Topic 4: Organic and Biological Chemistry

4.1 Systematic Nomenclature 4.2 Physical Properties 4.3 Alcohols 4.4 Aldehydes and Ketones 4.5 Carboxylic Acids 4.6 Amines 4.7 Esters 4.8 Amides 4.9 Proteins 4.10 Triglycerides 4.11 Carbohydrates

Organic Chemistry

Biological Chemistry

Introduction to hydrocarbons

Alcohols, aldehydes, ketones and Carbohydrates

Carboxylic acids, esters and triglycerides (fats and oils)

Amines, amides and proteins

Topic 4: Organic and Biological Chemistry

Organic chemistry - the study of hydrocarbons (compounds of hydrogen and carbon) and their derivatives.

Carbon:

the element of life on earth

4 valence electrons

it has room for 4 covalent bonds to 4 other atoms

Able to form single, double and triple bond

Organic compounds - molecules with carbon atoms as main elements.

7 million organic compounds

1.5 million inorganic compounds

Introduction

Molecular Formula

- Number of atoms of each element present

Structural Formula

- Shows the individual atoms in a molecule and how they are arrange

Modeling Organic Compounds 1-hexanol C6H14O

Molecular formula: C5H8O2

Other structural formula:

Saturated & Unsaturated HC

When C=C or CC bonds are present in the hydrocarbon chain, where the hydrocarbon contain less than the maximum number of hydrogen atoms, its an unsaturated hydrocarbon.

If hydrocarbon chain contain only C-C bonds, it is refer to as saturated hydrocarbon.

Unsaturated Saturated Saturated

Cyclics (cycloalkanes or cycloalkenes) are alkanes or alkenes which form into a ring structure.

Cyclics

CH2

CH2

CH2

CH2CH2

CH2

H2C

CH2

CH2 H2C

H2C CH2

CH2

CH2

CH2

CH2H2C

H2C

Cyclopropane Cyclobutane

Cyclopentane Cyclohexane

An aromatic compound has aryl group/ benzene ring as its functional group:

In benzene ring, the electrons in the carbon to carbon double bond are not held between just two

carbon atoms, but are spread over the whole ring,

the electrons are said to be delocalised.

Aromatics

CH

CH

CH

CH

CH

CH

Molecular

formula:

C6H6

Structural formula:

Physical Properties of Hydrocarbons

All hydrocarbons (HC) are non polar molecules,

HC molecules are attracted to each other only by

weak dispersion forces as secondary interactions.

As the length of hydrocarbon molecules increases,

the dispersion forces between molecules also

increases.

Small molecular mass hydrocarbons (< 5C), have

low boiling points and are gases at room

temperature (Eg. methane, propane, pentane).

Larger molecular mass hydrocarbons (> 5C) have

higher boiling point and usually liquid at room

temperature (Eg. hexane, octane, decane).

Alkanes 1. General formula: R R

2. Functional group: none

3. Systematic naming / nomenclature: alkane

4. Physical properties:

Non polar molecules

Molecules are held by very weak dispersion forces

small molecular mass alkanes gases at r.t.p. but big molecular mass alkanes liquid at r.t.p. (more dispersion forces between molecules)

have very low MP and BP (weak DF betw mol.)

not soluble in water (cannot form H-bond with

very polar water molecules)

5. Chemical properties:

Alkanes - generally considered chemically unreactive because they contain no reactive functional group.

But can undergo two main types of reaction:

(I) Complete combustion

CH4 + 2 O2 CO2 + 2 H2O

(II) Substitution forming haloalkanes, where hydrogen is substituted by a halogen in the presence of light.

CH4 + Br2 CH3 Br + HBr

6. Preparation: through fractional distillation of petroleum.

Alkene & Alkyne 1. General formula: R R RCCR RCCR

2. Functional group: Carbon to carbon Carbon to carbon

double bond triple bond

2. Systematic nomenclature: alkene alkyne

3. Physical properties:

Non polar molecules

Molecules are held by very weak dispersion forces

small molecular mass alkenes gasses at r.t.p. but big molecular mass alkanes liquid at r.t.p.

have very low MP and BP

not soluble in water

5. Chemical properties: More reactive than alkanes

(I) Complete combustion

CH3CH=CHCH3 + 6 O2 4 CO2 + 4 H2O

(II) Addition reaction

Hydrogenation add H2 across the double bond, with metal catalyst (nickel or platinum); used commercially to convert unsaturated vegetable oils to saturated fat. [Fats and Oils]

CH3CH=CHCH3 + H2 CH3CH2CH2CH3

Halogenation react with halogens (Br2, Cl2)

Bromine Test: Bromine water (Br2 / H2O), a reagent used to test the presence of double bonds because orange bromine solution will be decolorised.

CH3CH=CHCH3 + Br2 CH3CHBrCHBrCH3

Hydrohalogenation the hydrogen halides (HBr, HCl) can added across a double bond.

CH3CH=CHCH3 + HBr CH3CH2CHBrCH3

Hydration the addition of water (catalysed by an acid) to alkenes is an important reaction industrially, eg. to

produce ethanol (alcohol) from ethene.

CH3CH=CHCH3 + H2O CH3CH2CHOHCH3

Addition polymerization many alkenes and alkenes can add to themselves to form very long-chained

macromolecules called polymers. [Topic 5: Materials]

6. Preparation: cracking of short chain alkanes with the

presence of platinum as catalyst

C C + A B CA C B

Systematic naming / Nomenclature IUPAC naming

Identify longest chain of carbon atoms containing functional group (parent name).

Number the carbon atoms - start with C nearer to the functional group.

Determine functional groups location and type.

When two same functional groups are present on the same carbon atom, use the number twice.

When two or more functional groups are identical, indicates this by the use of prefixes di-, tri-, tetra-, and so on.

When branching first occurs at an equal distance from either end of the longest, choose the name of that gives the lower number at the first point of difference.

When two or more chains of equal length compete for selection as the parent chain. Choose the chain with greater number of substituents.

Between a number and a number:

Between a number and an alphabet:

Between an alphabet and an alphabet:

3-bromo-2-chloro-3-methylpentane

2-chloro-5-methylhexane-3-ene

2,4-dibromo-3,5-dichloropentan(e)-1,3-diene

Derivatives of Hydrocarbons

R = hydrocarbons (saturated / unsaturated /

cyclic / aromatic) or hydrogen atom

X = functional group / reactive site

atoms or groups of atoms that govern

the physical and chemical properties of

an organic compound

Organic Families

Each family has a functional group to identify it.

1. Alcohols (-OH, hydroxyl group)

2. Aldehydes (-CHO, aldehyde group)

3. Ketones (-CO-, ketone group)

4. Carboxylic acids (-COOH, carboxyl group)

5. Esters (-COO-, ester group)

6. Amines (-NH2, amino group)

7. Amides (-CONH2, amide group)

Homologous Series Homologous series has an associated functional group.

The formula of each member conforms to the same general formula.

The formula of each member contains more CH2 group than that of the previous member.

The physical properties of the members of a series gradually changes as the molecules become heavier and more complex

Physical state changes from gas to liquid to solid

Boiling point and melting point gradually increases

Solubility in a given solvent gradually decreases

The chemical properties of all the members of a series are similar. If the chemical properties of the first members are known then those of later members can be deduced.

Types of Organic Reactions

Combustion

Condensation (eg: esterification)

Addition (eg: hydrogenation, hydration, bromination, chlorination)

Acidic hydrolysis

Alkaline hydrolysis (eg: saponification)

Redox reaction

Most organic reaction require special apparatus set-

up to carry out the reaction due to volatile organic

compounds and also the very slow reaction rate.

Organic reactions apparatus

Reflux apparatus

To prevent the loss of volatile

organic compound and to

increase the rate of organic

reaction by giving extended

heating

Reflux process: repeated

vaporisation and condensation

Most organic reaction require special apparatus set-up

to carry out the reaction because organic compounds

are volatile and also to speed up the rate reaction.

2. Distillation apparatus Fractional distillation: To separate two miscible liquid with different boiling point, so as to purify / concentrate one of the organic compound.

Buchner filtration apparatus

To separate precipitate formed in an aqueous solution.

Separation apparatus

To separate two immiscible liquid

Boiling chips

To prevent over heating, bumping of solution and to

make sure heat is distributed evenly throughout the

liquid during reaction.