Structure and Bonding

Every living organism is made of organic

chemicals, (food, medicine, proteins, DNA..etc).
Therefore organic chemistry was defined
accordingly as chemistry of compounds found in
living organisms.
Nowadays chemistry of organic and inorganic is
unified the only distinguishing characteristic of
organic chemicals is that all contain the element
carbon, then organic chemistry is the study of
carbon compounds.
30 million presently known chemical
compounds, more than 99% of them contain
carbon.
 Carbon electronic structure and its consequent
position in the periodic table (group 4), can share
four valence electrons and form four strong
covalent bonds, carbon atoms can bond to each
other to form chain and rings i.e carbon can form
from methane one carbon atom to DNA 100
million carbons.

Organic chemistry touches the live of everyone.

Its study is a attractive undertaking.
Group 4A
Atomic structure: The nucleus
Nucleus (proton + neutron)

Electron orbitals

Atomic number Z
Atomic mass A
Isotopes
Atomic Structure: Orbitals
Orbital describes the volume of space around a
nucleus that electron is most like to occupy.

In other word orbital represents the space where

an electron spends most (90% - 95%) of its time.

There are four different kinds of orbitals denoted

s, p. d and f each with different shape. Of the four
only s and p are the most common in organic and
biological chemistry.
 The s orbitals are spherical with the nucleus at
their centre; p orbitals are dumbbell-shaped and
four of the five d orbitals are cloverleaf-shaped
Figure 1.

s orbital p orbital d orbital

Figure 1
 The orbitals in atom are organized into different
layers called electron shells.

Different shells contain different numbers and

kinds of orbitals and each orbital within a shell
can be occupied by two electrons.

The first shell contains only a single s orbital ,

denoted 1s and thus hold 2 es. The second shell
contains 2s orbital and three 2p orbitals thus holds
a total of 8 es. The third shell contains a 3s orbital,
three 3p and five 3d orbitals that is of capacity of 18
es.
 3d
3rd shell 3p
(capacity 18 electrons)
3s

Energy
2nd shell 2p
(capacity 8 electrons)
2s

1st shell
(capacity 2 electrons) 1s

The energy levels of electrons in an atom

 The three p orbitals at a given shell are consist of
two lobes perpendicular to x, y and z axices
known as px, py and pz each two lobes separated by
act region of zero electron known as node

Y Y
Y

X
X X

Z Z
Z
Atomic structure: Electron configurations
Lowest energy arrangement or ground state electron
configuration, of an atom is a listing of the orbitals
occupied by electrons. The arrangement prediction
based on the following rules:
Rule 1: The lowest energy orbitals fill up first,
according to the order 1s 2s 2p 3s 3p
4s 3d, the 4s orbital lies between 3p and 3d in
energy.
Rule 2: Only two electrons occupy an orbital, the two
electron in each orbital spin into two orientation
denoted as up and down i.e opposite spin.
Rule 3: If two or more empty orbitals of equal energy
are available, one electron occupies each with spins
parallel until all orbitals are half- full.
Some examples of how these rules apply shown in table below

Element Atomic number configuration

Hydrogen 1 1s

Carbon 6 2p
2s
1s
Phosphorus 15 3p

3s

2p
2s
1s
Problem: Give the ground state electron
configuration for each of the following elements:
a) Oxygen (b) Silicon ( c) Sulfur
Development of Chemical Bonding Theory
1885 Kekule and Arhibald Couper proposed that
in all its compounds, carbon is tetravalent-it
always forms four bonds when joins other
elements to form stable compounds.
Carbon atoms can bond to one another to form
extended chains.
Later the possibility of multiple bonding between
atoms was suggested C-C triple bond in acetylene,
C-C douple bond in ethylene.
Kekule add an other major advance that carbon
chain can joined back to form a ring.
The four bond of carbon sit at the corner of
regular tetrahedron, with a carbon in the centre.
 Bonds in plane of page
Bonds moving back of page

H C
H
H

Bond coming out of plane

 Why do atoms bond together? How bonds can be
described electronically?
Atoms bonds together because the compound
that result is lower energy and thus more stable
than the separate atoms.
Energy flow out when bond made and if we need
to break bond energy required.
Atoms usually seek to complete their outer shell
or the valence shell with 8 electrons (Octet) for
the special stability of the noble-gas elements of
group8A in periodic table: Ne(2+8); Ar(2+8+8);
Kr(2+8+18+8).
 The Ionic bond:
The alkali metal in group1A, for example achieve a
noble-gas configuration by losing single s e from
their valence shell to form cation (electropositive),
they said to be of low ionization energy. (ionization
energy is the tendency of an atom to loose electron)
Halogens in group 7A accept a p electron to fill the
valence shell and made anion (electronegative), they
said to be of higher ionization energy (impossible to
lose electron).
Attraction of opposite charge result is Na+ Cl- joined
by ionic bond (electropositive to electronegative.
Covalent bond:
Elements in the middle of periodic table e.g in
CH4 the bond is not ionic because its too much
energy for carbon (1s2 2s2 2p2) to gain or lose four
es to achieve noble-gas configuration.
Carbon bond by sharing electrons this bond
proposed by Lewis 1916 is called covalent bond.
A simple way to represent covalent bonds to use
what called Lewis Structures or electron-dot
structure i.e valence electrons represented as
dots.
Each atoms achieved an Octet ( 8 es) and two for
hydrogen to similar to noble-gas.
H
H C H H N H H O H
H H
 The simpler representation of covalent bond is
Kekule structures or Line-bond structures, in
which a two-electron covalent bond is indicated
as line between atoms.

H H

H C H
H N H H O H H C O H

H H H
ammonia water
methane methanol

Numbers of covalent bonds an atom forms

depend on how many additional valence electrons
it need to reach a noble-gas configuration.
Hydrogen (1s1) carbon (2s2 2p2) nitrogen (2s2 2p3)
oxygen (2s2 2p4) Neon configuration is (2s2 2p6)
 Non bonding
Lone-pair electrons

C
N Cl H O

Four bonds Three bonds One bond One bond Two bonds

Valence electrons that are not used for bonding are

called lone-pair electrons or nonbonding electrons
e.g nitrogen, oxygen and halogens.
In line structure usually the lone-pair electrons
omitted but you still need to keep them in mind since
they are crucial in chemical reaction.

H N H H O H

H
The nature of the chemical bonds:
Valence bond theory
How does electron sharing lead to bonding between
atoms?
Two models describe covalent bond:
1) Valence bond theory
2) Molecular orbital theory
Valence theory is the most easily visualized.
According to this theory a covalent bond form when
two atoms approach each other closely and a singly
occupied orbital (atomic orbital) of one atom overlaps
a singly occupied orbital of the other atom. The
electrons are then paired in an overlapping orbitals
(molecular orbital) and attracted by both nuclei thus
bonding the two atoms together.
 H + H H H

1s 1s H2 molecule
H-H bond formed by overlapping of two 1s orbitals of
two hydrogen atoms (bond length 0.74 , 1 = 1o-8 cm).
Such bond formed by the overlap of two atomic orbitals
along a line drawn between the nuclei called () bond.
Sigma bond has cylinderically symmetrical shape
During the bond-forming reaction 2H H2
104 Kcal/mol energy is released, i.e H2 is 104 Kcal/mol
less energy than the starting 2H.
This means the product H2 is more stable than the
reactant and H-H has bond strength of 104 Kcal/mol in
other word we have to put 104 Kcal/mol energy to break
H-H bond.
 The distance separate the two nuclei in the H2
molecule is called the bond length, which is a
distance just enough to prevent repletion of the
two positive nuclei and allow the overlapping for
bond formation.
Every covalent bond characterize by bond
strength and bond length
2H H2
Two hydrogen atoms
Energy

Released when bond forms

104 kcal/mol
Absorbed when bond breaks

H2 molecule
 Another example formation of fluorine molecule (F2)
Fluorine electronic configuration:
1s2 2s2 2px2 2py2 2pz1

Outer shell has 7es

It could be seen that one of the p orbitals has an
unpaired electron available for bond formation.
Overlap of this p orbital with another p orbital of another
fluorine will lead to bond formation.
Two possibilities are available for such overlap ( A head on
fashion or a side ways fashion.
The head-on overlap of fluorine atoms result in a bond
with the same general shape as H-H bond i.e cylinderically
symmetrical about the line joined the two nuclei.
 A head-on fashion

Aside ways fashion

 F-F bond length is 1.42 and strength of 38
Kcal.
These two examples show that a covalent bond
results from overlap of two atomic orbital to
form molecular orbital occupied by a pair of
es.
Each kind of a covalent bond has a
characteristic length and strength
Shapes of molecules
Hybridization-sp3 hybrid Orbitals and the structure
of methane (tetrahedral hybridization)
The bond in both hydrogen molecule and
fluorine is straightforward, but the slightly more
complicated bonding in the organic molecules
with tetravalent carbon atoms.
C6 1s2 2s2 2px1 2py1 2pz (carbon lowest energy
ground state configuration)
Carbon promote on of the 2s electron to 2p orbital
and move to excite state (higher energy state).
The excite state carbon has four unpaired es
 Methane, CH4 carbon has four valence es (2s2 2p2) and
forms four bonds.
Carbon used two kinds of orbitals for bonding, 2s and
2p accordingly we expect methane to have two kind of
C-H bonds but in fact all the four C-H bonds in
methane identical and are oriented towards the
corner of tetrahedron.
The s and p orbital hybridize to form equivalent
atomic orbitals with tetrahedral orientation and
called sp 3hybrid (4 sp3 orbitals).
The 4 sp3 orbitals to be a part are arrange directed to
the corners of tetrahedron.
The angle between each two is 109.5
Overlap of each sp3 hybrid orbital of carbon with an s
orbital of hydrogen result in methane.
 2s

2py

2pz Hybridization

Four tetrahedral sp3 orbitals

2px

An sp3 orbital
 The C-H bond has the bond strenght of 104
Kcal/mol aand the bond length of 1.09 and angle
between the any 2 C-H bonds is the tetrahedral
angle 109.5.
C-H bond in methane is cylinderically
symmetrical (sigma bond)

109.5
H
H C
H H
The structure of ethane and other alkanes
In ethane because C is attached to 4 other atoms
its also uses sp3 hybrid orbitals to attach itself to
the other carbon and the 3 hydrogen.
The C-H bonds similar to that in methane ( abit
weaker being 98 Kcal/mol for ethane while 104
Kcal/mol for methane).
C-C 1.54 length and 88 Kcal /mol sp3-sp3.
All the bond angles in ethane are tetrahedral
angle i.e 109.5
 109.5
H
H C H
H C H
H

1.54
Sp2- hybridization(Trigonal hybridization)
structure of ethylene
H H
C C
H H
H H C C
H H
In stead of sp3 hybrid imagine only 2s orbital
combines only two of the three available 2p
orbitals. Three sp2 hybrid orbitals result and one
2p orbital remain unchanged.
The three sp2 orbitals to be a part lies in a plane at
angle of 120 to one another i.e a trigonal
arrangement, with left p orbital which
perpendicular to the sp2 plane.
 sp2
2p
90 120

sp2

p
sp2 sp2
Side view Side view
 Overlap of 2 of the sp2 hybrid orbitas with s orbital of
H and the 3rd sp2 orbital with the sp2 hybrid orbital of
the other carbon will give.
H H Sp2-s
C C
C C H
H
Sp2-sp2

Each carbon has still a p orbital. This orbital consist of

two lobes one above and one below the plane of the 3
sp2 orbitals. Overlap of the p orbital of the two carbon
atoms give another bond called bond (pi bond),
consist of two part e cloud above and below the plane.
-bond formed by side way overlap of the 2 p orbitals ,
then its weaker than sigma bond.
 The side way overlap of the p orbitals can only
occur when the 2 C carbon and the 4 h lie in one
plane, therefore ethylene is a flat molecule.
C-H bond is 1.08.
C-C double bond is made of a strong single bond
() and a weak bond. It has total energy of 146
Kcal, C-C distance in ethylene is less than ethane
it is 1.34.
Double bond is shorter and stronger than single

bond.

C C
Sp-hybridization(Digonal): structure of acetylene
In addition to its ability to form single bond by
sp3 hybridization and double bond by sp2
hybridization, carbon can form a 3rd type of bond
called triple bond thro sp hybridization as in the
case of acetylene
H C C H
C6 1s 2s px py pz Ground satate C

promotion

excite state
Sp orbital with more s character than sp2
 To be as a part as possible, the two sp orbitals lie a
long a straight line that passes through the carbon
nuclues at 180 angle. p

180
sp

sp
p

Overlapping of the two sp orbitals one with the s

orbital of the hydrogen and the other with the sp
orbital of the other carbon will give

H C C H
 Each carbon left with 2p orbitals, each p orbital
consist of two lobes perpendicular to the line
joined the two carbon nuclei and to the axes of
the other p orbital and contain a single electron.
Overlapping of the p orbitals of one carbon with
the other carbon will form 2 bond each of
electron cloud of 2 es making cylindrical sheath
about the line join the two nuclei.
 Triple bond is made of strong and 2 weak bons
of total strength 198 Kcal. It stronger than double
bond of ethylene (146 kcal) or the C-C single bond
of ethane (88 Kcal) and it is shorter than both 1.21
.
C-H in acetylene is 1.06, even shorter than C-H of
ethylene because sp orbital is small because of
the great s character.
 Hybridization of other atoms:
Nitrogen and formation of ammonia:
The covalent bond is not only restricted to carbon
compounds. Other elements can also form
covalent bonds although the situation may be a
bit complex.
Let us look NH3 as an example of covalent
bonding involving Nitrogen
N7 1s 2s px py pz ground state

Sp3 hybridization
4 sp3 hybrid orbital
3 containing one e each and the
4th contain 2 es
 Sp3 orbitals of one electron can now form a covalent
bond with three hydrogen atoms.
Experiment showed that H-N-H angle is 107.1, which
near to 109.5 of the tetrahedral value 109.5 which
confirm that the shape of the ammonia molecule is a
tetrahedron, hydrogen occupies three corners and the
4th corner occupied by the unshared electron.

N
H H
H

107.1
 The unshared es can be donated to electron deficient
reagent eg an acid H+ then ammonia is a base.
NH3 + HCl NH4+Cl-
The bond angle (107.1 ) slightly smaller than
tetrahedral angle 109.5, this because the unshared
electron larger in size than H, then repel and compress
the other N-H bonds, if H replaced by CH3 the angle
almost 109.5 e.g trimethylamine.

N
H3C CH3
CH3

109.5
 The N-H bond in NH3 is 1.01 and its strength is 103
kcal.
Like carbon nitrogen can form sp2 and sp hybrid
orbitals e.g

H3C C N
H H 3C C C N
CH3 H2

Sp2-hybridization
Sp-hybridization
Oxygen and formation of water molecule
Let us consider the oxygen in the water molecule
O8 1s 2s px py pz oxygen at ground state

It may be expected oxygen will form 2 covalent bond

with 2H atoms by using 2p orbitals which
perpendicular to each other , then H2O may
expected to have O-H of 90.
O H

H
 In fact this picture is wrong. O-H angle was found
to be 105, nearly the tetrahedral angle.
Oxygen hybridizes its 2s orbital with the 3p
orbitals to give 4 sp3 hybrid orbitals

O8 1s 2s px py pz

Sp3 hybridization

4 sp3 hybrid orbitals

2 with 2es each and
other 2 one electron each
 Overlapping of 2 sp3 orbitals with two hydrogen
gives H2O.
The 2 H in water occupy 2 corners of tetrahedron
while the other 2 corners are occupied by
unshared pair of electrons.

H
O
105
H
The O-H angle is smaller than 109.5, the
tetrahedral angle because the 2 pair of unshared
es compresses the angle together.
If the 2 H replace by CH3 angle almost 109.5
Boron and structure of BF3
Boron 5 1s 2s px py pz at ground state

excite state of boron

Sp2 hybridization

BF3 is flat with 120 with vacant p orbital

Beryllium in beryllium chloride BeCl2
B4 1s 2s px py pz at ground state
promotion

excite state

Sp hybridization

Beryllium chloride is linear molecule of 180 angle

because its sp hybridization
B
sp sp

180
Formal charges:
This is the charge (+) or (-) which we must put on
an atom covallently bonded to another atom
when the no. of es in the outer most shell are
bigger or smaller than the no. of es which the
atom has when it is on its own.

H N H Charge is zero it is neutral molecule

H

H N H Ammonium ion charge +1

H
H O H No charge neutral molecule

H O H

Hydronium ion protonated water charge (+1)

O
O N
(-1)
O
(0)
(+1)
 H3C C N O

Acetonitrile is a solvent have +ve charge on N and a ve charge

on O although acetonitrile as a whole is electrically neutral ,
specific atoms are charged. Such molecules are called dipolar
molecules
F. C = 0
O

Nitromethane
H3C N
O
F. C = -1

F. C = +1
Formal -ve charge on oxygen
Forma +ve charge on sulphar

H
H
O C
S H
H
C
H H

Dimethylsulphoxide (solvent)
 Number of Number of bonding Number of non
F.C = valenceElectron - 2 - bonding electrons
electrons
in free atom

Problems:Calculate the formal charge on the atoms with

asteriks(*) and indicate shape of the molecules.
O
H * *
H3C N
H3C C O H3C N C
* *
*
H
acetate methylisocyanide
methylamine
O
* S *
*
O H2C N N diazomethane
* Sulphur dioxide
Resonance: Mesomerism
Let consider carbonate ion CO32- and acetate ion.

O O O

C C C
O O O O
O O
1 2 3

3 structure can be drawn for the carbonate ion 1, 2,

and 3 the difference between the three is the
arrangement of the electrons.
 Whenever we can draw 2 or more structure to
represent a molecule and the difference between
structure is the position of a pair of es we say
there is a resonance.
Structure of carbonate ion is neither 1 nor 2 or 3
but is a hybrid of the 3 structures. Each of the 3
structures is said to contribute to the hybrid.
The bond between the C and O is neither single
nor double but something in between.
-
All C-O bonds are equivalent are 1.27
where C-O is 1.35 and C=O is 1.20 . O

C
O O

 Acetate ion electrostatic map shows equal ve
on both oxygen
 The three structure of the carbonate and the two
structure of the acetate ion are called resonance forms
and relationship between them indicated by the
double head arrows between them.
The only difference between them is the position of
the electrons and the non-bonding valence
electrons.
Rules of resonance forms:
Rule 1: individual resonance forms are imaginary not
real, the real form is a resonance hybrid of the
different forms.
Rule 2: resonance forms differ only in their placement of
or non bonding electrons neither the hybridization
nor the position of atoms change in resonance forms
only the position of the electrons or non bonding
electrons
 The movement of the electrons or bonds
represented by curved arrow

O
O
C
C
O O
O O
Rule 3: Different resonance forms of a substance
dont have to be equivalent e.g acetone when
converted to anion by strong base

O O O
Base
H3C C CH3 H3C C CH2 H3C C CH2
 Rule 4: Resonance forms obey normal rule of
valency, e.g acetate ion

O O
H 3C C O H 3C C O

H 3C X
C O
 Rule5: The resonance hybrid is more stable than
any individual resonance form, general speaking
resonance lead to stability in other word the
larger number of resonance forms substance is
greater stability
Polar covalent bond, Electronegativity:
The C-C bond in ethane is covalent bond the
bonding two electrons are shared equally between
the symmetrical carbons.
Some bond between two atoms said to be polar
bond this means that the bonding electrons were
attracted by one atom more than the other which
result in that the electrons distribution is not
symmetrical
+ -

X : X X : Y X+ : Y-

Covalent bond Polar Covalent bond ionic bond

 The ability of atom to attract the electrons of the
covalent bond towards it is called
electronegativety (EN).
The most electronegative atoms are located in the
upper right-hand corner of the periodic table.
 As lose guide, bonds between atoms whose
electronegativety difference less than 0.5 are non-
polar bond, whereas atoms whose
electronegativity difference 0.5 2.0 are polar-
bonds. Atoms with the difference more than 2 are
largely ionic (see EN on periodic table).
C-H bond (C EN 2.5) (H EN 2.1) non-polar.
C-O (O EN 3.5) polar bond C-N (N EN 3.0) polar
Bond in these polar bonds C has + whereas O and
N are - as they withdraw electrons towards them.
C-Li ( Li EN 1.0) polar bond C has - whereas Li +
(partial charge)
Direction of bond polarity with the head electron rich
 When speaking about ability of atoms to polarize
bond we use the term inductive effect which is the
shifting of electrons in bond in response of
electronegativety of nearby atoms.
Metals such as Lithium and magnesium inductively
donate electron whereas non-metals such as oxygen
and nitrogen inductively withdraw electrons.

Problem 1 : Which element in each of the following pairs

is more electronegative
a) Li or H b) B or Br c) Cl or I d) C or H.

Problem 2: Use the +/- rule to show the direction of

expected polarity for each of the bonds indicated.
a) H3C-Cl b) CH3-NH2 c) NH2-H
d) CH3-SH e) CH3-MgBr f) CH3-F
Polar covalent bond, dipole moment( )Mu:
As individual bonds are polar, molecules as a whole
are polar their polarity is the sum of the bond polarity
and lone pair contribution (H2O and NH3).
Strong polar substance are soluble in polar solvent
like water.
This net polarity of a molecule is measured by
quantity called dipole moment, (Greek Mu)
measure in unit called Debye (D).
The dipole moment is equal to magnitude of the
charge (Q) (in esu )at each end of the molecule dipole
time the distance separate (r) the two charge in (1 =
1o-8 cm)
= Q (e) X r
The dipole moment of HCl is = 1.08 D
All molecules that have polar bonds will have dipole moments
Br-Br = 0
O-O = 0
H-F = 1.75 D
NF3 = 0.24
The H-F (1.75 D) small molecule but has high this is due
to the high electronegativity of F

Dipole moment () of some compounds

 In carbon tetrachloride although the bonds are
polarized bonds but the whole molecule = 0.
This because of the tetrahedral arrangement
which result in the vector sum of the polarization
to be zero.

Cl
Cl Cl
C

Cl
=0
 In comparing NH3 with NF3 ammonia = 1.47
whereas NF3 is only 0.24 although F is strong
eelectronegative, this is due to the direction of
unshared electrons contribution.

N N
H H F F
H F
= 1.47 = 0.24

We are going to see with time that the physical

and chemical properties of compounds depends
to large extend on the polarity of bonds.
Bond dissociation energy:
Homolysis and heterolysis of covalent bonds
There are three way in which a covalent bond may
break or cleave : 1) homolysis (lysis = break, homo
greak work means same)
two neutral
A B A + B
fragments called
free radicals
2) heterolysis (hetero = different)

A + B
A B Charged fragments
A + B
 The amount of energy consumed to cleave (break) a
bond is called BOND DISSOCIATION ENERGY (DH*)
and it equal to the energy liberated when a bond is
formed.
The amount of DH* depends upon the way that the
bond breaks i.e whether homolytically or
heterolytically.
Examples:
Bond Homolytic Hetrolytic
DH* Kcal/mol DH* Kcal/mol
H-H 104 401

H-F 135 370

CH3-Cl 84 227
 It could be noticed that homolytic bond
dissociation energies are considerably smaller
than heterolytic bond disociation energies.
Homolysis produces neutral particles which need
much less energy to separate them than oppositly
charged particles which need a great deal of
energy to separate them.
Then if bond dissociation mentioned without
specifying any of them this means its a homolytic
cleavage as its easy to occurs.
 We must not confuse bond disociation energy (DH*)
with another measure of bond strength called bond
energy (E). We said bond dissociation energy is the
energy required to break a specific bond in a molecule
CH3H CH3. + H. DH* = 104 Kcal/mol
CH3. CH2. + H. DH* = 106 Kcal/mol
CH2. CH. + H. DH* = 106 Kcal/mol
CH. :C: + H. DH* = 81 Kcal
It could be seen that each bond has specific bond
dissociation energy.
On the other hand bond energy E is a single
average value CH4 :C : + 4H. E (C-H) =
397/4 Kca/mol = 99.25 kcal/mol
 One of DH* uses is calculation of enthalpy change
H*

H H + Cl Cl 2HCl

DH* =104 DH* = 58 DH* 2(103)

+162 Kcal /mol -206 Kcal/mol
needed for bond cleavage is evolved in bond
formation
Overall the rxn from calculation is exothermic and
H* = (-206 +162) = -44 Kcal/mol this called heat of
reaction.
 Therefore we could express bond dissociation enery
and bond energy in the following way:
CH3H CH3. + H.
DH* = 104 Kcal/mol or H* 104 kcal/mol
While bond energy could be expresse as
CH4 :C : + 4H. E (C-H) H* = 397/4 Kca/mol =
99.25 kcal/mol
Physical properties and molecular structure
The physical properties such as melting point,
boiling point and solubility etc are based on the
structures of the substances and the forces
holding molecules and ions together.
What are these forces. How do they affect the
m.p., boiling point and solubilities of a
compounds
1) Ion-ion forces (inter ionic forces)
The m.p of a substance is the temp at which an
equilibrium exist between the well-ordered
crystalline state and the more random liquid
state.
 In an ionic compounds such as NaCl (Na+Cl-) each
+vely charge sodium ion is surrounded by 6 chloride
ions at both side, one above and below and in front
and back site arranged in a very regular way each ve
Cl- ion is also surrounded by 6 +ve sodium ions.

Cl-

Na+
 Sod. Chloride crystal The units are Na+ and
Cl- when liquified
A particular sod. Ion does not belong to any one chloride
ion, but is equally attracted to six chloride ion and the
same for chloride ion.
This electrostatic attraction forces will give an extremely
strong crystal. Hence a v. high temp is needed to overcome
the interionic force this give NaCl high m.p. (801)
 Also sodium acetate an ionic organic compound
CH3COO- Na + strong electrostatic forces hold +ve and
ve ions in the orderly crystalline structure.
Each sod. Is surrounded by vely charge acetate ion
and each acetate ion is surrounded by Na ion. A large
amount of thermal energy is required to break up the
orderly structure of the crystal into disorderly
structure of a liquid. As a result the temp at which sod.
Acetate melts is quit high, 324
The boiling point of ionic compounds are higher still,
so that most ionic organic cpds decompose before
they boil.
Boiling involve the breaking away from the liquid of
individual molecules e.g C2H5OH molecules or pairs
of oppositely charged ions e.g Na+ Cl-in Nacl or
CH3COO- and Na+ in Na acetate. Boiling occurs when
the vapour of the liquid equal the vapour pressure of
the atmospheric above it.
Intermolecular forces:
What kind of forces hold neutral molecules to each
other.
Like interionic forces, these forces are also
electrostatic in nature but weaker compared to
interionic electrostatic attraction.
There are 2 kind of intermolecular forces:
1) Dipole-dipole interaction : this is the attraction of
+ve end of polar molecule to the ve end of another
molecule.
In methyl chloride (CH3Cl) for example, relatively
positive methyl of one molecule is attracted to the ve
chloride of another molecule

1) H3C Cl
 As a result of dipole-dipole interaction, molecules of a
polar compounds are generally held to each other
more strongly than non-polar compounds of
comparable molecular weight.
2) Hydrogen bonding:
Hydrogen bonds especially strong dipole-dipole
attraction and found in compounds in which
hydrogen is bonded to strongly electronegative
elements.
The strong electronegative atom will attract the es in the
bond towards it leaving a +vely charged hydrogen
nucleus.
The attraction of +vely hydrogen of one molecule by the
ve charge of the electronegative atom of the second
molecule is called hydrogen bond and indicated by
broken line (..)

H F H F
 H
H H

H N
H N H N H O

H H H H

O O
N H

O Intramolecular H-bond

O
O

N O

O N
O

H O

intermolecular
 For hydrogen bonding to be important, the
electronegative atom must come from the group:
F, O and N. Only hydrogen bonded to one of these
elements are +ve enough, and only these elements
are ve enough for the necessary attraction to
exist.
The hydrogen bond strength 5 Kcal/mol and is
thus much weaker than the covalent bond.
Hydrogen bond account for the very high
differences in bp between compds having nearly
the same Mwt but one shows H-bonding while
other lack it
Compound Mwt bp

H 16 -162
H C H

H
H-O-H 18 100

CH3-O-CH3 46 -25

CH3CH2OH 46 78.5
 Compds whose molecule are held together by
hydrogen bonding are called associated liquids.
Their abnormally high bp is due to the energy
required to break the millions of hydrogen bonds
present despite the fact that only 5 Kcal of energy
is required to break a single hydrogen bond.
3) Van der Walls forces:
Polar compds molecules are held together by
dipole-dipole interaction, what forces, then
hold
together molecules of non-polar compds since
these compds can be present as liquids or even
solidified.
Example methane has m.p of -183 and bp of
-162. so methane has the m.p and bp which are
very small then force hold them v. small, its
force hold non-polar molecule is called Van
der Waals forces.
 Electrons are moving in an orbital, on the average, the
electron distribution in a non-polar molecule is
uniform over a period of time. At any given instant,
however , because electrons move, the electrons and
thus the charge may not be uniformly distributed,
electrons may in one instant be slightly accumulated
on none side of the molecule as a sequence a small
temporary dipole will occur.
This temporary dipole in one molecule can induce
opposite dipole in an other molecule result in
attractive forces between non-polar molecules which
makes possible either existance as liquids or solid
state
Van der waal forces operate at small distances in
between the molecule and hence increase with size
and surface thus depend on shape of the molecule.
 Temporary diploe and induce one
CH3 CH3
H3C C CH3 H 3C C CH2CH3 CH3CH2CH2CH2CH3
H
CH3

bp 9 bp 28 bp 36

All of these compds of comparable Mwt

Solubility:
Dissolution of a solid in a liquid is, in many
respects, like melting of a solid. The ordered
crystal structure of a solid is destroyed and the
result is the formation of a more disorderly
arrangement of the ions or molecules in solution.
As in melting energy is also required in
dissolution to overcome the interionic or
intermolecular forces
Where does the necessary energy come from?
The energy required to break the bonds between
the solute particles i.e ions and molecules comes
from the formation of new attractive force
between the solute and the solvent.
 Let us consider first the case of an ionic compd as
an example:
A great deal of energy is required to overcome the
powerful electrostatic forces holding together an
ionic lattice. Only H2O and few other highly polar
solvents dissolve ionic .
Considerably they do this by surrounding the +ve
and ve ions as they freed from the crystal surface.
Positive ions are surrounded by H2O molecules
with the ve end of the water dipole pointing
towards the +ve ions, the +ve charged ions
surrounded in exactly the opposite way


H
O Polar solvent
H

Crystal lattice
 The electrostatic attraction between the +ve ion
and the ve end of the water molecules and the
ve ion and the +ve end of the water molecules,
although relatively weak but in the aggregate they
produce enough energy to overcome both the
lattice energy and the interionic energy that
compd dissolves.
The surrounding of ions by solvent is called
solvation. When the solvent is H2O it is called
hydration.
The attractions between ions and dipoles of the
solvent are called ion-dipole bonds.
Water is superior solvent for ionic compounds,
because of the high dielectric constant ( ability of
solvent to separate oppositely charges ions)
Dissociation of non-ionic compds:
The solubility of non-ionic compds depends
chiefly on their polarity
Non-polar or weakly polar compds dissolve in
non-polar or weakly polar solvent.
Highly polar compds dissolve in highly polar
solvents.
A rule of thumb for predicting solubilities is that
like dissolve like
Methane dissolve in CCl4 because the force
holding methane molecule to each other and CCl4
to each other is van-der-waals interaction are
replaced by very similar force holding methane
and CCl4 molecules together.
 Neither methane nor CCl4 is soluble in H2O. The
highly polar water molecules held to each other
by the very strong dipole-dipole interaction
hydrogen bonds.
therefore could be very weak attraction between
polar H2O molecules and non-polar methane
molecules which shows no solubility of methane
in water.
In contrast, the highly polar ethanol C2H5OH is
quite soluble in H2O. Hydrogen bonds between
water and ethanol molecules can readily replace
hydrogen bonds between different ethanol
molecules and different water molecules
 H H
C2H5 C2H5
O H O
O H O
H O H
H
H

Ethanol molecules water molecules

Held together by H-bonds Held together by H-bonds

C2H5 C2H5
O H O H
H O H O
H
H

Ethanol and H2O molecules held together by H-bonds

 For liquid in liquids miscible is used rather than
soluble e.g ethanol is miscible with water.
Diethyl ether (C2H5-O-C2H5) and n-butanol
C4H9OH are functional group isomers. They have
equal solubility or miscibility in water but
C4H9OH have a b.p. 83 higher than
C2H5-O-C2H5.

CH3CH2CH2CH2 OH

H3CH2C O CH2CH3
Acids and bases:
There are a number of ways for defining an acid
and a base
The Bronsted-Lowry definition:
According to this definition an acid is a substance
that give a proton, and a base is a substance that
accept a proton.
When H2SO4 dissolves in H2O, the acid H2SO4
donates a proton to the base H2O to form an new
acid H3O+ and a new base HSO4-.

H2SO4 + H2O H3O + HSO4

Stronger acid Stroner base Weaker acid Weaker base

The equilibrium favour the weaker acid and base

 Likewise when the acid HCl reacts with base
ammonia. The new acid ammonium ion and the new
base Cl- are produced.

HCl + NH3 NH4 + Cl

Stronger acid Stronger base Weaker acid Weaker base
According to this definition, the strength of the acid
depend upon how readily it can give its proton and
the strength of the base depend on how readily will
accept the proton.
H2SO4 and HCl are strong acids since they can give
their protons readily and hence bisulphate and
chloride must be weak bases since they have little
tendency to hold on to a protons
 The product of the base when gain a proton is
called conjugate acid of the base (H3O+ , NH4+)
whereas the product of an acid when lose a proton
is called conjugate base of an acid (HSO4- , Cl-)

HCl + H2O H3O + Cl

acid base Conjugate acid Conjugate base
Organic acids:
Methanol and acetic acid contain hydrogen
bonded to electronegative oxygen (O-H).
Acetone contain hydrogen bonded to carbon next
to C=O (O=C-C-H).
Methanol contain OH and its a weak acid, acetic
acid contain OH to somewhat strong acid.
The acidity is due to the fact that the conjugate
base result from loss of a proton, contain a
negative charged stabilized by a strong
electronegative atom, oxygen.
Acetic acid conjugate base in addition is
stabilized by resonance.
 H H H H
- H+
C O C O

H H H

Anion stabilized by having

Pka = 15.54 negative charge on highly
electronegative atom

O O
O
- H+ C O
C O C O
H3C H3C
H 3C H

Anion stabilized by both having

Pka = 4.76 negative charge on highly
electronegative atom and by resonance
 The acidity of acetone is due to that the conjugate base result
from the loss of the a proton stabilized by resonance and
placed the negative charge on high electronegative atom

O O O
- H+ CH2
H3C C CH3 H3C C CH2 H3C C

Pka = 19.3
The Lewis definition of an acid and base
All compds containing hydrogen can be included
under the Lowry-Bronsted concept of acidity.
Lewis acid and base definition is not limited to
acid or base donate or accept aproton,
Lewis acid is substance that accept electron pair
whereas a base is a substance that donate electron
pair, the donated pair is shared between acid and
base in a covalent bond.
Boron trifluoride has only six es in the outer shell
and has an empty or vacent p-orbital and need a
pair of es to complete its octet (therefore Lewis
acid)
 While diethyl ether has a pairs of unshared es
(therefore Lewis base), therefore boron trifluoride
and diethyl ether can react together to give an acid
base complex.

F
C2H5 F C2H5
+ O F B O
B
F C2H5 F C2H5
F

Lewis acid Lewis base Borontrifluoride-

etherate complex
 Aluminium trichloride (AlCl3) also has six es in its
outer shell and is a powerful Lewis acid.

CH3
CH3
+ HN
AlCl3 Cl3Al NH
CH3
CH3

The transition metal compounds such as ZnCl2,

FeCl3 and SnCl4 are also excellent Lewis acids. The
bonding in such compds is more complex, since it
involves d-orbital hybridization, but like other
Lewis acids they have low-energy orbitals that can
accept es pair
 Finally, to be acidic in the Lowery-Bronsted sense,
the molecule must contain a hydrogen. The
degree of acidity depends on the a)
electronegativety of the atom to which the
hydrogen is attached and b) its size.
Thus within a given raw of periodic table acidity
increase with electronegativety e.g
H-CH3 < H-NH2 < H-OH < H-F also H-SH < H-Cl
With a given family acidity increase as the size
increases e.g HF < HCl < HBr < HI similarly
H-OH < H-SH < H-SeH (hydrogen selenide).
In the compds to which H is attached to a halogen
(halogen family), acidity increases as the size
increases
Isomerism:
Compounds that have the same molecular
formula but different chemical structures are
called isomers and the phenomenon is called
isomerism
isomerism

Structural stereoisomerism
isomerism

Optical isomerism Geometrical

isomerism
Structural isomerism:
This isomerism is due to the difference in
structure and is exhibited in 3 different ways
a) Chain isomerism: compds here differ in the
arrangement of the carbon skeleton e.g C4H10.
H
H C CH CH CH H3C C CH3
3 2 2 3
n-butane CH3
isobutane
b) Position isomerism: Compds here have the same
carbon skeleton but differ in the position
occupied by a substituent gp e.g H
H3C C CH3
CH3CH2CH2OH
OH
n-propyl alcohol Isopropyl alcohol
C) Functional group isomerism:
Compds here have different functional gp

CH3CH2 OH H3C O CH3

Ethyl alcohol Dimethyl ether

Stereoisomerism will be taken later in coming

chapters.
 Analysis of organic compounds
Before trying to analyse an organic compound we
must purify it: common methods for purification
are:
1) Recrystallization from suitable solvents
2) Distillation (a) at atmospheric pressure (b) at
reduce pressure
3) steam distillation
4) chromatography
Qualitative analysis
The elements commonly found iin organic
substances are carbon (always: by definition),
hydrogen, oxygen, nitrogen, sulphar, halogen,
phosphorus and metals

Test for carbon and hydrogen:

Ignition of the sample and formation of a residue
this means that the sample contains carbon
condensation of water from the vapour confirm
presence of hydrogen.
Another way is heating in test tube the sample in
presence of CuO (cupric oxide) which result in
CUO
C, H CO2 + H2O
 CO2 can be tested for by lime water (Ca(OH)2) to
give CaCO3 (insoluble) white precipitate.
H2O condense as water droplets on the cooler part
of the test tube.
 Nitrogen, Halogen and sulphur
These are all detected by the Lassaigne sodium
fusion test.
In this test compounds containing these elements
fused with sodium which result in convert them
from covalent bonded elements to ionic bonded

Na2S Sod. sulphide

Na, Fuse
C, H, O, N, S, X NaCN Sod.cyanide
in dry test tube
NaX (X = Cl, Br, I, F)

Sod.halide
Test for sulphur:
Na2S (from fusion) + Pb(CH3COO)2 PbS
Acidified first by acetic acid black precipitate

Test for nitrogen:

Nitrogen converted into sod, cyanide is tested for by
firstly adding ferrous sulphate and then ferric
chloride, the bright blue colour of ferric
ferrocyanide appears
NaCN + Fe2+ Fe(CN)2 ferrocyanide
Fe(CN)2 + Fe3+ + Na+ + 4 CN- Na Fe[Fe(CN)6]
sod ferric ferrocyanide

Prussian blue
 -4
N
N
N C
C C
Fe
Na+ C C
Fe3+
C N
N
N

Sodium ferric ferrocaynide

Tests for halogen:
The halogens as halide ions are tested for by addition
of AgNO3 to a solution of the ions acidified with
HNO3. A ppt of AgX is formed if there is any halogens.
AgNO3 + Na+X- AgX

Phosphorous: In the fusion mixture phosphorous is

converted into metallic phosphate which can be tested
for by inorganic tests for phosphates
Test for phosphates: All phosphates give a bright
yellow ppt of ammonium phosphomolybdate when
dissolved in HNO3 and warmed (not boiled) with
ammonium molybdate solution.

(NH4)3PO412MoO3xH2O
Quantitative analysis
C and H are estimated by burning a known weight
of a substance with CuO at about 900 where by
C [O] CO2 this absorbed by a known wt of
dry NaOH weighed before and after the
combustion.

H [O] H2O thus absorbed by Mg perchlorate

Weighed before and after combustion.
From the weight of CO2 and H2O obtained the % of
C and H can be calculated.
Nitrogen: by the Dumas method
In the Dumas method, N is oxidized by CuO to
nitrogen oxides and the nitrogen oxides thus
obtained are reduced back to nitrogen by Cu and
the nitrogen obtained collected and its volume
converted to vol at STP and from this volume the
weight and consequently the % of nitrogen
Determined.
The halogen, sulphur and phosphorous are estimated
by the oxygen flask combustion method
Determination of oxygen is difficult usually its %
composition determined by the difference when other
elements in a compound were determined.
Calculation of the Empirical formula and
molecular formula
The empirical formula of a compound is the simple
ratio of atoms present in such compound.
The molecular formula is the actual number of atoms
present in a compound.
Suppose we have a new compound whose elemental
analysis gave the following:
C 67.95%
H 5.69%
N 26.2%
Total 99.84
Since the total of these percentage is close to 100% the
small difference is experimental error that is there is no
other element like oxygen.
 To calculate the empirical formula:
1) Convert the % mass of each element to moles by
dividing the % mass with atomic weight of the
particular element
C = 67.95/ 12 = 5.66 mole
H = 5.69/1 = 5.69 ,,
N = 26.2/14 = 1,87 ,,
2) Divide the mole ratios with the smallest number
and then round ration to the nearest whole number
C: 5.66/1.87 = 3.03 which 3
H: 5.69/1.87 = 3.02 which 3
N: 1.87/1.87 = 1
Thus the empirical formula of the compound is C3H3N
To find the molecular formula it is necessary to know
the molecular weight.
 The older methods for determining molecular wts are
1) vapour density method
2) Freezing point depression method
3) Elevation of b.p
However these methods are not used now, and the most
accurate method to find Mwt is mass spectroscopy.
Eample 1:
Histidine an amino acid isolated from protein gave the
following elemental analysis: C, 46.38%, H, 5.90%, N,
27.01%.
Total is 79.29 in this case the difference is oxygen i.e
100- 79.29 = 20.71%
 To get the ratios as moles divide by atomic weight:
C: 46.38/12 = 3.86 H: 5.9/1.0 = 5.90 N: 27.29/14 = 1.94
O: 20.71/16 = 1.29
Now divide with the smallest number which is 1.29
C: 3.86/1.29 = 2.99 X 2 = 5.89
H 5.90/1.29 = 4.57 X 2 = 9.19 9.0
N: 1.94/1.29 = 1.5 X 2 = 3
O: 1.29/1.29 = 1.0 X 2 = 2
If the ratios numbers are too far multiply with factor
(2 or 4).
In the above example we need to multiply by 2 and
the empirical formula is C6H9N3O2
 Mass spectroscopy showed that histidine has the
molecular weight 155
The empirical formula weight 155, therefore
molecular formula of histidine is also C6H9N3O2.
The way in which these atoms are joined together
to give histidine is called the molecular structure
of histidine this determine by both physical and
chemical methods
HO HO
O O
H2N H2N

Histidine
HN N N
N
C6H9N3O2 H
C6H9N3O2
Exact Mass: 155.07
Exact Mass: 155.07
Mol. Wt.: 155.15
Mol. Wt.: 155.15
C, 46.45; H, 5.85; N, 27.08; O, 20.62
C, 46.45; H, 5.85; N, 27.08; O, 20.62
Problem1:
Nutra Sweet is 57.14% C, 6.16% H, 9.52 N calculate the
empirical formula and find the molecular formula (Mwt
294.3 g/mol).
Problem2:
Citral is a chemical responsible for the odour of lemon.
Combustion analysis shows that citral to contain 78.9%
C, 10.6% H. Assuming that the reminder I oxygen what is
the empirical formula of citral.
If citral has a molecular wt of 152 what is its molecular
formula
 NH2
O

N
N
N
N N
N

Mol. Wt.: 313.31

C, 53.67; H, 4.83; N, 31.29; O, 10.21

C14H15N7O2