Doc Brown's Chemistry Clinic

 KS4 Science Extra GCSE-IGCSE information revision notes on

 Extra ORGANIC CHEMISTRY

As well as describing the various types of organic compounds, this page also describes aspects of food and drug chemistry and ozone depletion.

See also Oil and its useful products, including other fossil fuels - coal, natural gas, introduces alkanes and alkenes, global warming and pollution from fossil fuels and plastics etc. and the page has an alphabetical keyword list.

Page section index: 1. combustion of organic compounds * 2. alkane/alkene 'families' * 3. alcohols like ethanol * 4. other organic molecule families e.g. carboxylic acids, esters, polymers * 5. Natural molecules - carbohydrates, sugars, amino acids, proteins and cooking, natural fats & oils etc. * 6. Vitamin C, Drugs-analgesics and Food Additives * 7. CFC's, Ozone and free radicals * and on other associated pages on this site: basic Oil Products notes - what you want may be here if not on this page * enzymes * multiple choice quiz and EMAIL query?comment

1. What is produced when organic compounds are burned?

Some organic compounds are used as fuels. Other organic compounds, including plastics, are burned as waste. Burning these organic compounds releases gases into the atmosphere.

• All organic compounds consist partly of carbon atoms and many contain hydrogen and other atoms such as oxygen and nitrogen. Coal, crude oil, natural gas (methane) and wood contain organic compounds
  • all are used as fuels, either directly like coal or natural gas,
  • or indirectly as coke from coal or petrol from crude oil etc.,
  • and apart from wood, they are finite (limited reserve) fossil (from decayed organic material) fuels.
• Many hydrocarbons are fuels i.e. a substance burned to release heat energy.
• When organic compounds are burned in a plentiful supply of air the carbon is oxidised to carbon dioxide and the hydrogen is oxidised to water.
• In a limited supply of air incomplete combustion occurs forming carbon monoxide and/ or carbon. Carbon monoxide is poisonous because it reduces the capacity of blood to carry oxygen.
• Combustion equations and tests for combustion products are all on the Oil Notes web page, lots of examples and diagrams too.
• Each fossil fuel has a different cost, efficiency and cleanliness on burning. Generally speaking in 'cleanliness' the order is methane (natural gas) > alkanes in petrol > heavy oil and from left to right there is also an increase in C/H atom ratio in the molecule so more CO₂ produced too. Some notes on other fuels (but they are designed for more advanced level courses) and a fossil fuel survey on Oil Products Notes page
• The combustion of plastics (and other organic compounds) which contain chlorine and nitrogen produce poisonous fumes when burnt e.g. choking hydrogen chloride HCl and toxic hydrogen cyanide HCN respectively. Especially where there is a limited supply of air. The combustion products of carbon (toxic CO and CO₂) and hydrogen (H₂O) are also formed.

• Hydrogen gas can be used as fuel.

  • It burns with a pale blue flame in air reacting with oxygen to be oxidised to form water.

  • hydrogen + oxygen ==> water or 2H_2(g) + O_2(g) ==> 2H₂O_(l) 

  • It is a non-polluting clean fuel since the only combustion product is water and so its use would not lead to all environmental problems associated with burning fossil fuels.

  • It would be ideal if it could be manufactured by electrolysis of water e.g. using solar cells.

  • Hydrogen can be used to power fuel cells on the "Extra Electrochemistry" page.

2. Why are there families of organic compounds? - variety !

Alkanes and alkenes were introduced on the Oil Notes page and give details of (i) alkane combustion (ii) the reaction of bromine with alkenes and (iii) the basics of alkene polymerisation.

2a INTRODUCTION

Organic compounds [*] belong to different families, though all organic compounds are based on carbon C, hydrogen H, and other elements such as oxygen O (e.g. ethanol CH₃CH₂OH and nitrogen N e.g. H₂NCH₂COOH the simplest amino acid (lots more examples on this page somewhere!). Most food is chemically organic in nature, apart from some minerals, and many drugs and plastic materials are composed or organic molecules, consequently, organic compounds and organic chemistry's rather important to us!

The compounds in each family have a similar chemical structure and a similar chemical formula. Each family of organic compounds forms what is called a homologous series. Different families arise because carbon atoms readily join together in chains (catenation) and strongly bond with other atoms such as hydrogen, oxygen and nitrogen. The result is a huge variety of 'organic compounds' which can be classified into groups of similar compounds i.e. different homologous series.

The term organic compound comes from the fact that most of the original organic compounds studied by scientists-chemists came from plants or animals, i.e. of natural origin. These days most organic compounds are synthesised from raw materials, in particular the physical separation and chemical manipulation of the products of crude petroleum oil.

[* Note: Inorganic compounds are all the other compounds not based on carbon, except for carbon monoxide CO and carbon dioxide CO₂, which are considered to be inorganic. Examples are: water H₂O, ammonia NH₃, sodium chloride NaCl.]

• A homologous series is a family of compounds which have a general formula* and have similar chemical properties because they have the same functional group of atoms (e.g. C=C alkene, C-OH alcohol or -COOH carboxylic acid).
  • * Match the general formula pattern with the alkane and alkene examples shown below.
• members of a  homologous series have similar physical properties such as appearance, melting/boiling points, solubility etc. but show trends in them e.g. steady increase in melting/boiling point with increase in carbon number or molecular mass.
• The molecular formula represents a summary of all the atoms in the molecule (see examples below).
• The structural or displayed formula shows the full structure of the molecule with all the individual bonds and atoms shown (though there are different 'sub-styles' of varying detail, see examples below).
• When a specific group of atoms in a molecule give it a particular set of characteristic reactions, that group of atoms is called the functional group of the molecule. Examples of functional groups include:
  • the double carbon-carbon bond C=C in alkenes,
  • the oxygen-hydrogen atom group of the -OH in alcohols,
  • and the group of four atoms constituting the -COOH group in carboxylic acids.

2b ALKANES - saturated hydrocarbons

• These are obtained directly from crude oil by fractional distillation (see oil notes).
• The saturated hydrocarbons form an homologous series called alkanes with a general formula C_nH_2n+2
• Saturated means the molecule has no C=C double bonds, only carbon-carbon single bonds, and so has combined with the maximum number of atoms i.e. no atoms can add to it. The alkanes don't really have a functional group and have quite a limited chemistry BUT they are still a clearly defined homologous series.
• Alkane examples: The gases (names and molecular formula): methane CH₄, ethane C₂H₆, propane C₃H₈, butane C₄H₁₀, liquids: pentane C₅H₁₂, hexane C₆H₁₄ etc. The first four alkane structures are shown on the oil notes page. Names end in ...ane
• Carbon always forms 4 bonds with other atoms and hydrogen 1 bond with other atoms e.g. Propane: molecular formula C₃H₈, structural and displayed formula styles include ...
  • or or
• Isomerism occurs when two or more compounds have the same chemical formula but have different structures. e.g. for the molecular formula C₄H₁₀ there are two possibilities - one 'linear' and one with carbon chain 'branching', both are shown in three ways ...
  • butane:
  • or or
  • and its isomer methylpropane:
  • or or
• Can you work out the structures of the 3 isomers of C₅H₁₂ ? (you will find enough to work out the answers on the Advanced Level page ALKANES)
• Isomers show variation in physical properties which depend upon the strength of the intermolecular forces. Intermolecular forces are due to weak electrical attractive forces that exist between all molecules.
• (a) For a homologous series the strength of intermolecular forces increases as the carbon chain length increases
• (b) For isomers (same C number), the forces decrease as the amount of chain branching increases.
• This is because the attractive forces are a function of the potential surface-surface contact i.e. the compactness of the molecules.
  • (a) as the chain length increases the surface-surface contact must increase per molecule,
  • (b) for isomers, with more branching, the chain length decreases and the molecule is more 'compact' reducing the surface-surface contact per molecule.
• For example in the series ...
  • (a) from methane ... ethane ... propane ... petrol ... oils ... grease ... waxes etc. the melting point/boiling point rises and so does the viscosity (stickiness!) as the carbon chain length increases. This trend also indicated by the change from gases to liquids to solids. See Oil Products page for more details
  • (b) 'linear' butane has a higher boiling point than 'branched' methylpropane (diagrams above).
• Alkanes and alkenes undergo combustion reactions (see Oil Products notes for plenty of details).
• CHLORO-ALKANES: Alkanes are usually not very reactive unless burned! BUT they will react with reactive chemicals like chlorine when heated or subjected to uv light to form chlorinated hydrocarbons.
  • Despite the reactivity of chlorine you still need something extra to initiate the reaction.
  • A substitution reaction occurs and a chloro-alkane is formed e.g.
  • a hydrogen is swapped for a chlorine and the hydrogen combines with a chlorine atom
  • ethane + chlorine ==> chloroethane + hydrogen chloride
  • C₂H₆ + Cl₂ ==> C₂H₅Cl + HCl
  • + Cl₂ ==> + HCl
  • Chloro-alkanes are useful solvents in the laboratory or industry but though their vapours can be harmful.

2c ALKENES - unsaturated hydrocarbons

• These cannot be obtained directly from crude oil and must be made by cracking (see oil notes).
• The unsaturated hydrocarbons form an homologous series called alkenes with a general formula C_nH_2n Unsaturated means the molecule has a C=C double bond to which atoms or groups can add.
• Alkene examples: Names end in ...ene
  • ethene
    • C₂H₄ or or
  • propene
    • C₃H₆ or or or
  • butene
    • or
• The alkenes are more reactive than alkanes because of the presence of the carbon=carbon double bond. The alkenes readily undergo addition reactions in which one of the carbon=carbon double bonds breaks allowing each carbon atom to form a covalent bond with another atom such as hydrogen or bromine.
• Examples of addition reactions are: with hydrogen under pressure and in the presence of a nickel catalyst to form an alkane

  • + H₂ ==>

    • ethene + hydrogen ==> ethane

  • + H₂ ==>
    • propene + hydrogen ==> propane
• Alkenes react by 'addition' with bromine and decolourises the orange bromine water because the organic product is colourless, and this is a simple test to distinguish an alkene from an alkane.
  • see Oil Notes for equations for ethene and propene
• Vegetable oils contain unsaturated fats and can be hardened to form margarine by adding hydrogen on to some of the carbon=carbon double bonds using a nickel catalyst. The process is called hydrogenation,
  • and the change in an 'unsaturated' part of an oil molecule is
  • -CH=CH- + H₂ ==> -CH₂-CH₂-
  • so producing a 'saturated' section in the molecule.
  • The structure of 'fatty' saturated/unsaturated/hydrogenated-fats-oils and uses are described in section 5c.
• Alkenes can add to themselves by addition polymerisation to form 'plastic' or polymeric materials (see below or oil notes)
• Alkenes are isomeric with cycloalkanes e.g. the molecular formula C₆H₁₂ can represent hexene or cyclohexane
  • hexene CH₃-CH₂-CH₂-CH₂-CH=CH₂  or  cyclohexane  
  • and note that ....
    • hexene is an unsaturated hydrocarbon with a double bond,
    • the isomeric cyclohexane does not have a double bond and is a saturated hydrocarbon,
    • so a simple bromine test could distinguish the two similar colourless liquids,
      • because only the hexene would decolorize the bromine water test reagent.

3. What is ethanol and how can we make it? - the 'alcohol' of the homologous series of alcohols!

What we call alcohol in everyday life is a substance whose chemical name is ethanol.  Ethanol is just one member of a family of substances called alcohols which have a C-OH functional group in their structure.

• Ethanol structure
  • or or or
• Ethanol is used as a solvent, as a bio-fuel (can be mixed with petrol or used directly), and used to make 'ethyl esters' (see below) as well as the 'potent' chemical present in alcoholic drinks!
  • The % alcohol in wines, spirits and beer varies from 1-40%.
    • The fermentation chemistry to produce alcoholic drinks is outlined below.
  • There are health and social issues about the medical and behavioural aspects of alcohol consumption. Alcohol causes liver damage and addiction problems. Binge drinking and alcohol dependency can cause major social problems both within a family and for the wider community.
  • Methylated spirit is mainly ethanol but poisonous and nasty tasting chemicals like methanol are added so it is not used as a beverage!
• Ethanol can be produced by fermentation of sugars. The raw materials are mixed with water and yeast at just above room temperature. The yeast contains enzymes which are biological catalysts. The sugars react to form ethanol and carbon dioxide. The carbon dioxide is allowed to escape and air is prevented from entering the reaction vessel to stop oxidation of ethanol to ethanoic acid ('acetic acid' or vinegar!). When the reaction is over the ethanol is separated from the reaction mixture by fractional distillation to make a petrol additive fuel or whisky!
  • e.g. glucose == enzyme ==> ethanol + carbon dioxide
  • C₆H₁₂O_6(aq) ==> 2C₂H₅OH_(aq) + 2CO_2(g) 
  • The progress of the fermentation can be followed by measuring the density of the fermented liquid with a hydrometer. Ethanol/alcohol is less dense than water/sugar so the density changes as the sugar is converted into alcohol.
  • Ethanol, from a solution made from fermented sugar cane, can be concentrated by fractional distillation. In Brazil it is blended with petrol to give an alternative motor vehicle fuel i.e. an example of a bio-fuel.
    • C₂H₅OH_(l) + 3O_2(g) ==> 2CO_2(g) + 3H₂O_(l) 
• Ethanol can also be produced by the reaction of steam and ethene (from oil cracking) in the presence of a strong acid catalyst (Phosphoric acid). The reversible reaction is carried out at a moderately high temperature (e.g. 300^oC) and a high pressure (e.g. 60 x atmospheric pressure). The higher temperature and catalyst speed up the reaction and increasing pressure moves the equilibrium to the right (side least gaseous molecules at 300^oC)
  • + H₂O ==>
• Advantages and disadvantages of the two methods of making ethanol:
  • advantages of fermentation: cheap and renewable resource like sugar cane (Brazil), sugar beet
  • disadvantages of fermentation: slow reaction and made by an inefficient  batch process, poor quality product e.g. low aqueous concentration, other organic chemicals formed to and yeast cell residues to remove. Large areas of agricultural land are needed.
  • advantages of ethene route: fast and efficient continuous process, relatively pure product, country may have local oil supply (e.g. North Sea for UK, Middle East countries)
  • disadvantages of ethene route: using a non-renewable finite resource (crude oil/cracking)
• The alcohols form a homologous series with the functional group C-OH. It is the presence of this functional group that gives alcohols their characteristic properties. The simplest homologous series of alcohols have the general formula C_nH_2n+1OH e.g.
• Ethanol is shown above, but the simplest alcohol with the lowest carbon number of one is methanol (the 1st in the homologous series alcohols is shown below).
  • or or
  • All the alcohols are flammable colourless liquids with a characteristic 'pleasant'? odour.
  • They all behave chemically in the same way but the boiling point steadily rises with increase in molecule size.
• The next three are propanol (propan-1-ol, 3rd in series), butanol (butan-1-ol, 4th in series) and pentanol (pentan-1-ol, 5th in series), note their the names also end in ...ol, which means the molecule is an alcohol.
  • propanol or
  • butanol
  • pentanol
• ESTERS: Ethyl ethanoate, an ester,  is formed by the reaction of ethanoic acid with ethanol e.g.
  • ethanoic acid + ethanol ethyl ethanoate + water
  • + + H₂O
  • General word equation: carboxylic acid + alcohol ==> ester + water
  • The procedure for preparing an ester are illustrated in the diagram below.
  • 
  • This technique is called 'heating under reflux', and ensures the reaction occurs the fastest at highest possible reaction temperature, the boiling point of the mixture. However, to prevent vapour loss by boiling/evaporation, the vapourised liquids are condensed back into the reaction flask.
    • The diagram shows a bunsen burner being used to supply the heat ('my days'), these days its more likely, and safer, to use an electrical heater that the round bottomed flask fits in snugly.
  • The colourless ester liquid is separated and purified from the reaction mixture by fractional distillation which is fully explained on the Elements, Compounds, Mixtures Notes (the example described is separating an ethanol/alcohol mixture, but the same principal applies in separating the ester from the water, unreacted alcohol and acid and the sulphuric acid catalyst.
  • You can make butyl ethanoate by the reaction:
    • ethanoic acid + butan-1-ol ==> butyl ethanoate + water
  • Its an equilibrium, and starting with the pure acid plus pure alcohol, you heat the mixture in and you get about ²/₃rds conversion* to the ester, and the preparation reaction is catalysed by a few drops of concentrated sulphuric acid.
    • * This means a theoretical maximum reaction yield of about 67%.
    • For more on % yields and 'atom economy' see calculations section 14.
  • If the ester is warmed with water or any dilute acid (faster), it changes back into the original acid and alcohol. This reverse reaction is called hydrolysis i.e.
    • ethyl ethanoate + water ==> ethanoic acid + ethanol
    • whereas esterification is
    • ethanoic acid + ethanol ==> ethyl ethanoate + water
      • (more on reversible reactions and chemical equilibrium)
  • Esters are usually sweet/pleasant smelling and occur widely-naturally in plants used as fragrances (e.g. perfumes) and food flavourings (more details in USES of ESTERS section) .
• Alcohols react with sodium to form hydrogen.
  • normal fizzing is observed and the salt product is soluble in the alcohol itself.
  • e.g. ethanol + sodium ==> sodium ethoxide + hydrogen
  • 2C₂H₅OH + 2Na ==> 2C₂H₅O^-Na⁺ + H₂ 
• Ethanol can be oxidised to form ethanoic acid which is a useful organic chemical. BUT it is this oxidation of ethanol that results in alcoholic drinks turning sour (e.g. cider, wine) when exposed to air. Ethanoic acid (old name 'acetic acid') is the basis of vinegar and is also used in making esters (e.g. pear drop essence, or .
  •   + O₂ ==>  + H₂O
  • This oxidation can also be done by heating the ethanol with a mixture of sulphuric acid and potassium dichromate(VI) solution. The mixture turns from orange to green.
  • When burned, ethanol, like any alcohol, forms carbon dioxide and water
    • CH₃CH₂OH_(l) + 2O_2(g) ==> 2CO_2(g) + 3H₂O_(l)
• Ethanol can be dehydrated to ethene by passing the alcohol vapour over heated aluminium oxide catalyst.
  •   ==> + H₂O
  • This reaction is potentially an important source of organic chemicals e.g. plastics from a renewable resource since the ethanol can be made by fermentation of carbohydrates etc.
• Alcohols from propanol upwards, i.e. from carbon number 3 or greater, will form isomers.
  • You will find plenty of examples on the advanced organic chemistry page for alcohols.

The steroid, cholesterol, contains the alcohol group -OH. Cholesterol is an essential steroid to humans but if too much is produced it can cause heart disease. The image on the right gives the skeletal formula structure of cholesterol (this structure representation is usually only dealt with at advanced level). All the lines in the structure represent bonds between carbon atoms except the 'wedge dash' to the -OH alcohol group in the bottom left of the molecule. Also note the 'alkene' double bond functional group to the right of the -OH group. [Cholesterol image from NIST]

4. What other families of organic compounds are there? more variations !

4a. The acids that we find in fruits and in vinegar belong to a homologous series called carboxylic acids and many fragrances and food additives are esters. (ester preparation and uses of esters).

4b. Polymers do not form a homologous series but they are all organic compounds having very long molecules.

4a. CARBOXYLIC ACIDS and ESTERS

• Carboxylic acids form another homologous series and have the functional group -COOH.
• The structures of the first three members are given below: Names end in ...oic acid.
  • methanoic acid (old name 'formic acid')
    • or or
  • ethanoic acid (old name 'acetic acid', in vinegar)
    • or or
  • propanoic acid (old name 'propionic acid')
    • or or
• Vinegar contains ethanoic acid (old name 'acetic acid'), see above in section 3 oxidation of the alcohol ethanol. It is used as a preservative and in food flavourings.
• Ethanoic acid is used in the manufacture of the fibre, acetate rayon.
• Citrus fruits like oranges and lemons and many soft drinks contain the tri-carboxylic acid citric acid. and contribute to the 'tarter' or 'sour' taste of fruit. The molecule contains three acidic carboxylic acid groups -COOH.

  • Citric acid is a natural preservative (E330 on food labels) and is found in the largest quantities in lemons, limes and grapefruit. It is an anti-oxidant. Metal salts from citric acid, i.e. citrates, are used in dietary supplements to deliver trace metal minerals in a biologically available/absorbable chemical form.
  • Citric acid can be used in baking powder to react with sodium bicarbonate giving the raising action from carbon dioxide gas formation. The same combination can be used to give the fizzy drink effect in medicines like ant-acid stomach powders.

• Aspirin is a carboxylic acid. Aspirin is a drug used for pain relief and is taken regularly by those at risk from heart attacks (see also 6b Drugs).
• Ascorbic acid (vitamin C) is another carboxylic acid and is present in fresh fruit and vegetables and is vital for good health AND the body cannot synthesise it, so you must eat fruit and vegetables regularly!
  • A lack of vitamin C can cause the disease scurvy. The symptoms of scurvy are skin sores, spongy gums and bleeding from mucous membranes. This is one example of malnutrition diseases caused by a vitamin deficiency in a diet.
• Carboxylic acids are weak acids, typically solutions are around pH3 (yellow-orange-pink with universal indicator).
  • [see theory on Extra Aqueous Chemistry page]
• They react and are neutralised by ... with examples ...
  • metals react to form salts and hydrogen e.g.
    • ethanoic acid + magnesium ==> magnesium ethanoate + hydrogen
    • 2CH₃COOH + Mg ==> (CH₃COO)₂Mg + H₂
  • alkali bases react to form a carboxylic acid salt and water  e.g.
    • ethanoic acid + potassium hydroxide ==> potassium ethanoate + water
    • CH₃COOH + KOH ==> CH₃COOK + H₂O
  • insoluble bases dissolve and react to form salt and water e.g.
    • zinc oxide + ethanoic acid ==> zinc ethanoate + water
    • ZnO + 2CH₃COOH ==> (CH₃COO)₂Zn + H₂O
  • carbonate and hydrogencarbonate bases to produce a carboxylic acid salt, water and carbon dioxide  e.g.
    • ethanoic acid + sodium hydrogen carbonate ==> sodium ethanoate + water + carbon dioxide
    • CH₃COOH + NaHCO₃ ==> CH₃COONa + H₂O + CO₂
    • OR propanoic acid + sodium carbonate ==> sodium propanoate + water + carbon dioxide
    • 2CH₃CH₂COOH + Na₂CO₃ ==> 2CH₃CH₂COONa + H₂O + CO₂
  • aqueous ammonia solution forms ammonium salts e.g.
    • methanoic acid + ammonia ==> ammonium methanoate
    • HCOOH + NH₃ ==> HCOONH₄
    • ethanoic acid + ammonia ==> ammonium ethanoate
    • CH₃COOH + NH₃ ==> CH₃COONH₄
    • Strictly speaking, ammonium hydroxide doesn't really exist, but in older texts you will find these reactions written in this way e.g.
    • propanoic acid + ammonium hydroxide ==> ammonium propanoate + water
    • CH₃CH₂COOH + NH₄OH ==> CH₃CH₂COONH₄ + H2O
• ESTERS: Carboxylic acids react with alcohols to form members of another homologous series called esters. Concentrated sulphuric acid acts as a catalyst in this reaction. See the preparation & formation of ethyl ethanoate above in section 3. above.
  • Structures of other esters made from ethanoic acid:
    • methyl ethanoate using methanol, and
    • propyl ethanoate from using propan-1-ol (n-propyl alcohol).
  • and what would the structure of their original alcohols be and what would the structure of butyl ethanoate be?
• Esters occur widely in nature and are usually sweet/pleasant smelling liquids and widely used as fragrances (e.g. perfumes) and food flavourings. Natural substances are used in many cosmetics but many mixtures contain synthetic organic compounds.
  • Examples of plant ester sources:
    • Lavender oil essence is distilled from the lavender plant
  • Examples of flavouring esters:
    • Pear drop sweet essence is an ester.
  • Factors affecting perfume design e.g. using esters:
    • Sorry, NOT finished - working on this section at the moment.
    • Designing a perfume - several issues to address by way of design factors.

4b. POLYMERS - synthetic macromolecules

• Some basic notes on polymers and plastics in the Oil Products Notes e.g. the formation of poly(ethene), polypropene and poly(chloroethene) PVC.
• Some important structure, strength and 1D, 2D 3D dimension structural concepts) in the "Chemical Bonding" notes.
• Most polymers (plastics) are made from alkene compounds containing the -C=C- bond by addition polymerisation.
• The general reaction is small monomer molecule ==> long polymer molecule as the small molecules link together to form a long chain.
• Poly(chloroethene) is made from chloroethene (old name 'vinyl chloride), CH₂=CHCl but the polymer is generally called polyvinylchloride, PVC. The general equation and the formation of ^*poly(ethene) and poly(propene) are shown on the Oil notes page. (^*old/wrong names: polythene, polyethylene AND polypropylene). The formation of PVC is shown below.

• Polymers (plastics) consist of a tangled mass of very long molecules in which the atoms are joined by strong covalent bonds to form long chains, but there are much weaker intermolecular forces holding the material together.
• In thermosoftening plastics like poly(ethene), poly(propene) or poly(chloroethene) PVC, because the inter-molecular attractive forces between the chains are weak, the plastic softens when heated and hardens again when cooled. It also means the polymer molecules can slide over each other. This means they can be easily stretched or moulded into any desired shape.
  • However it is possible to manufacture and process plastics in which the polymer chains are made to line up. This greatly increases the intermolecular forces between the 'aligned' polymer molecules and strong fibre strands of the plastic can be made.
  • Examples: The addition polymer poly(propene) and the condensation polymers nylon and Terylene
• When a thermosetting plastic is first heated covalent bonds are formed between adjacent chains of the polymers. These strong covalent cross-linkages give the material a high melting point and greatly increased strength and rigidity. They also prevent thermosetting plastics from being softened with heat and therefore from being stretched or re-shaped. However it does make a much stronger material and not as flammable. On heating strongly they do NOT melt, but tend to char, gradually giving off gases.

• 

• Melamine (used in furniture) and many glues are examples of thermosetting polymers.
• Problems with using plastics are on the Oil Products Notes page.
• Some important structure, strength and 1D to 3D dimension concepts  are described in the "Chemical Bonding" notes.

4c. Other Synthetic Polymers - macromolecules

Condensation polymerisation involves linking lots of small monomer molecules together by eliminating a small molecule. This is often water from two different monomers, a H from one monomer, and an OH from the other, the 'spare bonds' then link up to form the polymer chain.

• Nylon (a polyamide) is formed by condensation polymerisation, the structure of nylon represented below where the rectangles represent the rest of the carbon chains in each unit. (more advanced representations on the Organic Nitrogen Compounds advanced structure page.
• (3 units etc.)
• This is the same linkage (-CO-NH-) that is found in linked amino acids in naturally occurring macromolecules called proteins, where it is called the 'peptide' linkage.
• Terylene (a polyester) is formed by condensation polymerisation and the structure of Terylene represented as
•    (3 units etc.)
• This is the same kind of 'ester linkage' (-COOC-) found in fats which are combination of long chain fatty carboxylic acids and glycerol (alcohol with 3  -OH groups, a 'triol').
• Terylene and nylon are good for making 'artificial' or 'man-made' fibres used in the clothing and rope industries. In the manufacturing process the polymer chains are made to line up. This greatly increases the intermolecular forces between the 'aligned' polymer molecules and strong fibre strands of the plastic can be made.
• Some important structure, strength and 1D to 3D dimension concepts are in the "Chemical Bonding" notes.

5. Naturally Occurring Molecules from plants and animals

Small Molecules <=> Natural Polymers = Macromolecules like starch and protein

Carbohydrates, Proteins and Fats are the main nutrient constituents of food.

Most naturally occurring molecules are based on the elements carbon, oxygen and hydrogen, together with smaller proportions of nitrogen, phosphorus, sulfur (sulphur) and sometimes metal ions like iron (in the haemoglobin molecule) and magnesium (in the chlorophyll molecule).

5a. Carbohydrates

• Carbohydrates are a whole series naturally occurring molecules based on the elements carbon, hydrogen and oxygen.
• They are an important source of chemical energy in our diet.
• The smaller
• Historically the name 'carbohydrate' comes from the fact that all their formulae seemed to be based on C_x(H₂O)_y (see key above) BUT this is not the way to think of their formula.
• They range from relatively small molecules called monosaccharide (means one basic unit), or disaccharide (two basic units combined) to very large natural polymers or macromolecules called polysaccharides (many units combined). A summary of them is shown in the key diagram above along with some familiar names from biology.

Glucose is one of the simpler sugar molecules  (a monosaccharide). The structural formula is shown on the left and you should be able to see that there are 4 bonds to each carbon, 2 to each oxygen and just 1 bond to each hydrogen atom. The right-hand 'shorthand' skeletal formula version uses short straight lines to represent bonds. Most H's and their bonds are not shown, and at AS-A2 level it is assumed you can interpret these structures 'back to' a full structure!, but they are handy for describing large 'biochemical' molecules (see polysaccharide below)

• The formation of complex carbohydrates:
  • These are made of smaller carbon, hydrogen and oxygen based molecules combining together e.g. the polysaccharides starch and cellulose are formed from glucose, molecular formula C₆H₁₂O₆.
• Their formation can be described in terms of a large number of sugar units joined together by condensation polymerisation
  • e.g. the 'box' diagram below shows 4 units of a natural carbohydrate polymer being formed
  • Note: Condensation polymerisation means the joining together of many small 'monomer' molecules by eliminating an even smaller molecule between them to form the linkage.
    • e.g. HO-XXXXX-OH + HO-XXXXX-O-XXXXX-OH + H₂O etc.
• n C₆H₁₂O₆ ==>  (C₅H₁₀O₅)_n + nH₂O (where n is a very large number to form the natural polymer)
• The XXXXX or the [rectangles] below, represent the rest of the carbon chains in each unit (more detail in the 3rd diagram below).

plus many H₂O etc.

This diagram of starch or cellulose is in 'skeletal formula' style and both are polymers of glucose - can you see the connection between each 'unit' and the structure of glucose itself?

• The resulting natural polymer is called a polysaccharide.

• Acid hydrolysis of complex carbohydrates (e.g.. starch) gives simple sugars.

  • This can be brought about by e.g. warming starch with hydrochloric acid solution to form glucose.

  • (C₅H₁₀O₅)_n + nH₂O ==> n C₆H₁₂O₆ (where n is a very large number)

• The hydrolysis products from polysaccharides can be analysed with paper chromatography.

5b. Proteins and Amino Acidsand DNA

• Amino acids are carboxylic acids (like ethanoic acid) but one of the hydrogen atoms of the 2nd carbon atom is substituted with an amino group (a nitrogen + two hydrogens gives -NH₂). Another hydrogen on the same 2nd carbon can be substituted with other groups of atoms (R) to give a variety of amino acids.
• or The simplest is aminoethanoic acid or 'Glycine'
• and another amino acid called 2-aminopropanoic acid or 'Alanine'
• All amino acids have the general structure H₂N-CH(R)-COOH (see diagram by 5b heading).
  • R can vary, think of it as the 'Rest of the molecule!
  • R = H for Glycine, R = CH₃ for Alanine.
• Amino acids can polymerise together, by condensation polymerisation, forming proteins or polypeptides.
  • The peptide linkage is formed by elimination of water between two amino acids.
  • HNH-CH(R)-COOH + HNH-CH(R)-COOH ==> H₂N-CH(R)-CO-HN-CH(R)-COOH + H₂O etc. so ...
  • n H₂N-CH(R)-COOH ==> -NH-CO-CH(R)-NH-CO-CH(R)-NH-CO-CH(R)-NH-CO-CH(R)- etc. n units long
  • So proteins are condensation polymers of amino acids.
• Proteins have the same (amide) linkages as nylon but with different units.
• Proteins are an important component of tissue structure and enzymes (powerful biological chemical catalysts) are also protein molecules. Proteins tend to adopt a particular three dimensional shape (3D) which aids its function.

• When proteins are heated with aqueous hydrochloric acid or sodium hydroxide solution they are hydrolysed to amino acids.

  • see chromatography below, about how amino acids are identified in proteins.

• DNA (deoxyribonucleic acid) are the molecules that carry the genetic code or molecular 'blueprint' for all forms of life. For example it encodes through its base components the exact sequence of amino acids needed to synthesise a particular protein.

• A spot of cooking chemistry!

  • Food is cooked for several reasons:

    • The high cooking temperature kills harmful microbes-bacteria, as long as cooked for the required time at a high enough temperature.

    • It may improves the texture.

    • It may improve the flavour and taste (but remember some foods might taste better raw e.g. lettuce!)

    • It makes it easier for the body to digest the food.

  • 

  • Most of meat from animals consists of protein together with smaller amounts of water and fat. Eggs and fish are also good sources of protein.

  • Protein molecules have a definite shape (diagram 1. above).

  • During the cooking of meat irreversible chemical changes take place.

  • The complex and specific structure of protein molecules is partly broken down in the cooking process.

  • The high cooking temperature promotes particular chemical reactions to happen.

  • The structure changes and some of the chemical bonds are broken and new molecules can be formed that have a different taste-flavour and texture giving the food its own characteristic 'cooked' character.

  • The breaking down of protein complex protein molecules is called denaturing.

  • A similar process happens in the cooking of carbohydrate foods like potatoes which are broken down into far more readily digestible molecules.

• -

5c. Fats, Oils and Margarine

• Oils and Fats are an important way of storing chemical energy in living systems and are also a source of essential long-chain fatty acids.

• Most of them are esters of the tri-alcohol ('triol') glycerol (systematic name propane-1,2,3-triol, but that can wait until AS-A2 level).

• The carboxylic acids which combine with the glycerol are described as 'long-chain fatty acids'.

• The resulting ester is called a 'triester' or 'triglyceride' and they are major components in animal fat, vegetable oils, processed fats like margarine etc..

• The 'long-chain fatty acids' can be saturated, with no C=C double bonds, and so forming saturated oils or fats (1st diagram below of the triglyceride formed from palmitic acid).

• The 'long-chain fatty acids' can be unsaturated, with one or more C=C double bonds, and so forming unsaturated oils or fats (2nd diagram below of the triglyceride formed from oleic acid).

• Some sub-notes on Oil and Fat Structure: (health issues dealt with further down)

  • They have the same linkages as Terylene but with different units.

  • They are not as big as polymer molecules, but a lot bigger than a single petrol or sugar molecule.

  • There can be 1 to 3 different saturated or unsaturated fatty acid components, so lots of variation possible in structure of the oil or fat. The diagrams just assume three molecules of the same 'fatty' acid.

  • Monounsaturated fats have one C=C double bond in them, polyunsaturated fats usually have at least three C=C bonds in their molecular structure.

  • For the same molecular size in terms of carbon number, unsaturated fats have slightly lower intermolecular forces because the C=C double bond produces a kink in the carbon chain and they can't pack as closely together as the saturated molecules.

    • This gives unsaturated fats a lower melting point and so they tend to occur as e.g. vegetable oils rather than saturated low melting solids from meat and dairy products.

  • However, this means these unsaturated oils are not as conveniently 'spreadable' as 'butter'.

    • To overcome this problem, 'margarine' was invented. The vegetable oils are reacted with hydrogen gas using a nickel catalyst. Theses are called hydrogenated fats and have higher melting point so that they are a low melting solid at room temperature rather than the sticky vegetable oil you might use is cooking and salad dressings.

    • This reaction adds hydrogen atoms to the double bonds making a more saturated and more 'spreadable' higher melting soft solid fat that we call 'margarine'.

    • Saturated means no double bond and unsaturated means double bond in this context.

    • The reaction for any double bond is: >CH=CH< + H₂ ==> -CH₂-CH₂-, which is converting an unsaturated part of the molecule to a saturated structure.

    • BUT it does mean that it is more like animal fat now but various blendes have been developed to suit your dietary needs or desires!

    • Margarine and other 'spreadable' fats based on vegetable oils are quite a mixture of molecules known as an emulsion. A typical mixture might be

    • 14-21% saturated fats (triglycerides with almost no double bonds in the hydrocarbon chains)

    • 15-30% monounsaturates in which there is about one double bond per molecule.

    • 14-22% polyunsaturates which have more than one double bond per molecule.

      • In terms of melting points, the order is saturates > monounsaturates > polyunsaturates.

    • Sodium chloride and water ('salt' solution'), small amounts of protein and carbohydrate and whey or buttermilk are added to the fat/oil mixture.

    • To stop the salt solution separating out from the 'oily' fats an emulsifier is added, which keeps the aqueous salt solution dispersed in the fats or they would separate into two layers and affect the look and taste. Incidentally the emulsifiers may be mono- or di-glycerides of fatty acids, that is molecules like the vegetable oils but only 1 or 2 fatty acids attached to the glycerol rather than 3, which leaves 2 or 1 -OH hydroxy groups on the glyceride molecule. These molecules have the bifunctional structure because through the action of intermolecular forces they bind with both fats (via hydrocarbon chain, 'water hating' hydrophobic end of molecule) and bind with water too (via hydroxy group OH, the 'water loving' hydrophilic end of molecule) so holding the emulsion or dispersion together.

• Since fats and oils are important to our diet, there is the ever present danger of over-consumption (speaking as someone who loves chips and spicy crisps!). So there are health and social, as well as 'molecular' issues to address!

  • We need oils and fats as sources of important essential fatty acids.

  • We need both saturated and unsaturated fats or oils.

    • The main sources of saturated fats are from meat and dairy products e.g. 'dripping' and butter.

    • The main sources of unsaturated fats are plant oils e.g. olive oil.

  • It is recommended that we do not overdo the fat intake but we do need both saturated and unsaturated fats.

    • However, too much saturated fat raises cholesterol levels and is not too good for the heart.

SOAP

• 'Traditional' soap is a product of the hydrolysis of fats.

  • 'Soapy' soaps (not modern detergents) are the sodium salts of long chain fatty acids formed by heating fatty oils with sodium or potassium hydroxide to hydrolyse them.

  • This reaction breaks the fat molecule down into one glycerol molecule (triol alcohol) and three sodium salts of the long chain carboxylic fatty acids.

5d. Chromatography - a method of analysis

• Hydrolysis means breaking down a molecule with water to form two or more products.

  • Hydrolysis is accelerated if the substance is heated with acid or alkali solutions.

• When proteins are heated with aqueous acid they are hydrolysed to amino acids.

• Acid hydrolysis of complex carbohydrates (e.g.. starch) gives simple sugars.

• (1)  (2)  (3)

• Paper or Thin layer chromatography is used to separate coloured compounds (illustrated above).

• 1 to 5 represent five pure compounds, 6 is a mixture. Red, brown and blue make up the mixture because its spots horizontally line up with the three known colours.

  • The substances (solutes) to be analysed must dissolve in the solvent, which is called the mobile phase because it moves. The solvent may be water or an organic liquid like an alcohol (e.g. ethanol) or a hydrocarbon, so-called non-aqueous solvents.

  • The paper or thin layer of material on which the separation takes place is called the stationary or immobile phase because it doesn't move.

  • The distance a substance moves, compared to the distance the solvent front moves (top of grey area on diagram 2) is called the reference or R_f value and has a value of 0.0 (not moved - no good), to 1.0 (too soluble - no good either), but R_f ratio values between 0.1 and 0.9 can be useful for analysis and identification.

  • R_f = distance moved by dissolved substance (solute) / distance moved by solvent

• However, amino acids and sugars are colourless, but can still be separated in this way, so read on!

• Thin layer or paper chromatography can still used to separate and identify the products of hydrolysis of carbohydrates and proteins because you make them coloured by using another chemical reagent.

  • The hydrolysis can be done by boiling the carbohydrate or protein with hydrochloric acid.

  • The hydrolysed mixture is then 'spotted' onto the pencil base line of the chromatography paper.

    • Known sugars or amino acids are also spotted onto the base line too.

    • The prepared paper is then placed vertically in a suitable solvent, which rises up the paper.

  • Since the products are colourless, the dried chromatogram is treated with another chemical to produce a coloured compound.

    • Ninhydrin produces purple spots with amino acids

    • and resorcinol makes coloured spots with sugars.

  • You can then tell which amino acids made up the protein or the sugars from which the carbohydrate was formed.

    • The number of different spots tells you how many different amino acids or sugars made up the natural macromolecule.

    • Spots which horizontally match the standard known molecule spots confirm identity.

    • Starch gives one spot because only glucose is formed on hydrolysis.

      • (C₅H₁₀O₅)_n + nH₂O ==> n C₆H₁₂O₆ (where n is a very large number)

  • More on thin layer/paper chromatography.

  • Note that if organic compounds are gases or volatile (easily vapourised) liquids, they can be analysed using gas-liquid chromatography (in section 6. of the GCSE Extra Industrial Chemistry page).

6. Vitamins, Drugs-analgesic medicines and Food Additives

• 6a Vitamins are particular essential molecules with particular roles in living systems which are NOT proteins, carbohydrates, fats or mineral salts.

• One of the most important ones in any diet is Vitamin C or Ascorbic Acid. Its structure is related to 'simple' sugars but humans are one of the few mammals that are unable to synthesise vitamin C.

  • It is essential for healthy tissue and one of its functions is the removal of dangerously reactive chemical species called free radicals (see further on).

  • Vitamin C is present in fruit and vegetables but the amount is reduced by prolonged storage and cooking..

  • 250 years ago, as many as ²/₃ of a ship's crew died from vitamin C deficiency causing scurvy. In 1747 it was decided to give sailors citrus fruits to recover from scurvy but wasn't until 200 years later that vitamin C was recognised.

  • In contrast to the other water-soluble vitamins, vitamin C has no clear cut role as a catalyst or part of an enzyme. It does, however, have a range of other important functions:

    • Collagen formation. Vitamin C in collagen formation which is found wherever tissues require strengthening, especially in tissues with a protective, connective, or structural function. Collagen is critical to the maintenance of bone and blood vessels and is essential in wound healing.

    • Antioxidant activity. Ascorbic acid can act as an antioxidant by donating electrons and hydrogen ions, and reacting with reactive oxygen species or free radicals.

    • Iron absorption. Vitamin C is important for the effective absorption of iron and reduces iron(III) Fe³⁺ to iron(II) Fe²⁺.

    • It helps in the synthesis of vital cell compounds. During times of physical and emotional stress, as well as during infection, there is increased production of oxygen radicals. Therefore there is increased reliance on vitamin C's activity as an antioxidant.

    • Vitamin C is vital for the function of the immune system, but the effectiveness of large doses of vitamin C in preventing and alleviating the symptoms of the common cold is still a matter of debate.

  • Two of the earliest signs of deficiency (prevention of collagen synthesis) relate to its roles in maintaining the integrity of blood vessels. The gums around the teeth bleed more easily, and the capillaries under the skin break spontaneously producing tiny haemorrhages. If you are short of vitamin C for say 20 days, scurvy can develop and is characterised by further haemorrhaging, muscles depletion, rough-brown-dry-scaly skin, deep bruising. Wounds fail to heal properly and bone fails to rebuild properly too and you are further likely to suffer from anaemia and infections.

  • SO EAT yer fruit and veg 'guys' (as well as a few crisps!) AND keep yer health and still pass those dreaded exams!!!!

• 6b Drugs e.g. in analgesic medicines can be defined as an externally administered substances which modifies or affects chemical reactions in the body, usually for the bodies greater well-being. Poisons can be defined in the same way, but hopefully not intentionally and have undesired effects! A 'drug' is a specific molecule with a particular pharmacological or physiological action on an organism/animals chemistry and a medicine is the complete formulation of the means of administering the drug to a patient i.e. the method of delivery.

  • Analgesics are drugs used to reduce pain and are a type of anti-inflammatory agent.

  • The molecular structure of three well known analgesics are shown in the diagram below.

  • All are used for 'headache' treatment, and hopefully using this website and others will help minimise their use!

The central hexagonal ring of 6 carbon atoms is called a 'benzene' or 'aromatic' ring. The 4th outer electron of carbon (group 4) is delocalised, so the expected 4th bond per C atom forms part of a 'communal' system (more on this at advanced level, but the covalence rule of 4 for carbon is not broken!, you have seen this situation before, check out graphite. You can show a benzene ring as a simple hexagon with a circle in it)

from + NaOH ==> + H₂O

• The modern pharmaceutical industry has its origins in herbal and other traditional medicine.

• e.g. An extract of willow herb extract can be made from the leaves, bark and seeds of the willow tree. Amongst other ailments it was given to help curing feverish headaches and relief of pain in childbirth. When ingested the body hydrolyses and oxidises the naturally occurring 'precursor' molecule to form salicylic acid* which is the 'active' molecule in the body. in the 1890's the German chemist Hoffmann experimented with various chemical modifications of salicylic acid and found the best and chemically stable form was 'aspirin' (shown below). He tried the variations on his own father! who survived to provide valuable 'clinical trials' - hardly acceptable these days! * 'Oil of winter green' from certain plants is the methyl ester of salicylic acid and has similar 'medicinal effects'.

• Aspirin (and the others shown) are not very soluble in water. Soluble aspirin is made by neutralising the carboxylic acid with the alkali sodium hydroxide to make the much more soluble sodium salt of the acid. The reaction, using skeletal formula, is shown in the diagram below the three analgesic drug structures.

• New drugs and testing them:

• It costs a lot of money to develop a new medicine so the price charged by the pharmaceutical company must cover the cost of research, production and marketing.

• Patents are taken out to protect the company's commercial interests in the new medicine.

• Th