Standard answers Organic Chemistry AQA CHEM/AS Revision/Standard...Organic Chemistry – Standard answers 3.2 Alkanes Explain the insolubility of alkanes in water • Water forms H

Organic Chemistry – Standard answers

3.2 Alkanes Explain the insolubility of alkanes in water

• Water forms H bonds • Alkanes form VDW forces of attraction • H bonds are stronger than VDW forces of attraction

Explain the trend in boiling points of the alkanes down the homologous series

• More electrons • Stronger VDW forces of attraction • More energy required to overcome

Explain the lower boiling points of branched alkanes

• Less points of contact / surface area • Weaker VDW of attraction • Less energy required to overcome

Fractional distillation of crude oil

• The column has a temperature gradient • Fractions with low boiling points (low numbers of carbons)

rise to the top of the column and condense. • Fractions with high boiling points (high numbers of carbons)

condense in the lower chambers • The largest hydrocarbons will not vaporise and are tapped off

at the bottom of the column. • Each fraction contains a mixture of hydrocarbons with similar

boiling points and similar numbers of carbon atoms in the molecules.

• The flask is heated. • Fractions with low boiling points (low numbers of carbons)

evaporate first and condense in the condenser first. • Fractions with high boiling points (high numbers of carbons)

evaporate at higher temperatures then move into the condenser.

• Fractions of similar boiling points are collected in the flask.

Combustion of the alkanes

• Balance using CHO • Complete combustion à CO2 • Incomplete combustion / gas product àCO • Incomplete combustion / solid product à C • If balancing other functional groups

remember to account for any O in the organic molecule when balancing O

Thermal cracking

• 1000K 70 atm approximately 1s • Any C-C bond can break which gives a mixture of alkanes and • High % of alkenes made

Catalytic cracking:

• 800K 2atm approximately 4s • Zeolite catalyst consists of Al2O3 and SiO2 • Produces branched, cyclic alkanes and aromatic compounds

which are good fuels in the motor industry.

The effects from pollution: Carbon - May cause breathing problems Carbon monoxide - toxic gas Carbon dioxide - global warming Nitrogen oxides - Breathing problems / acid rain Sulphur dioxide - acid rain Hydrocarbons - photochemical smog

The catalytic converter:

• Pt Rh Pd metals • Honeycombed structure to increase surface area

Removal of NO and CO in Catalytic converter

2NO(g) + 2CO(g) à N2(g) + 2CO2(g)

2NO(g) à N2(g) + O2(g) Removal of unburnt hydrocarbons:

Hydrocarbon + Nitrogen monoxide à nitrogen + Carbon dioxide + Water C8H18(g) + 25NO(g) à 121/2 N2(g) + 8CO2(g) + 9H2O(g)

Hydrocarbon + Oxygen à Carbon dioxide + Water

C8H18(g) + 121/2 O2(g) à 8CO2(g) + 9H2O(g)

Flue gas desulphurisation:

• A spray of water and CaO or CaCO3 reacts with the SO2:

CaO(aq) + SO2(g) à CaSO3(s)

CaCO3(aq) + SO2(g) à CaSO3(s) + CO2(g)

3.3 Halogenoalkanes Reactivity of the halogenoalkanes

• More reactive due to the polar bond Discuss the boiling points of the halogenoalkanes

• As the halogen changes from RF à RI it becomes less polar • Therefore, weaker dipole – dipole forces of attraction • Therefore, should be decrease in boiling points

Also • As the halogen changes from RF à RI it has more electrons • Therefore, stronger VDW forces of attraction • Therefore, should be increase in boiling points

Trend • Check the trend in boiling points to see which has the greater effect

Discuss the rate of hydrolysis of the halogenoalkanes: • The weakest bond breaks first as it will have the lowest activation energy

bond Enthalpy / kJ mol–1

C–F +467 C–Cl +340 C–Br +280 C–I +240

• A mixture of ethanol and aqueous AgNO3 is used • Water / aqueous hydrolyses the halogenoalkane.

RX + OH- à ROH + X-

• The Ag+ ions then form a precipitate, AgX X –(aq) + Ag+

(aq) à AgX(s)

• The C - I bond is the weakest bond and would break more readily. • This means that it would give the fastest reaction.

Substitution vs elimination Substitution Elimination

Aqueous conditions – substitution predominates

Ethanolic conditions – Elimination predominates

OH- behaves as a nucleophile OH- behaves as a base (accepting a proton)

50 : 50 mixture of water : ethanol means substitution : elimination equally likely

How the ozone layer works:

• Ozone absorbs UV radiation breaking the molecule:

O3(g) + UV à O2(g) + O(g)

• The oxygen atom then reacts with an oxygen molecule:

O(g) + O2(g) à O3(g) + Heat

• Overall, UV is converted to heat energy and this process continues until the 2 reactions reach an equilibrium:

O(g) + O2(g) D O3(g)

HCFC’s as an alternative:

• Contains less Cl therefore less chance of Cl radicals being formed

3.4 Alkenes

The nature of the double bond:

• Alkenes are more reactive due to the electron dense C=C • The p bond is weaker so breaks first in reactions. • The p bond changes the shape to trigonal planar / bond angle of 120o: • Planar double bond locks the molecule around the double bond • No free rotation about these bonds.

What features give rise to geometric isomerism / E Z isomerism

• No free rotation around the C = C • Each C in the C = C has 2 different groups attached

E/Z determination using Cahn - Ingold - Prelog nomenclature (CIP):

1) Assign a 1 or 2 to each atom attached to each carbon in the double bond using Ar’s 2) If the highest priority atoms are on Z zame zide of the C=C assign Z isomer 3) If the highest priority atoms are on opposite sides of the C=C assign E isomer 4) If two atoms have the same atomic number, move to the next atom along the chain.

Cl has highest

priority Cl has highest

priority Cl has highest

priority Cl has highest

priority Priority groups on opposite sides, E

isomer Priority groups on same side, Z isomer

Test for alkenes

• Bromine water • Orange à colourless

Explain why there is a major / minor product

• Major product goes via 3o carbocation • Minor product goes via 2o carbocation • 3o carbocation are more stable than 2o carbocation • Make sure it is specific to the structures you are referring to ie could be 2o and 1o

Addition polymerisation

• Remove p bond • Extend bonds out from the C’s that were part of the C = C

• Identify repeat unit • Remove extended bonds replace p bond

Properties of Polymers

No branching

• No branching can pack closely together. • Van der Waals forces of attraction stronger • A rigid material is formed

Branching

• Branches cannot pack closely together. • Van der Waals forces of attraction weaker • A flexible material is formed

Electronegative side groups

• Chlorine is more electronegative than carbon • Permanent dipole is formed. • The d- chlorine is attracted to the d+ carbon in the next polymer. • The material is therefore hard but brittle.

Plasticisers

• Plasticisers get between the polymer molecules pushing them further apart. • This weakens the intermolecular forces of attraction. • The material is more flexible as they can slide past each other more easily. • Electrical cable insulation.

3.5 Alcohols Why are alcohols more reactive than alkanes:

• The more electronegative oxygen produces a polar bond • This makes the alcohols more reactive

Alcohols have higher than expected boiling points / draw a diagram:

• They can form hydrogen bonds with each other • This gives the alcohols a higher boiling point than

their corresponding alkanes

Are alcohols soluble in water / draw a diagram:

• They can form hydrogen bonds with water • This makes the first 3 alcohols soluble in

water. • After that, the long alkyl chain interferes

with the H bonds

Classification of alcohols:

Primary (1o)

The OH carbon (*) is attached to

1 other carbon atom.

Secondary (2o)

The OH carbon (*) is attached to

2 other carbon atoms.

Tertiary (3o)

The OH carbon (*) is attached to

3 other carbon atoms.

Making ethanol a) Fermentation: C6H12O6(aq) à 2CH3CH2OH(g) + 2CO2(g)

Conditions: Yeast / anaerobic conditions (without oxygen) / 30 – 40oC b) Hydration of ethene: H2C=CH2(g) + H2O(g) CH3CH2OH(g)

Conditions: Steam / 300oC / 60 atm / solid H3PO4 catalyst

c) Comparing the processes:

Process Hydration of Ethene Fermentation Raw material Ethene from crude oil – non renewable Sugar – renewable resource

Quality of product Pure Impure – requires fractional distillation

Rate of reaction Fast Slow

Type of process Continuous Batch

Costs High set up / low labour Low set up / high labour

Ethanol as a fuel:

Advantages Disadvantages Sugar – renewable resource Food vs Fuel

Carbon neutral Deforestation – removes trees that absorb CO2

Trees from deforestation burnt – CO2 released

Loss of habitats

Fertilisers – pollute water systems

Modern car engines need to be modified

Oxidation of alcohols

1o alcohol à Aldehyde à Carboxylic acid 2o alcohol à Ketone 3o alcohol

• Sodium dichromate / sulphuric acid. Orange à green • Reflux for carboxylic acids • Distil for aldehyde

3.6 Organic analysis

Functional group tests

a) Test for Alkenes – Unsaturation – C=C

Orange Colourless

Chemical test for alkene - C=C / unsaturation:

• Add bromine water, Br2 • Orange to clear and colourless

b) Test for Halogenoalkanes RX (X is a halogen)

RCH2X + OH- à RCH2OH + X- Ag+

(aq) + X-(aq) à AgX(s)

Precipitate (white / cream / yellow)

Chemical test for halogenoalkane:

• Add sodium hydroxide, NaOH / warm • Acidify with Nitric acid, HNO3 • Add silver nitrate, AgNO3 • Precipitate white / cream / yellow

c) Test for carboxylic acid, RCOOH

a) Carboxylic acids react with sodium metal, Na (all alcohols do too):

RCOOH + Na à RCOONa + ½H2

b) Only Carboxylic acids react with sodium carbonate, Na2CO3

RCOOH + Na2CO3 à RCOONa + H2O + CO2 CO2(g) + Ca(OH)2(aq) à CaCO3(s) + H2O(l) White Precipitate

Chemical test for carboxylic acids:

• Add sodium carbonate, Na2CO3 • Collect CO2 with a pipette • Bubble through limewater – white precipitate (goes cloudy)

d) Test for alcohols, ROH

i) All alcohols and carboxylic acids react with sodium metal:

RCH2OH + Na à RCH2ONa + ½H2

ii) Only 1o 2o alcohols can be oxidised

The oxidising agent – Potassium dichromate (VI) / sulphuric acid Cr2O7

2-(aq) + 14H+

(aq) + 6e- à 2Cr3+(aq) + 7H2O

Orange Green • This is orange in colour and is a mixture of Sulphuric acid, H2SO4 (H+) and K2Cr2O7.

Chemical test for alcohols:

• Add sodium, Na – fizzing with all alcohols, 1o, 2o and 3o • Add potassium dichromate, K2Cr2O7 / sulphuric acid, H2SO4 and warm • 1oand 2o alcohols orange à green

e) Test for aldehydes

• Aldehydes can oxidise further to carboxylic acids / Ketones cannot.

RCHO + [O] à RCOOH i) Add potassium dichromate, K2Cr2O7 / sulphuric acid, H2SO4 and warm

Cr2O72-

(aq) + 14H+(aq) + 6e- à 2Cr3+

(aq) + 7H2O Orange Green

ii) Add Tollens’ reagent, AgNO3 dissolved in ammonia – Silver mirror test Ag+

(aq) + e- à Ag(s) Colourless Silver ppt

iii) Fehling’s solution – CuSO4 / NaOH / Warm CuSO4(aq) à Cu2O(s) Blue Red 2Cu2+

(aq) + 2OH-(aq) + 2e- à Cu2O(s) + H2O(l)

Chemical test for aldehydes:

a) Add potassium dichromate, K2Cr2O7 / sulphuric acid, H2SO4 and warm • Orange à green

b) Add Tollens’ reagent, AgNO3 dissolved in ammonia – Silver mirror test • Silver precipitate / mirror

c) Add Fehling’s solution – CuSO4 / NaOH / Warm

• Blue à red

Summary of functional group tests

Test Functional groups Observations Bromine water Alkene C=C Orange à colourless

Hydrolysis of halogenoalkane with AgNO3

Halogenoalkane AgX precipiatate (white, cream, yellow)

Oxidation with K2Cr2O7 / H2SO4

1o 2o alcohols / aldehydes Not 3o alcohols

Orange à green

Fehlings / Benedicts solution Aldehydes Red precipitate

Tollens reagent Aldehydes Silver mirror

Sodium carbonate solution / Limewater

Carboxylic acids Fizzing / limewater goes cloudy

What affects the frequency at which a bond will vibrate in IR spectroscopy

• Bond strength • Bond length • Mass of atom at either end of the bond

IR spectroscopy

• Peaks that are absent are as important as peaks that are present • Quote the values and draw the bond responsible for a peak

How can a specific molecule be identified using IR spectroscopy

• 1000 – 1500 cm-1 is the fingerprint region. • These are unique to a particular molecule. • Compared with a spectra database to identify a specific compound.

Global warming

• Radiation from sun is absorbed by the Earth and re emitted as IR. • Some IR radiation is absorbed by gases in the atmosphere. • These molecules absorb IR radiation then re emit it as energy. • This energy warms up the atmosphere.

Factors affecting GWP (Global Warming Potential)

1. Its concentration in the atmosphere 2. Its ability to absorb IR radiation 3. Its lifetime in the atmosphere

High resolution mass spectroscopy

• Work out the Mr’s to the number of decimal places given • Allows identification of specific molecule • Allows identification of a contaminant – shown as 2 peaks in the MS

Combustion analysis

• Any mass left over is oxygen. • Tip: You may not be told that the other element is oxygen so always add the carbon and

hydrogen masses together to see if it equals the sample mass. • If it doesn’t, the difference is always oxygen, O

Example:

A 0.2500 g sample of a compound known to contain carbon, hydrogen and oxygen undergoes complete combustion to produce 0.3664 g of CO2and 0.1500 g of H2O. What is the empirical formula of this compound?

Element CO2 à C H2O à H O Masses CO2 / H2O 0.3664 0.1500

0.3664 x 12/44 0.1500 x 2/18

Masses of C / H / O 0.0999 : 0.0166 : 0.2500 –

(0.0999 + 0.0166) = 0.1335

0.0999 / 12 : 0.0166 / 1 : 0.1335 / 16

Moles of C / H / O 0.00833 : 0.0166 : 0.00834

( / smallest) 0.0833 / 0.0833 : 0.0166 / 0.0833 : 0.00834 / 0.0833

Whole No Ratio 1 : 2 : 1

Empirical formula CH2O

3.7 Optical isomerism:

• 4 different groups attached Chirality:

• 2 optical isomers are called enantiomers. • The carbon is the chiral centre / asymmetric carbon. • Racemic mixture / racemate – 50:50 mixture of the 2 enantiomers

Property of optical isomers:

• Rotate plane polarised light which is measured through a polarimeter • One isomer rotates it in the clockwise direction (+) • The other in the anticlockwise direction (-).

How are optical isomers formed in a racemic mixture:

• Planar molecule • Attack can come from above or below which are equally likely.

Nature:

• Only one of the optical isomers are made as synthesis in nature tends to use enzymes which are stereospecific:

Stereoisomer: A Molecule with the same structural formula but its atoms are arranged differently in space

Optical isomer: These are non superimposable mirror images

Racemate / Racemic mixture: Is a mixture of equal amounts of the 2 enantiomers

Synthesising drugs:

• Drugs and medicines interact with biological molecules such as proteins etc. • These have a 3D structure that will only bind to a drug molecule with a specific shape. • The 3D structure of the drug must 'fit' with the receptor site in a biological system:

• This determines the pharmacological activity Synthesis vs Nature

Synthesis Nature

Isomers Both one Made In the laboratory In the body Dose Twice needed Half needed Side

effects Probably None

Cost Cheaper Expensive Cost of

separation in lab

Expensive - isomers have same physical and chemical properties

Cheap as only one isomer made

3.8 Aldehydes and ketones: p's to p's

• O is more electronegative than C the p electrons will be attracted to the O atom. • This sets up a permanent dipole across the C=O bond:

1) Tollens’ reagent – Silver mirror test

Reagents Silver nitrate dissolved in ammonia, Ag(NH3)2+

Observations Aldehyde Silver precipitate / mirror formed Ketone No reaction

CH3CHO + [O] à CH3COOH

Ag(NH3)2

+ (aq) + e- à Ag(s) + 2NH3(aq)

Colourless Silver ppt

2) Fehling’s solution –

Reagents CuSO4 / NaOH / Warm Observations Aldehyde Red precipitate Ketone No reaction

CH3CHO + [O] à CH3COOH

Cu2+

(aq) + e- à Cu+(s)

Blue solution Red ppt

Reducing aldehydes and ketones:

Reduction of aldehydes:

CH3CH2CHO + 2[H] à CH3CH2CH2OH

Reduction of ketones:

CH3COCH2CH2CH3 + 2[H] à CH3CH(OH)CH2CH2CH3

Nucleophilic addition reactions:

1) Reduction

CH3CHO + 2[H] à CH3CH2OH

Conditions: NaBH4 - a source of hydride ions, H-

2) Hydroxynitriles

CH3CHO(aq) + HCN(aq) à CH3CH(OH)CN(aq)

Conditions: KCN followed by dilute acid (HCl) – This produces HCN

• CN- is the nucleophile and is attracted to the d+ carbon in the carbonyl group. • In practise, KCN is added. • This is because HCN is a weak acid (partially dissociates) giving a low [CN-] • Optical isomers often made

3.9 Carboxylic acids and derivatives:

• Solubility – C1 - C4 carboxylic acids mix readily:

• C5 à solubility reduces due to length of insoluble R chain.

Melting points

• All carboxylic acids hydrogen bond • With increased R chain, VDW also increases:

Acidic nature of carboxylic acids:

Carboxylic acid Carboxylate ion Hydrogen ion

• Carboxylic acids are acidic enough to react with metals, alkalis and carbonates. • Like inorganic acids they behave in the same way:

Metal + Acid à Salt + Hydrogen

RCOOH + Na à RCOONa + ½H2

Metal hydroxide + Acid à Salt + Water

RCOOH + NaOH à RCOONa + H2O

Metal Carbonate + Acid à Salt + Water + Carbon dioxide

2RCOOH + Na2CO3 à 2RCOONa + H2O + CO2

• Remember the test for a carboxylic acid is fizzing with NaHCO3:

RCOOH + NaHCO3 à RCOONa + H2O + CO2

Esters

Esterification - making esters:

• The reaction is known as esterification. • It is a reversible reaction:

1) Alcohol comes 1st becomes ‘yl’ 2) Carboxylic acid 2nd becomes ‘oate’

Uses of esters

• Flavourings – due to their sweet smells / tastes • Perfumes – Due to their sweet smells

1) Hydrolysis of esters: • It is the reverse reaction of esterification:

a) Acid hydrolysis: Reagent: dilute aq sulphuric or hydrochloric acid Conditions: Ruflux

• The hydrolysis of any carboxylic acid derivative results in the carboxylic acid.

b) Alkaline hydrolysis: Reagent: dilute aq sodium hydroxide Conditions: Ruflux

• When a base is used, the product is the carboxylate ion / salt of the carboxylic acid:

*Note: The carboxylate can be converted to the carboxylic acid by adding an acid, eg HCl, H2SO4

Fats and oils • Are esters made from propan-1,2,3-triol or glycerol and long chain carboxylic acids called

fatty acids:

• Fats are solids: • These have saturated fatty acids allowing them to pack efficiently

• Oils are liquids • These have unsaturated fatty acids and don’t pack together as efficiently:

Hydrolysis of fats and oils:

• The sodium carboxylate can be converted to a carboxylic acid with a strong acid, HCl. Biodiesel:

• The R group in the biodiesel comes from the fatty acid. • The molecules have the same properties as diesel.

Carbon neutral:

• In terms of CO2 taken in to make the plants and CO2 given out during combustion. • It doesn’t however include planting, watering, harvest, transporting etc

Acyl chlorides • The Cl is substituted with an O or N containing group. • HCl is always given off – white fumes are seen as they react with water vapour in the air

1) With water:

2) With alcohol:

3) With ammonia:

4) With primary amines:

Acid anhydrides: • The RCOO is substituted with O or N containing group. Carboxylic acid is given off 1) With water:

2) With alcohol:

3) With ammonia:

4) With primary amines:

Aspirin:

• Ethanoic anhydride is used instead of the acyl chloride as it is: Ø Cheaper Ø Less reactive / corrosive therefore safer to use Ø Doesn’t form HCl fumes

3.10 Arenes

Kekulé structure Vs Benzene: 1) Thermochemical evidence:

Ø Does not explain why it did not react with bromine.

Ø The structure is planar Ø It was found that all the C-C bond

lengths were equal in length and in between C – C and C = C bond lengths

Ø It is more stable / unreactive than corresponding alkenes

A new model: The delocalised structure of benzene

• 6 p orbitals can overlap forming a system of p orbitals spread over all 6 carbons.

• The 6 electrons can be anywhere in the p orbital formed.

• These electrons are delocalised over all 6 carbons.

6 x p orbitals p delocalised orbital The unreactivity of benzene:

• Electron density is less between the C’s than alkenes. • This means they are not as good at attracting electrophiles.

Reactions of benzene – Electrophilic substitution 1) Nitration:

Reagents and conditions:

Concentrated nitric acid and concentrated sulphuric acid (catalyst) / Reflux at 55oC

2) Fiedel – Crafts - Acylation:

Reagents and conditions:

Acyl chloride and AlCl3 (Halogen carrier / catalyst) / Heat under reflux

3) Reduction of nitrobenzene à Phenylamine: In the specification

Reagents and conditions: i) Sn and concentrated HCl / Heat under reflux: Gives the salt of the amine ii) Add NaOH: Gives the amine

Overall Equation:

Reaction Type: Reduction

Uses:

• Explosives • Manufacture of dyes

Extension –reactions and mechanisms 4 and 5 are not in the specification. 4) Fiedel – Crafts - Alkylation:

Reagents and conditions:

Halogenoalkane, RCl and AlCl3 (Halogen carrier / catalyst) / Heat under reflux

5) Halogenation: Reagents and conditions:

Halogen, Cl2 and AlCl3 (Halogen carrier / catalyst) / Heat under reflux

Comparing the reactivity of alkenes and benzene

Cyclohexene Benzene• Will decolourise bromine water: • Only reacts with bromine with a halogen

carrier:

Addition reaction

Substitution reaction

High electron density: localised electrons Low electron density: delocalised electrons• Reacts readily as it can attract

electrophiles more readily• Requires a catalyst to produce a (+) ion

in order to react with benzene

The mechanism:

The mechanism:

AlBr3 + Br2 àAlBr4- + Br+

AlBr4- + H+ àAlBr3 + HBr

Electrophilic addition Electrophilic substitution

3.11 Amines:

Primary Secondary Tertiary Quaternary Ammonia amine amine amine ammonium ion Naming amines: With 2 or more alkyl groups on the nitrogen:

N – methyl propylamine N,N – dimethyl butylamine N,N – Ethyl methyl butylamine Solubility

• The amines form hydrogen binds with water (and themselves). • The solubility decreases with the increase in the alkyl chain

Preparation of amines: 1) Preparation of amines from halogenoalkanes (AS):

Reagents: Excess ethanolic ammonia (excess to prevent further substitution) Conditions: Reflux • Ethylamine can react further (like the ammonia) with more chloroethane:

CH3CH2Cl à 2CH3CH2NH2 à (CH3CH2)2NH à (CH3CH2)3N

2) Reduction of nitrobenzene to aromatic amines:

Reagents: 1) Sn and concentrated HCl 2) NaOH

Conditions: Reflux

• NaOH is added to release phenylamine from its salt (with the HCl) • This is an important reaction as it is used in the manufacture of dyes.

3) Reduction of nitriles to amines:

• This reaction converts a nitrile to amines:

Reagents: H2 and Ni Conditions: High T and P The basicity of the 1o amines: The inductive effect

• The strength of the basicity depends upon the availability of the nitrogen’s lone pair electrons:

pH 8 pH 10 pH12

Phenylamine Ammonia Butylamine

Ø Negative inductive effect: Ø Lone pair electrons on the

nitrogen delocalise with the delocalised p electrons in benzene

Ø This decreases the electron density on the nitrogen.

Ø This makes it a weaker lone pair donor.

Ø Which makes it a weaker base.

Base line: No inductive effect Ø Positive inductive effect: Ø Alkyl groups give a small

push of electrons towards the nitrogen.

Ø This increases the electron density on the nitrogen.

Ø This makes it a better lone pair donor.

Ø Which makes it a stronger base.

Base reactions of amines:

• Just as ammonia forms salts with acids so do amines: Ammonia:

Base + Acid à Ammonia salts

NH3 + HCl à NH4Cl Amines:

Base + Acid à Alkylammonium salts

RNH2 + HCl à RNH3Cl The amines can be recovered by adding NaOH (a stronger base):

CH3NH3Cl + NaOH à CH3NH2 + NaCl + H2O

Nucleophilic substitution reactions involving amines: The reactions with the halogenoalkanes:

1) With ammonia, NH3, to form 1o amines: Year 1, recap: The nucleophilic substitution

• This reaction converts a halogenoalkane to amines R1X + 2NH3 à R1NH2 + NH4

+ X-

Reagents: Excess ethanolic ammonia

Conditions: Reflux 2) With 1o amines, RNH2, to form 2o amines, R2NH:

R2X + 2R1NH2 à R2R1NH + R1NH3

+ X-

3) With 2o amines, R2NH, to form 3o amines, R3N:

R3X + 2R2R1NH à R3R2R1N + R2R1NH2

+ X-

4) With 3o amines, R3N, to form quartenary ammonium salt, R4N+:

R4X + R3R2R1N à R4R3R2R1N+ X- Summary: Ammonia 1o Amine 2o Amine 3o Amine 4o Amine

Ø Unless an amine is used in excess, further substitution occurs, a quaternary salt is made.

Cationic surfactants Surfactant: A compound that is partly soluble and partly insoluble in water

• Quartenary ammonium salts are one of these types of compounds:

As detergents:

• The non-polar hydrocarbon chain will dissolve in a non-polar substance (such as grease).

• The positively charged region will dissolve in water. • This allows spots of grease to mix with water and therefore

be washed away: As conditioners:

• Wet hair and fabrics pick up negative charges. • The wet hair / fabric attracts the positively charged region creating a coating. • This prevents the build-up of further charges (static electricity) – smooth hair / soft fabric.

Nucleophilic addition – elimination reactions using amines as nucleophiles: Reactions with acyl chlorides: From 3.9 Carboxylic acids and derivatives: 1) With ammonia:

2) With primary amines:

3.12 Polymers: 1) polyesters:

• A polyester is made by condensing an alcohol and carboxylic acid.

a) 2 monomers: A Diol and a Dicarboxylic acid:

• It is described as a condensation reaction as water is eliminated as the ester link is formed.

Uses:

Ø Plastic bottles Ø Clothing Ø Carpets

b) 1 monomer: Hydroxycarboxylic acid

• It is still a condensation reaction as water is eliminated as the ester link is formed.

2) Polyamides:

• Polyamides are made by an amine / carboxylic acid condensation reaction.

a) 2 monomers: Diamine and Dicarboxylic acids:

• It is a condensation reaction as water is eliminated as the amide link is formed.

Uses:

Ø Bullet proof vests Ø Crash helmets Ø Fire resistant material

b) 1 monomer: Hydroxycarboxylic acid / Amino acids:

• A monomer with an amine group at one end and a carboxylic acid group at the other.

From amino acids:

• It is still a condensation reaction as water is eliminated as the amide link is formed.

Comparison of addition and condensation polymers:

Addition polymerisation Condensation polymerisation

Polyester Polyamide Functional groups C=C COOH / OH COOH / NH2 No monomers 1 1 or 2 1 or 2

Products poly(alkene) polyester + water / HCl polyamide + water / HCl

linkage C-C

Physical properties

à Increase in rigidity à à Increase in intermolecular forces between chains à

VDW between chains Permanent dipole between chains

H bonding between chains

Breaking down polymers

Addition polymers: Cannot be broken down as they are chemically inert – Non-biodegradable Condensation polymers: Can be hydrolysed - Biodegradable

1) Hydrolysis of polyesters:

2) Hydrolysis of polyamides:

Methods of disposal:

Land fill - burying: • Cheap • Non-biodegradable

• Requires land • Degradable waste often produces

CH4 • Decomposition releases water

soluble toxins à water supply Combustion: • Produces heat energy • CO2 released – greenhouse gas

• CO released – toxic • C released – respiratory problems• Styrene produces toxic styrene

vapour• Chlorinated polymers release HCl

gas which would need to be removed

Sort and recycle

• Remoulded • Conserves oil reserves • Long polymers can be ‘cracked’

into shorter molecules. • Saves energy from oil refining • Waste not going to landfill • CO2 not emitted

• Collection and transporting – expensive

• Polymers cannot be separated by machinery – man power – expensive

• Often cannot be re used as same plastic

3.13 Amino acids, proteins and DNA: • a amino acids have the NH2 and COOH attached to the same carbon:

Zwitterions:

• The amino acid and carboxylic acid can interact with each other to form a zwitterion:

Zwitterion: Is the pH at which the ion has no net electrical charge

• The zwitterion has no overall charge • This + / - charge increases the attractive forces between amino acids considerably. • They are often described as having unusually high melting points.

The isoelectric point and R groups:

• Acidic R groups lower the pH of the isoelectric point. • Basic R groups increase the pH of the isoelectric point .

The effect of pH on the zwitterion / amino acid structure:

pH < Isoelectric point: pH > Isoelectric point:

Proteins Amino acids and condensation reactions:

• 2 amino acids = dipeptide. • 3 amino acids join together we call it a tripeptide. • Many join together we call it a protein or polypeptide. • Polypeptides are synthetic, proteins are natural and are usually larger than polypeptides.

• The functional group is an amide group (CONH) • 2 different amino acids can join to form 2 different dipeptides (swap them over) • Dipeptides still have an NH2 and a COOH group which means they can undergo further

condensation reactions. Hydrolysis of polypeptides and proteins:

• Can all be hydrolysed back into their constituent amino acids. • This is done by using an acid or alkaline catalyst. (review polyamide hydrolysis).

Acid hydrolysis: Conditions: 6 mol dm-3 HCl / reflux 24 hours:

• Note: If HCl is used in the equation then the chloride ion would need adding to the balanced equation above.

Alkali hydrolysis: Conditions: Solution of aq NaOH above 100oC

• Note: If NaOH is used in the equation then the sodium ion would need adding to the

balanced equation above.

Simple structure of protein: • Each amino acid in the protein chain is referred to as an amino acid residue.

• These can be hydrolysed and separated by chromatography. Separation and identification – Thin layer chromatography (See Chromatography)

• Amino acids have different R groups. Each have different solubilities in the same solvent. • As amino acids are clear and colourless. • Ninhydrin a developing agent is used to locate the different amino acids – seen as a violet

spot under UV light. 2-Dimensional TLC • Amino acids can often have similar Rf values as R groups can be similar • 2 – dimensional TLC is used to separate components:

• The plate is turned through 90°.

• The chromatogram is run again with a different solvent.

• This gives two Rf values for each component - one for each solvent. • The two Rf values are compared to known Rf values for each solvent. • It gives a greater confidence in the identification of the amino acids.

Structure of protein: • Long chain of amino acids have complex structures in 4 levels:

Ø Primary Ø Secondary Ø Tertiary Ø Quartenary (although this structure isn’t required)

1) Primary Structure:

• This is the sequence of amino acids in the protein chain:

2) Secondary structure:

• The peptide links can form hydrogen bonds with each other in one of 2 ways:

a) a Helix: • The primary structure forms a helical structure held together by hydrogen bonds.

• The R groups point outwards of the helix structure.

b) b Pleated sheets • The primary structure folds back on itself and held together by hydrogen bonds. • Looks like a ‘pleat’ with the R groups alternating up and down along the plane.

• The R groups point outwards of the sheet structure. 3) Tertiary structure:

• The secondary structure folds and coils on itself to give a 3-dimensional structure. • This structure is held together by interactions between different R side groups:

a) Van der Waals’ forces of attraction

Ø Between the alkyl R side groups

b) Hydrogen bonds • Between OH / NH / C=O in the R side groups and the main chain.

c) Ionic bonds

• Between – COO- and – NH3+ in the R side groups

d) Disulphide bonds (sulphur – sulphur bonds) • Suplhur – sulphur covalent bonds are formed between cysteine residues

Summary:

• Temperature and pH can affect hydrogen bonding, ionic bonds and disulphide bonds which in turn will change the shape of the protein or polypeptide.

Enzymes

• They often contain co – factors: Small organic molecules or metal ions. Stereospecific nature of enzymes:

• They only react with specific substances called substrates. Active site:

• Only molecules that exactly fit the exact shape of the hollow / active site are catalyzed. Substrates:

• This is the ‘lock and key’ mechanism: • Within this hollow there are amino acid residue R groups. • Activation energy lowered / bonds in the substrate are weakened - Catalysing the reaction. • So stereospecific that enzymes only catalyse one enantiomer of optical isomers: • Allows chemists to synthesise one enantiomers in chiral drug synthesis. • Avoids undesirable side effects.

Inhibitors: • These are molecules with a similar shape to the substrate. • The difference is that they block the active site and no reaction follows.

• The level of inhibition depends upon 2 factors:

1) The relative concentration of the inhibitor : substrate: Ø High concentration of inhibitor : substrate à Little substrate gets to the active site. Ø Low concentration of inhibitor : substrate à More substrate gets to the active site.

2) How strongly the inhibitor bonds to the active site

Drugs:

• Many drugs work using inhibitors to stop an enzyme working. Penicillin:

• It blocks the active site in the enzyme that bacteria use to build cell walls. • The bacteria cells effectively ‘burst’

Drug design:

• Historically enzyme inhibitor drugs were produced by trial and error. • Modern day techniques use computer modelling. • These are then tested in the lab.

DNA:

• Deoxyribonucleic acid: Contains all the genetic information of living organisms. • It is made up of 3 components:

Phosphate group:

Pentose sugar – 2 deoxyribose: Base:

• The circled N are the atoms that form a bond to the 2-deoxyribose molecule. • The red circles highlight where these molecules join each other at.

Nucleotides: • These are formed from these 3 components joined together. • A simplified model:

Example: Cytosine nucleotide:

Polynucleotides:

• These join by a covalent bond between the phosphate and the sugar.

• It is a condensation polymerisation reaction where a water molecule is lost. • A phosphodiester bond (linkage) is formed • It makes a sugar – phosphate backbone along the chain • The bases are attached to the sugar on the back bone:

• This polynucleotide chain is one of the 2 strands that make up DNA DNA structure:

• DNA is formed from 2 polynucleotide strands that form a double helix. • The 2 polynucleotides are held together by hydrogen bonds between the bases: • Each base can only hydrogen bond with one particular base.

AT Greenhead College

Adenine with Thymine Guanine with Cytosine

Ø Only adenine has the right atoms in the right place to hydrogen bond with thymine

§ 2 hydrogen bonds between the pairs.

Ø Only guanine has the right atoms in the right place to hydrogen bond with cytosine

§ 3 hydrogen bonds between the pairs.

• Any other pairing would not have the right atoms the right distance or alignment to form these hydrogen bonds.

DNA replication:

• The DNA strands (polynucleotides) unwind. • Fee nucleotides align with their base pair on the unwound

strand (polynucleotide). • A new strand (polynucleotide) forms against the original

unwound strand producing a new double helix of DNA – Replication.

Anti cancer drugs: Cisplatin:

• Cancers cells divide and reproduce uncontrollably to form tumours.

• The DNA strands (polynucleotides) must unwind to allow the complimentary base pairs to align forming an identical DNA strand

• Cisplatin is a drug that interferes with this reproductive procedure stopping reproduction.

• As Cisplatin enters the cell it becomes hydrolysed as [Cl-] within the cell is lower.

• An N in the guanine base forms a dative covalent bond with the Pt replacing the water ligand (ligand substitution).

• An N in the guanine base forms a dative covalent bond with the Pt replacing the water ligand (ligand substitution).

• A second N from a neighbouring guanine molecule can replace a second chloride.

• This second guanine could be on the same strand or the opposite strand (polynucleotide).

• The cisplatin by binding to the DNA blocks replication. • When bound to the DNA strand(s) it causes a kink. • This means they can’t unwind and be replicated.

Side effects: • Cisplatin will bind to the DNA in normal cells that replicate quickly as well as cancer cells. Hair loss Suppress immune system Kidney damage

• These side effects can be lessened by:

lower doses Direct delivery to tumor

3.14 Organic Synthesis:

• These are always designed with the following aims: Ø Non-hazardous starting materials: Limits the impact of accidents causing damage /

environmental damage. Ø High % yield and atom economy: Avoids waste. Ø Fewest steps: 80% of 80% of 80% is just over a total of 50% yield. Ø Avoid solvent use (as much as possible): Hazardous waste / flammable / toxic /

separation from product creates waste.

Synthetic routes – Make sure you know all your routes with essential conditions and reagents.

3.15 NMR Nuclear spin

• With an odd number of nucleons there will be one nucleon that is not paired. • A spinning nucleus such as hydrogen behaves as a spinning charge and

generates a magnetic field.

Environment - Nuclear shielding:

• The magnetic field felt by a nucleus depends on:

1) Strength of the externally applied magnetic field

2) Environment: Surrounding electrons and nearby atoms affect nuclear shielding

• The electrons in an atom also produce tiny magnetic fields which 'shield' the nucleus from the applied magnetic field.

• This is nuclear shielding and the extent depends upon nearby atoms or groups of atoms:

Chemical shift: Environment / Nuclear shielding

• With less shielding from the external magnetic field, the (magnetic) nuclei is more strongly held.

• A higher frequency is required to resonate the nuclei (as it held strongly). • This frequency is called chemical shift, d. • The chemical shift (frequency) tells us the environment we find that nuclei.

The scale: • The scale is measured against a reference signal, TMS = 0, TMS is Tetramethylsilane:

• This molecule has 12 equivalent H’s / 4 equivalent C’s giving rise to a single peak.

• This peak is assigned the value = 0 • It is far away from any peaks produced by sample

molecules

Carbon - 13 NMR spectroscopy

13C NMR:

• 2 things can be obtained from 13C NMR is: 1) The number of different carbons – number of peaks 2) The carbon environment – chemical shift 1H NMR spectroscopy

• In addition:

3) Relative ratio of all the protons 4) Adjacent protons – splitting patterns, n + 1 rule Integration traces:

• The area under the peak is proportional to the relative number of protons. The solvent

• The solvent used needs to be proton free. • It needs to be volatile so it can be evaporated off afterwards. • CCl4, CDCl3, C6D6 are the common solvents where D it deuterium, 2H.

Interpretation:

Always start with the chemical shift to identify environment:

Use the integration to identify how many H’s giving the signal – add these to the previous diagram

Use the splitting pattern to identify the neighboring H’s – add these to the previous diagram

3.16 Chromatography 1) Thin Layer Chromatography - TLC 2) Column Chromatography - CC 3) Gas Chromatography – GC How does chromatography work?

• Components have different affinities for Stationary phase - Retention and Mobile phase

Phases and intermolecular forces of attraction: Solid phase:

• Molecules interact with solid phases by – ADSORPTION Liquid or gas phase:

• Molecules interact with the mobile phase by – SOLUBILITY Stationary phase – slows down their movement - RETENTION Mobile phase – speeds up their movement OVERALL – It is the difference between the SOLUBILITY in the MOBILE PHASE and

RETENTION in the STATIONARY PHASE that separate the components 1) Thin Layer Chromatography - TLC

• Solid stationary phase and liquid mobile phase Ø Retention by adsorption with stationary phase vs movement by solubility in the

mobile phase

• Liquid stationary phase and liquid mobile phase Ø Retention by solubility with stationary phase vs movement by solubility in the mobile

phase 2) Column Chromatography - CC

• Solid stationary phase and liquid mobile phase Ø Retention by adsorption with stationary phase vs movement by solubility in the

mobile phase 3) Gas Chromatography - GC

• Solid stationary phase and gas mobile phase Ø Retention by adsorption with stationary phase vs movement by solubility in the

mobile phase

• Liquid stationary phase and gas mobile phase Ø Retention by solubility with stationary phase vs movement by solubility in the mobile

phase

Phase: Is the physical state – solid, liquid or gas

Stationary phase: The molecules can’t move – a solid, can be a liquid (viscous) on a solid support

Mobile phase: The molecules can move – always a liquid or gas

Retention factor, Rf values:

Rf = Distance moved by component Distance moved by solvent front

Limitations: • Similar compounds often have too similar Rf values. • Unknown compounds have no Rf value for comparison. • Small temperature change can affect the Rf value

Alternatively:

• Comparisons can also be made against pure components run against the mixture:

Colourless components:

• Locating agents are added to reveal the location of the separated components / spots. 1) Fluorescent dye: Added to the stationary phase. Dark spot under UV light.

2) Locating agent: Iodine vapour / ninhydrin. Seen as purple spots.

Gas chromatography - Retention times:

• Is the time taken for a component to pass from inlet to detector. Area under each peak

• The area under each peak is equivalent to the amount of that component. • The relative concentrations of each component can be estimated by comparing peak areas.

Limitations of gas chromatography: • Thousands of chemicals have similar retention times, peak shapes. This means that most

compounds cannot be positively identified. Gas Chromatography - Mass Spectroscopy - GC-MS

Gas Chromatography, GC Separates components Mass Spectroscopy, MS Gives detailed structural information