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Organic Chemistry Lecture Notes
Teacher Notes



What is pencil lead made of if it isn't lead?
Pencil lead is a mixture of graphite and clay. Graphite is one form of the element carbon. Other forms of carbon are diamond - the hardest naturally occurring substance on the earth, soot, charcoal and coke.

Pencils used to be made with lead, many years ago. Lead is poisonous and so sucking the end of your pencil could be quite dangerous. We now use graphite and clay because it is safer and because we can make pencils of different hardness.

What are living things made of?
All living things are made of the element carbon combined with a number of other elements. You have probably heard lots of science fiction programs on TV talking about human beings as 'carbon-based life forms'.

The most important elements to join with carbon are hydrogen, oxygen, nitrogen, phosphorus, sulfur. The processes that happen in living things, such as digestion, movement, growth are all very complicated chemical reactions, but they all involved compounds which contain carbon.

What is organic chemistry?
We used to describe organic chemistry as the chemistry of living things. Since the chemistry of living things is based on carbon, the chemistry of carbon compounds has come to be known as organic chemistry. It now includes the study of carbon compounds which are not found in living things and so is an incredibly large branch of modern chemistry.


Why is life based on the element carbon?
There are two important properties of carbon that make it a suitable element to form the compounds in living things:

Firstly, carbon atoms can link together to form stable chains of great length. (This process is called catenation.) Carbon atoms bind strongly to each other and so often form very large molecules which are built around a carbon 'backbone'. The covalent bond between two carbon atoms is strong so that the backbones are stable. In all of these compounds simple sub-units called monomers are linked together by condensation reactions. Carbohydrates, proteins and nucleic acids are formed when large numbers of these sub-units bond together to form huge macromolecules called polymers.

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Secondly, it is a valency IV element - each atom of carbon can form four covalent bonds. The arrangement of electrons around the carbon atom allows it to make 4 single bonds (or 2 double bonds, or one triple and one single bonds) with other elements. The branched chains of carbon atoms can form an almost limitless number of possible compounds. This provides the variety of chemistry that allows living things to achieve great complexity.

Silicon is similar to carbon. Why are there no life forms based on silicon?
Silicon is unsuitable because, although it is a valency IV element like carbon, the Si - Si covalent bond is not strong enough for it to form long stable chains. It could therefore not form molecules of the complexity needed to make up cells.


What is the major source of organic chemicals?
Crude oil, which is thought to be the fossilized remains of forms of life which existed on earth many millions of years ago, is the major source of organic chemicals.

Crude oil is a mixture of hydrocarbons which belong to the alkane series. The components of crude oil are separated by fractional distillation into fractions, which are used as different fuels. Examples include: petrol, paraffin, diesel and gaseous fuels.

The alkanes make up a series of saturated hydrocarbons, called an homologous series because they have similar properties and have the same general formula:

The first four members of the series are gases at room temperature and are called:
methane, CH4;
ethane, C2H6;
propane, C3H8 and
butane, C4H10.

Alkanes with increasing numbers of carbon atoms have names are based on the Greek word for the number of carbon atoms in the chain of each molecule. So you can get, for example, pentane (5), hexane (6), heptane (7) and octane (8).

From pentane onwards, approximately the next thirty alkanes in the series are liquids. Alkanes with even longer chains are waxy solids. They are typical covalent compounds, insoluble in water but miscible (able to mix) with each other. Alkanes burn in oxygen to produce carbon dioxide and steam.




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Why is it dangerous to burn many fuels in a limited air supply?
If the supply of air is limited, alkanes and other carbon based fuels burn to give carbon monoxide and carbon (soot) instead of carbon dioxide. When this happens we say that incomplete combustion has occurred.

Carbon monoxide is very poisonous and carbon monoxide poisoning is responsible for a lot of accidental deaths. Gas fires, for example, when the get very old and haven't been serviced for a long time can burn gas incompletely. If someone has the gas fire on in a poorly ventilated room, the build up of carbon monoxide can cause the people in the room to drift into a coma, and die if they are not found.

Apart from having things like gas fires and gas boilers serviced regularly, you can now buy carbon monoxide detectors which warn you of the presence of this dangerous gas by sending out a loud bleeping noise, a bit like a smoke detector does.

What are polymers?
Polymers are substances made up of very large molecules, formed by joining together large numbers of small molecules, called monomers. The process is called polymerization.
There are two types of polymerization, condensation polymerization and addition polymerization.
Man made polymers are often useful as plastics or fibers including polythene, PVC, nylon. All living things are made of natural condensation polymers including proteins, DNA, RNA and cellulose.

How are carbon atoms joined together in organic compounds?
First, a reminder of some basic information about covalent bonding:
Covalent bonds
A covalent bond is formed when electrons are shared between atoms, rather than being transferred from one to the other.

A covalent bond is a pair of electrons, usually one from each atom, (but occasionally one atom provides both electrons - a coordinate bond) shared between both atoms. One of the electron orbitals of one atom overlaps an electron orbital of the other atom. Where the electron orbitals overlap there is a region of greater negative charge density, which attracts the nuclei of both atoms.

The bond formed by the shared pair of electrons acts as 'electron glue' which joins the two nuclei together. (Remember, electrons are negatively charged and nuclei are positively charged).

When one pair of electrons is shared between two atoms, this is called a single covalent bond. A single bond, also called a sigma () bond has the region of overlap of the electron orbitals directly between the two atoms.
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A second or a third bond formed by sharing one or two more electron pairs must be formed by orbitals which overlap on opposite sides of the axis of the sigma bond. These are called pi () bonds.
If two pairs of electrons are shared between two atoms, this is a double covalent bond and if three pairs are shared, this is a triple covalent bond.

The strength of covalent bonds depends on the nature of both of the atoms which are linked by the bond. In general, the shorter the bond, the stronger it is. Multiple bonds are stronger than single bonds, but not double or triple the strength. This is because pi bonds are not as strong as sigma bonds.

Now, back to carbon...
Carbon atoms in organic compounds are linked by covalent bonds. Single (sigma) and double (sigma and pi) bonds are common; triple (one sigma and two pi) bonds also occur.

Lots of carbon compounds seem to be isomers. What is an isomer?
In organic chemistry, there are many examples of different compounds which have the same molecular formula as each other, but different arrangements of the atoms in their molecules, (different structural formulae). These compounds are said to be isomers of one another. Isomerism also occurs in inorganic chemistry, but it is less common.

There are two types of isomerism common in organic chemistry: structural isomerism and stereo isomerism.
Structural isomers of a compound have the atoms of their molecules linked in a different order. This can come about in one of three ways:
* different carbon skeletons in the molecule (chain isomerism),
* functional group linked to different carbon atoms (positional isomerism),
* different functional groups (functional group isomerism).

Stereo isomers of a compound have the same structural formula as one another, but the atoms of their molecules are orientated differently in space. Two common forms of stereo isomerism are:
* geometric isomerism (also called cis /trans isomerism), which occurs due to lack of free rotation about double bonds,
* optical isomerism, which occurs because of an asymmetry of a carbon atom with four different groups attached to it.

If isomers have the same atoms in them, surely they have the same properties, so what's the point?

In fact, these small changes in structure can have significant effects on the properties of the substance:

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* Chain isomers of the same compound are very similar. There may be small difference in physical properties such as melting or boiling point due to different strengths of intermolecular bonding. Their chemistry is likely to be identical.
* Positional isomers are also usually similar. There are slight physical differences, but the chemical properties are usually very similar. However, occasionally, positional isomers can have quite different properties e.g. oxidation of alcohols.
* Functional group isomers are likely to be both physically and chemically dissimilar.
* Geometric isomers of one another usually have very similar physical and chemical properties.
* Optical isomers are physically and chemically identical in every respect except one: they rotate the plane of polarization of polarized light in opposite directions. But, it is important to realize that this can have significant effects in a living system. One optical isomer of glucose, for example, can be used by a living cell, but the other isomer cannot. This is because the enzyme in the cell which recognizes glucose is sensitive to only one form.


Since so many organic compounds contain the same elements, how do you name them?
There is a system of naming organic compounds which is based on the name of the alkane with the same number of carbon atoms as the longest carbon chain in the molecule of the compound.
Number of carbon atoms Name of alkane Prefix if compound is not analkane, haloalkane or amine

1 Methane Methan-
2 Ethane Ethan-
3 Propane Propan-
4 Butane Butan-
5 Pentane Pentan-
6 Hexane Hexan-
7 Heptane Heptan-
8 Octane Octan-
Side-chains of carbon atoms or other functional groups attached to the molecule are called substituents. The carbon atoms of the longest chain need to be numbered to show where the substituents are joined on.
When you are naming the organic molecule you put the number of the carbon atom that the substituent is joined to first, then the name of the substituent, then the name of the parent molecule (longest chain of carbon atoms). If there is more than one substituent then you put them in alphabetical order.
Here is a list of some functional groups with their names:
Structure Structure Name
CH3- methyl -
-OH hydroxy-, -ol
CH3CH2- ethyl-
-COOH -oic acid
CH3CH2CH2- propyl-
-NH2 amino-, -amine
-F fluoro-
-NO2 nitro-
-Cl chloro-
-CHO -al
-Br bromo-
-CO -one
-I iodo-
-C6H5 phenyl -

What are the important properties of alkanes?
Alkanes have the typical properties of covalent compounds. The physical state at room temperature depends on the strength of the intermolecular forces, which depend on the size of the molecule.

Chemically, they are relatively unreactive because of the non-polar nature of their molecules.
They burn in a plentiful supply of oxygen to give carbon dioxide and steam.

What are CFCs and why are they important?
CFCs are chlorofluorocarbons (really chlorofluoroalkanes). They are chemically inert, non toxic gases which can readily liquefy under compression and hence are used as aerosol propellants and circulating liquid in refrigerators and freezers.

Their use is now discouraged, because it has been discovered that they cause ozone depletion in the upper atmosphere.

What is alcohol and how are alcoholic drinks made?
The alcohol in wine, beer and spirits is ethanol, a member of the alcohol family. Alcohols make up an homologous series of general formula: CnH2nOH
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The OH group gives the alcohols their characteristic chemical properties.

The alcohols are named according to the same pattern as for alkanes:
methanol, CH3OH
ethanol, C2H5OH
propanol, C3H7OH and so on.

The alcohol in drinks is made by a process called fermentation. This process is achieved by the anaerobic respiration of yeast.

Yeast is added to solutions containing sugar (such as grape juice, apple juice or malt from barley) and the mixture left in a container fitted with an airlock which excludes air but allows carbon dioxide to escape. Fermentation may take several weeks, and ends when the alcohol content builds up to about 15%. This makes the yeast inactive and the process stops.

Alcohols can also be formed by addition of water to alkenes, and by hydrolysis of halogeno-alkanes and esters.

Stronger alcoholic solutions (those with an alcohol content greater than 15%) are made by fractional distillation of fermented products.

The lower alcohols, e.g. methanol, ethanol, are water-like liquids. They dissolve well in water, less well in other solvents. Alcohols burn in a plentiful supply of air to give carbon dioxide and steam. They can be oxidized to organic acids - ethanol, for example, is oxidized to ethanoic acid. This is the change that takes place when wine changes to vinegar.


What are the important properties of alcohols?
1 Physical properties
The physical properties of alcohols are influenced by the OH group. The lower alcohols are liquids, miscible with water and other hydrogen bonded liquids.
Alcohols can be classified as primary, secondary and tertiary according to how many other carbon atoms are attached directly to the carbon bonded to the OH:
* 0 or 1 - primary alcohol
* 2 - secondary alcohol
* 3 - tertiary alcohol
The position of the OH group has a slight effect on the physical properties, since, if it is surrounded by alkyl groups (tertiary alcohol) there is less opportunity for the OH group to be involved in hydrogen bonding. Thus tertiary alcohols are more volatile than isomers which are secondary and primary alcohols.
The position of the OH group has little effect on the chemical properties except in their response to mild oxidizing agents.