Dr Louis Farrugia Room A4-36 Course Secretary: Fiona Ironside ...

Course Head: Dr Louis Farrugia Room A4-36
Course Secretary: Fiona Ironside Room A4-04

Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
The course head is Dr Louis Farrugia, Room A4-36
E-mail: louis@chem.gla.ac.uk or Tel: 0141 330 5137 (direct).
You are welcome to contact Dr Farrugia at any time about any aspect of the course, either directly
or through the Course Secretary, Fiona Ironside, Room A4-04,
Email: fionai@chem.gla.ac.uk or Tel: 0141 330 8618.
LECTURE COURSES
Compulsory Lecture Courses (Core 1 and Core 2): the eighteen compulsory courses are listed
in the timetable. They are given during weeks 1 - 11.
Option Courses: There are eight MSci option courses. Designated “O” in the timetable. You
must attend at least three of these. You make your course selection on the notice board in week
10. Only those courses with sufficient interest (normally a minimum of 4 students) will actually run
and you may be required to alter your choice as a result of this.
Code Course Lecturer
H1 Advanced Organic Synthesis Dr R. Marquez
H2 Pericyclic Reactions Dr A. Sutherland
H3 Heterocyclic Systems Prof J. S. Clark
H4 Colloids & Macromolecules Dr A. Freer
H7 Metals in Medicine Prof L. Cronin
M1 Industrial Medicinal Chemistry Organon
M2 Cancer & Modern Drug Discovery Dr Hartley
M3 & 4 Pharmacology 1 & 2 Prof Martin, Dr Skett & Prof Stone
C1 Processing Chemical Data Prof C. J. Gilmore
C2 Heterogeneous Catalysis Dr D. Lennon
C3 Physical Organic Chemistry Dr G. Bucher
C4 Inorganic Materials Design Prof D. Gregory
C5 Reactivity of Transition Metal Organometallic Dr L. J. Farrugia
Compounds
C6 Asymmetric Synthesis Dr L. Soler
C7 NMR Spectroscopy Prof S. Wimperis
C8 Organic & Bioorganic Supramolecular Chemistry Dr G. Cooke
C9 The Periodic Table from an Electronic Perspective Prof J. McGrady
Minimum of 3 of the following options:
O1 Advanced Bio-Inorganic Chemistry Prof L. Cronin
O2 Organometallics in Synthesis Prof P. Kocovsky
O3 Modern Techniques in Surface Science Dr M. Kadodwala
O4 Protein Structures-Design & Engineering Prof N. Isaacs
O5 Advanced Retrosynthesis Dr R. Hartley
O6 Molecular Magnetism Dr M. Murrie
O7 Molecular Modelling Dr H. Senn
O8 Total Synthesis of Natural Products Prof J. S. Clark
O9 Applications of Synchrotron and Neutron Radiation Prof C. C. Wilson
Refer to Level 4 Courses Handbook for Aims and Objectives
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
Attendance at Alchemist Club and local R.S.C. meetings, which are held on Thursdays at 4 pm, is
recommended and encouraged.
Lectures in Pharmacology: Before starting the pharmacology lecture courses M3 and M4, all
students must read section 1 of Rang, H.P., Dale, M.M. & Ritter, J.M. (1999) “Pharmacology” 4th
Edition. They must also read chapter 1 of Gibson, G.G. & Skett, P. (2001) 3rd Edition
“Introduction to Drug Metabolism”. Before starting the CNS option course, students must read
section 4 of Rang, H.P., Dale, M.M. & Ritter, J.M. (1999) “Pharmacology” 4th Edition.
The pharmacology lectures are given in a style which chemistry students may find unfamiliar. The
material is presented more descriptively. It will not usually be possible to copy down every spoken
word. Students are advised to try to understand the lecture content at the time of presentation and
to make a summary of the concept/theory in note form rather than in full sentences. They can
also include relevant examples or annotated diagrams. Notes should be amplified later by
referring to lecture handouts or textbooks. Past examination questions (reprints available from the
Alchemist Club) indicate the breadth/depth of understanding required. Some Biology 2 material
will be covered for the benefit of CMC 4H students who did not previously study Biology 2.
Students who feel they have already seen this material should not absent themselves from
lectures but should regard them as an opportunity for revision.
Lectures by Visiting Speakers: The 4-M class are required to attend a number of the talks by
external speakers in weeks 1- 24. These will normally be held on Thursdays or Fridays at 4pm.
Details of which talks you should attend will be communicated to you nearer the time and a
reminder will be sent by e-mail.
TUTORIALS
Organic: Alternate weeks 3-24 Mondays at 4 pm in tutor’s office.
Physical: Alternate weeks 4-23 Mondays at 4 pm in the Carnegie or Physical Lecture Theatre.
Inorganic: Inorganic staff will indicate when they are available.
Pharmacology: Weeks 8-11 as marked on timetable.
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
STUDENT PROGRESS
Your performance of class work will be considered satisfactory only if you:
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
Regularly attend lectures and tutorials.
Carry out a research project in weeks 2-24 following the timetable given later in this
handbook.
Give a short oral presentation on your MSci placement project (15 mins + 5 mins for
questions) in weeks 3-5.
Attend selected talks by external speakers.
Submit an essay introduction to your project (as outlined in your third year documentation)
by Friday of week 5 to Fiona Ironside (A4-04).
Attend MSci placement talks on Friday afternoons of weeks 3-5, and attend MSci research
talks in week 27.
Give a Powerpoint presentation on your research project (15 mins + 5 mins questions) in
week 27.
Provide the Chemistry Department with two bound copies of a thesis on your project to be
submitted to Fiona Ironside (A4-04) by 4pm on the 16th March. A further copy should be
prepared and retained by you for your oral.
During weeks 2-24 you are expected to devote at least 20 hours per week to your project.
Persistent absentees from tutorials, lectures or laboratories will be asked to explain their behaviour
to the Head of Department and credit for the course may be denied (i.e. you may not be allowed to
sit the exams if you do not attend the course fully).
EXAMINATIONS
The degree examinations consist of a research project and six written examinations. There is also
a third year carry-over mark and there are marks for essays and the oral presentation. Two of the
written papers are each of three hours duration. All other written papers are of two and a quarter
hours duration. The research project will be assessed on the basis of the thesis (30%), the work
performed during the project (50%), and an oral examination on the contents of the thesis (20%).
All students must be available for oral examination by the external examiners on Tuesday
9 th June 2009 at 8:45 am. This is an integral part of the degree examination.
A summary of all marks for your degree:
Marks
Carry-over from 3rd year 50
Placement 100
Placement talk to department 40
Project Essay 30
Level-4 examination papers (4x2.25h, 2x3h) 500
Distance Learning 30
Research project 100
Research project oral presentation 40
Total 890
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
EXAM STRUCTURE
The final exam papers have a greater emphasis on 4th year material.
MSci in Chemistry with Medicinal Chemistry
Paper 1 MSci Physical Core 1 and Core 2
3 questions from 4
2 h 15 min
75 marks
Paper 2 MSci Inorganic Core 1 and Core 2
3 questions from 4
2 h 15 min
75 marks
Paper 3 MSci Organic Core 1 and Core 2
4 questions from 6, [2 sections, at least 2 from section B (core 2)]
3 h
100 marks
Paper 4 Medicinal Chemistry and Pharmacology
3 questions from 4
2 h 15 min
75 marks
Paper 5 MSci Options
3 questions from approximately 8
3 h
100 marks
Paper 6 MSci Problems based on Core 1 and Core 2 but including data from fundamental
techniques and basic chemistry/medicinal chemistry assumed from earlier years in Core 1 and
Core 2 courses.
3 questions from 6, [Section A 2 organic, 1 medicinal and pharmacology. Section B: 3 drawn from
physical and inorganic. At least 1 from each section]
2 h 15 min
75 marks
Total marks = 500
Important: The total number of questions on a paper is approximate and may change.
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
CONFERENCE ROOM
You are welcome to use the Conference Room as a place to study provided that (a) it is not
required for other departmental purposes, (b) you leave when requested by the janitors and (c)
the room is kept quiet and tidy.
ILLNESS AND ABSENCE FROM CLASSES
If you are unable to attend classes you must follow the new University guidelines regarding
absence, which are available at the following link:
http://senate.gla.ac.uk/academic/policies/student_absence_policy.html
You should also contact Dr Farrugia as soon as possible to explain the reasons for your absence.
If you believe that your performance in the course has been adversely affected for reasons, which
you wish to draw to the attention of the Board of Examiners, it is essential that you write to Dr
Farrugia to inform him of the circumstances.
CHEMISTRY DEPARTMENT LIBRARY
The Librarian, Mrs Denise Curry, has a selection of recommended textbooks which are available
for short term loan. During term 1 she will run courses on how to make best use of the library.
CAREERS TALK AND DISCUSSION
Thursday 16th October 3 pm. "Careers for Chemists" Speakers from industry, the Department
and the Careers Service will present their views of possible careers. This will be followed by an
open-ended discussion.
Individual interviews for all students will be arranged early in Term 1 to discuss their choices of a
future career.
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
FOURTH YEAR PROJECT TIMETABLE
Week 1 Students contact supervisors at 12 noon on Tuesday 23rd September.
Supervisors give students two copies of a synopsis of the project including a title and
leading references.
One copy of the project synopsis should be given to Fiona Ironside (Room A4-04).
Week 2 Practical work begins from the start of week 2. A COSHH form must be completed,
signed by the supervisor and handed into the Departmental Office (Room A4-04).
If the nature of the research changes during the project new COSHH forms must be
completed.
Week 4 Project assessors announced.
Students contact assessors.
Week 24 Friday: Last day of practical work.
Week 25 Friday: Final draft of thesis approved by supervisor.
Week 26 Monday: Deadline for submission of theses. Two bound copies to be submitted to
Fiona Ironside (Room A4-04) on 16th March no later than 4pm. Students should
retain an extra copy for themselves.
Week 27 Thesis talks (15 mins + 5 mins questions - assessed).
Weeks 26-27 Oral examinations: these will be conducted by the assessor and a second member
of staff. The supervisor will not be present. You must arrange the time of this oral
examination with your assessors.
Please note that there is a very short time between the end of practical work and submission of
the thesis. Be sure to begin writing your thesis before you finish work in the laboratory.
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
SAFETY
The Departmental Safety Committee has issued the following guidelines.
1. Experimental work should normally not start before 9.00 am and should finish by 5.00 pm.
2. Prior approval by the supervisor must be obtained should it be necessary for a student to
work even for short periods outwith these hours. The usual rules for late working will apply.
If the supervisor has to leave before experimental work is complete, written permission must
be given and in such cases a designated proxy (academic, post-doctoral or senior technical
staff) must be present in the building.
3. Access to IT equipment will be available only when Janitors are present in the building.
POLICY ON SUMMATIVE ASSESSMENT
All feedback on coursework used in assessment, including mid-year class exam/class test marks
and laboratory grades, is strictly provisional for your guidance only, and is subject to ratification by
the Board of Examiners and external examiners at the end of the academic year. You must retain
all copies of assessed work (lab notebooks, exam scripts, etc.) and have them available for
inspection by the examiners if requested at the end of the year. You will be given reasonable
advance warning should this be required.
PLAGIARISM
Plagiarism is the submission of someone else’s work as one’s own without acknowledgment. As
recent cases have shown, it is regarded as a serious offence against University discipline. You
must read the Senate-approved Plagiarism Statement on pages 9 – 11 which explains university
policy on plagiarism.
Degrees from Glasgow University recognise personal achievement. It follows that any work you
submit must be your own. It may be proper, and even desirable, to include words, data or ideas
taken from books or articles, the world-wide web or even from other students in work you submit
for assessment. But you must make it completely clear what is yours and what you have taken
from others. If you copy someone else’s words you must enclose them with quotation marks. You
should also give a verifiable reference: for example F.A. Cotton and G. Wilkinson, Advanced
Inorganic Chemistry, Fifth Edition, John Wiley & Sons, New York, 1988, page 1219 or J. Smith,
Level-3 Inorganic Laboratory Report, April 2 nd , 2000.
This regulation applies to all work submitted for assessment, including lab reports, class tests and
research projects unless you have specifically been told otherwise, for example in the case of a
group project or when a number of students share experimental data.
You will be required to sign a form stating that any work you hand in is your own.
See University Guidelines at the following address:
http://senate.gla.ac.uk/discipline/plagiarism/index.html
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
GUIDELINES FOR PRESENTING AND WRITING A THESIS
The thesis counts for 40% of the marks assigned to the project and, in addition, is the only
tangible result of the sixteen weeks of work which can be shown to the External Examiners. It is
therefore important that you do not let yourself down by a badly written or produced thesis.
TECHNICAL POINTS
The thesis should be word processed (the Department now has an adequate number of PC’s with
WORD 97 installed).
The font should be clear. Fonts normally used are Times New Roman or Arial (usually 10, 11 or
12 point). This document is written in Arial 10 pt with main headings in 12 pt bold and subheadings
in 10 pt bold.
The thesis should use 1.5 line spacing and have a reasonable margin on the left hand side to
allow for binding. Margins of 3.17 cm left and right and 2.54 cm top and bottom are acceptable.
Pages should be numbered consecutively, as should diagrams and spectra. Since the word
processor will do the numbering for you, it is easier if you do not include whole page diagrams or
spectra in the page numbering, but this is a matter of choice.
Chemical structures can be drawn using ChemDraw or ChemWindow and copied into WORD 97.
On the other hand there is nothing wrong with Xeroxing in structures (and indeed diagrams)
provided that the result looks neat and clear.
REFERENCES
Referencing work is very important and is frequently badly done. The format shown in the
following examples is that employed by the Royal Society of Chemistry. It should be used unless
your supervisor suggests an alternative.
1. Journal articles: (Journal in italics, year, volume no in bold, page no)
I. A. Fallis, L. J. Farrugia, N. M. Macdonald and R. D. Peacock, J. Chem. Soc. Dalton Trans.,
1989, 931.
C. Macleod, R.C. Hartley and D.W. Hamprecht, Org. Lett., 2002, 4, 75-78.
other possibilities are:
unpublished work, in press, personal communication.
2. Books: (Authors, Title in italics, publisher, place, year, vol no, page if necessary)
F.A. Cotton and G. Wilkinson, Advanced Inorganic Chemistry, Fifth Edition, John Wiley &
Sons, New York, 1988, page 1219.
3. Theses:
N. M. Macdonald, Ph. D. Thesis, University of Glasgow, 1994.
P.A. Lovatt, B. Sc. Thesis, University of Glasgow, 1993.
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
CONTENT
The thesis should contain:
• Title page
• Acknowledgements
• Contents page (with page numbers)
• A one page Abstract
• Introduction
• Experimental Section,
• Results and Discussion (or Results and Discussion as separate sections)
• Conclusions
• References
The above order is customary but sometimes the Experimental Section appears between
Conclusions and References - consult your supervisor.
The INTRODUCTION should set the work in context, review previous work (fully referenced),
describe any techniques or theories with which you were unfamiliar when you began the research,
and describe what you intended to do.
The EXPERIMENTAL SECTION should give full experimental details of all reactions or
experiments carried out. It is particularly important to indicate which are literature preparations
and which are novel. If a literature preparation is reported it is important to note if you modified it
or if it behaved in an unexpected way. New compounds should be as fully characterised as
possible. It is a good idea to include the actual spectra of new compounds (and other bulky
supporting data) in one or more Appendices.
The DISCUSSION is extremely important and is often where students do not do themselves
justice. A project where absolutely nothing has worked can be made interesting by discussing
WHY things went wrong. In any case, the discussion is often where you show how much of the
project you understood!
The CONCLUSIONS should summarise the work and suggest how it could be continued in the
future.
The ABSTRACT will be similar to the Conclusions but should be concise and incisive - it is the first
thing an examiner will read, and should encourage him or her to read the rest of the thesis!
Finally: SPELL CHECK YOUR THESIS.
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
CHEMISTRY-3H & 4H: RECOMMENDED TEXTBOOKS FOR 2008-2009
(a)
ESSENTIAL PURCHASES Level-4 Students will already have most of these books.
• Molecular models, table molecular model kit such as Organic/Inorganic Orbit kit, Orbit
Molecular Building System, Cochranes of Oxford Ltd, Leafield, Oxford OX8 5NT, £13.20.
• EITHER Inorganic Chemistry, Shriver, P W Atkins and C H Langford, OUP, 4th Edition, 2006,
£37.99 OR Inorganic Chemistry, Houscroft and A.G Sharpe, Prentice Hall, 2nd Edition, 2004.
• Biocoordination Chemistry, D E Fenton, Oxford Science Publications, £10.99.
• Spectroscopic Methods in Organic Chemistry, D H Williams and I Fleming, McGraw-Hill, 5th
Edition Revised, £39.99.
• Organic Chemistry, J Clayden, N Greeves, S Warren and P Wothers, OUP, £36.99.
• Physical Chemistry, R A Alberty and R J Silbey, John Wiley, 4th Edition, £37.95.
• Introduction to Molecular Symmetry, J S Ogden, Oxford Chemistry Primers, £10.99
• Molecular Quantum Mechanics, P W Atkins and R S Friedman, 4th Edition, OUP, 2004,
£35.99.
(b)
RECOMMENDED READING
• Basic Solid State Chemistry, Second Edition, A R West, John Wiley, £29.95.
• Structural Methods in Inorganic Chemistry, E A V Ebsworth, D W H Rankin and S Craddock,
Blackwell, 2nd Edition. Currently out-of-print but second hand copies may be available.
Particularly useful for laboratory and tutorial work and helpful in problem solving.
• The Mechanisms of Reactions at Transition Metal Sites, R A Henderson, Oxford Science
Publications, £10.99.
• Crystal Structure Determination, W Clegg, Oxford Chemistry Primers, £10.99.
• Foundations of Science Mathematics, D S Sivia and S G Rawlings, Oxford Chemistry Primers,
£10.99, uses relevant chemical problems to illustrate the mathematical material. There is an
accompanying text of Worked Problems (ISBN 019 850429) in the same series. Also worth a
look is
• Beginning Mathematics for Chemistry, S K Scott, OUP, £22.99.
ESPECIALLY RELEVANT TO LEVEL-3 COURSES
• Workbook for Organic Synthesis: The Disconnection Approach, S Warren, Wiley, £29.95.
• Reactive Intermediates, C J Moody and G H Whitham, Oxford Chemistry Primers, £10.99.
• Stereoselectivity in Organic Synthesis, G Procter, Oxford Chemistry Primers, £10.99.
• Chemical Aspects of Biosynthesis, J Mann, Oxford Chemistry Primers, £10.99.
• Stereoelectronic Effects, A J Kirby, Oxford Chemistry Primers, £10.99.
ESPECIALLY RELEVANT TO LEVEL-4 COURSES
• Aromatic Heterocyclic Chemistry, D T Davies, Oxford Chemistry Primers, 1997, £10.99.
• Pericyclic Reactions, I Fleming, Oxford Chemistry Primers, £10.99.
• Ions in Solution, J Burgess, Horwood Publishing, Chichester, 2nd Edition, 1999, ISBN 1-
898563-50-0.
• Chemical Bonding and Molecular Geometry, R J Gillespie and P L A Popelier, Oxford
University Press, New York, 2001, ISBN 0-19-510496-X, £29.99.
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
CHEMISTRY ONLY
• Beginning Group Theory for Chemistry, P H Walton, OUP, 1998, £29.99.
• Molecular Symmetry & Group Theory, R L Carter, Wiley, 1998, £40.95.
NOTE: All prices are subject to change by publishers at any time.
(c)
BOOKS AVAILABLE FOR CONSULTATION IN THE CHEMISTRY BRANCH LIBRARY
INORGANIC CHEMISTRY
• Advanced Inorganic Chemistry, F A Cotton and G Wilkinson, John Wiley, 6th Edition.
• Chemistry of the Elements, N N Greenwood and A Earnshaw, Pergamon, 2nd Edition.
More of a reference book than a text book, but contains factual information, particularly for main
group elements, which is more complete than in Cotton and Wilkinson.
• Some Thermodynamic Aspects of Inorganic Chemistry, D A Johnson, Cambridge U.P, 2nd
Edition. (Out of Print)
• Inorganic Chemistry, A G Sharpe, Longman, 3rd Edition.
• Orbitals, Terms and States, M Gerloch, John Wiley, out of print.
A small book that should help to clarify difficulties in understanding the nature of orbitals, terms
and states. Relevant to many courses in Inorganic and Physical Chemistry.
• The Elements, Their Origin, Abundance and Distribution, P A Cox, O.U.P.
Useful background and revision materials for Radiochemistry courses.
• A Guide to Modern Inorganic Chemistry, S M Owen and A T Brooker, Longman.
Sets out to answer the questions that are asked most often by students. A revision aid.
• Heterogeneous Catalysis. Principles and Applications, G C Bond, O.U.P.
• Environmental Chemistry – A Global Perspective, G W van Loon and S J Duffy, O.U.P.,
2005, 2nd Edition
ORGANIC CHEMISTRY
• A Guidebook to Mechanism in Organic Chemistry, P Sykes, Longmans, 6th Edition.
• Some Modern Methods of Organic Synthesis, W Carruthers, Cambridge U.P, 4th Edition.
• Guidebook to Organic Synthesis, R K Mackie, D M Smith and R A Aitken, Longman, 3rd
Edition.
• Advanced Organic Chemistry - Reactions, Mechanisms and Structure, 5th Edition, J March,
John Wiley. The definitive reference work which is an excellent and complete source of
references.
• Secondary Metabolism, J Mann, Carendon Press, 2nd Edition.
• Medicinal Chemistry, C R Ganellin and S M Roberts, Academic Press, 2nd Edition.
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Level 4M Chemistry With Medicinal Chemistry Session 2008 - 2009
ESPECIALLY RELEVANT TO LEVEL-4 COURSES
• Heterocyclic Chemistry, T L Gilchrist, Longman, 3rd Edition.
• Heterocycles in Life and Society, A F Pozharskii, A T Soldatov and A R Katritzky, Wiley.
• Non-Benzenoid Conjugated Carbocyclic Compounds, D Lloyd, Elsevier. (Out of print)
• Molecular Biology of the Gene, Volumes 1 & 2, J D Watson et al., Benjamin//Cummings, 4th
Edition.
• Organic Chemistry - A Guide to Common Themes, T Kitson, Edward Arnold.
A very readable overview of concepts and reaction types.
PHYSICAL CHEMISTRY
• Chemical Applications of Group Theory, F A Cotton, John Wiley, 3rd Edition.
• Tables for Group Theory, P W Atkins, M S Child and C S G Phillips, O.U.P.
• Chemical Bonding Theory, B C Webster, Blackwell Scientific, Oxford, 1990.
• Modern Spectroscopy, 4th Edition, J M Hollas, John Wiley.
• Fundamentals of Molecular Spectroscopy, C N Banwell, McGraw-Hill, 4th Edition.
• Crystal Structure Analysis: A Primer, J P Glusker and K N Trueblood, O.U.P., 2nd Edition.
• Symmetry and Structure, S F A Kettle, John Wiley.
• Biophysical Chemistry, C R Cantor and P R Schimmel, W H Freeman & Co.
• Physical Biochemistry, D Freifelder, W H Freeman & Co.
• Protein Structure - A Practical Approach, T E Creighton, IRL Press, 2nd Edition.
• Introduction to Protein Structure, C Branden and J Tooze, Garland Publishing, 2nd Edition.
• Physical Biochemistry: Principles and Applications, D Sheehan, Wiley.
• Physical Chemistry, P W Atkins, OUP, 8th Edition.
• Molecular Modelling. Principles & Applications, A R Leach, Addison Wesley Longman, 2nd
Edition, 2001
• Computational Chemistry, G H Grant and W G Richards, Oxford Chemistry Primers.
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