Department of Chemistry


Class Handbook


Course Documentation








Modules 2X and 2Y

Session 1999 - 2000




Welcome back to the Department as a member of the Chemistry-2 class. Whether you are doing just one module or both, we hope you will find these courses stimulating and the staff friendly and approachable.

In Chemistry-1 you received a general introduction to the foundations of the subject. During your second year you will build on this foundation and commence a more serious study of chemistry which you will undoubtedly find more rigorous and challenging. Nevertheless, in designing the Chemistry-2 Modules our main objective has been to produce courses which are interesting, enjoyable and useful, not only for those who wish to proceed to Honours in Chemistry, but also for those who intend other degree courses.

Successful completion of Chemistry-2 (2X and 2Y) will allow you to proceed to Honours BSc courses in Chemistry or the new MSci. degree courses. During term 2 we will give you details of the various courses in Chemistry-3H and -4H, invite one or two representatives from industry to explain the types of employment which are available for Chemistry Honours graduates, and describe briefly the wide range of research being pursued within the Department. Those of you who proceed to Chemistry-4H will have the opportunity to undertake a research project within one of the research groups.

We are sure you will find that, as you explore the subject in greater breadth and depth, you will begin to realise how far-reaching chemistry becomes and how fascinating it can be. It is our intention to make your second year both enjoyable and successful. If you have any problems please inform your tutor immediately, or go to Dr. Freer, your class head, or to the appropriate lecturer so that they can help you - that is our job and that is why we are here. But we can only successfully help those who bring their problems to us before it is too late.

Finally, we would ask you to read the contents of this booklet and associated documentation very carefully. All sections are important, but we should draw your attention in particular to those sections dealing with "Course Assessment" and "Absence". It is most important that Dr. Freer is kept fully informed of any illness or other extenuating circumstances which might affect you during the year, so that these can be taken into account in assessing your overall performance at the end of the year.

Professor P. J. Kocienski

Head of Department




Outline of Course Content

Lecture Course

The level two chemistry course comprises two modules. Chemistry-2X , Molecules Matter - the Fundamentals, and Chemistry-2Y, Chemistry of the Natural World. The lectures, which are in the West Medical Building at 11 a.m. each day, form the central core of each module and are compulsory. Chemistry-2X is on Tuesdays and Thursdays and some Mondays, while Chemistry-2Y is on Wednesdays and Fridays and intervening Mondays (check lecture timetable on page 13 for details). Each module comprises 7 lecture blocks with 8 lectures in each block. Lectures provide only part of the information required for each topic and the student is expected to amplify this knowledge by attending tutorials and laboratory sessions as well as private study.

Talking during lectures is a distraction to both the lecturer and your fellow students and is probably the commonest problem raised at staff/student meetings. If persistent talkers are sitting next to you let them know of your, and your classmates’ resentment at their unsociable behaviour!


Practical work is divided into three main laboratory periods: physical, organic and inorganic, each of 5 weeks duration. Attendance is compulsory. Each module demands one afternoon session per week and is arranged, as far as possible, to accommodate other subjects. Students taking both modules will therefore be required to do two afternoons per week (normally Wed. & Thurs. or Mon. & Tues.) while single module students will normally be allocated a Monday or a Tuesday to dovetail with possible IBLS modules. Normal laboratory hours are 2:00 - 5:00. A charge (£15) is made to help cover the cost of laboratory manuals, notebooks, handouts, graph paper etc. This is collected during the afternoon enrolling session when laboratory days are assigned.

How many lab. experiments do I have to do?

This is the commonest question asked in any of the labs. The answer: as many as you can manage. Since the duration of individual experiments varies (some take only 2 hours, others 4 hours including write up) then some students may get through five or even six experiments and others only 4 (which would be regarded as a minimum) per module in the five week period. The number of modules you are doing, and any difficulties encountered in the experiments, is taken into account when the overall mark is assigned. Laboratory assessment contributes 10% to your final assessment.

The design study.

Since the design of an experiment involves a book or literature search, as well as an extensive write - up over two lab. afternoons, only students doing both modules will be assigned a design experiment. This is credited as two experiments and hence the write up should be relatively substantive.

NB. Students intending to do Chemical Physics only do one laboratory session per week and do not do a design study.

All chemical substances present a certain risk. Learning how to handle them is part of your training. Information and safe handling procedures are provided in the laboratory manuals.

Interactive Teaching Units with an Industrial Dimension

During weeks 8 and 16 students are required to participate in the interactive teaching units (ITUs) on industrial chemistry. Attendance for one unit per module (i.e. both units if you are doing both modules) is compulsory with each unit contributing 5% towards your final assessment. All Chemistry-2Y students are required to complete ITU 1 in week 8. Only Chemistry-2X students are required to do ITU 2 in week 16. Each unit is roughly equivalent to a laboratory practical slot and will last 3 hours. The units provide an insight to the range of issues typically faced within the chemical industry and illustrate the role of chemists in a modern and dynamic industrial environment.

Students will be spilt into small groups to work through problems of major interest to the modern chemical industry. In addition to covering specific areas of chemistry, which will complement that presented in lectures, broader issues such as economic and environmental issues will also be addressed. The units operate in an interactive manner, with small groups having to adopt a team approach to problem solving. Assessment will be by attendance as well as a short written report.

Unit 1 : The Age of Refrigeration. Unit 2 : Mercury, Membrane or Diaphragms


Tutorials begin in week 3 and run on alternate (odd) weeks throughout the session, except for week 13 which is class exam week. Attendance at tutorials is mandatory. Tutorial groups normally consist of six students meeting with the staff tutor at a time convenient to both students and tutor. Tutors are normally assigned during week 2. Tutorial work is taken from the problems set in the in the tutorial handbook for the appropriate week and must be handed in to the tutor in advance. This is important as it gives the tutor a guide to underlying problems in specific areas of the course and can form the basis of one to one or small group discussion. The work handed in is graded and a record of attendance is kept. Answers to the tutorial problems will be displayed on the Chemistry-2 notice board the week after the tutorial. The content and format of many of the questions in the tutorial book closely mimics class and degree exams questions. Students will therefore find tutorial sessions very helpful. The tutorial system is organised by Dr. A. Benniston (room A4-32c) and any problems associated with the tutorials should be taken up with him directly.


In some of the lecture blocks a problem solving workshop is substituted for one of the lectures. You will find the relevant workshop in the tutorial handbook. Students are encouraged to tackle as many of the questions as possible since the material covered in the workshop is often used as the basis for exam questions.

Voluntary Organic Tutorials (VOTs)

Experience has taught us that students often find difficulties in two particular areas of the Organic Chemistry course, viz. stereochemistry and curly arrow representation of organic mechanisms. To help students improve in these two areas we have set aside an hour slot on the Friday of week 9 for an extra stereochemistry tutorial and Monday and Thursday of week 19 for curly arrow tutorials. Further details of times and locations will be given nearer the time. Do come along and benefit from these extra tutorials.

Study Advice

Your lecturers will have spent many hours ensuring that the contents of their lectures are both relevant and up to date. However, in the time allocated to the lecture blocks it is impossible to adequately cover all aspects of individual topics. You are therefore encouraged to read the relevant sections of the recommended textbooks and make additional notes. The Chemistry branch of the University Library is located on the top floor of the Joseph Black Building and you may find it useful to browse through additional books for a different interpretation of a particular topic. If you are having problems with any part of the course seek advice sooner rather than later either from the lecturer giving the course or from Dr. Freer.

Finally, as term progresses you will experience great pressure to complete essays for other subjects and perhaps put chemistry studies ‘to another day’. This is a recipe for disaster! You should therefore try and keep up with the volume of work by studying as much as possible in the evenings and integrating the tutorials and workshops into your study regime.


Course Assessment

The final mark for the course is made up as follows:

Minimum Requirements for the Award of Credits

Students may be awarded credits for the course only if they meet the following requirements:

Normally no grade or credits shall be awarded to a candidate who has not met these requirements.


The mid-session Class examination is provisionally on the Thursday afternoon of week 13. It is in the form of one 1½ hour paper per module (i.e. 2 x 1½ hours for those doing both modules). Only work covered in Term 1 is examined. An example of the Class examination is given at the back of this course documentation.

It is important that you do well in the Class Examination as this forms 35% of your final assessment. A poor performance will put pressure on you to work significantly harder for the degree exam. You do not get a second chance with the class exam. It is vitally important for you to plan your work from the start with this in mind.

Extenuating circumstances (e.g. illness) at exam times must be reported to Dr. Freer at the time and supported by a medical certificate or other appropriate documentation.

The end of course examination is in the form of one 3 hour paper per module (i.e. 2 x 3 hours for those doing both modules). It will include compulsory questions on topics covered in Terms 2 and 3 plus a choice of questions from work across the entire year.

Exam papers from previous years can be purchased from the Alchemist Club but it should be borne in mind that changes have been made to the course in recent years and hence exam questions on some topics may be different from the current course.

Laboratory assessment

In each section (physical, organic and inorganic) lab. grades are determined by various factors, including the number of experiments completed and the marks awarded for written work and your overall comprehension of the experiment undertaken.

There is no minimum number of experiments - you are expected to attend all laboratories sessions, though you will be given credit for reasonable explained absence due to illness or other circumstances.

It is your responsibility to ensure that lab. reports are submitted for marking in time - usually on completion of each experimental exercise. Credit may not be given for work handed in late.

The overall lab grade, determined by performance in all three sections, contributes up to 10% of your final assessment. Grades and their contribution to the assessment are as follows:-

Grade Contribution (%) to final assessment

A (Excellent) 9-10

B (Very Good) 7-8

C (Satisfactory) 5-6

D (Disappointing) 3-4

E (Must Improve) 1-2

F (Award of credits doubtful) 0

Rough guidance for the sort of typical performance required to achieve such grades are as follows:-

Number of and

Grade experiments Average

per section* Mark/10

A ³ 8 ³ 8 [* Half this for single

B 8 7-8 module students.]

C 6-7 6-7

D 5-6 5-6

E < 5 -

F < 3 -


Notice to Students - 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.)

Grade point averages: Guidelines



Grade descriptor

Grade points







very good




















very poor


Total grade points = sum of credits x grade points

Grade point average (GPA) = Total grade points/ Total credits

The grade point average and credit level requirement for B.Sc. and M.Sci. are given in full in the University of Glasgow Calendar 1998-1999. Some of the key points are listed below. Please consult your adviser of studies for full details.

Diploma of Higher Education (General Science)

240 credits (with at least 140 in Science) with grade point average of at least 8.5


360 credits (with at least 200 in Science and 120 above level 1) with grade point average of at least 10 and at least 50% of grade points and at least 60 of credits above level 1 must be at grade D or better.

B.Sc. in General Science

Must have a broad spread of Science Subjects (biological, mathematical, physical).

If grade point average is greater that 12 - awarded with merit

If grade point average is greater that 14 - awarded with distinction

B.Sc. in a Designated Subject (e.g. Chemistry)

Must have at least 80 credits with at least 800 grade points at level 3 of the designated subject. Merit and distinction as above.

Admission to B.Sc. Honours

Must have at least 240 credits (with at least 140 in Science) with a grade point average of at least 11. At least 60 credits should be above level-1. In addition, each department sets a minimum grade in certain subjects e.g. Chemistry B.Sc. Honours requires D grade or higher passes in both 2X and 2Y.



Admission to M.Sci.

Must have at least 240 credits (with at least 140 in Science) with a grade point average of at least 12. At least 100 credits should be above level-1. In addition, each department sets a minimum grade in certain subjects e.g. Chemistry M.Sci. normally requires grade A passes in both 2X and 2Y.

Student Responsibilities

Absence From Classes


should be explained by a doctor's medical certificate or similar document which MUST be submitted to the Registrar’s Enquiry Office, Main University Building

The medical certificate will be copied by the Registrar’s Office to all the Class Heads of the subjects you take and your Adviser of Studies.


may be explained by a 'Self Certificate of Absence' (available in the Science Faculty Office and submitted to the Science Faculty Office, Boyd Orr Building

For the overall assessment of the course, attendance credits will only be given if absence was adequately explained by one or other of these routes.

Student feedback

We hope that the course will operate smoothly, but if there are difficulties, bring them to the attention of Dr. Freer immediately they arise so that we may try to resolve them as quickly as possible. Play an active part in the staff/student liaison committee, either directly or through your class representative. Please take time to complete the evaluation questionnaires and try to provide constructive comments. This helps to modify and improve the course for the future.

Class representatives

During the first week of the new term you will be invited to elect two members of the class to represent you on the Staff-Student Liaison Committee and for liaison between staff and students. The names of the Class Representatives and notices of forthcoming meetings will be posted on the Chemistry-2 notice board.

Staff-Student Liaison Committee

The Staff-Student Liaison Committee, which includes the Head of Department, all other Class Heads and the Class Representatives from other years, meets once or twice every term in the Conference Room (A4-41) in the Chemistry Department. Students may have any items they wish included in the agenda and are also free to raise any matters they wish at the meetings without prior notice. Minutes of the meetings will be posted on the class notice board.


Students are reminded that regulations regarding plagiarism (copying) apply to all work contributing to assessment, including lab. reports, class tests, and research projects. Except where specifically directed, as part of a group project for example, all assessed work must be your own. Copying of lab reports, for example, is plagiarism - students may share data, where appropriate - but the report must be your own.

"The University's degrees and other academic awards are given in recognition of the candidate's personal achievement. Plagiarism is therefore considered as an act of academic fraudulence and as an offence against University discipline. Plagiarism is defined as the submission or presentation of work, in any form, which is not one’s own without acknowledgement of the sources. With regard to essays, reports and dissertations, a simple rule dictates when it is necessary to acknowledge sources. If a student obtains information or ideas from an outside source, that source must be acknowledged. Another rule to follow is that any direct quotation must be placed in quotation marks, and the source immediately cited." (University of Glasgow Calendar, 1998-99, p.16)

Other Information


Students doing both modules should obtain their own copies of:-

1. Atkins: "Physical Chemistry" (6th. Edn.)

2. Shriver, Atkins & Langford: "Inorganic Chemistry"

3. Bruice, "Organic Chemistry" (2nd Edn.)

When purchasing Bruice you should find a voucher inside that enables you

purchase a set of Orbit Molecular Building Models at half price.

Also recommended:-

4. Webster: "Chemical Bonding Theory"

5. Tebbutt: "Basic Mathematics for Chemists"

Students doing Chemistry-2Y only will find it useful to obtain a copy of Bruice.

Other books held in the library will be recommended occasionally for consultation. A set of Orbit molecular models is a compulsory requirement for the stereochemistry lecture course. They may be taken into examinations if you find them useful. (Get them half-price!!)

Notice Boards

The Chemistry-2 notice boards (2X and 2Y) are situated on the ground floor of the Joseph Black (Chemistry) Building opposite the IBLS computing suite. Class exam results, laboratory grades and general course information as well as answers to tutorials and workshops will be displayed here.

Medical Conditions

Students with long term medical conditions or other disabilities which may interfere with their course work should let Dr. Freer know, in confidence, of the situation.

Careers Talks

Towards the latter half of the second term (normally Monday and Tuesday afternoons of week 18) several speakers are invited from the Chemical Industry to describe the various career opportunities in chemistry and allow students to find out more about the diversity of a career in chemistry. For students thinking of staying on for a higher degree a synopsis of some of the current research being undertaken in the department will also be given.

Industrial Visits

We hope to arrange some short site visits for small groups of students to local chemical and biotechnology companies. These will be co-ordinated via your Class Representatives. More details will be given nearer the time (normally week 20).


Up to date course documentation, research details and other goodies are available on the Chemistry Department home page (

It is also worth noting that some of the recommended textbooks and further information can be found at the appropriate publisher website. Details of the addresses will be given at the lectures when they become available.



CHEMISTRY 2X and 2Y STAFF 1999-2000

Room No.* e-mail

x1 AC Thermodynamics Prof. Alan Cooper B4-20c alanc

x2 DMC Solid State Chem. Dr. Dave McComb A3-23 davidm

x3 SA Stereochemistry Dr. Susan Armstrong C5-03 s.armstrong

x4 AC Quantum Mechanics, Prof. Alan Cooper B4-20c alanc

x5 JW Main Group Prof. John Winfield A4-08 johnwin

x6 PK Reaction Pathways Prof. Philip Kocienski C4-04 philk

x7 RC Organometallic Chemistry Dr. Ron Cross A4-32d ronc


y1 RH Spectroscopy Dr. Bob Hill A4-35 bobh

y2 CG Kinetics Prof. Chris Gilmore A5-27 chris

y3 JM Aromatic Chemistry Dr. Jennifer Matthews C5-19 j.matthews

y4 ACB Co-ordination Chem. Dr. Andy Benniston A4-32c andrewb

y5 AF Biophysical Chem. Dr. Andy Freer A4-13 andy

y6 RH Applied Organic Chemistry Dr. Bob Hill A4-35 bobh

y7 RCH Organic Synthesis Dr. Richard Hartley C4-11 richh



Class Head: Dr. Andy Freer (330 5945) A4-13 andy

Tutorial Administration: Dr. Andy Benniston A4-32c andrewb

Class Secretary: Lesley Bell (mornings only) A4-42 lesleyb



Laboratories: Staff Senior Technician

Physical Speakman (A3-07) Dr. Andy Freer Mr. Jim Gorman

Organic Cullen (A3-25) Dr. Peter McCabe Mr. Jim McIver

Inorganic Cullen (A3-25) Dr. Diane Stirling Mr. Jim McIver


* All room numbers refer to the Joseph Black (Chemistry) Building.

†e-mail addresses suffixed by, e.g.














SESSION 1999-2000






Title: Molecular Thermodynamics: a hitch-hikers guide.

Duration: 8 Lectures.

Lecturer: Prof. A. Cooper (Room B4-20c).

Aims: To give an introduction to the molecular basis of thermodynamics and show how basic thermodynamic concepts and properties of matter are related to chaotic molecular properties by a common-sense statistical approach, with examples and applications in simple systems


  1. Define internal energy and enthalpy, heat and work, in molecular terms and appreciate why a statistical approach is needed to describe the molecular basis of thermodynamics.
  2. Express and explain the meaning of the Boltzmann probability expression and apply it to numerical calculations in various circumstances.
  3. Calculate average thermal kinetic energies of particles, describe evidence in support of molecular thermodynamics.
  4. Understand chemical equilibrium from a statistical viewpoint, derive the expression for the Gibbs free energy of a simple chemical reaction from the Boltzmann formula, show how this leads to a molecular definition of entropy.
  5. Understand how intermolecular interactions might modify simple molecular thermodynamics expressions and show how this leads to the concepts of activity and activity coefficient.
  6. Appreciate the relationship between the free energy of a process and the work available.
  7. Define chemical potential and understand how this applies in complex mixtures, with reference to phase equilibrium processes. Define standard states.
  8. Relate and use the concepts and methods outlined here to other areas of the chemistry curriculum, and other molecular thermodynamics problems.

Course Outline: Energy and the First Law; Heat vs Work; Internal Energy (U) and Enthalpy (H = U + PV); molecular/statistical view of chemical equilibrium; Probability and statistics, statistical derivation of K = 4 for H/D exchange; Boltzmann exponential formula, p(E) = w.exp(-E/kt); examples (i) population of molecular vibrational levels, (ii) barometric formula. Average thermal (kinetic) energy = 3kT/2 per molecule; use of U or H in different circumstances; w = "number of ways" in which molecules may take on energy E; probability distribution, means, fluctuations in simple descriptive terms; Brownian motion, blue skies, chemical kinetics as examples of fluctuations; demonstration of critical point fluctuations. Chemical equilibrium; D G° = -RTlnK from Boltzmann formula; entropy S = kln(w) per molecule (=Rln(w) per mole); free energy as an alternative way of writing probability; statistical meaning of the Second Law; "the most probable things generally happen"; corrections for intermolecular interactions: activity and activity coefficients; dS = dQ/T; D S for ideal gas expansion; free energy and work; D G (not D H) = maximum work; complex mixtures; chemical potential; G = å nim i ; phase equilibrium and mixtures; m i (phase 1) = m i (phase 2) at equilibrium; m i = m i ° + RTln(ai), and different forms for liquids, solutions, gases, etc., standard states.


Title: Solid State Chemistry - Beyond the molecular world

Duration: 8 Lectures

Lecturer: Dr. D. W. McComb (Room A3-23).

Aims: To examine the patterns adopted by atoms/ions in simple solids and consider why one arrangement may be preferred to another; to consider how the properties of a solid are influenced by the packing arrangement in metals, ionic crystals, covalent crystals and some minerals.


  1. Close-packing in solids: Be able to describe the characteristics of cubic and hexagonal close packing. Be able to identify the geometry, inter-atomic spacings and composition of the unit cells. Be able to discuss the structure of metals and alloys in terms of close packed solids and qualitatively relate the properties to the crystal structure. Have an understanding of the relative sizes of atoms/ions and how these influence the structure adopted by a given material.
  2. Ionic Crystals : Be able to identify and describe the key structures (rock salt, zinc blende, fluorite, antifluorite, caesium chloride, rutile) that can be used to describe ionic crystals. Understand and be able to identify the types of hole present in the crystals and the location of the ions in the close-packed sites and holes. Be able to describe some applications of these materials and relate the properties to the crystal structure.
  3. Covalent/Network Crystals: Understand and be able to describe the structure-property relationship observed in the allotropes of carbon. Be able to describe the formation of intercalated compounds and discuss the structure-property relationship.
  4. Silicate Crystals : Understand and be able to describe some of the basic silicate mineral structures such as nesosilicates, disilicates, chain structures, layered structures and zeolites. Understand and be able to describe how the structure of zeolites can be utilised in technological applications.


Course Outline: The initial part of this lecture series will expand upon some of the first year inorganic course. Students are, therefore, encouraged to reacquaint themselves with some aspects of their first year notes. In particular, students should know the different simple crystal packing patterns of (i) simple cubic, (ii) body-centred cubic (bcc) and face-centred cubic (iii), and be able to calculate co-ordination numbers, interatomic distances and ions per unit cell. This will lead in to discussion of more up-to-date topics outlined above. The solid-state experiment in the second year teaching laboratory will give students the opportunity to build, examine and use models of many of the structures discussed.



Title: Organic Stereochemistry: shape matters

Duration: 8 hours

Lecturer: Dr. S. K. Armstrong (Room C5-03)

Aims: To give an understanding of the importance of molecular shape, and to introduce the principles governing stereospecific reactions in organic chemistry.


Objectives: by the end of the course students should be able


  1. To draw accurate representations of three-dimensional molecules using various conventions, including wedge-and-hash, Newman, Fischer and sawhorse projections
  2. To illustrate the conformations available to acyclic organic molecules, and their relative energies
  3. To label chiral centres accurately as R or S, and double bonds as E or Z, using the Cahn-Ingold-Prelog sequence rules, and to know the meanings of the D/L and +/- conventions for labelling chiral compounds
  4. To define and give an example of a "stereospecific reaction"
  5. To explain why SN2 reactions proceed with inversion of configuration, whereas SN1 reactions may proceed with complete racemisation.
  6. To define "syn" and "anti" addition to double bonds, and give an example of each
  7. To illustrate and explain the stereochemical course of the reactions of alkenes with reagents such as bromine, hobr, hydrogen (catalysed), borane, peracids, and osmium tetraoxide
  8. To identify the products of such addition reactions as chiral, achiral, meso, diastereomeric, or identical; and to appreciate that chiral products will be formed as racemic mixtures
  9. To explain why E2 reactions usually proceed from antiperiplanar conformations, whereas E1 reactions need not; and to predict whether E1, E2, SN1, SN2, will be observed for a given molecule
  10. To draw accurate representations of the common conformations available to cyclohexanes (including conformational ring inversion or "ring flip"), with substituents, and to label the substituents correctly as "axial" or "equatorial"
  11. To appreciate that low-energy cyclohexane conformations are chair-shaped with equatorial substituents, and that a sufficiently bulky group ("locking group") can prevent conformational inversion, and so affect the chemistry of the ring.


Course Outline: Drawing molecules: stereochemical conventions; chirality, enantiomers and the Cahn-Ingold-Prelog sequnce rules. Substitution reactions. Alkenes: E and Z double bonds, syn and anti additions to alkenes. Compounds with more than one chiral centre: diastereomers, meso compounds. Physical properties of enantiomers and diastereomers contrasted. Conformational analysis of ethane and related compounds. Elimination reactions. Cyclohexane conformations; substituents on cyclohexanes; ring flip and its prevention.


Title: Quantum Mechanics, Chemical Bonding and Symmetry

Duration: 8 Lectures

Lecturer: Prof. Alan Cooper (Room B4-20c)

Aims: To introduce the basic concepts of quantum mechanics and its application to the electronic structure of atoms and molecules, chemical bonding and the elements of symmetry.


1. Appreciate the wave-particle duality of matter and the Heisenberg uncertainty principle.

2. State and apply the de Broglie relation.

3. Recognise the different components of the Schrodinger equation.

4. Appreciate what is meant by a wavefunction.

5. Understand the origin and shape of the different atomic orbitals, as obtained from the study of the hydrogen atom.

6. Apply electron spin and the Pauli exclusion principle.

7. Appreciate how molecular orbitals (chemical bonds) may be made up by a combination of atomic orbitals.

8. Understand how the shape of an object may be described in terms of basic symmetry properties.

9. Know the basic symmetry elements and define what is meant by a point group and a space group.

10. Apply these concepts to the understanding of the properties of simple molecules.


Course Outline: (to follow)


Basic text:- Atkins "Physical Chemistry" (OUP, 6th edition.)

Additional reading:-

P.A.Cox "Introduction to Quantum Theory and Atomic Structure" (Oxford Chemistry Primers #37)

M.J.Winter "Chemical Bonding" (Oxford Chemistry Primers #15)

Title: Main Group Chemistry : from acids and superacids to crowns and crypts.

Duration: 7 lectures, 1 workshop.

Lecturer: Professor J.M. Winfield. (Room A4-08).

Aims: To convey the diversity and usefulness of main group chemistry through discussion of key compounds in areas that provide useful reagents for organic chemistry or which challenge simple ideas of structure and bonding.


  1. Be able to recognise a Brønsted acid and super acid, to be able to differentiate between Brønsted and Lewis acids and to understand their applications for protonation in carbocation and non-metal cationic chemistry.
  2. Be able to use oxidation states and VSEPR to interpret the chemistry of interhalogens and noble gas compounds; be able to use the solvent system concept to describe BrF3 solution chemistry; be able to recognise that molecular structures (e.g. XeF6) may depend on the state of matter.
  3. Appreciate the importance of atomic size, electronegativity and bond energies in determining the properties of C-F vs. C-H compounds.
  4. Be able to use oxidation state diagrams (Latimer and Frost) to interpret the main features of chlorine-oxygen and nitrogen-oxygen chemistry in aqueous solution.
  5. Be able to appreciate the relationship between simple bonding descriptions of nitrogen oxides and the main features of their chemistry.
  6. Understand how ionic size and hence lattice energy can determine the properties of simple ionic salts; understand what is meant by solvation and the applications of the HSAB principle to anion-cation interactions in water.
  7. Know the features that make crown ethers and cryptands useful ligands for simple cations and the behaviour of the e- in strongly basic solvents; hence understand the conditions necessary for synthesis of alkalides (e.g. Na-) and electrides.
  8. Be able to apply simple 3c, 2e bonding pictures to B2H6 and higher boranes.
  9. Be able to apply the knowledge and principles contained in 1-8 to unknown situations.


Course Outline: Properties of and chemistry in, HF, HSO3F and CF3SO3H; effect of SbF5 and generation of carbocations by protonation or cracking. Interhalogens and noble gases focusing on BrF3 and XeF6. The mirror image situation for fluorocarbons vs. Hydrocarbons. Chemistry of Cl-O and N-O compounds with particular reference to HClO4, HOCl, HNO3, N2O42NO2 and NO. Simple salts of Groups 1 and 2 cations, size and lattice energy effects in Li3N and Mg3N2. Simple models for solvation of ions. Co-ordination chemistry of s block metals focusing on polydentate crown ethers and cryptands. Liquid NH3 and amines for the production of the solvated e- . Birch reduction, preparation of Na-, and e- salts. The nature of e- deficiency and the simple 3c, 2e- bonding model applied to B2H6 and other simple BnHm species. A problem-solving workshop.

Title: Reaction Pathways: carbanions and the mechanisms of key steps in organic chemistry.

Duration: 8 Lectures.

Lecturer: Professor P. J. Kocienski (Room C4-04).

Aims: To convey the importance of the carbonyl group and to show how carbonyl groups are valuable (i) in carbanion generation and subsequent carbon-carbon bond formation and (ii) as electrophiles.


  1. Appreciate the structure of the carbonyl group and recognise its importance in the natural occurrence of ketones, aldehydes, carboxylic acids, esters and amides. Know why e.g. urea is a solid but but-2-methylpropene is a gas.
  2. Understand nucleophilic attack on carbonyl carbon with e.g. LiAlH4, Grignard reagents, cyanide ion and semicarbazide, appreciate how protected cyanhydrins act as defence mechanisms in plants.
  3. Appreciate the acidity of protons on carbons adjacent to the carbonyl group and pKa values of ketones, understand how enolates are formed, how they stabilise negative charge on carbon, how they react as nucleophiles; understand how enols are formed in acidic solution and their relation to phenols.
  4. Understand the mechanism of a -halogenation, a -deuteriation, a -alkylation and a -racemisation of ketones and the mechanism of the iodoform reaction.
  5. Understand how enolates are formed from ethyl acetonate (EAA) and diethyl malonate (DEM) and then used in the Claisen and Dieckmann condensations for the synthesis of b -keto esters and ketones. Understand the mechanism of decarboxylation of b -keto acids.
  6. Understand the pathway of the aldol reaction, including its reversibility, and the subsequent dehydration sequence. Appreciate its use in the synthesis of enones including the Robinson annelation reaction.
  7. Understand how the Michael addition reaction occurs and its utility in synthesis of 1,5 dicarbonyl compounds.
  8. Be able to apply the knowledge and principles contained in 1-7 to novel situations.

Course Outline: Polarity of carbonyl group in ketones, esters and amides; dipolar character of amides. Carbonyl carbon as the site of nucleophilic attack by LiAlH4 etc. Reversibility of cyanhydrin formation; locking of cyanhydrin by sugar in nature and use of this as a defence mechanism. Base-induced enolate formation, relationship with EZ elimination; pKa as index of acidity of a -proton. Acid-induced enol formation. Enolates as bidentate nucleophiles, react via C toward R-hal, D2O and iodine; racemic products where appropriate. Very acidic central proton in EAA and DEM; reaction of derived enolate anions with esters to give b -keto esters (Claisen); its cyclic variant Dieckmann condensation. Decarboxylation of derive b -keto-acids. Reaction of enolates with ketones (aldol) to give a -b enones; ring forming reactions (Robinson annelation). Addition of nucleophiles to a -b unsaturated ketones (i.e. to C3 of >C3 = C2 - C1 = 0) Michael addition; synthesis of 1,5 diketones.

Title: Organometallic Chemistry - metal meets carbon.

Lecturer: Dr R.J. Cross (Room A4-32d).

Aims: To introduce the chemical diversity and value of organometallic compounds of both the main group and transition elements.


1. Be familiar with the range of organometallic compounds of main group metals (groups 1, 2, 12 - 15) and be able to relate their reactivity to the metal electronegativity (e.g. reactions with water, oxygen, donor solvents).

2. Know the main methods of synthesis of main group organometallic compounds, and be able to devise appropriate methods to prepare a stated compound.

3. Know the nature of Grignard reagents in solution, and understand the evidence for this.

4. Know which organometallic compounds are likely to be electron deficient, and understand the structural, bonding and reactivity consequences of electron deficiency.

5. Appreciate how the reactivity of organometallic compounds can be modified to suit particular objectives.

6. Understand the stoichiometries and structures of transition metal carbonyl complexes, and be able to explain the bonding in such compounds in terms of synergic systems involving p -bonding.

7. Understand the basis and use of the 18-electron rule to explain or predict the stoichiometries of low oxidation-number transition metal complexes.

8. Be able to apply the principles of 6 and 7 to transition metal compounds containing nitrosyl, alkene and other p -bonded ligands.

9. Know the operation of the b -process, oxidative addition/reductive elimination and insertion reactions of s -bonded (h 1) organo-transition metal complexes, and understand the role of spectator ligands in stabilising s -bonded organo-transition metal compounds.

10. Appreciate how the above reactions feature in processes catalysed by transition metal compounds, and know the key steps in the hydroformylation reaction catalysed by CO2(CO)8.

11. Be able to apply the knowledge and principles embodied in the above to previously unseen examples and situations.

Course Outline: The chemistry of main group element organometallics will be developed first, as many of the principles encountered here also apply to transition metal derivatives. Reactivity patterns, structures and bonding will be related to periodic position of the elements involved, and examples of applications and uses cited throughout. Preparative methods will be explained.

Transition metal organometallics will be developed via metal carbonyls and other p -bonded complexes, before proceeding to h 1-derivatives. The use of the 18-electron rule will be emphasised. Typical reactions of s -bonded organo-transition metal compounds will be explained, and rationalisation made of the structures of organo-transition metal complexes. The applications of these reactions in catalytic processes will then be illustrated by the cobalt carbonyl catalysed hydroformylation (OXO) reaction.













SESSION 1999-2000







Title: Spectroscopy: seeing molecules in different lights.

Duration: 8 Lectures.

Lecturer: Dr R A Hill (Room A4-35).

Aims: To explain the different ways in which electromagnetic radiation may interact with molecules and how this may be used to determine molecular structure; to introduce the theory behind electronic and vibrational spectroscopy and NMR and mass spectrometry; to enable students to use UV/visible spectroscopy for quantitative analysis and IR and NMR spectroscopy for simple structure determinations.


  1. Understand the relationship between light absorption and colour and appreciate the range of the electromagnetic spectrum and the units in which electromagnetic radiation is measured.
  2. Appreciate the idea of a chromophore; understand the origin of the p ® p * transition in terms of a simple M.O. diagram; understand the origin of charge transfer spectra; know and be able to use Beer’s law.
  3. Know the equation relating the wavenumber of an IR transition to the force constant and reduced mass; be able to draw the normal modes of vibration of H2O and CO2 and understand the selection rule for IR spectra (change of dipole moment).
  4. Appreciate the idea of group frequencies and know the approximate wavenumber of the IR absorptions of the common functional groups.
  5. Appreciate the basis of NMR spectra and understand the origin of 1H chemical shifts in terms of electron density surrounding the nucleus; know the approximate chemical shifts of common groups.
  6. Understand the origin of spin-spin splitting and be able to work out the number of nearest neighbours based on the splitting pattern.
  7. Interpret simple 1H, 13C, 31P and 19F NMR spectra.
  8. Understand the principles of mass spectrometry.

Course Outline: Principle of absorption spectrometer and how absorption spectra relate to colour of samples. The electromagnetic spectrum and units of measurement. Electronic spectra and chromophores: d® d and p ® p * transitions and charge transfer complexes. The Beer-Lambert law and its use in analysis. Vibrational spectra, mathematical interpretation and reduced mass. Vibrational spectra of polyatomic molecules: H2O, CO2, CH2O. Group frequencies. Nuclear magnetic spectroscopy, chemical shifts and spin-spin coupling. Interpretation of 1H, 19F, 13C and 31P NMR spectra. Mass spectrometry.

Title: Kinetics, Explosions, Oscillations and Chaos: A look at very fast, oscillating and inherently chaotic reactions, catalysis and other topics.

Duration: 8 Lectures.

Lecturer: Prof. C. Gilmore (Room A5-27).

Aims: To explore what controls the rates of chemical reactions and how to measure them; to explain the basis for very fast reactions and explosions; to describe modern examples and applications of periodic and chaotic chemical phenomena.


  1. Be able to describe various experimental methods to study the speed at which chemical reactions take place.
  2. To identify experimental methods appropriate in particular practical circumstances.
  3. Relate experimental results to aspects of the reaction mechanism involving concepts such as: elementary reactions, rate-determining steps and the steady-state approximation.
  4. Apply these concepts and experimental methods in the understanding of real processes, including catalysis (enzymes), oscillating reactions, chain reactions and explosions.

Course Outline: Chemical kinetics - the measurement of how fast chemical reactions take place and the molecular factors that control these rates. How a reaction rate is defined and how it is measured: traditional experimental methods for slow reactions; rapid reaction techniques, including stopped-flow, chemical relaxation, spectroscopic methods, temperature-jump, flash photolysis. Reaction mechanisms, elementary reactions, consecutive reactions, rate-determining steps, the steady-state approximation. Applications to real systems: catalysis, enzymes and enzyme inhibition, Michaelis-Menton mechanism; oscillating reactions; chain reactions and explosions. Recent developments in chaos theory: what are chaotic systems, and how can this explain certain reaction behaviour?

Title: Aromatic Chemistry: tastes, smells, colours, bangs.

Duration: 8 Lectures.

Lecturer: Dr. Jennifer L. Matthews (C5-19).

Aims: To examine the many ways that aromatic compounds impinge on our daily lives, in smells and flavours (e.g. vanillin), in dyes, in drugs (e.g. salicylic acid), in detergents, in plastics, in insecticides and even in explosives (e.g. TNT).


  1. Know that aromatic hydrocarbons usually undergo substitutions, unlike alkenes (addition).
  2. Be aware of Hückel's (4n+2) p-electron rule; be aware of the criteria that must be fulfilled for a compound to be classified as aromatic; be aware of the criteria for antiaromaticity.
  3. Be aware of examples of aromatic compounds which contain one or more heteroatoms within the aromatic ring and understand the features that make these compounds aromatic.
  4. Know the reagents required, the electrophilic species involved, and the reaction pathways for the bromination, chlorination, nitration, sulfonation, alkylation and acylation of aromatic compounds.
  5. Know which substituents direct electrophilic substitution mainly ortho and para to themselves and which direct mainly meta and be able to explain why.
  6. Know which substituents increase the rate of electrophilic attack and thus require mild conditions, and which substituents are deactivating and thus require forcing conditions.
  7. Be able to account for the moderation of the activating influence of amino and hydroxyl substituents observed after acylation of these two groups.
  8. Know a method for reduction of a nitrobenzene to an aminobenzene.
  9. Know how to convert primary aromatic amines into diazonium salts; know the various reactions of solutions of these salts, with and without loss of nitrogen.
  10. Appreciate why phenols are acidic, how to separate a phenol from a neutral compound, and know how ethers and esters are prepared from phenols.
  11. Know about the requirements for nucleophilic aromatic substitution.
  12. Be able to use the basic principles of retrosynthetic analysis to plan routes for the synthesis of aromatic compounds with a variety of substituents.

Course Outline: This course will consider the basis of aromaticity and the preparation, reactions, reactivity, properties and importance of simple benzene derivatives.

Title: Co-ordination Chemistry - At the Centre of Life

Duration: 7 Lectures, 1 Workshop

Lecturer: Dr. A C Benniston (Room A4-32c)

Aims: To introduce students to the co-ordination chemistry of transition metals and ligand field theory, and to show how this can lead to an understanding of magnetic and spectroscopic properties. To introduce macrocyclic ligands and how they can be used as models for bio-co-ordination chemistry


1: Be able to write down the first row transition metals and to know their common oxidation states; write down the electron configurations of the atoms and of the ions in any oxidation states.

2: Know the reaction types (redox, ligand exchange, acid/base, geometry change) undertaken by transition metal complexes, and relate these to relevant considerations such as oxidation level, d-orbital configuration.

3: Be able to recognise stepwise stability constants in simple co-ordination chemistry. Know what denticity of a ligand means. Understand why linked bidentate ligands have an increased thermodynamic stability over monodentate ligands (chelate effect).

4: Have a basic definition of what a macrocycle is, and know the difference between an oxa (crown), aza and thia macrocyclic ligand. Know that macrocycles show an even greater thermodynamic stability over chelating ligands.

5: Understand the way in which the d-orbital energies split in (a) octahedral (b) tetrahedral and (c) square planar co-ordination, and be able to predict whether a complex is high or low spin.

6: Remember the spin-only formula for the magnetic moment and be able to determine the number of unpaired electrons in a complex from the value of its magnetic moment.

7: Understand the origin of the absorption spectra of the Ti3+ and Cu2+ ions, and the origins of colour in other complexes.

8: Remember the spectrochemical series, and know the factors which affect the size of D o

9: Be able to draw a molecular orbital diagram for a (s -bonded octahedral complex and indicate how the t2g and eg energy levels are changed by (p -bonding; be able to use the diagrams to explain the spectrochemical series.

10: Understand the concept of ligand field stabilisation energy (LFSE); be able to calculate LFSE and understand its use in explaining thermodynamic, structural and kinetic properties of some transition metal ions.

11: Understand the Jahn-Teller effect, and be able to predict when it might apply.

12: Have an appreciation of how macrocyclic ligand complexes may be used as model for metallo-biosites.

13: Be able to apply the reasoning of any of the foregoing to unseen situations.

Course Outline: The chemistry of transition metals covering the objectives outlined above will be presented with various relevant examples.

Title: Biophysical Chemistry: structure and function of biological macromolecules.

Duration: 8 Lectures.

Lecturer: Dr A. Freer (Room A4-13).

Aims: To introduce the factors which determine how biological macromolecules behave in solution. Describe how physical and chemical properties can be used to isolate and purify proteins. Introduce biophysical techniques which can be used to study macromolecular structure.


  1. How the Henderson-Hasselbalch equation, when applied to biological buffers, allows us to understand their mode of action.
  2. Understand how the state of ionization of amino acids depends very much on the pH of the solution.
  3. Appreciate the meaning of isoelectric point, pI, and how this influences the charge on the protein.
  4. Use of UV absorption to measure the concentration and activity of macromolecules.
  5. Describe how the physical properties of macromolecules are used to isolate a single species from a biological extract based on solubility, size, charge and polarity.
  6. Determination of molecular size using gel filtration, electrophoresis and mass spectrometry
  7. Briefly describe ways in which molecular conformation may be detected by different physical techniques. CD spectroscopy, X-ray diffraction and fluorescence.

Course Outline: Biological macromolecules; the chemical nature of the very large molecules DNA and proteins; proteins consist of twenty different amino acids which vary in size, shape, polarity and hydrophobicity; based on these differences we can use chemical techniques to purify proteins by precipitation, gel filtration, ion exchange and affinity chromatography; the pH of the protein solution very often determines the characteristics of the macromolecule. Protein concentration and biological activity are used to assess purity; describe physical techniques used to gain information about macromolecular size, shape, and detailed atomic structure; SDS electrophoresis, mass spectrometry, CD spectroscopy, NMR and X-ray crystallography and fluorescence.

Title: Applied Organic Chemistry

Duration: 8 Lectures

Lecturer: Dr R A Hill (Room A4-35)

Aims: To provide a general introduction to the applications of organic chemistry including medicinal, biological and supramolecular chemistry and utilisation of natural products and their ecological significance.


  1. Know the properties of organic molecules such as size, charge distribution, polarity, shape and electronic structure and from these be able to predict intermolecular interactions involved in medicinal and biological applications.
  2. Be able to use stereochemical descriptors (R, S, E, Z) and understand biodiscrimination of enantiomers and diastereomeric interactions.
  3. Relate the structures of membrane components to their properties and understand how membrane active agents function.
  4. Be able to define partition coefficient and know the factors that affect lipophilicity.
  5. Predict the state of ionisation of various functional groups in a biologically active substance and how this affects its properties and be able to estimate pKa values and use them to calculate ionisation ratios.
  6. Relate the structure of a sunscreen to its function
  7. Be aware of the structural and biological diversity of natural products and how these substances are involved in inter- and intra-species interactions.
  8. Understand the intermolecular interactions involved in supramolecular chemistry and how such molecules can be used in catalytic or biomimetic applications.
  9. Understand the mechanisms of intercalation and reactions with DNA.
  10. Be aware of modern theories of mechanisms involved in taste and smell with reference to sweeteners, flavours and perfumes.
  11. Be aware of the substances that are used to modify nerve transmission, act as insecticides or as herbicides and how they function.


Course Outline: Intermolecular interactions, stereochemical descriptors, enantiomers and diasteroisomers, biodiscrimination, membrane structure, phospholipids, membrane disrupting agents, partition coefficients, lipophilicity, pKa values and calculations of the state of ionisation at various pH’s, UV absorption of sunscreens, natural product classification in structural and biological terms, pheromones, feeding deterrents, interactions involved in supramolecular chemistry with applications, phase transfer catalysis, biomimetic applications, intercalation of DNA, nitrogen mustards, neighbouring group interactions, olfactory mechanisms, sweetness, aspartame, sugars, acetylcholine, anaesthetics, opiates, insecticides, herbicides.

Title: Organic Synthesis

Duration: 8 lectures

Lecturer: Dr Richard C. Hartley

Aims: To introduce synthetic strategy with particular emphasis on chemoselectivity and protecting group chemistry; to illustrate the course with the synthesis of chemicals used in every day life such as pharmaceuticals, perfumes, and flavourings.



  1. Know how carbonyl groups react with nucleophiles, draw curly arrow mechanisms for these reactions, and be able to explain the relative electrophilicity of different carbonyl groups.
  2. Design syntheses involving reactions of carbonyl groups with nucleophiles (in particular Grignard reagents), oxidations and reductions.
  3. Explain the importance of chemoselectivity in the synthesis of molecules containing many functional groups, recognise when chemoselectivity is possible, and know and be able to apply given chemoselective reagents.
  4. Know the limitations of protecting group chemistry and when to use it; understand the principle of orthogonal sets and the principle of atom economy.
  5. Recognise a number of protecting groups and know their use, stability, and the reagents for and mechanisms of protection and deprotection.
  6. Provide synthetic schemes for multi-step transformations using protecting groups for aldehydes, ketones or hydroxyl groups.
  7. Know how protecting group chemistry is used in polypeptide synthesis (e.g. Aspartame) and be able to design syntheses of simple dipeptides. Be aware of the use of protecting group chemistry in DNA, RNA and oligosaccharide synthesis.


Course Outline: Revision of nucleophilic addition and nucleophilic acyl substitution reactions; relative reactivity of carbonyl compounds to electrophiles; Grignard reagents; synthetic planning and retrosynthesis; oxidisng and reducing agents; complex functionality and chemoselectivity; Protecting groups – when to use them, requirements for, and the principle of orthogonal sets; atom economy; a selection of protecting groups for aldehydes, ketones, carboxylic acids, amines, and alcohols and their use in synthesis; polypeptide synthesis, in particular dipeptide synthesis; other biological polymers (DNA and RNA).