PREPARATION GUIDE FOR YEAR 2

PREPARATION GUIDE FOR

YEAR 2

Don’t spend your whole summer vacation

forgetting all of the chemistry you’ve learned

…a little bit of preparation will help your performance

in Year 2

…a little bit of summer reading will expand your independent learning skills

(which employers are very keen on)!

CONTENTS:

GENERAL INFORMATION

Summer Reading List 1

Revision Guide 3

A Quick Guide to Differentiation & Integration 6

Symmetry, Structures of Simple Solids & Basic Crystallography 18

Structure and Spectroscopy 40

REVISION of 1st YEAR ORGANIC CHEMISTRY 42

UNIT CONTENTS:

6F5Z2101 Laboratory techniques 2

62

6F5Z2102 Solid State, d-block and f-block Chemistry

6F5Z2103 Chemistry of the Carbonyl Group

6F5Z2110 Structure and Spectroscopy

6F5Z2105 Instrumental Analysis

6F5Z2104 Thermodynamics and Kinetics

6F5Z2108 -option Chemistry in Society 2

6F5Z2109 -option Green Chemistry

6F5Z2106 Formulation Fate and Biometabolism

6F5Z1103 Applied Molecular Biology

6F5Z1104 Biochemistry

6F5Z2107 Pharmaceutical Analysis and Quality Control

Dr. Debra Whitehead [email protected] 1

Summer Reading List

Preparing for your 2nd Year

To stop you from getting bored in the long, long holidays, here’s a copy of your summer reading list…in case you are near to a library – to help you find out which bits of chemistry that you like! All good preparation for career (& exam) success in the future.

Recommended Books for Yrs 2 & 3: We arrange a book pack of the 3 recommended texts which will cover Years 2 & 3 from OUP at a reduced price of £125.99 (20% reduction & the cost works out at ~12-17p / day). Usually you can purchase these from Portland Bookshop (MMU Student Union) or Blackwell Bookshop “Physical Chemistry” by Atkins & de Paula (Newest: 11th edition - 2017) + “Organic Chemistry” by Clayden, Greeves & Warren (Newest: 2nd edition - 2012) + “Inorganic Chemistry” by Weller, Overton, Rourke & Armstrong (Newest: 7th edition - 2018) Chemistry3 will still be a useful introductory textbook – but you will also need the depth of information presented in the other recommended texts. “Maths for Chemistry” will help explain & provide lots of practice questions for the maths that you will encounter in Years 2 & 3.

General Comments

In general, the following series of books are all good for getting a more in-depth idea about one topic – but I would not recommend that you buy them. They are all well written & light! See if you can find copies in a library. I’ve noted how many copies of each book that there are available in the MMU library – please don’t take out all of these books & keep them sitting in a dark corner for the whole vacation. Just take one book – and try reading it. (NB: Not in one sitting!) Return any books as soon as possible. You might pick a topic that you’ve found especially difficult this year or the subject you’ve liked the best. Revising your notes from this year of anything you’ve found particularly topic is always a good start! Let me know which books you like the best (or least) & if you have any other recommendations.

Royal Society of Chemistry (RSC) Tutorial Texts: http://pubs.rsc.org/bookshop/search?searchtext=Tutorial+texts Oxford Chemistry Primers: http://ukcatalogue.oup.com/category/academic/series/chemistry/ocp.do Open University/RSC "The Molecular World": http://www.rsc.org/molecularworld (The OU is particularly good at writing texts that enable you to teach yourself = Key Grad Skill.)

Supplementary Book “A Guide to Modern Inorganic Chemistry” by Steven M. Owen & Alan T. Brooker – There are 2 copies in the library – but if you ever find cheap used copies on Amazon or e-bay then I would recommend buying it.

http://pubs.rsc.org/bookshop/search?searchtext=Tutorial+texts

http://www.oup.co.uk/oxfordtextbooks/chemistry/ocp/

http://www.rsc.org/molecularworld


Summer Reading Do not buy these books – just get them from the library

1. Foundations of Organic Chemistry by Hornby & Peach

(Oxford Chemistry Primers) - 4 copies - Practice of functional group, nucleophile & electrophile identification - Revise 1st year notes - Revise Chemistry3 (especially if you don’t get one of the copies of the primer) - Highly recommended - essential prior to Year 2 Organic Chemistry

2. “Physical Chemistry: Understanding our Chemical World” by Paul Monk - 11 copies in the library - Written by a former MMU lecturer. - Easy to read guide to physical chemistry – introducing you to key concepts by trying to answer questions about things that we observe in the world around us…like “Why do we sneeze?”, “How is smoke in horror films made?” - Especially Chapters 3, 4 – 10 - Useful for Thermodynamics & Phase Equilibria lectures – Year 2 - Highly recommended.

3. “Molecular Symmetry & Group Theory” by Alan Vincent - 6 copies (1 – 1977, 5 – 2001) in the library - A unique book that actually gets you to teach yourself a topic in a step-by-step guide. - It gives you a good head-start getting your head around symmetry elements – don’t be put off by the maths…and try building molecules using Scigress if you need help visualizing the structures. - Useful for Symmetry lectures – Year 2 & Spectroscopy lectures - Highly recommended.

4. d- and f-block chemistry by C. J. Jones

(RSC Tutorial Text) - 1 copy in library - Transition metal chemistry lectures – Year 2

5. “Basic Atomic & Molecular Spectroscopy” by J. Michael Hollas

(RSC Tutorial Text) - 1 copy in library

- Spectroscopy lectures (Phys. Chem.) – Year 2

Other libraries – Check!! In the UK the MMU library can issue you with a SCONUL card which allows you to visit (but not borrow) books from all UK university libraries.


REVISION GUIDE

PREPARATION FOR

YEAR 2


Revision Guide

Preparation for Year 2

During the long, long vacation you will probably be ready to start doing some thinking and getting ready for your second year. There are lots of good reasons to do this:

Your second year marks count towards your final degree classification.

When you apply for jobs during your final year, employers will look at these marks to assess whether they should hire you – so make sure they are good!!

Many people find the 2nd year of the course a big jump up from the 1st year - therefore, it is important to revise your notes from last year in core topics, since we will assume that you already know & remember the content of these courses, without having to look them up.

If you “just” managed to pass the course (anything less than 100%!), then look in particular at topics that you found difficult and think about how you could have improved your performance in both coursework & examinations.

Independent study and practising questions on your own are essential elements to developing the problem-solving skills and knowledge required by employers to succeed.

Before asking a question, make sure you have searched fully for the answer.

Hard work now = Interesting & challenging job later

Essential Preparation Thermodynamics and kinetics

Guide to Differentiation & Integration (Separate Section) Essential 2

- If you don’t know how to deal with mathematical functions such asT

G

or dT

T

Cp (or if you

do vaguely but it makes you want to cry just thinking about it) then working through this simple guide will be your key to success in the Thermochemistry module. - Even if you got an A* at A-level you need to be fluent in this mathematics by the start of Year 2 … so yes, you should go through the guide too… - Warning: If you don’t try this guide, you will find the Thermochemistry course more tricky than it really is – it really is just a question of practising so that you are familiar with the content. (Practising = Read / do questions in guide 10 – 30 times … not just once.) - Highly recommended by this year’s 2nd years.

Monk & Munro’s “Maths for Chemistry” book (Chapters 14-20) - All exercises in all of these chapters … will help you gain the expertise & proficiency that you will need in the relevant mathematics required for this course & brush up on your independent learning skills as well … which will make your future employers v. happy!

Symmetry, Structures of Simple Solids & Basic Crystallography ESSENTIAL REVISION & PREPARATION Guide (Separate Section) - Chapters 3, 6 & 8 – “Inorganic Chemistry” by Weller et al. - Outline of key skills required to practise over vacation - Online Resources - Scigress Modelling Exercises

Notes from 6F4Z2104 Introduction to thermodynamics & Kinetics (Dr. Edge) - Especially the key principles, equations (memorised) & how to apply these.


Essential Preparation Organic + Inorganic

Review of Organic Chemistry required for 2nd year (Separate Section) - When learning organic chemistry, each new element builds on the foundation of all of the previous knowledge. It is essential that you know how to do the following WITHOUT looking at a text book at the start of the year. You MUST be fluent in the language of organic chemistry before term starts in September:

o Name compounds o Identify functional groups, sp2, sp3 carbons, electrophiles & nucleophiles o Curly arrows

- Should be able to draw mechanisms (without looking at notes) - Predict products of reactions based on Year 1 knowledge of chemistry

o A wide range of reactions (nucleophilic addition, SN1, SN2, E1 and E2, etc.) o Carbonyl group chemistry o Grignard reagents

- Overview of each - Additions to the C=O group of Grignard reagents

o Electrophilic addition to alkenes – Markovnikov’s rule

o Relative stability of carbocations & how that relates to electrophilic additions to alkenes (Markovnikoff & anti-Markovnikoff additions)

o Identification of primary, secondary, tertiary & quaternary carbons o R & S for naming enantiomers o 13C NMR and IR spectroscopy

- Read this review, memorise the key elements now & throughout the term. - This information has to be second nature to you - Otherwise you will struggle with the key elements during lectures and fall behind. - It is highly likely that you will be tested on this in the 1st week of term. - Highly recommended by this year’s 2nd years.

Recommendations from the current 2nd Years: Revise the following mechanisms (so that you know how to identify the key features – such as functional groups, electrophiles, sp, sp2 and sp3 carbons, draw the arrows and complete the mechanism WITHOUT reference to a textbook – this must be second nature to you):

Nucleophilic Substitution (SN1 and SN2)

Elimination reaction (E1 and E2)

Electrophilic addition to alkenes

Aromatic electrophilic substitution

Nucleophilic addition to carbonyl

Nucleophilic acyl substitution

Chemistry3 by Burrows, Holman, Parsons, Pilling & Price (Chapters 19-24 = excellent start)

Make sure you bring your 1st year notes & revision guides back with you - we will assume that you will be using them daily during term time.


ESSENTIAL REVISION & PREPARATION

GUIDE

TO DIFFERENTIATION

& INTEGRATION


A Quick Guide to Differentiation & Integration (Only 1 hour required)

Ignore the rumours – calculus (differentiation & integration to you & me) really isn’t the hardest topic in the universe – nor is it an unsurpassable mountain that you will never ever understand. If you follow this guide you will no longer fear the very mention of these words. You will be able to understand the basics so that you don’t feel like you have to lie down & take a nap every time you

see any of the following:pT

G

or

2

1

1T

T

dTT

.

Still awake? Excellent – such fortitude of spirit is exactly what is needed. Now, those of you who are thinking you don’t need to revise this topic or you can’t be bothered or that you are never going to understand it – think again! This v. short guide has been produced in response to previous survivors of the second year – including the ones who get 1sts – so no trying to escape – I’m expecting you to have tried to follow, understand & remember this guide. The emphasis is on the word “tried” (at least a couple of times). By the end of your 1st term, you will have seen these symbols so much that it will be second nature to you – it’s just a question of practice. There is, however, one basic test that you have to pass in order to follow this guide – so brace yourselves: can you add & subtract 1 from another number? If yes, then let’s crack on with making differentiation easier…if not, then practise adding and subtracting…& then start with this guide tomorrow.

Differentiation

Differentiation is just a mathematical function like addition, subtraction or taking a log. It is used to calculate:

rates of reaction (kinetics)

slopes of graphs

entropy and other thermodynamic quantities.

If y = a xn and we want to find the rate at which y changes as x changes

(i.e. the slope of the graph of y versus x) then we need to:

“differentiate” y (i.e. the equation) with respect to x to get dx

dy.

Note: This does not mean “dy” divided by “dx”.

General rules for differentiation y with respect to x: Learn these off by heart.

1. If y = xn, then 1 nxn

dx

dy

2. If y = axn where a is a constant, 1 nxna

dx

dy

3. If y = a where a is a constant, 0dx

dy

(Proof - write y = a as y = ax0 - since x0 = 1, n = 0, thus 00 10 xadx

dy)

4. If y = ln (ax) - do not panic - xax

a

dx

dy 1

5. If y = uv then:dy dv du

u vdx dx dx

= “1st x differential of 2nd + 2nd x differential of 1st”

(Product Rule applies to the product of two functions u & v which are both functions of x.)


So (apart from the example with the natural log (ln) and products), all you have to do is:

look at the expression for y

write down the constant, a (if present)

multiply by the power

multiply by x raised to the old power minus 1

Easy peasy!

Here are some quick examples - so you know what lies ahead.

1. y = x5 415 55 xxdx

dy 2. y = x 4 314 44 xx

dx

dy

3. y = x 3 213 33 xxdx

dy 4. y =

2

1

x

3

312 222

xxx

dx

dy

Hint: (y = x –2)

Can you see the pattern?

Remember:

n

nx

x

1

and 2

1

xx

Your Go - 1 Differentiate the following expressions: (Answers at the back)

1. y = x 7 2. y = x 8 3. y = 4

1

x

4. y = 5x 7 5. y = 5x 8 6. y = 4

3

x

Let’s make it a bit more complicated In real life, y is rarely so simple. It is often equal to a series of terms added together - but all you do is differentiate each term in turn.

1. y = x 7 + x 3 + 3 2626 37037 xxxxdx

dy

2. y = 2x 4 + 3

6

x+ 20

4

343 18803642

xxxx

dx

dy

Your Go - 2 Differentiate the following expressions:

1. y = x 6 - x 2 + 210 2. y = x 5 + 6

1

x+ 0.6

3. y = 3

2

4x

x 4. y = )6ln( xx


Where am I actually going to see anything like this?

You will see lots of equations involving differentials in your course – although probably not all with y and x as the variables.

You may need to investigate the rate at which y changes with respect to changes in x.

For macroscopic changes (ie. big changes that can be observed), this is written: x

y

For microscopic changes (ie. tiny changes that cannot be observed), this is written: dx

dy

Sometimes the change in a variable (such as free energy G) is dependent on changes in both pressure (written as dp) and temperature (written as dT). This would be written:

Arrrgghhhh – this looks horrible. But let’s think about what it means:

δG is used rather than dG since G is dependent on more than one variable

(p and T). Rate of change of G with respect to p = The slope of the graph of G against p. The T subscript just means “whilst holding the temperature variable constant”.

So each term contributes to the total change in G:

Term 1: dpp

G

T

Rate of change of G with respect to p x the actual change in p

Term 2: dTT

G

p

Rate of change of G with respect to T x the actual change in T

If you still find that difficult to understand: - all we are doing is taking the slope of a graph & multiplying by the change in the x coordinate

to find the change in the y coordinate – which is pretty simple maths.

Maxwell’s relations tell us that: Vp

G

T

and S

T

G

p

so if we look at graphs of G against p or T for a substance (in gas, liquid and solid states), we can understand more about its thermodynamic properties.

Differentiation will help you check any integrations you do.

dTT

Gdp

p

GdG

pT

Tp

G


Product Rule You will only see the Product Rule in one derivation during this course and in the Physical Chemistry course in Year 3. However, it is important that you know this rule, since at first sight it looks completely counter-intuitive and could lead to one (or maybe two) moments of confusion during lectures! First let’s look at a few really simple examples of the Product Rule, in order to prove to you that it really is true: 1. y = x7 x x3 u = x7 (“1st function”) and v = x3 (“2nd function”)

we can easily calculate: 67du

xdx

and 23dv

xdx

Substituting into the formula:

dy dv du

u vdx dx dx

= “1st x differential of 2nd + 2nd x differential of 1st”

gives us:

7 2 3 63 7dy

x x x xdx

which simplifies to become:

910dy

xdx

This is fairly trivial example since we can see that y = x7 x x3 = x10 and therefore using the 1st rule of

differentiation: 910dy

xdx

.

2. We will practise this one more time:

9

2

1y x

x u = 2

2

1x

x

and v = x9

we can easily calculate: 3

3

22

dux

dx x

and 89

dvx

dx

Substituting into the formula gives us:

8 9

2 3

1 29

dyx x

dx x x

which simplifies to become: 8 9

6 6 6

2 3

9 29 2 7

dy x xx x x

dx x x

This is fairly trivial example since we can see that 9 7

2

1y x x

x and therefore using the 1st rule

of differentiation: 67dy

xdx

.

Your Go - 3 Differentiate the following expressions using the Product Rule:

1. y = x6 x x2 2. 8

6

1y x

x


Application:

In the derivation of the Gibbs-Helmholtz equation, we must differentiate the following expression by T (rather than x – but the principle is exactly the same):

y = 1GG

T T u = 11

TT

and v = G

we can easily calculate: 2

2

11

duT

dT T

and

dv dG

dT dT

Substituting into the formula gives us:

2

/ 1 1d G T dGG

dT T dT T

We know that G = H – TS, therefore dG

SdT

2

/ 1d G T GS

dT T T

We can substitute in for S in terms of G: G H

ST

(by rearrangement of G = H – TS)

2 2 2 2 2

/ 1d G T G H G G H G H

dT T T T T T T T

Leaving us with a very useful expression,

2

/d G T H

dT T

from which we can derive the Gibbs-Helmholtz equation by integration:

2 1

2 1 2 1

1 1G GH

T T T T

Clearly your next step has to be to learn about integration!


Integration

Right so you’ve seen how easy differentiation is - integration is just the opposite of differentiation (just as subtraction is the opposite of addition). Integration is used to calculate:

Area under a graph (either general expression in terms of “x” or between specific limits)

A simpler relationship for a system represented by a differential equation. Indefinite Integrals

If nxadx

dy and we want to find an equation relating y and x then we need to:

“integrate” the expression above with respect to x which is written as dxxay n. Since there are

no limits, we will just get a general expression for y in terms of x. This is called an indefinite

integral.

Note: should never ever be referred to as “big S” or “that squiggly thing” – it is the integral sign.

General rules for integration of simple functions Learn these off by heart. (NB: c is just a constant.)

1. Basic: cn

xdxx

nn

1

1

2. Multiply by constant, a: cn

xadxxa

nn

1

1

3. Constant, a: cxadxa

4. Complicated case: cxadxx

a )ln( - You will see this often in thermodynamics.

So (apart from the example with the natural log (ln)), all you have to do is:

add 1 to the power

divide by the new power

add a constant No problem!

Here are some quick examples – so you know what lies ahead – (c is a constant).

1. cx

cx

dxx

514

5144

2. cx

cx

dxx

413

4133

3. cx

cx

dxx

3

5

1255

3122

4. cx

cx

cx

dxxdxx

2

2133

3 2

1

213

1

x

y


Whenever, you integrate an expression – CHECK that when you differentiate the result it is the same as the original.

Check:

1. 4

45

55

5x

x

dx

dyc

xy Yep – it works!

Now you should check Examples 2 – 4.

Your Go – 4 Integrate the following expressions:

1. dxxy 7 2. dxxy 83 3.

dxx

xy4

5 1

4. dxx

y5

2 5. dx

xy

3 6.

dx

xy

15

Integrating with limits (definite integrals) Sometimes we want to find the integral of something between 2 different limits. For instance we might want to know the area under the graph y = 2x 2 + 4x + 6 between x = 3 and x = 10.

In this case, we want to calculate the value of the expression with x = 10 (so substitute in 10 as the

value of x) and then subtract from this the value of the expression when x = 3 (by substituting in 3

as the value of x) – this will leave us with the value for the expression integrating between the limits

3 and 10. Confused? Just look at the mathematics below and all will become clear(er):

32

32

23

23

10

3

23

10

3

2310

3

2

872

54926

36323

32106102

3

102

623

2

62

43

2642

cc

cc

cxxx

cxxx

dxxx

Note that the constant c in each bracket cancels out. This always occurs when the integral has limits. Therefore, in these cases, we don’t bother to write in the constant c (as shown in the answers to the questions below).

Your Go – 5 Integrate the following expressions:

1. 1

0

3dxxy 2. 2

1

43 dxxy 3.

4

2

3

6 1dx

xxy


Application to Thermodynamics:

In thermodynamics, you will often see that the entropy change of the system ΔS as we change the temperature from T1 to T2 is:

2

1

T

T

pdT

T

CS

Two scenarios arise: a. If CP is constant (ie. Cp = 425 J K-1 mol-1) then if we can get a general form of the equation for this scenario by integrating:

1

2

12

ln

)ln()ln(

)ln(

1

2

1

2

1

2

1

T

TC

TTC

TC

dTT

CdTT

CS

p

p

T

Tp

T

T

p

T

T

p

(If you don’t understand how the last step is true then you need to revise the log laws.) Example: A liquid is heated from a temperature of 300K to 500K. Given that Cp = 425 J K-1 mol-1 for this liquid, calculate the change in entropy. (i) Assign labels to the values given in the question: T1 = 300K T2 = 500K Cp = 425 J K-1 mol-1

(ii) Starting from 2

1

T

T

pdT

T

CS , do the derivation above to give:

1

2lnT

TCS p

(Memorise this equation.)

(iii) Substitute values into the equation:

1.217300

500ln425ln

1

2

T

TCS p

J K-1 mol-1

b. If Cp is dependent on T (ie. Cp = (4 T + 10) J K-1 mol-1) then if we need to deal with each situation on an individual basis by substituting in for Cp and then integrating. Example: A liquid is heated from a temperature of 300K to 500K. Given that Cp = (4 T +10) J K-1 mol-1 for this liquid, calculate the change in entropy: (i) Assign labels to the values given in the question: T1 = 300K T2 = 500K Cp = (4 T +10) J K-1 mol-1


(ii) Starting from 2

1

T

T

pdT

T

CS , substitute in for T1, T2 and Cp

11

500

300

500

300

500

300

molKJ1.805

)300ln(103004)500ln(105004

)ln(104

104

1042

1

TT

dTT

dTT

TdT

T

CS

T

T

p

You will see integrals of this type v. often – so make sure you remember this result:

1

2ln12

1p

pdpp

p

p

or

1

2ln12

1T

TdT

T

T

T

Additional Terminology

n

i

iG1

add together G for each component 1 to n 321

3

1

GGGGi

i

n

i

iG1

multiply together G for each component 1 to n 321

3

1

GGGGi

i

Additional Mathematics to Revise

Using a calculator incorrectly is one of the most common sources of errors – always insert lots of brackets:

3418

20

+ 5 should equal 5.84 = (20 (18 + )34( )) + 5 = 20 (18 + )34( ) + 5

not 11.94 = 20 18 + )34( + 5 = 53418

20

not 7.36 = 20 18 + )534( = 53418

20

Clearly label variables – helps you to insert the numbers correctly into the equation.

Memorise equations as you proceed through the course – they have to be 2nd nature.

Write down equation to be used.

Insert units – ensure all variables converted to correct units. (ie. J not kJ, K not oC)

Rearranging equations

Logarithm rules


Answers

Your Go – 1

1. 67xdx

dy 2. 78x

dx

dy 3.

5

5 44

xx

dx

dy

(y = x–4)

4. 66 3575 xxdx

dy 5. 77 4085 xx

dx

dy 6.

5

5 1243

xx

dx

dy

Your Go – 2

1. xxxxdx

dy26026 515

2. 7

474 650)6(5

xxxx

dx

dy

3. 2

3

23 38

324 xx

xxdx

dy

(Remember: 2

2

1 xx

)

4. xxxxx

xx

xdx

dy 1

2

11

2

11

2

1

6

6

2

1

2

1

2

1

2

1 1

(Remember: 2

1

xx )

Your Go - 3

1. y = x 6 x x 2 u = x 6 and v = x 2

therefore: 56du

xdx

and 12dv

xdx

Substituting into the Product Rule formula gives us:

6 2 5 7 7 72 6 2 6 8dy

x x x x x x xdx

We can see that y = x 6 x x 2 = x 8 and therefore using the 1st rule of differentiation: 78dy

xdx

.

2. 8

6

1y x

x u = 6

6

1x

x

and v = x 8

therefore: 7

7

66

dux

dx x

and 78

dvx

dx

Substituting into the Product Rule formula gives us: 7 8

7 8

6 7 6 7

1 6 8 68 8 6 2

dy x xx x x x x

dx x x x x

We can see that 8 2

6

1y x x

x and therefore using the 1st rule of differentiation: 2

dyx

dx .

Your Go – 4


1. cx

dxxy8

87

2. cx

cx

dxxy 3933

998

3. cx

xc

xxc

xxdx

xxy

3

636146

4

5

3

1

636146

1

4. cx

cx

cx

cx

dxx

dxx

y

44

415

55 2

1

4

2

42

152

12

2

5. cxdxx

dxx

y )ln(31

33

6. dxxxdxx

dxx

y

2

1

2

15

15

15

cxxcx

xcx

x

2551

521

21

12

1

2

1

Your Go – 5

1. 4

10

4

1

4

0

4

1

4

441

0

41

0

3

x

dxxy

2. 53

53

596

552

1

52

1

4 185

13

5

23

533

x

dxxy = 18.6

3.

2

7

2

74

2

2

74

2

274

2

3

6

22

1

7

2

42

1

7

4

2

1

727

1

x

xxxdx

xxy

= 2322.4 (to 1dp)

CONGRATULATIONS!! You now know all the calculus necessary for your 2nd year

…if you’ve found this a bit tricky then come back tomorrow & go through it all again. Feeling confident about calculus just requires practice.

Dr. Stuart Langley [email protected] 18

ESSENTIAL

REVISION & PREPARATION

Symmetry, Structures of Simple Solids

& Basic Crystallography


Preparation for Symmetry, Structures of Simple Solids & Basic Crystallography

One topic that students find tricky in Year 2 is visualising the symmetry of different molecules and

crystal structures. Don’t worry you can fix this! The recommendations below are designed to help you

practise these skills so that you can really do well in this core module.

“Chemistry3” by Burrows et al.: Chapter 6 (Solids) - This is a useful concise introduction to these

topics.

In addition, the Yr 2 recommended textbook “Inorganic Chemistry” by Weller, Overton, Rourke &

Armstrong has three excellent chapters, which will act as a nice introduction

1. “Inorganic Chemistry”: Chapter 3 (The Structures of Simple Solids)

- Sections 3.1 – 3.10: Description of the structure of metallic & ionic solids

2. “Inorganic Chemistry”: Chapter 6 (Molecular symmetry)

- It is fully recommended that when reading chapter 6, you use a molecular bonding kit, or some

blue-tack and cocktail sticks, to build the molecules that are being focused upon so that you can

actually have a go at performing the symmetry operations. One of the hardest elements associated

with molecular symmetry operations is being able to visualise them, which many people struggle

with. So don’t make it hard for yourself, make some models!

3. “Inorganic Chemistry”: Chapter 8 (Physical Techniques in Inorganic Chemistry)

- Sections 8.1 and 8.2 (on X-ray and neutron diffraction).

“Molecular Symmetry & Group Theory” by Alan Vincent will also be of use here – the library has 6

copies.

It’s a pretty unique textbook in that you learn something & then immediately have to put it into

practice – so by the end of the book you have taught yourself how to apply these skills – which is really

useful.

Please bear in mind that the library has only six copies available … so you will need to move fast!

Online Resources:

Inorganic Chemistry by Weller et al. – Free online resources

global.oup.com/uk/orc/chemistry/ichem6e/

- Videos of chemical reactions

- 3D rotatable molecular structures for each Chapter (including Chapters 3, 6 & 8)

- Uses chemtube3d www.chemtube3d.com

Instructions for how this supports the text is given on first page of each chapter). There is a whole

section on symmetry (found within the structure and bonding tab), which provided you have Java

enabled on your device will allow to “spin” molecules around in order to see, in 3D, what the

symmetry transformation looks like.

http://www.chemtube3d.com/


Molecular Modelling Activities using SCIGRESS

The Scigress annual licence tends to run out at the end of July. Therefore, in order to do these

exercises using Scigress, you may need to download the latest version / new licence via the S: drive –

available via myMMU: S:\Faculty of Science & Engineering\School Of Science & The

Environment\Chemistry\Software\ Scigress_20xx

SCIGRESS has three relevant exercises that will support and further your understanding of these two

areas:

Experiment 11 – Crystal Lattices and Close Packing Sites

Experiment 12 – Identification and Execution of Symmetry Operations

Experiment 13 – The Relationship Between Infrared Spectra and Molecular Geometry


Overview

In this exercise you will enter lattice parameters obtained from crystallographic studies into a SCIGRESS document so as to represent the crystal structure of a compound in different ways. This will help to identify close packing sites which, in turn, aids in understanding why different compounds crystallize in different lattice types.

Recommended Exercises

No recommended exercises.

Background

Many substances crystallize in lattices based upon close packing schemes. In close packing, each atom or ion is considered to be a hard sphere. Each layer of spheres is arranged to pack the spheres as close together as possible. This will be the case if the spheres are in contact and if each row is offset from the neighboring row by half the diameter of a sphere. Close packing in three dimensions is achieved if the spheres of any one layer lie directly above the depressions in the layer immediately beneath it. Within a layer, there are depressions in the center of a triangular array of three spheres in contact with one another. Two close packing patterns are possible. If the third layer is aligned above the first, then the third and first layers are identified as A layers. The offset layer sandwiched between them is a B layer. The resulting pattern is ABABAB, referred to as hexagonal close packing (hcp).


An alternative to hexagonal close packing occurs if the third layer is offset from both the A and B layers, resulting in an ABCABC pattern known as cubic close packing (ccp).

ccp

In each close packing scheme, there are two types of spaces or holes between adjacent layers of spheres. A tetrahedral hole exists between a sphere and a triangular array of spheres in the layer directly below it. An octahedral hole exists between a triangular array of spheres in one layer and the triangular array centered directly below it in the adjacent layer.

Tetrahedral Hole in Center Octahedral Hole in Center

Metals tend to crystallize in close packed structures (ccp and hcp). Ionic compounds tend to crystallize in lattices based on close packed structures with the large ion (usually anion) in a close packed array and the counterion occupying holes (e.g. NaCl is ccp of Cl- with Na+ occupying octahedral holes).

Modeling Section

Aluminum Lattice. 1. Open the Workspace. 2. Select Action | Crystallize. A Crystal Shape box opens. Select the Main tab. 3. Scroll through the Space Group list and select F23. This identifies the crystal

system (face centered cubic) of metallic aluminum. 4. Enter a=4.04958 in the Angles section of the dialog window. The values for b, c,

α, β, and γ remain unchanged. 5. Select Infinite Lattice in the Build box.


6. Click the Fractional Coordinates tab, and enter the following values from the table below for atoms 1 to 4. Click OK and a crystal structure appears in the Workspace.

atom symbol x y z

1 Al 0 0 0

2 Al 0 0.5 0.5

3 Al 0.5 0 0.5

4 Al 0.5 0.5 0

7. Select View | Crystal Boundaries | Show Lattice Boundaries (this option is

turned on by default).

Viewing the lattice

1. Rotate and view the lattice from different angles. Find the arrangement of layers

(ABC or AB). View the lattice looking from one corner of the cube to its most distant diagonal.

2. Find a tetrahedral hole. Select the atoms which surround the tetrahedral hole. Alter the atom size by changing the van der Waals scale to better view the tetrahedral hole.

❏ Select View | Styles | Atoms... In the resulting Atom Attributes dialog box, click on the Shape tab. Type in a new scale value (0-1).

3. Narrow the window so that the boundary around the lattice is small. Copy the lattice and paste into a word processing document.

4. Find an octahedral hole and select the atoms which surround the hole. As in the preceding step, narrow the window, copy and paste into the same word processing document.

5. Orient the lattice to show that the octahedral hole exists between two staggered triangular arrays of atoms. Paste the lattice into a graphics application, and draw lines between the atoms to identify the two triangular arrays. Paste the result into the word processing document.


Sodium Chloride Lattice

Many ionic lattices result from a close packed array of the large ion with the small ion occupying either octahedral or tetrahedral holes. Proceed with the NaCl lattice as in the case of the aluminum lattice.

1. Select P4(2)32 from the space group list.

2. Edit the cell parameters by entering a = 5.64056.

3. Open Fractional Coordinates and enter the following values:

atom symbol x y z 14 Na 0.5 1 0.5 1 Na 0 0 0 15 Cl 0.5 0.5 0.5 2 Na 0.5 0.5 0 16 Cl 0.5 0 0 3 Na 0.5 0 0.5 17 Cl 0 0.5 0 4 Na 0 0.5 0.5 18 Cl 0 0 0.5 5 Na 1 1 1 19 Cl 0.5 1 0 6 Na 1 0 0 20 Cl 1 0.5 0 7 Na 0 1 0 21 Cl 0 1 0.5 8 Na 0 0 1 22 Cl 1 0 0.5 9 Na 1 1 0 23 Cl 0.5 0 1 10 Na 0 1 1 24 Cl 0 0.5 1 11 Na 1 0 1 25 Cl 1 0.5 1 12 Na 0.5 0.5 1 26 Cl 1 1 0.5 13 Na 1 0.5 0.5 27 Cl 0.5 1 1

4. Select Infinite lattice in the Build box. Click OK to close the Crystal Shape dialog box. The sodium chloride lattice appears in the window. However, the chloride ions will appear smaller than the sodium ions. You can fix this in the following way:

❏ Select Edit | Preferences | Periodic Table Settings... Select the Charge tab. Highlight Cl in the box to the right. In the left list the van der Waals radius and charge appears for a Cl ion. Click Change, and a small dialog box opens. Change the radius to 1.67Å. Click OK. Do the same for Na ion (1.16 Å). Click OK to return to the workspace.

5. View the NaCl lattice from different perspectives by rotating the lattice. Note

that the Na atoms form a face-centered cubic array with the Cl atoms in the positions of octahedral holes. In actuality, the Cl atoms also form a face- centered cubic array with the Na atoms in the positions of octahedral holes.

View an Extended Lattice

6. Go to the Crystal Shape window.

7. Edit the lattice boundaries so they range from 0 to 2 in the a, b and c directions.

❏ Click on Infinite lattice, and click OK to close the dialog box

Select View | Crystal Boundaries and select Show Unit Cell and Show Lattice Boundaries (this option is turned on by default).

8. There should now be eight unit cells within the lattice with one of the unit

cells outlined.


9. View the lattice from different angles. Choose one or more orientations to

copy and paste into your word processing document. Explain how the figure demonstrates that both the Cl and Na ions form ccp arrays.

Report Guidelines

The aim of the report is to demonstrate an understanding of close packing in atomic and ionic lattices. Select orientations of the lattice, or portion of the lattice, which clearly illustrate close packed layers, octahedral holes and tetrahedral holes. If, for purposes of clarity, you wish to eliminate part of a lattice, simply delete selected atoms or ions. Alternatively, you may select only the atoms you wish to emphasize. It may be useful to paste a structure into a graphics document to add arrows, lines and labels for explanatory purposes.


Instructor Notes

Typical Results

The following figures have been pasted from an editor document for the aluminum lattice. In some cases additional graphics were added by first pasting into a chemical graphics document and adding lines and labels before pasting into the word processing document.

Al unit cell Al atoms at faces Octahedral hole

Three different views of octahedral hole (in center).

Tetrahedral hole in center of cluster (scale=1)


+

NaCl lattice viewed along alternating close-packed layers of

Na and Cl- ions (8 unit cells, scale=1)


Overview

In this exercise you will learn how to locate elements of symmetry in molecules and how to demonstrate the results of symmetry operations.


Complete Exercises I, II, III, and IV before beginning this experiment.

Background

Molecular symmetry is of great value in understanding molecular bonding and spectroscopy. The symmetry of a molecule is expressed as a collection of symmetry operations or elements of symmetry. A molecule with a particular set of symmetry elements is said to belong to a particular point group. Molecular orbitals and vibrations within molecules also have symmetry properties.

Symmetry operations are manipulations of a molecule which result in indistinguishable representations of the molecule; that is, a molecule looks no different before and following a symmetry operation. The operation may exchange two identical atoms, or it may leave one or more atoms unmoved. The symmetry operations are as follows:

Identity (E): The identity is a trivial symmetry operation which involves doing nothing to the molecule. It is mentioned here only for the sake of completeness. All molecules possess an identity and, in some molecules, the identity is the only element of symmetry.

Axis of Rotation (Cn): An n-fold axis of rotation is a rotation about an

axis by 360°/n. Often, but not always, rotation axes correspond to bond

axes. For example, SF6 possesses a C4 axis which passes through opposing S-F bonds.

Rotation by 90° about the axis rotates each fluorine atom perpendicular to the axis into a position previously occupied by another fluorine atom.


6 3

3

SF also possesses 3 C axes of rotation which do not pass through bonds. In the following representation, the C

passes through the sulfur atom.

axis is perpendicular to the plane of the paper an


Rotate a molecule 1. Center the molecule in the window by selecting the entire molecule and

pressing ctrl + f on the keyboard. It may resize the molecule in the process of centering it. If the molecule is not centered in the window, it will wobble as the rotation commands are executed.

2. Rotate the molecule until the rotation axis is perpendicular to the screen. You

should now be looking directly down the rotation axis, which should be centered in the window.

3. Press r on the keyboard to enter rotation mode.

4. Press Z to rotate in the clockwise direction and z to rotate counter-clockwise.

Rotate around the x and y axes by pressing x, X, y or Y. Rotation occurs by 5° each time. Thus nine operations result in a 45° rotation, 12 - 60°, 18 - 90°, 24 - 120°, etc. You may rotate continuously by pressing the Space bar. To halt continuous rotation, press the Space bar again.

Plane of Symmetry or Reflection (σ): A mirror plane of symmetry is an operation in which reflection of an atom from one side of the plane to the other results in an indistinguishable representation of the molecule. Atoms which lie within the plan are unmoved. Examples of mirror planes are given below.

Reflect through a mirror plane

1. Orient the molecule so that the plane is parallel to the right and left sides of the window (perpendicular to the window or screen).

2. Select Action | Selection | Mirror.

Improper Rotation or rotation-reflection (S

n): An improper rotation is the result of

two operations in sequence; rotation by 360°/n, followed by reflection through a mirror plane perpendicular to the axis of rotation. An example of an improper axis of rotation is shown below.


2

Execute and demonstrate an improper rotation

1. Follow the procedures for rotation and reflection in sequence. 2. To demonstrate the example above, the following steps would be executed:

I II

II III

III III

The results of the successive operations of rotation and reflection are shown below.

Inversion (i): An inversion through the center of a molecule can usually be accomplished by a rotation by 180° followed by reflection through a plane (Mirror operation) perpendicular to the rotation. Note that this is identical to an S as in the


example below (rotation by 180° about the C-C axis followed by reflection through a plane perpendicular to the C-C axis).

For a planar molecule, an inversion is simply accomplished via rotation by 180° about an axis perpendicular to the plane since subsequent reflection through the plane leaves the molecule unchanged.

Modeling Section

Methane has several elements of symmetry, some of which are challenging to visualize. Build a model of CH

4 and view the atoms by number and the bonds

as cylinders. Center the molecule in the window by selecting only the carbon atom and pressing Control + f.

For each symmetry element, you should have one document to show the original orientation and one to show the result of the operation. Orient the molecule so as to make apparent the symmetry element (e.g. looking down a rotation axis). Adjust the size of the window so that you can simultaneously view documents showing the original atom placements and those following a symmetry operation. Once you have completed the operation, copy the structures and paste them into a word processing document.

Report Guidelines

Label (e.g. C3), and give the number of each type of symmetry element in the molecule to accompany the examples generated using SCIGRESS.


d

Instructor Notes

This exercise could be adapted to numerous other molecules and polyatomic ions.

Typical Results There are 4 types of symmetry elements in the T

point group, 4 C3 rotation axes, 6

σd mirror planes, 3 C2 axes, and 4 S4 improper axes.


Overview

In this exercise you will use SCIGRESS to compute the infrared spectra of small inorganic molecules. Group theoretical methods will be used to predict the number and symmetries of molecular vibrations possessed by a molecule.


Complete Exercises I, II, III, IV, and VI before beginning this experiment.

NOTE A basic understanding of the chemical applications for symmetry and group theory is necessary. It is advisable to review the relevant material in an inorganic chemistry text or other reference such as F.A. Cotton, Chemical Applications of Group Theory, 3rd ed., Wiley, New York, 1990.

Background

One of the applications of symmetry in chemistry is the prediction of vibrations which will be active in infrared (IR) and/or Raman spectroscopy. Such predictions can be confirmed by using MOPAC to generate IR spectra and to examine the vibrations responsible for the IR peaks. As an example, the symmetries of IR active vibrations in a water molecule are worked out below. The same method is applicable to other molecules. The water molecule belongs to the C2v point group for which the character table is as follows:


A

A

1 1

2 2

1. Determine each atom’s contribution to the character of the transformation matrix under each symmetry operation. If an atom moves, it contributes 0 to the character. If an atom remains stationary, determine the contribution of each coordinate. If a coordinate is unchanged, it contributes 1; if it is reversed in sign, it contributes -1; if it is something in between, it makes a fractional contribution.

a. The consequences of each operation type are summarized as follows:

E: All atoms remain and all coordinates are unchanged. Each coordinate contributes 1 to the character of the reducible representation. Thus, for water, the character for the E element is 9.

C2: The hydrogens move and thus contribute 0. Oxygen remains stationary

and the z coordinate remains unchanged, contributing 1. However, x and y are both reversed in sign and thus each contributes -1. The character is thus 1-1-1 = -1

v(xz) (plane of molecule): All atoms remain unchanged. The z and x

coordinates are unchanged, each contributing 1. Each y coordinate is reversed, contributing -1. For each atom, the contribution is 1 and the character is 1+1+1 = 3

v(yz): Only O is unchanged. The z and y coordinates contribute 1 each. The

x coordinate is reversed and contributes -1. Thus the character is 1+1-1 = 1.

b. The reducible representation is Γ = 9 -1 3 1

2. Determine the irreducible representations of the coordinates by making use of a group property.

3. The reducible representation represents the sum of the motions of all of the

coordinates: 3 of which result in translation (x, y, z) and 3 of which result in rotation (R , R , R ) for a nonlinear molecule. Thus, for water, there are 3

x y z

vibrations. If the irreducible representation of a vibration is that of a coordinate (x, y, or z), it will be IR active. Subtract the irreducible representations of translations and rotations. a. Translation (x = B1, y = B2, z = A1)

b. Rotation (Rx = B2, Ry = B1, Rz = A2)

c. The vibrations which remain:3 - 1 = 2 B 3 - 2 = 1

1 - 1 = 0 B 2 - 2 = 0


2

4. Of the 3 vibrations, 2 are A1 symmetry and 1 is B1 symmetry. A1 is the irreducible representation of the z coordinate and B1 is the irreducible representation of the x coordinate so all three vibrations are IR allowed.

Note that, for a particular point group, Γ will depend upon the number of atoms in the molecule.

If a symmetry operation is a multiple (e.g. 2C3 in C3v) the contribution to the irreducible representation must be multiplied by that multiple in calculating the number of irreducible representations.

If a vibration belongs to a degenerate irreducible representation (E or T), then there will be a single vibrational frequency, corresponding to 2 (E) or 3 (T) degenerate transitions. Likewise, when accounting for rotations and vibrations, if 2 rotations, say, belong to an E irreducible representation, that accounts for 1 E irreducible representation.

Modeling Section

Simulation of the Infrared Spectrum of H O(g)

1. Build a water molecule in the Workspace. 2. Optimize the molecule with MOPAC using PM3 parameters. Append a Force

calculation. When you append calculations, MOPAC executes the selected calculations in sequence; in this case, a geometry optimization followed by an IR/vibrational spectrum. ❏ Open a new experiment and select chemical sample, IR transitions, and MO-G

PM3 FORCE. The experiment manager automatically does an optimization followed by an IR calculation. Select Run.

3. View the vibrational spectrum. ❏ Activate the molecule window after the calculations are complete. Select Analyze | IR Transitions. An IR spectrum appears in a separate window. Each separate vibration is represented by a peak with a triangle symbol at the minimum.

4. Adjust the x and y axes as needed. For example, the water spectrum should be

displayed between 0 and 4000 cm-1 and should have no peaks at frequencies

below 1000 cm-1. To check frequencies above 4000 cm-1, double click just below the horizontal axis to open the Axis Attributes/ Axis Parameters dialog box.

❏ Enter a Wavelength Range of 6000 to 1000 cm-1. Click OK to rescale the spectrum. Rescale the spectrum, as desired, to view parts of the spectrum in greater detail.

5. Resolve overlapping peaks as needed.

❏ Click on a curve with the Select tool. A red line appears, defining

6. Click on a peak symbol to view the vibration corresponding to a particular peak. The structure window will rearrange to show the atom motions involved in the vibration. To better view the vibration, click anywhere in the structure window and reorient the structure.

7. Paste the spectrum and vibrations into a word processing document and assign each vibration to an irreducible representation.


N2F2

1. Build a molecule of N2F2 in the Workspace. Optimize and execute a Force calculation as in the case of the water molecule.

2. View the molecule and determine the point group. Obtain the character table for the point group.

3. Use the methodology given in the Background section to determine the number and symmetries of the vibrations of the molecule. Determine which of the vibrations are IR active.

4. View the computed IR spectrum of N2F2. View the vibrations, both IR active and IR inactive, and assign their symmetries (irreducible representations).

Report Guidelines

✎ Paste the spectra and vibrations for water into a word processing document and assign each vibration to an irreducible representation.

✎ Use group theoretical methods to determine the symmetries of the vibrational modes of N2F2 and determine which vibrations are IR active.

✎ Paste the spectra and vibrations for N2F2 into a word processing document and assign each vibration to an irreducible representation.


Instructor Notes

Typical Results

Water

N2F2

Number of each symmetry species:

nAg = 14 [(12)(1) + (0)(1) + (0)(1) + (4)(1)] = 4

nBg = 14 [(12)(1) + (0)(-1) + (0)(1) + (4)(-1)] = 2

nAu = 14 [(12)(1) + (0)(1) + (0)(-1) + (4)(-1)] = 2

nBu

= 14 [(12)(1) + (0)(-1) + (0)(-1) + (4)(1)] = 4

Reducible representations of translations (Au, 2B

u) and rotations (A

g, 2B

g).

Remainder are vibrations: 3Ag, 1A

u, 2B

u

IR active modes: 1Au, 2B

u


Further Discussion

An additional system worth studying is SF4. The structure is based on a trigonal bipyrimidal distribution of electron pairs, and since there is one lone pair, there are two structures possible. The two structures do not have the same number of IR active transitions, so that infrared spectroscopy provides an experimental criterion for determining the correct structure. One structure belongs to the C2v

point group and prediction of the number of IR active vibrations is straightforward. The other belongs to C

3v and here transformation of the atoms

under the C3 operation is more difficult.

SF4

The structure of SF4 is based upon a trigonal bipyramidal distribution of electrons, one being a lone pair. Thus there are two possible structures one with the lone pair in an axial position and one with the lone pair in an equatorial position.

Dr. Ryan Mewis [email protected] 40

ESSENTIAL REVISION & PREPARATION

GUIDE

TO Structure and Spectroscopy

Dr. Ryan Mewis [email protected] 41

Preparation for Structure and Spectroscopy

Revise conversions between frequency, wavelength and wavenumber.

Revise equation for calculating photon energy.

Recommended Reading:

Foundations of molecular structure determination Duckett, Gilbert and Cockett (OUP, 2nd Ed) Good all round text detailing IR, Raman, UV-vis, NMR, mass spectrometry and X-ray crystallography

Nuclear Magnetic Resonance Hore (OUP, 2nd Ed) Introductory primer that covers NMR

NMR: The Toolkit. How Pulse sequences work Hore, Jones and Wimperis (OUP, 2nd Ed) More advanced primer that covers pulse sequences

Review Yr 1 Notes: Specifically the Application of 13C NMR spectroscopy in organic chemistry (Dr Birkett).

Also refer to Dr Beatriz Macia-Ruiz’s notes in this document on 13C and IR spectroscopy.

Topics that will be covered this year:

A background on the inherent sensitivity issues of NMR and how this links to the NMR experiment

What the 1H NMR spectrum provides the spectroscopist with e.g. number of signals, integration ratio,

chemical shift of the signals and signal multiplicity

J-couplings due to first-order effects and the Karplus plot. Determination of geometric isomerism using

J-coupling will also be covered

Second order effects

Determination of geometric isomerism using J-coupling

J-coupling in aromatic ring systems

19F NMR spectroscopy

Advanced methods such as NOESY (Nuclear Overhauser Spectroscopy)

2D methods such as COSY (Correlation Spectroscopy) and HMQC (Heteronuclear Multiple-Quantum

Correlation)

Mass spectrometry – how the mass spectrum is collected

Production of fragments and their relative stability

Common fragmentation pathways e.g. retro Diels-Adler, McLafferty Rearrangement, retro-ene reaction,

tropylium and acylium ions

Deducing structures using a suite of analytical data

Beatriz Maciá Ruiz <[email protected]> 42

ESSENTIAL

REVISION of 1st YEAR

ORGANIC CHEMISTRY


NOMENCLATURE

Revise class notes, including nomenclature of (cyclo)alkanes, (cyclo)alkenes, (cyclo)alkynes, aromatic

compounds and organic compounds with functional groups.


1. ISOMERISM AND STEREOCHEMISTRY

Revise the concepts in the following diagram:

In particular, revise:

2.1. Stability in substituted cyclohexanes:

Isomers

(same molecular formula)

Structural Isomers

Chain Isomers

Position Isomers

Functional GroupIsomers

Stereoisomers

ConformationalIsomers

ConfigurationalIsomers

E-and Z- Isomers

Isomers with chiralcentres


2.2. CIP Rules (establish priority between substituents):

1st- Order by atomic number

Cl > F > O > N > C > H

…or in case of isotopes, by mass

2nd- If same priority at first atom: Go to first point of difference

3rd- Multiple bonds: Add double or triple representations of atoms at the respective other

end of the multiple bond.

2.3. Naming Z/E isomers (cis (same side)/trans (opposite side) double bonds, respectively)

2.3 Naming enantiomers: R/S nomenclature


2. REACTION INTERMEDIATES. Concepts to revise:

2.1. Electrophiles (species that accept e-)

2.2. Nucleophiles (species with e- to share)

2.3. Inductive effect (the most electronegative atom atracts the e- Polar bond)

2.4. Mesomeric effect (to delocalize e- through bonds)

Example:

2.5. Carbocations

2.6. Carbanions


2.7. Radicals

2.8. Language in organic chemistry

3. REACTIONS IN ORGANIC CHEMISTRY

3.1. Radical halogenation


3.2. Nucleophilic substitution (SN1 and SN2)

General picture:


3.3. Elimination reactions (the nucleophile acts as a base)


3.4. Additions to double bonds (hydrogenation, bromination, hydration and adition of HX)

General picture:

3.5. Aromatic electrophilic substitution (SE Ar) (halogenation, nitration, sulfonation, alkylation and

acylation)

General picture:

Mechanism:



3.6. Nucleophilic addition to carbonyl compounds



3.7. Nucleophilic substitution to carbonyl compounds

General picture:

Reactivity trend:

General mechanism:


4. SPECTROSCOPY: Molecular response to radiative stimulus

ΔE = hν ν = c/λ


IR - Generalities:

* Streching requires more en\ergy than Bending

- Streching vibration has higher than Bending vibrations

* To vibrate a short (and stronger) bond requires more energy than to vibrate a long (and weaker)

bond

- Streching C=C has higher than streching C-C

* Higher for the vibration of bonds with lighter atoms (Hooke’s law)

- Streching C-H has higher than streching C-D


13C NMR Spectroscopy - chemical shift () vs. absorption of energy (resonance) as the y-axis

Chemical shift for 13C NMR ( = 0 – 250 ppm)

Coupling to H is removed by “broad band” irradiation of all Hs

Each carbon atom in a specific carbon environment will produce one singlet in a 13C NMR spectrum.

Hybridisation and type of

carbon atom Approximate chemical shift range (ppm)

sp3 0 – 80 ppm (moves downfield (to higher values with

the change from CH3 to CH2 to CH to C)

sp 80 – 100 ppm

sp2 alkene 110 -140 ppm (alkene carbon signals tend to be more

upfield (lower values) than aromatic carbon signals)

sp2 aromatic 115 – 150 ppm

sp2 C=O

190 – 210 ppm

Carbonyl carbon signals are often the most downfield

signal in the 13C NMR spectrum


5. WHERE YOUR 2nd YEAR STARTS:

Second year lectures in the unit 6F5Z2006 (Core Concepts 1; Organic and Inorganic Chemistry) will

focus on the carbonyl group with some emphasis on the chemistry of enols/enolates.

Many aldehydes/ketones can exist as two forms – a keto and an enol. Consider acetone:

O OH

Ketoform

Enolform

The formation of an enol/enolate arises from deprotonation of the proton:

O

H

HH

B

O

H

H

O

H

H

Enolate

H

O H

O

H

H

H

Enol Mechanism of Formation of enols/enolates

This proton can be removed by base to give an anion that is resonance stabilised – we can delocalise the

anion over additional atoms so it is more stable than expected. This phenomenon is also observed

elsewhere, such as in nitro- and cyano-substituted compounds


Resonance Stabilisation of anions to carbonyls, nitro groups and cyano groups.

Thus, we can think of the proton of aldehydes/ketones/esters as being acidic

Acidity of α-protons

to a carbonyl:

Lower pKa means more acidic H H abstraction is easier when the carbanion generated (ENOLATE) is

more stable . As a result protons to carbonyl carbons are far more acidic than those on a simple

alkane such as butane (pKa~50) where no stabilisation can occur.

Enolates as nucleophiles:

Enols/enolates are far more than a curiosity in organic chemistry. They are very useful nucleophiles. In

first year lectures you saw how simple alkenes can act as nucleophiles and can undergo addition reactions

with protons and bromine for instance and the mechanism is very similar (See section 4.4 of these notes).

Enolates can be considerd as alkenes which are more powerful nucleophiles owing to the presence of

the O- group and can react with a wide range of electrophiles with regeneration of the carbonyl group:

O

R1

R2

EO

R1

R2

E

General mechanism for reaction of enolates with electrophiles

Enolates, being powerful nucleophiles can also react with carbon-based electrophiles such as haloalkanes

and are thus very useful species for forming carbon-carbon bonds – one of the most important

transformations in organic chemistry.


O

R2R1

H H

B

O

R2R1

H

R3X

X - Br, I

O

R2R1

H R3

NewBond

Reaction of enolates with haloalkanes

Enolates also react with other aldehydes/ketones (which have an electrophilic carbonyl carbon) in a

more complex process known as the aldol reaction.

B-

R'R

O

R'R

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General Mechanism of the Aldol Reaction

Next term:

we will look at these process in detail and their uses in synthesising useful organic molecules.

We will also look at other reactions associated with carbonyl groups:

Conjugate additions to -unsaturated carbonyls.

The Michael Addition.

The Robinson Annulation.

Oxidations and Reductions in Organic Chemistry.

In addition we will be discussing how to plan a synthesis of a target molecule in a logical fashion

applying what is known as Retrosynthetic Analysis.

If you would like to read ahead over the summer here are a few references:

For an introduction see: “Chemistry3”, Ch 23,p1054-1057, p1074-p1090.

For good coverage at second year level see:

“Organic Chemistry”, P.Y. Bruice, 5th Ed, Ch 18, p850-891, Ch 19, p908-920.

“Organic Chemistry With Biological Applications”, John McMurry, 2nd Ed, Ch 14, p 574 and p 588-

p592, Ch 17, p695-733.

For more advanced, but rigorous, coverage see:

“Organic Chemistry”, Clayden et al; 1st Ed, Ch 6, p139-141, Ch 10, p227-241, Ch 21, p523-538, Ch26

p667-671, p676-680, Ch 27, p689-698, Ch 29, p749-753, p760-762.

For good coverage of retrosynthetic analysis read Ch 30, p771-801.

Unit content 61

Unit specifications

Chemistry BSc Pharm Chem Med Bio

6F5Z2101 Laboratory Techniques 2

6F5Z2102 Solid State, d-block and f-block Chemistry

6F5Z2103 Chemistry of the Carbonyl Group

6F5Z2110 Structure and Spectroscopy

6F5Z2104 Thermodynamics and Kinetics

6F5Z1103 Applied Molecular Biology

6F5Z2105 Instrumental Analysis

6F5Z2107 Pharmaceutical Analysis and

Quality Control

6F5Z1104 Biochemistry

OPTION 6F5Z2106 Formulation Fate and Biometabolism 6F5Z2108

Chemistry in Society 2

6F5Z2109 Green

Chemistry

Unit content 62

TITLE Laboratory Techniques 2 UNIT CODE: 6F5Z2101

BRIEF SUMMARY: An introduction to some laboratory techniques and associated practical and analytical skills for interpreting data in inorganic, organic, physical, analytical & computational chemistry.

INDICATIVE CONTENT: Advanced synthetic techniques and skills unit. A balanced programme of experiments will be selected from inorganic, organic, physical and analytical chemistry. The practical exercises will introduce new advanced techniques and concepts, and will reinforce health and safety awareness and Good Chemical Laboratory Practice (GLP). A further element will focus on the application of modelling techniques to drug design. Learning will normally take place through the following activities: self-reflection and individual and group-based laboratory work.

ASSESSMENTS

ELEMENT 1 Laboratory proformas 40%

DESCRIPTION: The assessment consists of completing laboratory proformas (up to c. 2,000 words) to assess the students’ ability to collect, interpret and rationalise data obtained using analytical techniques and / or physiochemical techniques and their ability to synthesise materials using chemical techniques. These proformas will also be used assess the students competency of advanced laboratory techniques using safe laboratory practice.

ELEMENT 2 Laboratory portfolio40%

DESCRIPTION: The assessment consists of written practical reports (up to c. 2,000 words) and laboratory tests to assess the students’ ability to collect, interpret and rationalise data obtained using analytical techniques and / or physiochemical techniques and their ability to synthesise materials using chemical techniques. These proformas will also be used assess the students competency of advanced laboratory techniques using safe laboratory practice.

ELEMENT 3 Report20%

TYPE (COURSEWORK / EXAM)

DESCRIPTION: The assessment consists of a written practical report (up to c.1500 words) to assess the students’ ability to apply molecular modelling techniques in order to analyse and interpret protein-ligand interactions. The student will demonstrate that they can present experimental results of their collected and interpreted data in a professional format using appropriate IT software (for example Scigress) and formulate compelling and rationalised arguments for interactions present.

LEARNING RESOURCES

ITEMS FOR PURCHASE: Atkins, P. & de Paula, J. (2010) Physical Chemistry. 10th edition, Oxford :OUP Weller, M., Overton, T., Rourke J. & Armstrong F. (2014) Inorganic Chemistry. 6th edition, Oxford : OUP Clayden, J., Greeves, N. and Warren S. (2012) Organic Chemistry. 2nd edition, Oxford : OUP Burrows, A., Holman, J.S., Parsons, A.F., Pilling, G. and Price, G. J. Chemistry3: Introducing inorganic, organic and physical chemistry. 3rd edition, Oxford: OUP Monk, P. & Munro, L.J. (2010) Maths for chemistry: A chemist's toolkit of calculations. 2nd edition, Oxford : OUP

ESSENTIAL READING: Dean, J., Holmes, D., Jones, A. M. , Jones, A., Reed, R. & Weyers J. Practical Skills in Chemistry. 2nd edition, London : Pearson (Electronic copies available via the library)

Learn Sci videos techniques – on moodle

Unit content 63

TITLE Solid state, d-block and f-block Chemistry UNIT CODE :6F5Z2102

BRIEF SUMMARY: This unit covers transition metal complexes, molecular symmetry, crystallography, solid-state chemistry and f-block chemistry

INDICATIVE CONTENT: Element 1. Transition Metal Complexes (d-block chemistry) Topics include; Nomenclature, Isomerism, the chelate and macrocyclic effects. Crystal field theory. Coordination geometries and their d orbital splitting. Magnetic properties of transition metal ions. Electronic absorption spectra. MO theory applied to transition metal complexes. An Introduction to organometallic chemistry and the 18/16-electron rules. Element 2. Solid State Chemistry Crystalline solids; close-packing model of spheres. Metallic, ionic and covalent solids. Metallic alloys. Radius ratio rules to predict ionic lattice structures. Lattice defects and non-stoichiometric compounds. Properties and applications of solid state structures with an introduction to the band theory of solids. Amorphous solids; Introduction to glasses. Amorphous materials derived from silicates. Physical and chemical properties of glasses Element 3. f-block Chemistry Lanthanide chemistry; Introduction to the f-block elements. f-orbitals. Electron configuration of lanthanide atoms and ions. The lanthanide contraction. The coordination chemistry of lanthanides. Electronic and magnetic properties of lanthanides. Applied lanthanide chemistry. Element 4. Molecular Symmetry and Crystallography Molecular Symmetry in terms of rotational axes, planes of symmetry and centres of inversion, symmetry point groups. Group Theory; using symmetry to predict vibrational spectra, and construct MO diagrams of polyatomic molecules. Crystallography; basic crystallography concepts, unit cell, Miller indices, Bragg and d-spacing equations, systematic absences and indexing of peaks to determine structure. Analysis of experimental data.

ASSESSMENTS

ELEMENT 1 EXAM 60%

DESCRIPTION: Two hour examination (closed book), comprising a combination of short answer and longer description/calculation/problem solving questions. Preparation will be assisted by formative assessments and tutorials on all topics to provide feedback on interim stages of work.

ELEMENT 2 Coursework -Report 40%

DESCRIPTION: Students will be tasked with rationalising the structure of different crystalline forms from a group theory perspective. Students will be expected to deduce the symmetry mode responsible for the vibration and relate their deductions to the morphology observed in nature examples. Students will also be tasked to analyse experimental X-ray diffraction data to determine crystal phase and molecular structure. Students will write a small report (1000-1250 words) to detail their findings and observations that have enabled the crystalline forms to be elucidated.

LEARNING RESOURCES

ITEMS FOR PURCHASE: Weller, M., Overton, T., Rourke, J. and Armstrong, F. (2014). Inorganic Chemistry. 6th Ed. Oxford. Oxford University Publishing.

ESSENTIAL READING: Vincent, A. (2001). Molecular symmetry and group theory. 2nd Ed. John Wiley and Sons. Clegg. W. (2015). X-ray crystallography. 2nd Ed. Oxford. Oxford Chemistry Primers. West. A. R. (2014). Solid state chemistry and its Applications. 2nd Ed. John Wiley and Sons.

Unit content 64

TITLE Chemistry of the Carbonyl Group UNIT CODE: 6F5Z2103

BRIEF SUMMARY: The use of carbonyl groups as enabling functionality will be illustrated by discussion of a range of chemical transformations of these functional group.

INDICATIVE CONTENT: Chemistry of the Carbonyl Group Formation of carbonyls by oxidation. Reduction of the carbonyl group. Keto-enol equilibria. Alpha deprotonation of carbonyl compounds. Alkylation of 1,3-dicarbonyls using alkoxide bases, kinetic alkylation of ketones using LDA. Homoaldol and mixed aldol additions and condensations. Use of LDA to control products of the aldol reaction. The Claisen condensation. Conjugate Additions Chemistry of conjugated ketones. Conjugate addition of nucleophiles. 1,2 Versus 1,4-addition. The Michael reaction. The Robinson Annulation. Enamines and Imines Formation and reactions of enamines and iminium ions. Application to targeted synthesis. Enolates and iminium species in the synthesis of nitrogen heterocycles.

ASSESSMENTS

ELEMENT 1 Coursework Test 40%

DESCRIPTION: 1h unseen, closed-book test. The element of assessment will be supported by formative components and tutorials to provide opportunities for student feedback on interim stages of work. The test will consist of short answer, problem-solving questions testing ability to apply material in indicative content (part 1) to write mechanisms, predict starting materials/products as set out in LO 1.

ELEMENT 2 Exam 60%

DESCRIPTION: 2 hour unseen examination. The element of assessment will be supported by formative components and tutorials to provide opportunities for student feedback on interim stages of work. The exam will consist of a combination of short and long answer, problem-solving questions testing ability to apply material described in indicative content (parts 2 and 3) to write mechanisms, predict starting materials/products as set out in LOs 2/3.

LEARNING RESOURCES

ITEMS FOR PURCHASE: Bruice, P. Y. 2017. Organic Chemistry. 8th ed. New Jersey: Pearson

ESSENTIAL READING: Clayden, J., Greeves, N. and Warren, S. G. 2012. Organic Chemistry. 2ND ed. Oxford: Oxford University Press.

Unit content 65

TITLE Structure and Spectroscopy UNIT CODE: 6F5Z2110

BRIEF SUMMARY: Fundamental spectroscopic principles and structural elucidation using NMR, mass spectrometry and infra-red techniques and determination of molecular physical parameters from vibrational and rotational spectroscopies.

INDICATIVE CONTENT: The unit content will typically cover the following themes: - Structural elucidation: Combined application of 1H and 13C NMR, IR and mass spectroscopy to structural elucidation. 1H NMR and 13C NMR : how the experiment works, identifying chemical environments, the generation of multiplet structures, J-coupling (effect of bond length and angle), Karplus plot, chemical shift, shielding and deshielding effects, effects of EWG and EDG on aromatic proton environments, DEPT, 19F NMR and coupling constants. 2D NMR : experiments and exemplar spectra. Mass spectrometry : creation of ions, sensitivity of instrumentation, M+ and base peaks, fragmentation pathways, Stevenson-Audier rule, retro-Diels Adler reaction, McLafferty rearrangement, tropylium ion formation, common fragment ions. IR: identifying key stretches to enable structural elucidation of molecules. Application of structural elucidation to new drug molecules - Fundamental Molecular Spectroscopy: Electromagnetic radiation and the electromagnetic spectrum, energy within molecules. Boltzmann distribution and quantised energy levels, energy level occupancy for rotational and vibrational transitions, Beer-Lambert Law. Vibrational and rotational spectroscopy: Rigid rotor model for diatomics and triatomics, determination of moment of inertia and internuclear distances from microwave spectra. SHM oscillator model, anharmonic oscillator model, overtones, bond force constant. Introduction to Raman spectroscopy. Infrared and Raman spectra of AB2 and ABX molecules. - Professional / Career Development: A selection of workshops and online support to assess, develop, and identify acquisition of the following skill areas: CV preparation, work experience / graduate job searches, applications, psychometric tests, assessment centres and interview skills.

ASSESSMENTS

ELEMENT 1 Coursework Report 60%

DESCRIPTION: A technical skills exercise report on the NMR and IR focused practical to acquire data pertaining to unknown compounds in order to elucidate their structure and the mechanism of their formation (2000 words). Appended to the report will be a mock job application document including preparation of a CV and job application.


DESCRIPTION: A 1 hour test on the Fundamental Molecular Spectroscopy element of the unit consisting of questions designed to assess both breadth (short answer questions) and depth (longer, problem solving questions) of understanding. Tutorials and formative work will progress learning to the final goal and provide feedback mechanisms for students on interim stages of work.

LEARNING RESOURCES

ITEMS FOR PURCHASE: Atkins P.W. and de Paula J., 2014, Physical Chemistry, 10th Edition, OUP Weller M., Overton T., Rourke J. and Armstrong F., Inorganic Chemistry ,OUP Monk P. and Munro L.J , 2010, Maths for chemistry: A chemist's toolkit of calculations 2nd Edition, OUP

ESSENTIAL READING: Burrows A., Holman J.S. , Parsons A.F., Pilling G. and Price G.J., 2017, Chemistry3: Introducing inorganic, organic and physical chemistry, 2nd Edition, OUP Patrick G.L., 2009, An Introduction to Medicinal Chemistry , 4th Edition, OUP Hore P.J., Jones J.A. and Wimperis S, 2000, NMR : The Toolkit. How Pulse Sequences Work, OUP Hore P.J., 1989, Nuclear Magnetic Resonance, OUP

Unit content 66

TITLE Thermodynamics and Kinetics UNIT CODE: 6F5Z2104

BRIEF SUMMARY: Exploration of concepts required for study of physical chemistry including the study of interfaces, kinetics, thermodynamics

INDICATIVE CONTENT: The unit content will typically include: - Processes at Interfaces: Introduction to surface chemistry; Chemisorption and physisorption, thermodynamics of adsorption, entropy, enthalpy and Gibbs free energy of adsorption, associative and dissociative adsorption. Adsorption coefficient. Adsorption isotherms; Mono and multilayer adsorption, Langmuir and Freundlich adsorption, types of adsorption isotherms, BET isotherm. Applications; Experimental methods of investigating adsorption, Kelvin equation, pore size, measurement/calculation of surface areas of porous and non porous solids. - Thermodynamics: Entropy; Entropy and its statistical significance. Entropy as a function of temperature and pressure, Clausius inequality, Third law of thermodynamics, absolute entropy values, experimental determination of entropy; heat capacity and Kirchhoff equation. Introduction to chemical potential; Gibbs functions; temperature dependence of Gibbs free energy, Gibbs Helmholtz equation, composition dependence of Gibbs free energy, derivation and application of the van't Hoff Isotherm. Phase equilibria: pure substances; Phase equilibria of pure substances, one and two component systems (solid/liquid), critical temperature and pressure, phase diagrams, eutectics. Properties of mixtures; Clapeyron equation, Clausius-Clapeyron equation, Trouton’s rule, colligative properties and the elevation of boiling point and depression of freezing point, Raoult’s law, deviations from Raoult’s law, azeotropes, distillation, partition of a solute between two immiscible solvents. Application – fundamental understanding of chemical reaction energetics. - Kinetics: Kinetics; Rates of reactions; Reaction kinetics, integrated rate equations, determination of reaction order, pseudo-order reactions, reaction half-lives. Reaction mechanisms and molecularity; Rate determining step, consecutive/reversible reactions, steady-state approximation, chain reactions, unimolecular reactions, Lindemann treatment. Temperature dependence of reaction rates; Maxwell-Boltzmann distribution, collision theory, activation energy, Arrhenius equation, thermodynamics of activation; enthalpy, entropy and Gibbs free energy, activated complex theory, Eyring equation. Application – predicting and measuring rates of chemical reactions.

ASSESSMENTS


DESCRIPTION: Assignment one will be a 1-hour in-class test (unseen), comprising a mixture of multiple choice, short answer, and problem-solving questions. The element of assessment will be supported by formative components and tutorials to provide opportunities for student feedback on interim stages of work.

ELEMENT 2 Exam 60%

DESCRIPTION: Assignment two will be a 2-hour unseen examination comprising a combination of short answer and problem-solving questions. The element of assessment will be supported by formative components and tutorials to provide opportunities for student feedback on interim stages of work.

LEARNING RESOURCES

ESSENTIAL READING: Atkins' Physical Chemistry - Atkins, P. W., De Paula, Julio 2014

Unit content 67

TITLE Formulation, Fate and Biometabolism UNIT CODE: 6F5Z2106

BRIEF SUMMARY: Understanding the principles of drugs and medicine formulation, the interaction of biomolecules/drugs within biological systems, pharmacokinetics and toxicology in the context medicinal chemistry and drug discovery.

INDICATIVE CONTENT: This unit will focus on two principle elements: Element 1: Pharmacokinetics, toxicology and drug metabolism: Basic drug formulation and routes of administration. Basic pharmacokinetic calculations. ADME. Drug absorption, polarity of functional groups, membrane permeability, Henderson-Hasselbach equation and the effect of pH. Drug distribution, lipophilicity and distribution, plasma proteins, passive and active membrane transport, blood-brain barrier. Drug metabolism, Phase I and Phase II metabolism. First pass effect. Drug excretion, structure and function of the kidneys, drug polarity and excretion, enterohepatic circulation, clearance. Introduction to drug toxicology, LD50, measures of toxicity. Bioactivation of drugs. Mechanisms of toxicity, in-vivo formation of electrophiles and their reactions with biomolecules; Element 2: Biometabolism including primary and secondary metabolism (eg AcCoA, Shikimic acid pathway, alkaloids. Anti-metabolites, proteins, peptidomimimetics and biosisoterism. Introduction to the discovery of novel bioactives. Biosensing, synthetic receptors.

ASSESSMENTS

ELEMENT 1 Coursework- Essay 50%

DESCRIPTION: A concise (1500 word max) report summarising the pharmacokinetics and ADME process for a specified pharmaceutical or drug. The report will review and summarise the principles underpinning the specified drug’s formulation/administration, pharmacokinetics, ADME and toxicology. Using pharmacokinetic data, from scientific literature sources, interpret and summarise pharmacokinetic data, for the specified drug, coherently within the context of medicinal chemistry and the drug discovery process.

ELEMENT 2 Exam 50%

DESCRIPTION: 90 minute unseen examination, consisting of short and long answer questions, which will provide evidence of understanding of principles of biometabolism to predict metabolites and explain the discovery of novel bioactives, specifically primary and secondary metabolism (eg AcCoA, Shikimic acid pathway, alkaloids. Anti-metabolites, proteins, peptidomimimetics and biosisoterism. Introduction to the discovery of novel bioactives. Biosensing and synthetic receptors. The element of assessment will be supported by formative components and tutorials to provide opportunities for student feedback on interim stages of work .

LEARNING RESOURCES

ESSENTIAL READING: G. G. Gibson and P Skett Introduction to Drug Metabolism, 3rd Edition. H. Moynihan and A. Crean Physicochemical Basis of Pharmaceuticals, 1st Edition. M. K. Campbell, S. O. Farell, Biochemistry, 8th Edition.

FURTHER READING: G. Patrick, An Introduction to Medicinal Chemistry, 4th Edition. C.M. Dobson et al., Foundations of Chemical Biology, Oxford Chemistry Primer No. 98.

Unit content 68

TITLE Pharmaceutical Analysis & Quality Control UNIT CODE: 6F5Z2107

BRIEF SUMMARY: This unit develops an integrated knowledge and ability to apply the principles of analytical/bioanalytical techniques in the quantitative/qualitative analysis of drugs and related substances/samples (including biologicals).

INDICATIVE CONTENT: This unit aims to develop an integrated knowledge and ability to apply the principles of analytical/bioanalytical techniques and methods in the quantitative/qualitative analysis of drugs (either licit or illicit), and related substances/samples (including biologicals). The unit provides an understanding of (i) the quality control of pharmaceutical/drug materials; (ii) bioassays and/or binding assays; (iii) new analytical and/or bioanalytical techniques and (iv) the structure and content of monographs for pharmaceuticals and/or biopharmaceuticals. The class also introduces and provides an understanding of the principles of Total Quality Management in the production of medicines including (but not limited to): (i) Quality Control/Assurance and (ii) Quality Management of drugs and other related substances. Practical laboratory activities will support this unit and reinforce the lecture material within the context of pharmaceutical analysis and quality control. Advanced topics including (but not limited to): QA/QC practice; Pharmacopoeial monographs; ICH guidelines; Equipment Qualification; Near Infra-red in drug analysis; Analysis of counterfeit drugs; Analysis of drugs of abuse; Mass spectrometry in bioanalysis; Clinical applications of mass spectrometry; Metabolite identification in bioanalysis will be discussed within the context of current research and innovations in the subject area.

ASSESSMENTS

ELEMENT 1

TYPE (COURSEWORK / EXAM) Coursework Essay 50%

DESCRIPTION: Students will undertake a problem-based learning exercise/assignment to apply critical thinking and data analysis skills, within the context of pharmaceutical analysis. Specifically students will critique and describe the application of analytical/bioanalytical techniques or methods in the quantitative/qualitative analysis of a specific drug (either licit or illicit), and/or a related substance/sample (including biologicals).

ELEMENT 2 Exam 50%

DESCRIPTION: 90 minute unseen examination, consisting of short and long answer questions, which will provide evidence of understanding of principles and application of the qualitative and quantitative methods for the analysis/bioanalysis of biological agents, drugs and/or other related substances in formulations and biological media/samples. Describe in the context of pharmaceutical analysis, the principles, legislative requirements and issues relating to the principles, legislative requirements and issues relating to: (i) Quality Assurance (QA); (ii) Quality Control (QC); (iii) Good Pharmaceutical Manufacturing Practice (GMP); (iv) Good Control Laboratory Practice (GLP); (v) Pharmacopoeias and Pharmacopoeial Monographs and/or (vi) Regulatory Instruments; (vii) Analysis of counterfeit drugs and/or drugs of abuse; (viii) Application of mass spectrometry in bioanalysis, clinical applications and metabolite identification. The element of assessment will be supported by formative components and tutorials to provide opportunities for student feedback on interim stages of work.

LEARNING RESOURCES

ESSENTIAL READING: D. G. Watson Pharmaceutical Analysis: a textbook for pharmacy students and pharmaceutical chemistry, 4th Edition.

FURTHER READING: A. H. Beckett and J. B. Stenlake Practical Pharmaceutical Chemistry, Part I and Part II, 4th Edition. S. H. Hansen and S. Pedersen-Bjergaard Bioanalysis of Pharmaceuticals: Sample Preparation, Chromatography and Mass Spectrometry, 1st Edition. H. Moynihan and A. Crean Physicochemical Basis of Pharmaceuticals, 1st Edition.

Unit content 69

TITLE Instrumental Analysis UNIT CODE: 6F5Z2105

BRIEF SUMMARY: This unit is an introduction to key aspects of instrumental analytical chemistry: namely separative methods [chromatography], elemental analysis [atomic spectroscopy] and electrochemistry.

INDICATIVE CONTENT: Topic 1: Introduction to Separation Science, Sample preparation for instrumental analysis, especially solvent extraction and solid phase extraction. The basis of chromatographic separations. TLC and column chromatography. Typical stationary and mobile phases. Dead time, Retention time, capacity factor, selectivity, resolution and efficiency. Band spreading in chromatography - the Van Deemter equation. Instrumental Chromatography (GC & HPLC). Isothermal and temperature programmed GC. Isocratic HPLC and solvent programming in HPLC. Order of analyte elution. Chromatographic optimisation. Qualitative and quantitative analysis by GC and HPLC. Internal standardisation and relative response factors. Ion chromatography. Size exclusion chromatography. Analyte detection in chromatography. Topic 2: Elemental Analysis. Atomic Spectroscopic techniques: Theory of atomic emission and atomic absorption. Description of the basic instrumentation and instrument components. Techniques covered: flame emission spectroscopy (FES), inductively coupled plasma (ICP), flame atomic absorption spectroscopy (FAAS) and mercury cold vapour and hydride generation variations, electrothermal/graphite furnace AAS (ETAAS or GFAAS). Chemical, physical and spectral interferences. Background correction techniques. Molecular Spectroscopic Techniques: UV/Visible instrumentation. Absorption spectra and the Beer-Lambert Law. Deviations from the Beer-Lambert Law. The analysis of multicomponent mixtures. Topic 3: Equilibrium electrochemistry: Electrode potentials, half cell reactions and their role in redox systems. Oxidation state diagrams and their interpretation. Activities and activity coefficients in solution, ion solvent interactions, Debye-Hückel limiting and simplified laws. Reference electrodes; Thermodynamics of cell reactions. Ionic transport and liquid junction potential.

ASSESSMENTS

ELEMENT 1 COURSEWORK Test 40%

DESCRIPTION: 1h unseen, closed-book test. The test will consist of multiple choice questions relating to topic 3, and will require students to apply the electrochemical principles to a range of appropriate analytical case studies and examples.

ELEMENT 2 EXAM 60%

DESCRIPTION: 2 hour unseen examination. The element of assessment will be supported by formative components and tutorials to provide opportunities for student feedback on interim stages of work. The exam will consist of a combination of short and long answer, problem-solving questions testing learning outcomes 1 and 2.

LEARNING RESOURCES

ESSENTIAL READING: Quantitative Chemical Analysis (9th Edition) Daniel C. Harris

FURTHER READING: Exploring Chemical Analysis (5th Edition) Daniel C. Harris Fundamentals of Analytical Chemistry (9th Edition) Douglas A. Skoog, Donald M. West, F. James Holler and Stanley R. Crouch.

Unit content 70

TITLE Green Chemistry UNIT CODE: 6F5Z2105

BRIEF SUMMARY: This module will introduce the concepts of green chemistry and its role in moving towards a more environmentally sustainable and economically viable chemical industry.

INDICATIVE CONTENT: This unit will focus on the twelve principles of green chemistry as proposed by Anastas and Warner. It will use these twelve principles to show how industry, via the use of appropriate examples e.g. Monsanto and Cativa processes, is striving to integrate greener methodologies in to their practice to maximise efficiency as well as reducing waste.

ASSESSMENTS


DESCRIPTION: The assessment consists of a written report (up to 1500 words) to assess the students’ ability to rationalise the implementation of green chemistry to improve atom economy, to compare and contrast green chemistry synthetic transformations to conventional alternatives and the need to simplify the production of chemicals and drugs which avoids the need for derivatisation. Students will be tasked with focusing on one particular reaction and discuss the potential merits of implementing a green chemistry route using the twelve principles of green chemistry as a basis.

ELEMENT 2 Exam 50%

DESCRIPTION: Examination (closed book, 1.5h), comprising description/calculation/problem solving questions. These questions will be based around the twelve principles of green chemistry e.g. atom economy, energy efficiency, reducing the need for derivatives, renewable feedstocks, catalytic cycles. Preparation will be assisted by formative assessments and tutorials to provide feedback on interim stages of work.

LEARNING RESOURCES

ESSENTIAL READING: Lancaster, M. (2016) Green Chemistry : An Introductory Text. 2nd Ed., Cambridge : RSC Anastas, P. T., Warner, J. C. (2000) Green Chemistry : Theory and Practice. Oxford : OUP

Unit content 71

TITLE Chemistry in Society 2 UNIT CODE: 6F5Z2108

BRIEF SUMMARY: This module will introduce new, emerging and unusual (NEU) materials and their manufacturing processes.

INDICATIVE CONTENT: The module introduces the chemistry behind the materials that have had a significant impact on our society in the last few decades. For example, materials used in electronic devices such as microprocessor chips, photovoltaics, LEDs (Light emitting diodes), smart phone displays and television screens. The relationships between particle scale and properties that give rise to distinctive modern materials, will be illustrated through three study blocks: Block 1 – unique properties of nanoscale materials: common nanostructures; effect of nanometre length scale on various optical effects; Nanoparticles and Colloids: Colloids (emulsions, dispersions, aerosols), nanoparticles dispersions. Influence of surface energy on colloid stability; Properties of surfactants and association colloids; Methods of nanoparticles synthesis; Important applications of colloids and nanoparticles. introduction to quantum wires and dots; nanotubes; nanoparticle scattering effects; combined electron oscillation in metal nanoparticles. Block 2 – the physical properties of semiconductors and superconductors; principles of superconductivity; principles of semiconductor (band structure, charge transport, carrier generation, recombination processes in both equilibrium and non-equilibrium conditions, doping, PN junctions, optical absorption); semiconductor devices and applications with a focus on photovoltaics. Block 3 – coatings technology: Chemical vapour, plasma and atomic layer deposition techniques; magneton sputtering for production of optoelectronic components (photovoltaics, solar cells, organic light emitting diodes OLEDs).

ASSESSMENTS


DESCRIPTION: Students will be required to conduct a critical review (up to 1500 words) of research articles relating to surface coating techniques.


DESCRIPTION: Unseen, closed book, in-class test (1.5h) comprising combination of short and longer descriptive/calculation/problem solving questions: covering key concepts in semiconductor and nanoscale materials.

LEARNING RESOURCES

ESSENTIAL READING: Review articles and current primary literature (typically high-impact journals) as directed within each study block.

Unit content 72

TITLE APPLIED MOLECULAR BIOLOGY UNIT CODE: 6F5Z1103

BRIEF SUMMARY: This Unit will introduce students to the key principles that underpin many nucleic acid molecular methodologies, with a strong emphasis on the applications and context of these techniques.

Indicative Content: The key features of nucleic acids, Eukaryotic and Prokaryotic genomes and gene expression will be introduced. Polymerase Chain Reaction and alternative in vitro cloning (e.g. Q-PCR & loop-mediated isothermal amplification) in vivo cloning methodologies and next generation sequencing techniques will be discussed. A range of bioinformatics techniques will also be introduced. Lectures, tutorials and practical activity will support and underpin the students understanding of PCR methodologies, including primer design, PCR optimisation, and plasmid cloning techniques. The lectures will link to applications, current topics and ethical considerations in the subject area and be led by academic research interest. Delivery will include lectures (including multi-media delivery), laboratory practical sessions, online self-directed study tutorials, current topics session, virtual labs.

ASSESSMENTS


DESCRIPTION: The learning outcomes will be assessed in a 1 hour unseen in-class test delivered online via the unit Moodle area. The test will typically include multiple choice questions (MCQs), drag and drop, labelling diagrams and problem solving questions. Students should demonstrate their ability to recall, interpret and analyse theory and applications of molecular biology.

ELEMENT 2 Coursework 50%

DESCRIPTION: Practical report (up to 1500 words) based on analysis of molecular data generated using PCR or plasmid technology in the laboratory. The report will include a background section, aims, results, discussion and references. This assessment will assess students’ ability to discuss, and apply current molecular techniques and applications as well as interpreting and analysing data.

LEARNING RESOURCES

Unit content 73

TITLE BIOCHEMISTRY UNIT CODE: 6F5Z1104

BRIEF SUMMARY: This Unit will develop students’ knowledge of protein structure and function, including metabolic processes linked to cellular signalling and protein modification.

Indicative Content: This unit will review amino acid chemistry, primary, secondary and tertiary structure (linking basic amino acid chemistry to the 3D structure and functionality of proteins), the regulation of protein synthesis and decay, membrane and structural proteins, enzymes, post-translational modifications. The key metabolic pathways (carbohydrate, lipid, amino acid) that are integral to these processes and methodologies in protein analysis (e.g. affinity chromatography, SDS-PAGE, Western Blotting, enzymatic assays, Mass Spectrometry and NMR) will be covered. Lectures, tutorials and practical activities will support students learning and application of methods in protein analysis and computational sessions will reinforce learning of structural methodologies. Academic research interests will link to relevant and current developments in the subject area. Bioinformatics sessions will be used to explore protein structure.

ASSESSMENTS


DESCRIPTION: Lab report (up to 1500 words) to show critical appraisal and synthesis of information and analysis and interpretation of proteins resulting from practical work on protein expression and purification, enzyme activity assays and/or SDSPAGE/ western blotting and computational work using a range of software to probe protein structure.


DESCRIPTION: This assessment will be a 1 hour unseen in-class test delivered online via the unit Moodle area. The test will comprise a range of question types (e.g. multiple choice, text entry) which will test the student’s ability to critically appraise, synthesise and use information from the unit content as well as the student’s ability to use biochemical methodology.

LEARNING RESOURCES

Documents

PREPARATION GUIDE FOR YEAR 2