Graduate School of Chemistry

Director: Professor D.J. Robins

Graduate School of Chemistry

Session 1998-1999

Postgraduate Research Training Programme

Head of Graduate School of Chemistry

• Prof. D. J. Robins

Head of Department of Chemistry

• Prof. J.M. Winfield

Graduate School of Chemistry Committee

• Dr R. C. Hartley

• Dr L. Hecht

• Dr D.W. McComb

• Dr I. Pulford

Postgraduate Research Training Programme

As part of their formal training and in order to be awarded a Ph.D., all postgraduate research students in the Department are required to,

(i) attend the postgraduate safety training programme and, if appropriate, the radiation protection course before commencing any practical work

(ii) attend courses arranged by the Physical Sciences Graduate School

(iii) attend and be assessed on the content of postgraduate lecture courses

(iv) attend sectional colloquia

(v) participate in postgraduate research seminars

(vi) produce a research report in May and September of their 1st year and May of their 2nd year

(vii) undergo at least one oral examination after the May report is submitted and before the end of September.

(i) Postgraduate Safety Training Programme

This course is mandatory for all 1st year postgraduate students. It will be co-ordinated by Dr R.J. Cross and consists of four lectures presented on 5th, 6th, 7th and 8th October from 9-10 am in C4-07.

The content of the course will be examined at 9 am on 9th October in room C4-07 and the examination must be passed before practical work can be undertaken in the department.

Radiation Protection Course

This course is run by the Scottish Universities Research and Reactor Centre and the University Radiation Protection Service, and is mandatory for postgraduate students who intend to become "classified" radiation workers. As registration is required before the end of September, students who need to do this course will have been enrolled by their supervisor.

All lectures are given in room 222 in the Kelvin Building (Department of Physics and Astronomy) from 10.00 am to 5.00 pm on 6th and 7th October 1998. An examination on the content of the course will be held a week later. Those who intend to become "classified" radiation workers must sit this examination and others are strongly advised to do so. The results of the examination are not published but successful candidates are awarded a certificate indicating that they have attained a satisfactory standard. In the event of failure, another opportunity to take the examination is provided a few weeks after the original examination.

(ii) Physical Science Graduate School Courses

These will be outlined in a separate handout. The courses must be attended by 1st year postgraduate students and a certificate obtained before a Ph.D. can be awarded.

(iii) Postgraduate Lecture Courses

During the first 2 years, all students must obtain a total of at least 6 course credits by attending at least 3 courses in the 1st year and the remainder in the 2nd year. A credit is awarded for satisfactory attendance at a postgraduate lecture course AND successful completion of an assessment exercise based on the course material. Note that credits are not awarded for the Physical Science Graduate School courses, the safety training course or the practical experience courses.

Postgraduate courses (5 lectures - 1 credit) should be chosen from those detailed in the appendices. These courses may also be attended by undergraduates. Students wishing to undertake courses with Computing Services, or postgraduate lecture courses outside the Department, either in other Departments within the University or at the University of Strathclyde, may do so with the approval of the appropriate Head of Section. A 4th year option course (8 lectures - 1 credit) or an AFE/ENV Chemistry Honours Module (15 lectures - 2 credits) may be substituted for a postgraduate course only with the approval of the Head of Section. Documentation for the 4th year option courses and the AFE/ENV modules can be found at the Department of Chemistry web site (http://www.chem.gla.ac.uk).

All postgraduate students are required to inform Dr R.C. Hartley of those courses which they intend to undertake. This should be done using the tear-off slip at the back of this manual which should be returned by Friday 9th October.

PRACTICAL EXPERIENCE COURSES - These courses are intended to allow postgraduate students to gain "hands-on" experience in the use of advanced equipment and are considered essential before general access to the instruments is available to any particular student. Although numbers on any given course may be limited the course may be repeated in the light of demand. Students should discuss with their supervisors which courses are required for their research.

(iv) Sectional Colloquia

All postgraduate students are expected to attend the colloquia of their section of the Department.

(v) Postgraduate Seminars

Each student will be required to attend the postgraduate seminar programme organised within her/his own section and to give seminars to their appropriate section as required by the Head of Section. Each postgraduate student must give a talk on her/his own research during her/his final year. Attendance at all sectional seminars is mandatory for all research students. Training sessions (one hour per week) are organised within some research groups.

(vi) Research Reports

Each research student is required to submit a word-processed report on her/his research to the appropriate Head of Section in May and September of their first year and May of their second year. The deadlines for submission of these reports are 1st May 1998 and 1st September 1998. Section Heads will provide guidelines for these reports. A list of courses and colloquia attended should be appended to each report. The reports and subsequent oral examinations are designed to:

(i) Develop written and oral communication skills;

(ii) Provide guidance and continuous assessment;

(iii) Develop a sense of accountability;

(iv) Develop professional standards for the acquisition and reporting of experimental data;

(v) Train the student to formulate objectives and assess progress;

(vi) Ensure that the student prepares for the thesis in good time.

(vii) Annual Oral Examination

All 1st and 2nd year postgraduate students will be examined orally by the Head of Section and an internal examiner who is not the student's supervisor (normally the co-supervisor) on the content of (a) their research report(s); (b) postgraduate courses attended; (c) material from seminars and Departmental colloquia (lecture notes may be brought into this examination). Students whose performance in the oral examination is deemed unsatisfactory will be required to undertake remedial work on which they will be subsequently examined or, in extreme cases, be required to terminate their research studies.

Annual Report to Head of Department/Head of Graduate School

In accordance with Faculty policy on postgraduate student progress and supervision, supervisors will agree with Section Heads on a written report to the Head of Department/Head of Graduate School and to the student on the performance of each postgraduate student in her/his annual oral examination and on the content of their research report.

Submission of Thesis and Final Oral Examination

All students should have completed their practical work by the end of September in their final year and thesis writing should be well advanced by then. Theses must be submitted within one further year. It should be noted that any students requiring access to Departmental facilities beyond 30 September of their final year, (for students commencing their course of study in the Department on 1 October, or other appropriate date for students commencing their course of research study at other times) will be required by the University to matriculate and pay the appropriate "writing-up" fee. As the name implies this is only intended to allow students to have access to facilities for the purpose of writing their thesis. Under no circumstances will any student in this category be permitted to carry out additional practical work. If further practical work is necessary the express permission of the Head of Department/Head of Graduate School must be obtained and an appropriate fee paid to the University. As required by Senate and Faculty, the final oral examination will be carried out by a nominated external examiner together with an internal examiner who is not the student's supervisor. At the prior request of the examiners, students may be required to produce, at the oral examination, their laboratory notebooks, spectra, reference samples of key compounds, computer output, etc. which have been obtained during the course of their research. Notebooks, spectra, compounds prepared and computer output remain the property of the Department.

APPENDIX 1 : COURSES AVAILABLE

Specialist Postgraduate Courses

Unless otherwise stated, these modules carry 1 credit. Only those courses for which sufficient attendance is registered will actually run. Postgraduates will be notified in good time if a course is to be cancelled.

POSTGRADUATE LECTURES: Physical Lecture Theatre unless otherwise stated

Practical Experience Courses

These courses are organised within the Department and arrangements to take a course should be made by the student with the appropriate staff member listed below.

UV/IR spectroscopy Mrs V. Thomson (A3-26c)

Practical Chromatography Dr W.J. Cole (A5-12)

NMR spectroscopy Dr D. Rycroft (C3-04b)

There is a wide range of state of the art equipment within the department and training is available in techniques such as laser raman spectroscopy, analytical electron microscopy, X-ray crystallography, mass spectrometry, differential scanning calorimetry, thermogravimetric analysis and fluorescence spectroscopy by special arrangement with the appropriate staff member, who will be identified by the student's supervisor.

AFE/ENV Chemistry Honours Modules

These modules are each of 15 lectures and 2 credits will be awarded on successful completion of a course. All lectures will take place in Tutorial Room C4-07.

The following courses will be held at 10.00 am on Mondays, Tuesdays and Thursdays for 5 weeks starting on the date shown.

Postgraduate lecture courses at University of Strathclyde

All courses run in 2nd Semester except GB (S981e). See timetable below for dates, times and locations. All courses are worth 1 credit unless otherwise stated.

TIMETABLE FOR STRATHCLYDE UNIVERSITY POST-GRADUATE COURSES 1998-99

Note:

MA will be incorporated into the 4th Year Undergraduate course, P2, run in the 2nd semester --- see 4th Year timetable.

GB is in the 1st semester, 5,6,7th January.

APPENDIX 2 : POSTGRADUATE COURSE OUTLINES

Course Code: A982a

Value: 2 Credits

Title: Organic Synthesis Workshops 1

Duration: 12 hours

Lecturers: Dr R. C. Hartley and Dr J. L. Matthews

Aims: To teach students to use retrosynthetic analysis in the design of syntheses and to interpret spectroscopic data for the identification of compounds. Students will present their solutions to the problems distributed by RCH or JLM one week before each workshop.

Objectives: The following topics will be covered:

1. Synthesis of aromatic compounds.

2. Synthesis of amines.

3. Synthesis of 1,2-, 1,3-, 1,4-, 1,5-, and 1,6-difunctional compounds.

4. Synthesis of double bonds.

5. Mechanisms of organic reactions as appropritae to the above.

6. Interpretation of spectroscopic data.

Outline: (i) Aromatic compounds. (ii) Amines. (iii) 1,3-Difunctional compounds. (iv) Spectroscopy 1. (v) Double Bonds. (vi) 1,5-Difunctional compounds and Michael addition. (vii) Diels-Alder and 1,6-difunctional compounds. (viii) 1,2-Difunctional compounds. (ix) Spectroscopy 2. (x) 1,4-Difunctional compounds. (xi) Pyrroles. (xii) Spectroscopy 3.

Assessment: by the students' presentations in workshops.

Course Code: A982b

Value: 2 Credits

Title: Organic Synthesis Workshops 2

Duration: 12 hours

Lecturers: Dr S. K. Armstrong and Dr. D. J. Procter

Aims: To integrate a working knowledge of organic reactions and synthetic design and analysis, using the context of published syntheses. Discussion sheets will be distributed approximately 1 week before each workshop, and students are expected to bring written answers with them to the workshop.

Objectives: To give confidence and understanding in the interpretation of published syntheses, and in suggesting alternative synthetic strategies which could be investigated. In line with recent interview practice by chemical employers, some emphasis will be given to heterocyclic compounds.

Assessment: by the students' weekly presentations and/or by a final "open book" test.

Course Code: A981c

Value: 1 Credit

Title: Instrumental Chromatographic Methods

Duration: 5 hours

Lecturer(s): Dr M. C. Jarvis

Aims: To give a practically-oriented introduction to GC and HPLC methods and instrumentation for the analysis of organic and biological samples.

Objectives:

1. Learn how to select the most suitable GC or HPLC method for any particular application, based on systematic criteria.

2. Understand what controls resolution and sensitivity in different forms of chromatography, how they are interrelated and how to optimise them.

3. Learn how to choose columns and conditions for GC separations.

4. Learn how to choose columns and conditions for HPLC separations.

5. Tackle straightforward troubleshooting of GC and HPLC methods and equipment, including problems of interpreting integrator outputs.

Outline: Principles of chromatography. Performance criteria. Factors controlling resolution: the Van Deemter equation. Gas chromatography: capillary and packed columns. Stationary phases. Injection systems for capillary GC. The flame ionisation detector. Specialised detectors for trace analysis. GLC-MS. High-pressure liquid chromatography: chromatographic modes and column packing materials. Instrumentation for HPLC. UV detectors. Others detector systems. Integrators and chromatographic data handling.

Assessment: End of course assessment to be decided.

Course Code: A981d

Value: 1 Credit

Title: Advanced Structure Determination

Duration: 8 hours

Lecturer: Prof J. D. Connolly & Dr D.J. Procter

Aims: To show how a combination of modern spectroscopic techniques can be used for the elucidation of complex structural problems.

Objectives

1. To understand the basics of the NMR technique and how pulse sequences can be designed to achieve a particular output from an NMR experiment.

2. To familiarise students with more advanced NMR and Mass Spectrometric techniques.

3. To enable students to select appropriate techniques to solve particular structural problems.

4. To assign complex structures using a combination of modern spectroscopic techniques.

Outline: The majority of the material in the course will be dealt with in a workshop format. The course will begin with a brief introduction to the basic theory of NMR. This will include a discussion of the rotating frame, T1 and T2 relaxation times, and 90¡ pulses (and how to determine these values experimentally) and inverse detection. Techniques to be discussed will include one-dimensional experiments like spin decoupling and NOE difference and two dimensional experiments like direct proton-proton correlation (COSY), direct proton-carbon correlation (HMQC or HSQC), long range proton-carbon correlation (HMBC) and 2D NOE experiments (NOESY and ROESY). Emphasis will be on how to extract the required information from spectra obtained from these experiments. Finally, a brief discussion of advanced mass spectrometric techniques will conclude the course.

Course Code: A981e

Value: 1 Credit

Title: Molecular Recognition-Man-made and Natural

Duration: 8 hours

Lecturer: Dr M. C. Parker

Aims: To introduce molecular recognition in synthetic systems and illustrate these concepts by extensive reference to examples of molecular recognition in biological systems. Understand the role intermolecular forces and solvent play in binding processes.

Objectives: To understand what forces are important in controlling molecular recognition; be able to determine binding constants; knowledge of techniques to measure binding constants; prediction of design criteria and an understanding of the importance of molecular recognition in biological systems.

Outline:

1. Molecular recognition, what is it ?

2. Beginnings of host-guest chemistry, thermodynamic aspects of molecular recognition

3. Types of interactions; measuring binding constants; examples from literature; synthetic systems-underpinning principles of drug-design and examples from nature.

Course Code: A981f

Value: 1 Credit

Title: Modern techniques in surface science.

Duration: 8 hours

Lecturer(s): Dr M. Kadodwala

Aims: To introduce advanced methods of surface science, and give examples of how they are applied in the study of model adsorbate-surface systems

Objectives:

1. Outline laser/optical techniques of surface analysis.

2. Understand surface photochemistry and photochemical modification of surfaces, and their applications in nanotechnology.

3. Understand advanced structural probes.

Outline:

1. Basics: surface science, what is it all about ? Second harmonic generation and SFG.

2. Surface photochemistry: theory, some examples, nanosecond versus femtosecond excitation.

3. Advance techniques in surface structure: SEXAFS, photoelectron diffraction, X-ray standing wave (XSW), surface XRD, quantative LEED.

Course Code: A981g

Value: 1 Credit

Title: Electron distributions and chemical bonding

Duration: 8 hours

Lecturer: Dr P. R. Mallinson

Aims: To introduce experimental and theoretical methods for determining charge density distributions of molecules, and their application to chemical properties

Objectives:

1. Understand the relation of X-ray scattering by a crystal to light scattering (the relation of wavelength to resolution). Use the concept of Fourier transformation to define the structure factor.

2. State the Laue conditions governing the amplitude of the structure factor for a crystal.

3. Explain how space-group-forbidden X-ray scattering may arise from aspherical atomic densities. Define the terms promolecule density and deformation density. Be familiar with the X-X and X-N experimental techniques.

4. Be familiar with formalisms of the X-ray scattering factor and its relation to the structure factor: the isolated-atom approximation; the generalised scattering factor description of aspherical atoms. Describe the multipole model of the atomic density and know the principles of fitting multipole parameters to experimental structure amplitudes by least squares.

5. Be aware of ab initio molecular orbital methods for obtaining electronic charge distributions in molecules.

6. Interpret charge density in terms of modern quantum chemistry via the topology of the charge distribution. Understand the concepts of stationary values of the charge density, interatomic (zero flux) surface, Laplacian distribution, and their relation to chemical bonding.

7. Know the theoretical relations of X-ray structure factors and scattering factors to wavefunctions.

8. Know how various types of dynamic density distributions are obtained from multipole structure factors via Fourier synthesis. Know the principles of calculating static density distributions and other properties directly from the multipole model.

9. Be aware of some important aspects of charge density experiments: the effect of temperature, correlation of thermal and charge density parameters; the rigid bond test for reliability of the model. The use of synchrotron radiation.

10. Interpret physically the harmonic and anharmonic formalisms of the atomic temperature factor.

Outline: The geometrical and physical optics of X-ray diffraction in relation to resolution. Introduction of the aspherical model of atomic density into the structure factor, and the concept of deformation density. Experimental determination of charge distributions in crystals by multipole analysis of diffraction data. Theoretical determination of charge distributions; properties of atoms in molecules via topological analysis of the charge density. Derivation of chemical properties from the experimental multipolar density. Practical considerations of charge density experiments. Harmonic and anharmonic atomic vibrations and their effects.

Course Code: A981h

Value: 1 Credit

Title: Excited States of Inorganic Compounds

Duration: 8 hours

Lecturer: Dr R. D. Peacock

Aims: The aims of the course are to give an appreciation of the preparation, characterisation, properties and reactivity of excited states of inorganic compounds

Objectives: You should be able to:

1. Understand the information contained in Tanabe-Sugano, Jablonski and Potential Energy diagrams for the d3 electron configuration

2. Understand the vibronic structure of absorption and emission bands in terms of the Frank-Condon principle. Know how such vibronic structure can be used to determine the nature and magnitude of the geomtry change in going from the ground to the excited state

3. Know the deactivation routes for excited states - fluorescence, phosphorescence, non-radiative decay, quenching

4. Understand the reasons for fluorescence quenching in the chlorophyll dimer

5. Appreciate the nature of the charge-transfer excited state of [Ru(bipy)3]2+. Understand how this excited state can be quenched by oxygen to produce singlet oxygen. Understand how the redox properties of the excited state of [Ru(bipy)3]2+ are different from those of the ground state and how this can result in electron transfer and the "water splitting" catalytic cycle.

6. Understand why the photochemical reactions of Cr3+ differ in rate from the ground state reactions.

Outline: How the excited states of a molecule differ in physical and chemical properties from the ground state properties; revision of Tanabe-Sugano diagrams and the electronic spectra of transition metal ions; selection rules; potential energy and Jablonski diagrams; vibronic structure and the Franck-Condon principle; how to use vibronic structure to quantify geometry in the excited state; excites state spectroscopies; methods of deactivation of the excited state - fluorescence, phosphorescence, non-radiative decay, quenching; energy and electron transfer; photochemistry; examples from the photochemistry and photophysics of chlorophyll, Cr3+ complexes and [Ru(bipy)3]2+

Course Code: A981i

Value: 1 Credit

Title: Total Synthesis of Natural Products

Duration: 8 hours

Lecturer(s): Prof. P. J. Kocienski/Dr E. Colvin

Aims: To survey some of the recent strategies that helped guide synthetic chemists in the construction of complex natural products.

Objectives: To survey some of the recent strategies that helped guide synthetic chemists in the construction of complex natural products.

Outline: A selection of natural product syntheses from distinguished laboratories will be used to illustrate how strategic thinking has influenced the concision and efficiency of complex synthesis. The strategies will include (a) two directional synthesis; (b) desymmetrisation; (c) cascade (domino) reactions; (d) biogenetic approaches; (e) remote functionalisation. Lecture material will be accompanied by readings from the literature.

Course Code: A981j

Value: 1 Credit

Title: Organometallics in Organic Synthesis

Duration: 8 hours

Lecturer: Dr D.J. Procter

Aims: To explore further the use of transition metals and lanthanides in organic synthesis. The course will examine a wide variety of synthetically useful organotransition metal and organolanthanide processes.

Objectives:

1. Recall examples of organometallic reactions already seen in previous courses.

2. Discuss new organotransition metal reactions and look at their use in synthesis.

3. Understand the mechanisms of some of these reactions.

4. Examine the catalytic cycles involved in some processes.

5. Discuss important organolanthanide reactions and their use in synthesis.

6. Discuss the mechanism of some of these processes.

7. Examine the difference in properties between the transition metals and the lanthanides which give rise to their specific chemistry.

Outline: Few of today's syntheses are achieved without employing a metal or organometallic reagent at some stage in the route. This course builds on previous synthetic courses and aims to cover the important areas of organotransition metal and organolanthanide chemistry. Focusing on the synthetic value of each reaction, we will examine 'classic' organometallic processes and newer 'state of the art' reactions. The mechanistic aspects of both stoichiometric and catalytic processes will be addressed. All new reactions will be illustrated by examples taken from recent synthetic reports in the literature.

Course Code: A981k

Value: 1 Credit

Title: Clusters and Surfaces

Duration: 8 hours

Lecturer: Dr L. J. Farrugia

Aims: To introduce the concept of the cluster-surface analogy, and examine the validity of this model in terms of structure, reactivity and energetics of transition-metal cluster compounds.

Objectives:

1. To learn the types of cluster compounds formed by the transition metals

2. To learn how electron counting rules are used to rationalise metal framework geometries

3. To compare metal-atom geometries in clusters and bulk and particulate metals

4. To learn how ligands bind to clusters and how this may be compared with chemisorbed molecules

5. To learn about the dynamic processes in metal cluster compounds and how this relates to ligand dynamics on surfaces

Outline:

1. Introduction to cluster chemistry. Classification of cluster compounds. Types of ligands associated with cluster compounds. Electron counting in clusters - the role of ligand-ligand interactions.

2. Why study clusters? The validity of the cluster-surface analogy. A comparison of cluster structures and those in bulk metals, including a discussion of high nuclearity clusters.

3. Modes of ligand bonding in clusters with particular reference to catalytic models. Ligand and metal mobilities, and fluxional processes in cluster compounds

4. Reactivity of clusters, in particular with respect to multi-site coordination of ligands

Course Code: A981l

Value: 1 Credit

Title: Solids and Surfaces - A Chemist's View of Bonding in Extended Structures

Duration: 8 hours

Lecturer: Dr D.L. Lennon and Dr D.W. McComb

Aims: To describe and discuss the fundamental concepts of structure and bonding that underpin solid-state and surface chemistry

Objectives:

1. To learn about the fundamental inter-relationship between orbitals and bands

2. To learn how to sketch simple band structures from a chemist's viewpoint.

3. To learn how to interpret band structure and density of states diagrams.

4. To learn how to use the fundamental concepts to learn more about the structure and bonding in solid state structures.

5. To learn how to use these concepts to describe surfaces and to understand molecule-surface interactions.

Outline: Orbitals and bands in one dimension. Bloch functions, k-space and band structure. Band width and interpreting band structures. The Fermi level. Density of states. Solid state examples.

Setting up a surface problem. Molecule-surface interactions using density of states. The frontier orbital perspective. A surface case study. Barriers to chemisorption. Qualitative reasoning about orbital interactions on surfaces

APPENDIX 3 : Course Outlines for Postgraduate lectures at University of Strathclyde

Name

Room No.

Supervisor

Section Inorganic/Organic/ Physical

Year of Study 1st/2nd

I will attend the following postgraduate lecture courses during the 1997/98 session:

* If any of the courses selected are 4th year options courses or courses other than Glasgow Chemistry Department courses please indicate above and obtain the signature of the appropriate Head of Section.

Head of Section

Please note that first years must attain at least 3 credits. Second years and other postgraduates must complete all remaining credits as detailed on the postgraduate notice board.

Please return this form to Dr R. C. Hartley (Room C4-11)

by Friday 16th October, 1998