
Description* Introduction and Singlet states: Types of photochemical reactions. Photon energy.
Fluorescence – relationship of quantum yields to radiative and measured lifetimes.
Radiationless processes. Jablonski diagram. Triplet states: nature, population, spin-orbit
coupling, phosphorescence, energy transfer, reactions
Transient Spectroscopy: Fluorescence lifetime determination: laser flash photolysis,
femtosecond/picosecond methods, Transient IR and Raman.
Photoreduction of benzophenone and derivatives as an illustrative example of an organic
molecule in solution Another illustrative example of photo-reactions, e.g. Photo-induced
electron transfer reactions, photochemistry of co-ordination compounds, photochemistry of
nucleic acids. Solar energy conversion. Primary processes of photosynthesis and Gratzel
CH4008 – Advanced Physical Chemistry
Chemically modified electrodes. Preparation , characterization and properties of redox active
and inactive self assembled monolayer films on electrode surfaces. Preparation and
characterization of self assembled monolayer (SAM) thin films. Electrochemical and catalytic
behaviour of SAM film modified electrodes.Classification, synthesis and fundamental
properties of electroactive polymer materials. Ionic and electronic conductivity mechanisms
exhibited by electroactive polymers. The experimental determination of electronic and ionic
conductivity in electroactive polymers using microelectrode and complex impedance
spectroscopic methods. The use of electroactive polymer materials as amperometric
chemical sensor devices.
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4107
ADVANCED PHYSICAL CHEMISTRY II
5
Semester/term Semester 2
taught*
Contact Hours*
16 Hours of Lectures; 6 Hours of Tutorials
Module
Personnel
Learning
Outcomes
Module Learning
Aims
CH4007 – Quantum Chemistry
Module Content/
Description* Time-dependent theory: inversion in the NH3 molecule, Fermi Golden Rule. Quantum
chemical description of polymers: Bloch functions, Brillouin zone, energy bands. Rotation of
homonuclear diatomic (and some other) molecules, bosons and fermions, ortho and para H 2,
their interconversion and spectra.
CH4009 – Solid State
Point Defects: An introduction to the nomenclature and occurrence of point defects in a
variety of solids. A first principles derivation of the nember of intrinsic defects in ionic crystals
as given by ststistical thermodynamics. Grossly defective materials: the nature and
occurrence of non-stoichiometry in solids, its control and effects on the properties and the
modes of stabilisation of grossly defective crystals. Dislocations: the nature and occurrence
of dislocations, the energetics of dislocation formation and the effects of dislocations on the
strength of materials and on the rates of crystal growth and stabilisation. Surfaces: the
nature of grain boundaries and the energetics of surface formation and stabilisation, the
aggregation of defects.
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4108
OPTION MODULE
5
Semester/term Semester 2
taught*
Contact Hours*
Module
Personnel
Learning
Outcomes
Module Learning
Aims
In this module students select four advanced option courses:
Module Content/
Description* CH4003 - Aspects of Inorganic Chemistry
Bio-inorganic chemistry, metallo-enzymes, alkalides and electrides: definitions, synthesis,
structures and properties. Polyhedral silsesquioxanes and metallasilsesquioxanes and their
applications.
CH4021 - Molecular Dynamics
An introduction to the simple yet powerful method for solving the many particle equations of
motion for molecular systems; applications in chemistry.
CH4022 - Matter Transport in Solids
Ionic conductance and diffusion processes in solids considered from first principles;
applications include solid state reactions, including corrosion of metals and alloys, and fast
ion conductors and their uses in advanced battery systems and chemical sensors.
CH4023 - Quantum Chemistry
Quantum operators; perturbation theory and applications (Stark effect); beyond the HartreeFock limit; vibrations in solids (phonons).
CH4024 - Heterogeneous catalysis
The course will examine the basic principles of catalyst and catalyst design including
measures of catalyst activity. Examples of real world catalysts will be given including the use
of zeolites for acid catalysed reactions within the petroleum industry and the design and
performance of car exhaust catalysts and hydro-desulfurisation catalysts and there link to
environmental legislation.
CH4025 - Supramolecular Chemistry
Host-guest chemistry and molecular recognition including relevance to biological processes
and 'molecular engineering'. Self-assembly and anion sensing.
CH4027 - Topics in Structural Chemistry
A brief review of the preparation, structural chemistry and physico-chemical properties of (i)
Molecular Crystals and (ii) Copper oxide superconductors emphasising the interplay
between composition, structure and properties.
CH4030 - Statistical Thermodynamics
Application of statistical mechanics to study molecular motion in various states of matter;
Fermi-Dirac and Bose-Einstein statistics.
CH4031 - Organic Synthetic Methods II
The modern Aldol Reaction in the stereoselective synthesis of molecules of
medicinal/biological importance, particularly natural products that derive from the polyketide
synthetic pathway.
CH4034 - DNA Structure and Drug DNA complexes
Spectroscopic tools for studying nucleic acids; structure of DNA (A, B and Z); covalent and
non-covalent binding to DNA; relevance to drug design.
CH4036 - Bio-Organic Chemistry
Introduction; Catalytic antibodies; Combi-chem lite; Directed evolution; RNA world;
Proteomics
CH4037 - Electrochemical Biosensors
The physical principles underlying electrochemical sensors. A survey of surface immobilized
redox enzyme based biosensor devices using electrochemical transduction. Strategies for
enzyme wiring. Self assembled monolayer based biosensors.
CH4041 - Material Synthesis using Chemical Vapour Deposition
The aim of this course will be to provide students with an introduction to the increasingly
important technique of chemical vapour deposition (CVD). This method has extensive
applications in both industrial processes and academic research, and is used to deposit thin
films of various substances. Also, CVD has led to the synthesis of novel materials such as
nanowires and nanotubes. The course will cover the basic principles of CVD, its use as the
impetus for surface and gas phase reactions, and the various technological considerations
relevant to the development of the technique.
CH4042 - Fundamentals of Electrochemical Energy Conversion and Storage
The course will deal with the physical electrochemistry which underpins electrocatalysis, fuel
cells, batteries and super-capacitors.
CH4080 - Molecular Informatics
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
CH4401
Module Name*
ECTS Weighting*
Advanced Medicinal Chemistry I
5
Semester/term Semester 2
taught*
Contact Hours*
16 hours of lectures, plus tutorials
Module
Personnel
Learning
Outcomes
Module Learning
Aims
CH4050 - Central Nervous System
Module Content/
Description* * Cellular foundations of neuropharmacology: Cytology of the nerve cell, Bioelectric
properties of the nerve cell, The steps of synaptic transmission, Aspects of the metabolism in
the central nervous system
* Neurotransmitter Postsynaptic Receptors: Classification & Definition
* Modulation of synaptic transmission: Definitions, Second messengers
* Neurotransmitters and their receptors: Aminoacids
Glutamic acid –Glutamate: Synthesis & Metabolism, Glutamate receptors, NMDA receptor
Glycine:Glycine receptors
GABA: Distribution & Metabolism, GABA receptors: GABAA, GABAB & GABAC, Drugs
acting on GABA receptors: Benzodiazepines, Barbiturates & Spasmolytics.
*Neurotransmitters and their receptors: Acetylcholine (Synthesis -Choline acetyltransferase& Storage, Choline transportm Metabolism & Inactivation (Acetylcholinesterase), The
cholinergic synapse, Cholinergic receptors -Nicotinic Receptors & Muscarinic Receptors,
ACh drugs, ACh in disease states: Parkinson’s and Alzheimer’s diseases
* Neurotransmitters and their receptors: Serotonin (Synthesis & Metabolism, Serotonin
Transporter: A Representative Reuptake Pump, Location and Structure of the Serotonin
Transporter, Mechanism of Action of the Serotonin Transporter, Transporter Inhibition:
Selective Serotonin Reuptake Inhibitors, Serotonin receptors, Serotonin and Depression
*Neurotransmitters and their receptors: Noradrenaline and Adrenaline (Generalities:
Catecholamines, Synthesis and Metabolism of Catecholamines, Adrenergic neurons,
Metabolic actions of Catecholamines, Noradrenaline transporter: Desipramine,
Adrenoceptors -Classification
beta-Adrenoceptors: Subtypes, Location and Function, Agonists and Antagonists,
Transduction Mechanisms, Clinical Uses, beta-blocking drugs
Alpha1-Adrenoceptors: Subtypes, Location and Function, Agonists and Antagonists
Transduction Mechanisms, Clinical Uses, alpha1-blocking drugs: Benign Prostatic
Hyperplasia
alpha2-Adrenoceptors: Subtypes, Location and Function, Agonists and Antagonists
Transduction Mechanisms, Clinical Uses, alpha2- drugs: Analgesics and Antidepressives
Imidazoline Binding Sites
* Neurotransmitters and their receptors: Dopamine (Synthesis and Metabolism,
Dopaminergic neuron, Dopamine transporter & inhibitors, Dopamine receptors, Dopamine
and Parkinson’s disease, Dopamine and schizophrenia
* Neurotransmitters and their receptors: Neuroactive peptides (Generalities & differences
with small neurotransmitters, Coexistence with Neurotransmitters, Classification, Opioid
peptides and their receptors: agonists and antagonists, Vasopresin and Oxytocin and their
receptors, Tachykinins: Substance P and Neurokinins, Cholecystokinin
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4402
ADVANCED MEDICINAL CHEMISTRY II
5
Semester/term Semester 2
taught*
Contact Hours*
22 hours
Module I. Rozas and External from DCU
Personnel
Learning
Outcomes
On successful completion of this module students should be able to:
Module Learning
Aims CH4052:
• Explain computational methods that will help in the design of new drugs
• Compare the different computational methods used in drug design and choose and explain
which is the appropriate method for a given problem
• Assess the problems associated with computational drug design.
CH4056:
• Explain the separation processes involved in different analytical methods
• Select the most appropriate analytical method for the separation of potential drugs.
CH4052 - Computational Medicinal Chemistry
Module Content/ CH4056 - Analytical Methods
Description*
Computational tools in medicinal chemistry: data bases (Small molecules-cambridge vs. Big
molecules-brookhaven), mechanoquantic methods (Semiempirical -application/examples, Ab
initio and DFT- application/examples); computational methods based on clasic mechanics
(Molecular mechanics -application/examples, Molecular dynamics -applications/examples)
-examples done by students
Different approaches to drug design:
*selection of the biological target (receptor), selection and/or optimization of a leader
compound (ligand)
*receptor structure is known: 3d structure known (docking), 1ry structure known (protein
homology)
*receptor structure is unknown: Pharmacophore determination superimposing structures
(fitting), "de novo" design , 2d-qsar: linear correlations: different parameters, 3d-qsar.
Additional problems in drug design:
*different conformations: conformational analysis methods: Systematic search, Random
search -> Montecarlo
High temperature molecular dynamics, Annealing
*the environment: solvation models: Continuous, Discrete (solvent & membrane), Mixed
(QM/MM)
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4403
Advanced Medicinal Chemistry III
5
Semester/term Semester 2
taught*
Contact Hours*
16 Lectures; 2 Tutorials
Module
Personnel
Learning
Outcomes
Module Learning
Aims
CH4053 - Site Specific Drug Delivery Systems
Module Content/ CH4055 - Combinational Chemistry and Screening Methods
Description*
CH4053
Introduction – why a good in vitro profile is no indication of in vivo activity
Description and appreciation of Ehrlich’s “magic bullet” insight
The general methods of delivery are described (oral, implant, topical, i.v. etc) and the merits
of each approach considered. After illustrating that oral delivery is the preferred method of
delivery a drug’s journey is then considered in more detail.
The numerous issues effecting a drug, or other chemical’s journey from bottle to site of
action are discussed, including the acidity of the stomach, the phsysiochemical properties
required, for example, sufficient solubility in both aqueous and lipid (cell membrane) based
media (log P and log D). The drug must be water soluble enough for transport via the
bloodstream but lipophilic enough to diffuse through the cell wall lipid bilayer.
Other issues such as pKa, dissolution rate and site of absorption are discussed culminating
in Lipinski’s rule of 5.
Alternative methods of cell entry (aqueous pore, active transports, endocytosis)
Brief discussion of P450 system in terms of metabolism and the effects of other agents in
combination (ADME(T)/DMPK)
Overcoming problems using prodrugs
More specific look at options if a poor in vivo profile is observed and how to overcome the
variety of problems e.g. low lipophilicity – prodrugs (defined) offer the simplest solution.
Examination of the pitfalls, and the factors that can be influenced (solubility, tissue
penetration, presystemic metabolism, site specificity, rate of onset/duration of action, toxicity
(positive and negative), poor patient compliance, formulation problems).
Different classes of prodrugs (bi/tripartite and mutual (carrier linked) and bioprecurors.
Carrier linked
Esters of acids or alcohols and associated electronic and steric effects on release in vivo.
Sulfonates, phosphonates and amides described.
Numerous examples of bi/tripartite and mutual ester and amide prodrugs affecting the
various different factors of influence are provided. Examples applicable to topical absorption
are also included
Methenamine described.
Bioprecursors
The story of the development of the discovery of prontisil and bioprecursor prodrugs by
Domagk. Definition and numerous examples of oxidative and reductive activation, including
mechanisms of activation.
In depth analysis of the mode of action of acyclovir and how it exploits virus encoded
kinases to ensure selective activation solely in infected cells.
Macromolecular prodrugs
In which the drug is attached to a polymer. Physiochemical properties dominated by that of
the polymer. Uptake in the GI tract is poor and intravascular delivery is generally required,
size issues - capillaries (especially in the lungs) can become clogged). Loading is variable.
Diffusion across membranes is poor but endocytosis mechanisms can be effective.
Coverage of issues such as biodegradability, addition of solubilising side-chains and linkers
to aid release. Examples of natural hormones, contraceptives, methotraxate and
doxorubicin (PK1) on polymers.
The blood brain barrier
Examination of the extra issues involved for drugs to cross the blood-brain-barrier and how
dihydropyridine prodrugs can achieve this. Description of the mode of action of nerve
agents (via deactivation of acetylcholinesterase) and the associated effects. Mode of action
of antidotes for the peripheral nevous system and prodrug antidotes for the CNS. A
penicillin based prodrug to cross the BBB to treat bacterial meningitis. Discussion of LDopa’s ability to cross the BBB, mode of activation, mode of action and problems with
peripheral activation (preventing the active agent, dopamine, entering the brain). Use of
carbidopa and benzerazide (dopa decarboxylase inhibitors that don’t cross the BBB) to allow
low dosing and effective use of L-Dopa. Use of a MAOI prodrug activated by dopa
decarboxylase (in combination carbidopa to prevent peripheral activation) that is released
within the brain, preventing the incompatibilities of MAOIs within the periphery.
Liposomes as delivery devices
General theories, loading strategies, types of vesicles, phospholipids used, targeting issues
(concentration in the liver), transport in macrophages, stealth liposomes, targeted liposomes.
Case Studies
Case study – Prodrugs of Taxol, study of the attempts to improve the bioavailability of
Taxol by increasing its water solubility.
New Targets/Technologies
Case Study – Glivec a CML treatment. A brief discussion of the genetic events leading to
the formation of the Philidelphia Chromosome (and other mutants) responsible for the
expression of rogue kinases. Development of Glivec from a PKC inhibitor with activity
against BCR-ACL. Brief mention of Irresa and Tarceva, targeting EGFR, and active against
prostate, pancreatic, colorectal renal-cell and oesophageal
Case Study – Herceptin, a treatment for breast cancers in which HER2 is overexpressed.
Overview of human epithelial growth factor receptor 2 and the requirements for activity of
herceptin. Definitions and background (including chemical uses as catalysts) of monoclonal
antibodies including interaction and the use of HER2 as the antigen. Description of the
production and isolation of antibodies and the subsequent humanisation by gene conversion
mutagenesis, modelling and nucleic acid exchange to humanise the coding for the
recognition region.
mAbs alone can induce an immune response, block highly expressed and activated
receptors for growth factors or inhibit angiogenesis. They can also be used for targeting
radionucleides, cytotoxic drugs and toxins. Best example of FDA approved treatment is
Mylotarg (gemtuzumab) a humanised CD33 mAb linked to calicheamicin.
Finally mention of Antibody directed enzyme prodrug therapy
CH4055
Historical overview; biological combinatorial techniques; combinatorial strategiy. Drug
development process; time frames, costs, approach and strategies; lead discovery and
optimisation. Medicinal chemistry and drug development. Solid phase techniques, split and
mix techniques, instrumentation. Immobilized reagents; solid phase natural product
synthesis. Resins; supports; crosslinking agents; spacers. Synthetic examples; Ugi
reactions. Screening
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4404
ADVANCED MEDICINAL CHEMISTRY IV
5
Semester/term Semester 2
taught*
12 Lectures; 2 Tutorials
Contact Hours*
Module
Personnel
Learning
Outcomes
Module Learning
Aims
CH4051 - Medicinal Chemistry Cardiovascular System
Module Content/ CH4054 - Case Studies
Description*
CH4051
Introduction
Brief description of the types of disease and number of deaths associated with the
cardiovascular system.
Focus on hypertension, definition and associated problems, e.g. increased risk of stroke.
Treatments for hypertension
Beta blockers - Beta adrenergic antagonists
An overview – The nervous system and how the adrenergic (sympathetic) system fits into it.
The basic neurobiology of the somatic, sympathetic and parasympathetic systems
Biosynthesis and metabolism of adrenaline and noradrenaline
A detailed examination of adrenoreceptors – subtypes, structure, biochemical cascades
initiated and the associated physiological outcomes of activation of the different subtypes.
Important interactions of adrenaline with adrenoreceptors followed by the a/b selectivity
discovered by Ahlquist - larger alkyl groups on the amine enhance activity at the b receptors
– hydrophilic pocket hypothesis.
The effect of adrenaline in differtent organs with different levels of expression of different
subtypes. An overview of the biological effects of different subtype selective ant/agonists.
Focus on b-adrenoreceptor antagoniosts (b-blockers) and Black’s attempts to alleviate
angina leading to the development (via dichloroisoprenaline) of pronethalol – active against
angina with an additional antihypertensive effect. The first b-blocker used clinically.
The (serendipitous) discovery of propanolol (now the benchmark for activity), racemic
synthesis included. An overview of the positive and negative physiological effects.
Examples of other 1st generation b-blockers including SAR
2nd generation - Discovery of cardioselective (b1 (heart) activity > b2 (lung)) b-blocker
practolol - alleviating problems for asthmatics. Mention of the controversy around the
different activities of the o/m/p aromatic substitution patterns. Further side-effects (was
withdrawn) and other clinically employed 2nd generation b-blockers.
3rd generation b-blockers – extention from the amine, examples (focus on xalmoterol) and
SAR. Finally diverse uses of b-blockers.
b-blockers have a similar ether/hydroxy/amino backbone with varying R groups, syntheses
are similar but there issues with their chiral preparation which is discussed.
Angiotensin converting enzyme (ACE) inhibitors
Overview of the history and current knowledge of the Renin-Angiotensin System (RAS) and
assessment (not very promising to start with) of different targets within it.
Story of the development of the first ACE inhibitors from early (unsuitable) snake venom
peptides. Structural knowledge of ACE was limited - carboxypeptidase A (another zinc
protease) was employed as an analogous enzyme that cleave a single terminal aminoacid
raher than the two that ACE cleaves.
Analysis of the CPA active site and the elaboration of CPA inhibitor benzylsuccinic acid and
its elaboration to Captopril.
Two syntheses of captopril, racemic with resolution and asymmetric.
Side effects of Captopril and the extention of the byproduct inhibitor strategy resulting in the
formation of Enaprilat. Enaprilat is not absorbed too well making oral delivery difficult,
simple esterification (enapril) solves this – tie in with drug delivery.
Synthesis of enapril(at), lisinopril and quinapril(at).
Consideration of the bioactive conformation and synthesis of cilazapril and two syntheses of
ramipril. Synthesis of fosinopril
More recent information on ACE, N-domain, C-domain, new inhibitors, crystal structure data,
binding, modelling. Discussion of the mode of activity, not as simple as initially thought.
Another target in the RAS – Angiotensin II antagonists, development of losartan, including
two syntheses. Comparison of structures and intereactions with the AII receptor. Synthesis
of valsartan
Calcium Channel antagonists/blockers
Brief overview of calcium channels. And how the different classes of drugs have different
physiological outcomes are employed to treat different cardiovascular problems. A racemic
and chiral synthesis of verapamil. Synthesis of the dihydropyridines nifedipine, K8644 and
amlodipine and diliazam.
Diuretics
Overview of diuretics from the early mercury based compounds in the 1920s. The sites of
action of different diuretic drugs. Structures, uses and mode of action of: carbonic
anhydrase inhibitors such as acetazolamide; loop diuretics such as bumetanide and
furosemide; the thiazides such as chlorothiazide, hydrochlorothiazide, chlorthalidone and
indapamide; potassium sparing diuretics such as triamterine and amiloride. An aldosterone
antagonist spironolactone.
Miscellaneous
Very brief mention of organic nitrates isosorbide dinitrate, nitroglycerin and amylnitrate.
Very brief mention of the cardiac glycosides such as digitoxin.
Brief discussion of the “polypill” containing low doses of 3 antihypertensive drugs, folic acid,
aspirin and a statin at low doses.
CH4054
Asthma
Description of the disease, etiology and number of deaths associated with asthma.
Analysis of the potential targets for treatment, histamine, leukotrienes and their associated
problems. Adrenaline is known to dilate the airways – potential treatment?
Very quick reminder of the adrenergic nervous system (covered in more detail in the CVS
course) focusing on b2-agonists
Examination of adrenaline which can be employed in a clinical setting is not an ideal drug dramatic side effects and poor pharmacokinetics.
The work of Lands leading to the development salbutamol – Understanding the structural
alterations made to reduce metabolism by COMT but retain activity at the b2
adrenoreceptors.
Increasing the duration of action - salmeterol
Overview of other approaches and treatments available
Gastric and duodenal Ulcers
Description of the disease and hi-lighting the problems associated with ulcers prior to the
development of effective anti ulcer treatments.
Etiology of the disease and description of the risks SKF took pursuing histamine as a target other mediators and no proof of histamine subtypes mediating acid secretion at the time.
SAR studies based on the different effects of model compounds on uterus and heart tissue.
Development of histamine from an endogenous agonist to the effective antagonist cimetidine
- the usual methods of developing antagonist behaviour from agonists proved unsuccessful,
sales figures included.
Synthesis of cimetidine
Further work at Glaxo resulting in the development of ranitidine (no P450 issues) including
its synthesis and some sales figures.
SAR studies
Other drugs jumping on the bandwagon - tiotidine, famotidine (including synthesis). Glaxo’s
attempts to prolong activity
Proton pump inhibitors – omeprazole
The role of H. Plyori in ulcers and the introduction of triple therapies.
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4405
ADVANCED MEDICINAL CHEMISTRY V
5
Semester/term Semester 2
taught*
Contact Hours*
Module
Personnel
Learning
Outcomes
Module Learning
20 Lectures; 4 Tutorials
Aims
CH4025 - Supramolecular Chemistry
Module Content/ CH4031 - Organic Synthetic Methods II
Description* CH4034 - DNA Structure and Drug DNA complexes
CH4036 - Bio-Organic Chemistry
CH4025
The following topics will be covered in this lecture course (but many more will also be
featured): Non-covalent interactions: electron-pair donor-acceptor, electrostatic, hydrogenbonding, p-donor-p-acceptor, van der Waals. Importance of geometric control:
preorganisation. Role of solvent: hydrophobic interactions. Cation binding: crown ethers,
cryptands, acyclic receptors. Applications in sensors and phase-transfer catalysis. Anion
recognition: cationic, metal-based and neutral receptors. Recognition of neutral molecules by
hydrogen-bonding and/or p-p interactions in organic solvents, and by hydrophobic
interactions in water. Cyclodextrins, cyclophanes. Supramolecular catalysis, self-assembly of
supramolecular aggregates, coordination networks and crystal engineering. Molecular
motors and machines. Complexed structures formed by self-assembly and the basic
concepts of nanochemistry.
CH4031
Introduction
Overview of the history of chemotherapy as a weapon against cancer.
The Taxol story - screening isolation and so on Microtubule active agaents - Biochemical
background, mode of action
Taxol
Different disconnective approaches to Taxol Holton’s synthesis of Taxol, disconnection, key
points and the chemo-, regio-, stereoselectivity (as appropriate) of each step. Nicloaou’s
synthesis of Taxol, disconnection, key points and the chemo-, regio-, stereoselectivity (as
appropriate) of each step.Taxol SAR
Epothilone
Epothilone history and background information Nicloaou’s synthesis of Epothilone,
disconnection, key points and the chemo-, regio-, stereoselectivity (as appropriate) of each
step.
CH4034
Introduction.
Survey of properties of nucleic acids. Primary structure of DNA and RNA.
Spectroscopy. Ultraviolet, circular dichroism, infra-red and NMR spectroscopies. Evidence
for double-strand formation, base stacking, sugar pucker and nucleotide conformation,
Watson-Crick base-pairing.
Structures of A-DNA, B-DNA, Z-DNA. X-ray methods; fibres and oligonucleotides. Main
features such as pitch, tilt, major and minor groove nucleotide conformation etc.
Binding to DNA. Groove binders (e.g. netropsin), triplex-forming oligonucleotides.
Intercalators. Application of Uv/vis, fluorescence, NMR, X-Ray, viscosity and electrophoretic
methods (Cisplatin has also been considered in previous years
Quadruplex DNA Guanine tetrads, Hoogsten binding. Drug binding.
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
Module Code*
Module Name*
ECTS Weighting*
CH4601
MATERIALS CHEMISTRY 1
5
Semester/term Semester 2
taught*
Contact Hours*
6 Hours
Module
Personnel
Learning
Outcomes
Module Learning
Aims
CH4022 - Matter Transport in Solids
Module Content/ CH4063 - Simulation Techniques in Solids
Description*
CH4022
Mobility of defects in ionic solids - experimental determination of energies and entropies for defect
formation, migration and interaction.
Nature of diffusion in solids and some related phenomena - the diffusion coefficient, D, correlation factors - the Nernst-Einstein equation - techniques for measurement of values
of the diffusion coefficients in solids.
Solid-state reactions - transport processes in diffusion-controlled corrosion reactions - the
corrosion of silver by liquid sulphur - the high temperature corrosion of metals and alloys in
complex aggressive environments.
The nature of fast-ion-conductors, the operative transport mechanisms and the applicatioins
for which these the unique properties of theses materials are essential
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*
CH4602
Module Code*
Module Name*
ECTS Weighting*
MATERIALS CHEMISTRY 2
5
Semester/term Semester 2
taught*
Contact Hours*
18 hours Lectures
Module
Personnel
Learning
Outcomes
Module Learning
Aims
CH4006/CH4064 - Photochemistry
Module Content/
Description* Introduction (1 lecture). Absorption of light. Selection rules and transition probabilities.
Singlet states: (2 lectures) Fluorescence, quantum yields, lifetime measurements,
radiationless processes. Jablonski diagram.
Transient Spectroscopy: (1 lecture). Fluorescence lifetime determination: laser flash
photolysis.
Triplet states: (1.5 lectures) nature, population, spin-orbit coupling, phosphorescence,
energy transfer, reactions. Nanosecond and picosecond laster photolysis.
Photoreduction of benzophenone and derivatives as an illustrative example of an organic
molecule in solution (1.5 lectures).
Another illustrative example of photo-reactions, e.g. Photo-induced electron transfer
reactions or photochemistry of co-ordination compounds.
CH4008/CH4061 - Advanced Physical Chemistry
Electrochemistry:
Classification, synthesis and fundamental properties of electroactive polymer materials. Ionic
and electronic conductivity mechanisms exhibited by electroactive polymers. The
experimental determination of electronic and ionic conductivity in electroactive polymers
using microelectrode and complex impedance spectrosopic methods. The use of
electroactive polymer materials as amperometric chemical sensor devices.
Molecular Reaction dynamics:
Potential energy surfaces and molecular reaction dynamics. P.E. Surfaces. H3. Attractive
and repulsive surfaces. Molecular reaction dynamics. Monte Carlo methods. Reaction crosssection H + H2 reaction.
Molecular Beams and I.R. Chemiluminescence. Molecular beam methods. Reactive
collisions - forward, backward and sticky collisions. IRCL Technique. F + H2 D2; H + F2.
Tunnelling; MRD & ACT.
Recommended
Reading List
Module Pre
Requisite
Module Co
Requisite
Assessment Annual Examination
Details*