Notes on Organic Chemistry

4.1.1 Basic Concepts of Organic chemistry

Naming and representing the formulae of organic compounds

Hydrocarbons: Organic chemistry mainly concerns the properties and reactions of hydrocarbons,
compounds that conntain only carbon and hydrogen atoms. Hydrocarbons form series of
compounds with similar structures and formulae that can be represented in many different ways.
Nomenclature: The set of rules that outline how different organic compounds should be named and
how their formulas are represented.
Naming compounds: Compounds are named according to rules laid out by the International Union
of Pure and Applied Chemistry (IUPAC. This ensures each compound is universally named the
same, which helps to avoid potentially dangerous confusion.
Stem: The prefix of the chemical tells you the length of the longest unbroken chain of carbon atoms
in the compound.
Number of Carbon Atoms Prefix Alkane example
1 Meth- Methane
2 Eth- Ethane
3 Prop- Propane
4 But- Butane
5 Pent- Pentane
6 Hex- Hexane
7 Hept- Heptane
8 Oct- Octane
9 Non- Nonane
10 Dec- Decane

Functional groups: The ending (suffix) of the compound’s name tells you the functional group
present. If there is more than one functional group present, they are added as a prefix.
Functional group Suffix
Alkane -ane
Alkene -ene
Alcohol -ol
Carboxylic acid -oic acid
Ketone -one
Aldehyde -al
Ester -ate
Amine -amine

If a halogen is present, it’s represented by a prefix:

Functional Group Prefix
Fluorine Fluoro-
Chlorine Chloro-
Bromine Bromo-
Iodine Iodo-

Side chains: Carbon side chains are branched from the longest carbon chain are represented by a
prefix at the start of the word. These alkyl groups are made using the stems given above
(meth-,eth-,prop-, etc) and the syffix -yl.

General rules:
1. Functional groups and side chains are given, if necessary, with the number corresponding to
the carbon they are attached to.
2. Numbers are separated by commas.
3. Numbers and words are separated by hyphens.
4. If more than one particular side chain or functional group is present then one of the
following prefixes is added: di- (2), tri- (3), tetra- (4), etc.
5. The carbon chain is numbered in ascending order from the end of the chain nearest a
functional group
6. If multiple prefixes are present, they are included in alphabetical order.

Formulas: There are many different ways of writing and representing organic compounds:
1. Empirical Formula
- The simplest whole number ratio of atoms of each element in a compound
2. Molecular Formula
- The true number of atoms of each element in a compound
3. General Formula
- The simplest algebraic formula of a member of a homologous series. All members of a
homologous organic series follow the general formula.
4. Structural Formula
- The minimal detail that shows the arrangement of atoms in a molecule
- The carboxyl group will be represented as COOH and the ester group as COO
5. Displayed formula
- The relative positioning of atoms and the bonds between them. Shows every atom and
every bond in an organic compound.
6. Skeletal Formula
- The simplified organic formula of just a carbon skeleton and functional groups
- Shows only the bonds in a compound and any non-carbon atoms
- Vertices are carbon atoms
- Hydrogen is assumed to be bonded to them unless stated otherwise
7. Cyclic Compounds and Benzene
- These compounds are represented by different hexagonal shaped symbols
- Benzene is represented by a hexagon with three lines inside it

Functional groups

Homologous series: A series of organic compounds with the same functional group but with each
successive member differing by CH2.
Organic compounds are often part of a homologous series, in which all members follow a general
formula and react in a very similar way. There is an increase in boiling points as the chain length
increases.
Functional group: A group of atoms responsible for the characteristic reactions of a compound.
Alkyl group: A hydrocarbon chain with the general formula CnH2n+1. Sometimes R may be used to
represent alkyl groups, as well as other fragments of organic compounds not involved in reactions.
Aliphatic: An aliphatic compound is a compound containing carbon and hydrogen joined together in
straight chains, branched chains or non-aromatic rings.
Alicyclic: An alicyclic compound is an aliphatic compound arranged in non-aromatic rings, with or
without side chains.
Aromatic: An aromatic compound is a compound containnig a fully conjugated ring. Benzene is
aromatic.
Saturated: A compound is described as being saturated if it contains single carbon-carbon bonds
only.
Unsaturated: A compound is described as being unsaturated if it contains multiple carbon-carbon
bonds, including C=C, C≡C, and aromatic rings.

Isomerism

Isomers are molecules with the same molecular formula but a different arrangement of atoms within
the molecule. This gives isomers a different structural formula.

Chain Isomers: Have the same molecular formula but a different arrangement of the carbon
skeleton. The isomers’s carbon chain will differ – they can be straight chains or branched chains,
however they will always have the same molecular formula.
Position Isomers: Have the same functional group of the molecule but in a different position on the
carbon chain.
Functional Group Isomers: Functional group isomers have the same molecular formula, but the
molecules have a different functional group.

Reaction Mechanisms

A ‘curly arrow’ is used to describe the movement of an electron pair during a reaction. It can show
either heterolytic fission or the formation of a covalent bond.

Breaking a covalent bond is called fission.

In homolytic fission, each bonding atom recieves one electron from the bonded pair, forming two
radicals. Movement of one electron is shown by a single-headed curly arrow.

In heterolytic fission, one bonding atom recieves both electrons from the bonded pair. This leads to
the formation of a positive and negative ion. Movement of two electrons is shown by a double-
headed curly arrow. Most mechanisms involve heterolytic fission.

A radical is a species with an unpaired electron. Radicals are represented by a dot.

Types of reactions

Reactions can be classified according to what happens to the reactants during the reaction and what
the end products are. The main types of reaction are:

• Addition – the reactants combine to form a single product

 • Substitution – one functional group is replaced by a different functional group
• Oxidation – a species loses at least one electron, and is oxidised
• Reduction – a species gains at least one electron, and is reduced
• Polymerisation – a reaction in which many small molecules, known as monomers, join
together to form a long, repeating molecule called a polymer.

4.1.2 Alkanes

Properties of alkanes

Alkanes are saturated hydrocarbons containing single C-C and C-H bonds. These single bonds are
called Σ bonds. The overlap of orbitals is directly between the two atoms and there is free rotation
around the Σ bond.
Alkanes are part of a homologous serious with the general formula CnH2n+2. Cycloalkanes are an
exception to this formula but are still saturated hydrocarbons.
Each carbon atom in an alkane forms four Σ bonds. They have tetrahedral geometry and a bond
angle of 109.5 degrees. This shape minimises electron-electron repulsion between bonding pairs.

Variations in Boiling Points

Induced dipole-dipole interactions act between organic alkane chains and are affected by the chain
length and any branching. As the chain length of the alkane increases, so does the Mr of the
molecule. This results in stronger intermolecular forces between the chains and the compound has a
higher boiling point as a result.
Branching of alkane chains weakens London forces between the chains as they are less able to pack
tightly together. Therefore, the distance over which the intermolecular forces act is increased and
the attractive forces weakened. This means branched chain alkanes have lower boiling points than
straight chain alkanes.
Fractional distillation makes use of this variation in boiling points.

Reactions of Alkanes:
Alkanes have a low reactivity with many reagents due to the high bond enthalpy of the C-C bonds
and very low polarity of the Σ-bonds present.

Combustion of Alkanes:
Alkanes make good fuels as they release a lot of energy when burned. With sufficient oxygen
present, they undergo complete combustion to produce carbon dioxide and water.
If the oxygen present is insufficient, combustion is incomplete and carbon monoxide or carbon
particulates are produced alongside water.
Carbon monoxide is a toxic, gaseous product that is especially dangerous to humans as it’s
odourless and colourless. Carbon monoxide is dangerous because it replaces oxygen in the blood,
starving the brain and other organs of oxygen and causing people to suffocate.
Oxides of nitrogen and sulfur are also produced as a byproduct of alkane combustion along with
carbon paritculates from unburnt fuel. In clouds, these oxides can react with water and form dilute
acids, which result in acid rain.

Chlorination of Alkanes:
Alkanes react with halogens in the prescence of UV light to form haloalkanes. The UV light breaks
down the halogen bonds (homolytic fission) producing reactive intermediates called free radicals.
Free radicals are species containing an unpaired electron which is shown using a single dot. These
attack the alkanes, resulting in a series of reactions: Initiation, propagation and termination.
1. Initiation – The halogen-halogen bond is broken to form two free radicals.
2. Propagation – In each propagation step, the molecule containing the radical changes through
single electron transfer. Overall, a hydrogen is replaced and the Cl radical is reformed as a catalyst.
3. Termination – Two radicals join to end the chain reaction and form a stable product.
The propagation step can continue many times to result in multiple substitutions – this is a chain
reaction. The conditions of the reaction can be altered to favour the termination step and limit the
number of substitutions, however, termination could also occur at different positions in the carbon
chain. The nature of this reaction to produce multiple products limits it’s use in organic synthesis.

4.1.3 Alkenes

Introduction to Alkenes: Alkenes and cycloalkenes are unsaturated hydrocarbons with at least one
carbon-carbon double bond. They are part of a homologous series with the general formula CnH2n.
The carbon-carbon double bond is an area of high electron density, making it susceptible to attack
from electrophiles (species that are attracted to electron dense areas) It consists of a normal covalent
Σ-bond and a π-bond.
The π-bond is formed by sideways overlap of adjacent p-orbitals above and below the bonding C
atoms. The Σ-bond is formed by overlap of orbitals directly between the bonding atoms.
The C-H bonds are in the same plane as the C-C Σ-bond. There is trigonal planar geometry around
the carbon atom and a bond angle of 120 degrees. This angle minimises electron-electron
reppulsion between bonding pairs. The π-bond has electron density above and below the plane of
the Σ-bonds. There is restricted rotation in alkenes due to this π-bond.
Bromine water is used to identify an alkene double bond and other unsaturated compounds. Alkenes
cause bromine water to change colour from orange-brown to colourless. This is because bromine
forms bonds to the carbon atoms, removing the C=C bond, causing the compound to become
saturated.

Stereoisomers: Compounds with the same structural formula but a different arrangement of atoms
in space.

E-Z isomerism: A stype of stereoisomerism, which occurs due to the limited rotation around a
double carbon bond. The limited rotation means that ‘high priority’ groups attached to the C=C can
be ‘together’ or ‘opposite’. The Z isomer is on zhe zame zide.

Cahn-Ingold-Prelog (CIP) priority rules: There is a priority of different groups in molecules that can
display E-Z isomerism. The atom or group on each side of the double bond with the higher Ar or Mr
is given the higher priority. These high priority groups are used to determine if it’s the E or Z
isomer.

Cis-Trans Isomerism: A special case of E/Z isomerism in which two of the substituent groups
attached to each carbon atom of the C=C group are the same. These stereoisomers can be named in
the same process as above, but instead of using Cis- for when the groups are on the same side and
Trans- for when they are on different sides. It’s important to remember that use of E as equivalent to
trans and Z as equivalent to cis is only consistently correct when there is a H on each carbon atom
of the C=C bond.

Addition Reactions of Alkenes:

The carbon-carbon double bond in alkenes has a relatively low bond enthalpy. This makes them
relatively reactive. During their reactions, the double bond opens up to form single bonds to other
atoms. These are called addition reactions. The pi bond is an area of high electron density. This
attracts electrophiles.
Producing Alkanes: Alkenes can undergo electrophililc addition with hydrogen to produce alkanes.
The C=C bond opens up and forms single bonds to each of the hydrogen atoms. This reaction
requires a nickel catalyst.
This reaction is also known as a hydrogenation reaction. Catalytic hydrogenation is used in the
manfacture of margarine from unsaturated vegetable oils.

Producing Haloalkanes: Haloalkanes are organic compounds with single carbon bonds only and
halogen functional groups. Alkenes undergo addition reactions with halogens to form di-substituted
haloalkanes, and with hydrogen halides to form mono-substituted haloalkanes.

Producing Alcohols: Alcohols are organic compounds with a hydroxyl functional group, -OH.
Alkenes undergo addition reactions with steam to form alcohols. This reaction requires an acid
catalyst, such as phosphoric acid. Diols. Alcohols with two hydroxyl functional groups, can also be
formed from alkenes through an oxidation reaction. The double bond is oxidised by acidified
potassium manganate(VII) (KmnO4). The mangante ions must be cold, dilute and acidified.

Electrophiles:
Electrophiles are electron pair acceptors and are attracted to areas of high electron density. Some of
the most common elecrophile sources are:
• Hbr
• Br2
• H2SO4

Electrophillic Addition:
Electrophillic addition is the reaction mechanism that shows how electrophiles attack the double
bond in alkenes. When the double bond is broken, a carbocation intermediate forms. This is a
carbon atom with only three bonds, so it has a positive charge.
Carbocations can have varying stability, with tertiary being the most stable and primary the least.
The more stable the carbocation, the more likely it is to form. Therefore, in an addition reaction of a
hydrogen halide, multiple products can form but the major product will always be the one that’s
formed via the most stable carbocation possible.

E.g: The mechanism of propene with hydrogen bromide.

Hydrogen bromide is polar due to the difference in the electronegativities of hydrogen and bromine.
The electron pair in the double bond that transfers electrons to form a covalent Σ-bond to H. This
produces a positively charged carbocation intermediate on the other carbon, which attracts the
negatively charged bromide ion formed by cleavage of the H-Br bond in the first step.
The hydrogen joins to the carbon atom which is bonded to the most hydrogen atoms. The bromide
ion bonds to the carbon atom which is joined to the most carbon atoms. This is due to the tendency
for the reaction to proceed via the most stable carbocation intermediate. Hence, 2-bromopropane
forms more than 1-bromopropane in the mechanism of propane with hydrogen bromide. This makes
2-bromopropane the major product.

Addition polymers:
Addition polymers are produced from alkenes which are short chain monomers which join together
to form long chain polymers. The double bond of the alkene is broken to form a repeating unit – the
repetition of which would form the complete polymer chain.
The repeating unit must always be shown with extended bonds through the brackets, showing that it
bonds to other units on both sides.

Waste Polymers and Alternatives:

The energy and resources used to make waste polymers are large. Polymers are made from alkenes
which are obtained from crude oil, a non-renewable resource. The extraction and cracking of crude
oil are both high energy processes and additional energy is then required to convert these alkenes
into polymers.

Uses of polymers:
Polymers are unreactive hydrocarbon chains with multiple strong, non-polar covalent bonds. This
makes them useful for manufacturing many everyday plastic products such as poly(ethene)
shopping bags.
However, the unreactive nature of the bonds in addition polymers means they aren’t biodegradable
and can’t be broken down by species in nature.
Benefits of using cheap oil-derived plastics are counteracted by problems for the environment if
these go to landfill. It’s important to dispose of plastics effectively to improve the use of resources
and reduce the negative impact on the environment.

Disposal of Polymers:
Addition polymers are non-biodegradable which means disposal of them can be difficult. Waste
polymers can be processed in different ways. Some can be recycled, used as organic feedstock for
production of plastics and other organic chemicals, or combusted to produce energy from other
industrial processes.
Combustion can release toxic gases which must be removed to reduce the impact on the
environment. During disposal by combustion of chlorine-containing haloalkanes, HCL may be
released. This is toxic and needs to be removed.
As well as this, scientists are developing biodegradable polymers and photodegradable polymers to
overcome these waste issues. This helps to reduce dependency on finite resources and alleviates
problems from disposal of persistent plastic waste.