TOPICS

1. DETERMINATION OF STRUCTURE OF ORGANIC COMPOUNDS

2. ELECTRONIC THEORY IN ORGANIC CHEMISTRY.

DETERMINATION OF STRUCTURE OF ORGANIC COMPOUNDS

1. Identification of the Compound.

The first step in determining the structure of an organic compound involves proper identification
of the compound.
Identification stage involves the following three steps:
 Isolation and purification of organic compounds
 Qualitative test (Elemental analysis)
 Quantitative analysis (Empirical, Molecular formula and Percentage composition)

The General Steps Required to Determine the Structure of An Organic Compound

2. CHEMICAL AND PHYSICAL ANALYSES ( SPECTROSCOPIC METHODS)

TYPES OF SPECTROSCOPIC METHODS FOR STRUCTURE ELUCIDATION

• X-ray crystallography
• Infra-red spectroscopy
• Mass spectroscopy
 • UV spectroscopy
• Nuclear magnetic resonance (NMR) spectroscopy

ISOLATION AND PURIFICATION OF ORGANIC COMPOUNDS.

Purification of organic compounds is important because most synthetic reactions give mixture of
products. Also, most compounds of biochemical interest occur naturally in plants as components
of complex mixture from which they can be separated.
• A pure compound is a homogeneous sample consisting of molecules of the same structure. A
pure solid has a sharp and constant melting point or constant boiling point (if liquid).
• A mixture is a substance which consists of two or more components that are not chemically
combined together.
Separation of mixture into individual components can be achieved by differences in physical
properties such as differences in boiling point, solubility, volatility, size, density e.t.c.
Techniques used in separating organic mixture include :
 Filtration
 Centrifugation
 Crystallization
• Simple distillation
• Fractional distillation
• Decantation
• Evaporation
• Steam distillation
• Chromatography
• Solvent extraction (liquid-liquid extraction)
• Freeze drying

1. Filtration
This technique is used to remove or separate an insoluble solid from a liquid particularly when
the solid is suspended throughout the liquid. The solid/liquid mixture is called a suspension.

There are many small holes in the filter paper, these allow very small particles of the solvent and
dissolved solutes to pass through as filtrate while the larger insoluble particles are retained on the filter
paper as residue
2. Centrifugation
When there is only a small amount of suspension, or when much faster separation is required,
centrifugation is often used instead of filtration. The liquid containing the undissolved solids is put in
a centrifuge tube. The tubes are then put into the tube holders in a centrifuge.

A Centrifuge

The holders and tubes are spun around at a very high rate and are thrown outwards. The denser
solid is collected as a lump at the bottom of the tube with the clear liquid above

3. Crystallization
Solid organic compounds are rarely pure after isolation from reaction mixture; they are usually
contaminated with small impurities which are produced along with the desired product. The
purification of impure crystalline compound is affected by crystallization from a suitable solvent or
mixture of solvents. The most desirable characteristics of a solvent for crystallization are as follows:
1. It should not dissolve the solid (desired product) when cold but it should dissolve it when hot
2. It should dissolve the impurities readily or to only to a small extent
3. It should yield well-formed crystals of the purified compound.
4. It should be capable of easy removal from the crystals of the purified compound, i.e. possess a
relatively low boiling point.
a. Crystallization by Cooling a Hot Concentrated Solution
• To obtain crystals from an unsaturated aqueous solution, the solution is gently heated to
make it more concentrated. After, the solution is allowed to cool at room conditions.
• The solubilities of most solids increase with temperature When a hot concentrated
solution is cooled, the solution cannot hold all of the dissolved solutes. The “excess”
solute separates out as crystals.
 •

b. Crystallization by Evaporating a Cold Solution at Room Temperature

• As the solvent in a solution evaporates, the remaining solution becomes more and more concentrated.
Eventually the solution becomes saturated, then further evaporation causes crystallization to
occur.
• If the solution is allowed to stand at room temperature, evaporation will be slow and It may take days
or even weeks for crystals to form

•
Crystallization by slow evaporation of a solution (preferably saturated) at room
temperature

4. DISTILLATION
a. Simple Distillation

A method used to separate a solvent from a solution containing non-volatile solutes. When a solution
is boiled, only the solvent vaporizes, the hot vapour formed condenses to liquid again on a cold
surface. The liquid collected is the distillate.
Distillation is a joint process of vaporization and condensation. The method is used for the purification
of liquids which boil without decomposition and contain non-volatile impurities. The method can also
be used for separating liquids having sufficient difference in their boiling points.e.g: Chloroform (b. p.
334 K) and aniline (b. p. 457 K). Ether (b. p. 308 K) and toluene (b. p. 384 K)
Before the solution is heated, several pieces of anti-bumping granules are added into the flask to
prevent vigorous movement of the liquid called bumping to occur during heating ,therefore making
boiling smooth.
If bumping occurs during distillation, some solution (not yet vaporized) may spurt out into the
collecting vessel.
b. Fractional Distillation
This process is used for separating a mixture of two or more miscible liquids which have boiling
points close to each other. Since in this process, the distillate is collected in fractions under different
temperatures, it is known as fractional distillation. This process is carried out by using fractionating
columns.
A fractionating column is attached vertically between the flask and the condenser a column packed
with glass beads provide a large surface area for the repeated condensation and vaporization of the
mixture to occur
This method may be used to separate a mixture of acetone (b. p. 330 K) and methyl alcohol (b. p. 338
K) or a mixture of benzene and toluene.

The temperature of the escaping vapour is measured using a thermometer. When the temperature
reading becomes steady, the vapour with the lowest boiling point firstly comes out from the top of the
column.
When all of that liquid has distilled off, the temperature reading rises and becomes steady later on
another liquid with a higher boiling point distils out. Fractions with different boiling points can be
collected separately.
One of the technological applications of fractional distillation is to separate different fractions of crude
oil in petroleum industry into various useful fractions such as:
• gasoline,
• kerosene oil,
• diesel oil,
• lubricating oil etc.
c. Azeotropic distillation:
Azeotropic mixture is a mixture having constant boiling point. The most familiar example is a
mixture of ethanol and water in the ratio of 95.87: 4.13 (a ratio present in rectified spirit). It boils
at 78.13oC. The constituents of an azeotropic mixture can't be separated by fractional distillation.
Hence a special type of distillation (azeotropic distillation) is used for separating the constituents
of an azeotropic mixture..
d. Steam distillation
This method is applicable to the separation and purification of organic compounds (solids or
liquids) which are:
(a) insoluble in water
(b) volatile in steam
(c) possess a high vapour pressure (10-15 mm Hg) at 373 K and
(d) contain non-volatile impurities.

Aniline (b. p. 457 K) can be purified by steam distillation since it boils at a temperature of 371.5
K in the presence of steam
• Other compounds which can be purified by steam distillation are:
• nitrobenzene
• bromobenzene
• o-nitrophenol
• salicylaldehyde
• o-hydroxyacetophenone
• essential oil
• turpentine oil etc.

e. Distillation under reduced pressure

This method is used for the purification of high boiling liquids and liquids which decompose at or
below their boiling points. The crude liquid is heated in distillation flask fitted with a water
condenser, receiver and vacuum pump. As the pressure is reduced, the liquid begins to boil at a
much lower temperature than its normal boiling point.
• The vapour is condensed by water condenser and the pure liquid collected in the receiver.
• Glycerol which decomposes at its boiling point (563 K) under atmospheric pressure can
be distilled without decomposition at 453 K under 12 mm of Hg.
Similarly, sugarcane juice is concentrated in sugar industry by evaporation under reduced pressure
which saves a lot of fuel.
 5. SUBLIMATION

Sublimation is the direct change of a solid to vapour on heating, or a vapour to solid on cooling
without going through the liquid state.
This can be demonstrated by heating a mixture of two compounds in an evaporating dish as shown
below:
 One compound changes from solid to vapour directly and the vapour changes back to solid on
a cold surface
 The other compound is not affected by heating and remains in the evaporating dish.

Separation of a mixture of two compounds by sublimation process

6. CHROMATOGRAPHY:
This is a modern method used for the:
• separation of mixtures into its components,
• purification of compounds
• test the purity of compounds.
The name chromatography is based on the Greek word 'chroma' meaning colour and 'graphy' for
writing because the method was first used for the separation of coloured substances found in plants.
This method was described by Tswett in 1906

The technique depends on the distribution of the components of a mixture between a mobile phase
and a stationary phase. The stationary phase may be in form of a packed column (column
chromatography) through which a mobile phase can flow, or in the form of a thin layer adhering to a
 suitable form of packing material (thin layer chromatography) over which the mobile phase is
allowed to ascend by capillary action. The stationary phase may be a liquid or solid (silica or
alumina) and the mobile phase can be liquid or an inert gas Based on the arrangement of the
stationary phase and the mobile phase , chromatography can be classified as follows:
1. Paper chromatography (PC)
2. Thin layer chromatography (TLC)
3. Column chromatography (CC)
4. Gas –liquid chromatography(GLC)
5. High performance liquid chromatography (HPLC

Paper Chromatography / Thin Layer

The stationary phase is paper or glass plate coated with layers of solid stationary phase, which
adhere to the plate generally by virtue of a binding agent such as CaSO 4, which is incorporated. The
most common stationary phases are silica gel, alumina, sepahadex, cellulose powder. Many of these
are available with a fluorescent compound (e.g ZnS) incorporated in order to facilitate the detection
of the resolved components of the mixture which is then achieved by viewing the plates under UV
light. This technique is used to identify the number of components in complex organic mixture e.g.
extract from plants, dyes. It involves ascending of organic solvent (mobile phase) over the mixture
(spotted on the stationary phase) in the bid to separating the mixture into its components.
The movement of mobile phase over the stationary phase in a bid to separate the mixture is called
development or elution. The eluted paper or plate gives a chromatogram. Each spot is characterized
by a property called retention factor (RF). RF of each component depends on its rate of adsorption on
the stationary phase; this in turn depends on the polarity of the compound RF= distance moved by the
solute from origin/ distance moved by the solvent front from origin Note that 0<RF

COLUMN CHROMATOGRAPHY
This is used for separation of the constituents of organic mixture. The stationary phase is a column
packed with an adsorbent. The mobile phase is an organic solvent (known as eluant). This technique
involves using the eluent to elute each component of the mixture (after being adsorbed to the
stationary phase). Each component of the mixture is adsorbed to the stationary phase at different rates
and hence they move at different speed down the column. Aliquots (equal volumes) of the eluates are
then collected into test tubes or beakers. Components with the same RF values are then bulked
together.

7. SOLVENT EXTRACTION
This separation method involves extracting a component from a mixture with a suitable solvent.
Water is the solvent used to extract salts from a mixture containing salts and sand
Non-aqueous solvents (e.g., 1,1,1-trichloroethane and diethyl ether) can be used to extract organic
products. The technique often involves the use of a separatory funnel

When an aqueous solution containing the organic product is shaken with diethyl ether in a separating
funnel, the organic product dissolves into the ether layer. The ether layer can be run off from the
separatory funnel and saved.
Another fresh portion of ether is shaken with the aqueous solution to extract any organic products
remaining. Repeated extraction will extract most of the organic product into the several portions of
ether
Conducting the extraction with several small portions of ether is more efficient than extracting in a
single batch with the whole volume of ether
These several ether portions are combined and dried. The ether is distilled off,
leaving behind the organic product.

The organic product in an aqueous solution can be extracted by solvent extraction using diethyl ether

8. Freeze drying.
This is a process called lyophilization. This process is used when water is to be removed
from heat-labile materials e.g polysaccharides, enzymes and peptides
 QUALITATIVE ANALYSIS (ELEMENTAL ANALYSIS)

This method deals with detection of various elements present in an organic sample. Most
organic compound contains C,H O, and other elements such as N, S, P, halogens and
metals).

1. DETECTION OF C AND H
 Carbon and hydrogen can be detected by heating a small amount of the substance
with copper(II) oxide
 Carbon and hydrogen would be oxidized to carbon dioxide and water
respectively
Sample+ O2(g) CO2(g) + H2O(g)
 Carbon dioxide turns lime water milky
 H2O turns anhydrous CUSO4 from white to blue or anhydrous CoCl2 from blue
to pink Water turns anhydrous cobalt (II) chloride paper pink

2. Detection of N, S and halogens (Lassaigne’s sodium fusion test)

Lassaigne’s sodium fusion test is used to convert elements into soluble sodium
compound or to ionisable inorganic material by fusion of sodium metal with the organic
compound.
The organic compound is heated with excess sodium metal to redness and then plugged
into water in a mortar. After cooling, the content is then ground and filtered. The filtrate
is then divided into 3 portions:
[C, H, N, X,P, S] + Na (excess) NaCN + Na2S + NaX

[C, H ,N,X,P, S] + Na (limited) NaSCN + NaX

Na

NaCN + Na2S

1. Test for Nitrogen

To the first portion of the filtrate
Lassaignes fitrate + FeSO4 +FeCl3 Prussian blue solution.
Prussian blue solution indicates the presence of CN-, which in turn indicates the presence of N in
the organic sample.
Equations: NaCN + FeSO4 Na4Fe (CN)6 (aq) + Na2SO4 (aq)
3Na4Fe (CN)6 (aq) + 4FeCl3 Fe4[Fe(CN)6]3 + 12NaCl
Prussian Blue

2. Test for S
To the second portion of the filtrate, add dilute lead ethanoate and dilute nitric acid
Na2S + dil. Pb[CH3COO]2 dilute HNO3 PbS + 2CH3COONa
 Filtrate black ppt

3. Test for halogens

To the third portion

Lassaignes filtrate is first acidified with few drops of dilute H 2SO4 and boiled to remove S and CN in
the form of HCN (g) and H2S (g), these S2- and CN- ions can also interfere with the precipitating
agents such as AgNO3

NaX + AgNO3 dil.HNO3 NaNO3 + AgXs

NaX + AgNO3 dil.HNO3 NaNO3 + AgX

 White ppt soluble in excess aqueous NH3, it indicates the presence of Cl-
 Pale yellow ppt sparingly soluble in excess aqueous NH3, it indicates the presence of Br-
 Yellow ppt insoluble in excess aqueous NH3, it indicates the presence of I-
Quantitative analysis
(Percentage composition, Empirical and Molecular formulae)

Empirical Formula
The smallest possible whole-number ratio of subscripts of the elements in the formula. For
instance, the empirical formula of sulfur monoxide would simply be SO, as is the empirical
formula of disulfur dioxide S2O2.
Steps for Determining an Empirical Formula
• Start with the number of grams of each element, given in the problem.
• Convert the mass of each element to moles using the molar mass from the periodic table.
• Divide each mole value by the smallest number of moles calculated.
• Round to the nearest whole number.

Problem No 1:
A sample of copper metal weighing 2.50 g is heated to form an oxide of copper. The final
mass of the oxide is 3.13 g. Determine the empirical formula of the oxide.
• Step one: Determine mass:
Cu ⇒ 2.50 g, O ⇒ 3.13 g - 2.50 g = 0.63 g
Step two: Determine moles:
Cu ⇒ 2.50 g / 63.546 g/mol = 0.03934 mol
O ⇒ 0.63 g / 16.00 g/mol = 0.039375 mol
Step 3: Divide each mole value by the smallest number of moles calculated.
• 0.03934 mol 0.039375 mol
• 0.03934 mol 0.03934 mol
• =1 ( Cu) =1.000889 (O)
• Step 4: Round to the nearest whole number.
• The molar ratio between Cu and O is 1:1, then the empirical formula: CuO

Tutorial
1. A compound contains 16.7 g of Iridium and 10.3 g of Selenium, what is its empirical
formula?
2. A compound was found to contain 24.74% (by mass) potassium, 34.76% manganese,
and 40.50% oxygen. Determine the empirical formula.
3. Ammonia reacts with phosphoric acid to form a compound that contains 28.2% nitrogen,
20.8% phosphorous, 8.1% hydrogen and 42.9% oxygen. Calculate the empirical formula
of this compound
4. A bromo-alkane contains 35% carbon and 6.57% hydrogen by mass. Calculate the
empirical formula of this bromo-alkane.
C= 12g/mol, H= 1g/mol, Br= 80g/mol.
 MOLECULAR FORMULA
A compound is 19.3% Na, 26.9% S, and 53.8% O. Its formula mass is 238 g/mol. What
is the molecular formula?

Solution:
• 1) We start by assuming 100 g of the compound is present. This turns the above percents
into masses.
• 2) Calculate moles:
Na ⇒ 19.3 / 23.00 = 0.84
S ⇒ 26.9 / 32.1 = 0.84
O ⇒ 53.8 / 16.00 = 3.36
3) Look for lowest whole-number ratio:
3.36 / 0.84 = 4
The empirical formula is NaSO4
Empirical formula weight of NaSO4 is 119

Therefore, the molecular formula is given as :

M.F = Molecular weight
Empirical Formula Weight
238 / 119 = 2
Na2S2O8.

Tutorial B
1. A compound is found to contain 50.05 % sulfur and 49.95 % oxygen by weight.
What is the empirical formula for this compound? The molecular weight for this
compound is 64.07 g/mol. What is its molecular formula?
2. On analysis, a compound with molar mass 60 g/mol was found to contain 12.0 g of
carbon, 2.0 g of hydrogen and 16.0 g of oxygen. What is the molecular formula of
the compound?
3. What is the empirical formula and molecular formula for lactic acid if the percent
composition is 40.00% C, 6.71% H, 53.29% O, and the approximate molar mass is
90 g/mol?

Percentage yield & Purity

The quantity of product that is calculated to be produced when the entire limiting
reactant is used up is called the theoretical or calculated yield
The quantity of product that is actually produced through the reaction is called the actual
yield.
• The percentage yield is calculated using this formula:

Example 1:
For a reaction: 2H2+O2→2H2O.
Consider the case where 5 g of H2 reacted with 50 g of O2. The actual yield is found to be
40 g. Calculate the theoretical yield and percentage yield.
 No. of moles of H2 present: 5/2=2.5moles
No. of moles of O2 present: 50/32=1.56moles
Since 2.5 moles of H2 reacts with 1.25 moles of O2, there is an excess of O2. H is
the limiting reactant.

2.5 moles of H2 will yield 2.5 moles of H2O which equates to a theoretical yield of 45 g
of H2O.
Percentage yield: 40/45×100%=88.9%

Tutorial C
1. The medical drug aspirin is made from salicylic acid. 1 mole of salicylic acid gives 1
mole of aspirin. Given that the chemical formula for salicylic acid is C 7H6O3 and the
chemical formula for aspirin is C9H8O4.
In an experiment, 100.0 grams of salicylic acid gave 121.2 grams of aspirin. What
was the percent yield?

Percentage purity

Percentage purity of a substance can be calculated by dividing the mass of the pure
chemical by the total mass of the sample ( impure), and then multiplying this number by
100.
• Percentage purity indicates the amount of pure and impure substance present in a
sample.
• The percentage purity can be calculated by:
• % purity = Mass of pure
Mass of impure or Mass of Sample X 100