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A MIND MAP

Nearly every subject has a shadow, or imitation. It would I suppose,

be quite possible to teach a deaf and dumb child to play the piano.

When it played a wrong note, it would see the frown of it’s teacher,

and try again. But it would obviously have no idea of what it was

doing, or why anyone should devote hours to such an extraordinary

exercise. It would have learnt an imitation of music. And it would have

learnt to fear the piano exactly as most students fear what is supposed

to be mathematics.

What is true of music is also true of other subjects. One can

learn imitation history – Kings and dates, but not the slightest idea of

the motives behind it all; imitation literature – stacks of notes of

Shakespeare’s phrases, and a complete destruction of the power to

enjoy Shakespeare…….

(W. W. Sawyer)

Periodicity and Orbitals

(1) Remember the positions of the key elements in the periodic table

because this will help you understand their characteristics such as

atomic radius and electronegativity

(2) Electrons are arranged in orbitals around the nucleus that have

specific shapes and energy levels.

(3) the further away

from the nucleus

the electron/orbital,

the higher energy

it will be

(4) the greater the

number of nodes

an orbital has,

the higher energy

it will be

(5) The important orbitals for this course

are the spherical s orbitals

and the dumbell

shaped

p orbitals

The p orbitals are present

in every shell (other than

the 1st shell) as a set of 3

"degenerate orbitals" which

all lie in mutually

perpendicular planes

Hope fully it's not too hard to see how these two topics link together. We looked in the first lecture at the important types of orbitals we need to know about for this course. In the lecture 3 screencast we are looking at how these types of orbital can combine to give the types of bonds we see in the drug molecules.

Ionic Bonding and sp3

hybridisation

I also talked in the lecture about "aromaticity" this is a very specific type of conjugation phenomenon that will be covered in more detail later in the course. However I will put the criterior for aromaticity in here should you want to familiarise yourself with this concept now.

Polarity and Functional Groups

Assess the polarity of the following molecules:

Moderately polar

polar (water soluble)

non-polar

(crosses the blood brain

barrier)

Functional Groups

Part 2

Highlight and name all of the functional groups

in these molecules (you'll get the answer the next time

you click on the arrow).

Acids and Bases

Acids

Bases

Which nitrogen in each of the structures below do you think is the most basic (answers will appear the next time you click on the arrow).

We talked a lot about electronegativity in these lectures

if you are not sure what this is then refer back

to the periodicity content as well as the

first video in the functional

groups section

remember: The lower the pKa the stronger

the acid (and hence the weaker the base)

Key mechanisms:

Reactions of Functional Groups

Electrophiles and Nucleophiles

Stereochemistry

Assign the configurations of the chiral centres in each

of the molecules below:

Draw all of the possible isomers of isocitric acid

and describe the relationship between each compound

(enantiomer or diastereomer):

Nucleophilic Substitution

This is a direct extension on from the

reactions of functional groups lectures.

Nucleophilic substitution reactions are

reactions of electrophiles with nucleophiles.

SN1 and SN2

Example Questions

Hydrolysis

Base Promoted

Hydrolysis

Acid Catalysed

Hydrolysis

Example Questions

(1). Highlight the functional group in enalapril

that is the most susceptible to hydrolytic

degradation. Fully explain your answer

(2). Provide a full curly arrow mechanism for the acid

catalysed hydrolysis of enalapril

(3). Provide a full curly arrow mechanism for the base

promoted hydrolysis of enalapril

Ester and Amide

Synthesis

Ester Synthesis

Amide Synthesis

Example Questions

(i) Reaction of a carboxylic acid

with an alcohol using acid as a

catalyst

(ii) Reaction of an acyl chloride

with an alcohol.

(iii) Reaction of an acid

anhydride with an alcohol.

(iv) Transesterification

under basic or acidic

conditions.

(2). Provide an example mechanism for each of the reactions you have suggested

(iv). After the tutorial!

(2). Suggest a possible structure for compound A

and provide a full curly arrow mechanism

for the conversion of compound A into

Nicotinamide

Enolates, the Aldol Reaction and the Michael Reaction

Example Questions

After the Tutorial

lecture 18

The Michael Reaction

The generation of an enolate anion requires an "acidic proton" within the molecule

Hopefully it is clear to you now that you

need to understand functional groups to

be fully able to assess the acid base

character of the groups within a drug

molecule!

Test yourself

Polarity

Test Yourself

Part 1

Polarity of course links in with bonding and periodicity

because we need to understand the orbitals that are

making the polar/non-polar bonds as well as the

electronegatvity of the atoms within each bond

(periodicity).

Atoms, Orbitals and Bonds

The link between these two subjects is pretty clear

-and acid/base reaction is essentially an

electrophile/nucleophile reaction

The link between these two subjects is pretty clear

-if your not sure why refer to the SN2 lecture not where

I talk about the correlation between nucleophilicity

and basicity.

lecture 3

lectures 1 and 2

Life Sciences Chemistry

We looked in the first lecture at the important types of orbitals we need to know about for this course. In the lecture 4 screencast we are looking at how these types of orbital can combine to give double and triple bonds. We also see how pi electrons (which are in different orbitals to the electrons in sigma bonds) behave differently. The most notable example of this is the conjugation phenomenon that I introduced you to.

Key Points from the lecture:

It's hopefully quite easy to see how

these two concepts are connected

Hydrolysis Reactions are

Nucleophilic Acyl

"Substitution Reactions"

Lecture 4

sp2 and sp hybridisation as well as

a bit of conjugation!

If you are unsure about the exact structure

of an alkene then you should revisit the section

hybridisation before looking at the lecture 18

content

The p orbitals are present

in every shell (other than

the 1st shell) as a set of 3

"degenerate orbitals" which

all lie in mutually

perpendicular planes

Stereochemistry and conformations link nicely into bonding and

hybridisation. With stereochemistry and conformations we are

looking at the specific 3D shape of molecules which is of course

determined by the hybridisation state of the atoms and the types

of bonds present.

Addition Reactions to Alkenes

Ester and Amide synthesis Reactions are

Nucleophilic Acyl

"Substitution Reactions"

The connection between the SN1 and SN2 concepts and stereochemistry is very strong! For both of the nucleophilic substitution mechanisms we have considered the

"stereochemical outcomes".

Diastereomers

Configurations

Conformational

Isomerism

Conformations of

Cyclohexane

The between these concepts is appreciated when you

think about the stereo and regiochemical outcomes of

both of the electrophilic alkene addition mechanisms

that are covered in lecture 18.

(1). List 4 ways to synthesise an ester

(i).

(ii).

(iii).

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