Organic Chemistry

Organic and inorganic

Organic compounds are not limited to nature.
Organic compounds are compounds that contain carbon.
Why is carbon so special?
Carbons position in the periodic table
Li Be B C N O F
Carbon is in the center, to the left are elements that give up
electrons easily and to the right are elements that have a
tendency to accept electrons.
Carbon neither readily gives up or accepts electrons, instead it
shares electron with other Carbons.
Bond forming and bond breaking depend on electrons that are
shared, and in turn depend on the atom that they belong to.

The structure of Atom

Atom consists of a tiny dense nucleus
surrounded by electrons.
Nucleus contains positively charged protons
and uncharged neutrons.
Electrons are negatively charged.
Amount of positive charge on the proton is
equal to amount of negative charge on neutron.
Electrons move continuously and this kinetic
energy counteracts the attractive force of
the positively charged protons.
Protons and Neutrons have the same mass and
are 1800 times more massive than an electron.
Mass of an atom is defined by the nucleus and
the volume is defined by the electrons.
The atomic number of an atom is the number
of protons in the nucleus. Which is unique to a
particular element.
The mass number of an atom is the sum of its
proton and neutrons.

Nucleus (protons and Neutrons)

Electron cloud

 All atoms have same atomic number but not the same mass number.
The atomic number of Carbon is 6.
12

13

14

12C 98.89%
13C 1.11% are called isotopes.
14C is also an isotope, it is radioactive with a half life of 5730 years.

How are electrons distributed in an Atom?

Erwin Schrodinger proposed that the electrons in an atom can be
thought of as occupying a set of concentric shells that surround the
nucleus.
The first shell is the closest to the nucleus.
Each shell contains subshells known as atomic orbitals.
Each atomic orbital has a characteristic shape and energy and
occupies a characteristic volume of space.
The first shell consists of an s atomic orbital; the second shell
consists of s and p atomic orbital; the third s,p and d; fourth and
higher shells consist of s,p,d and f atomic orbitals.

Energy Level

Sub-shells
orbital

No. of A

1 (K-shell)

2 (L-shell)

s, p

1, 3

8 (2 in s, 6 in p)

3 (M-shell)

s, p, d

1,3,5

18 (2 in s, 6 in p, 10 in d)

4 (N-shell)

s, p, d, f

1,3,5,7

32 (2 in s, 6 in p, 10 in d,
14 in f)

Occupation of orbitals

Number of Electrons
1

Electrons fill orbitals in a way to

minimize the energy of the atom.
Therefore, the electrons in an atomfill
the principal energy levels in order of
increasing energy (the electrons are
getting farther from the nucleus)
Aufbau principle

http://chemwiki.ucdavis.edu/Inorganic_Chemistry/Electronic_Configurations

Pauli exclusion principle No more than two electrons can occupy each atomic orbital
The two electrons must be of opposite spin.
Hunds rule When there are two or more atomic orbital with the same energy, an
electron will occupy an empty orbital before it will pair up with another
electron.

B (Z=5) configuration: 1s2 2s2 2p1

C (Z=6)configuration:1s2 2s2 2p2
N (Z=7)configuration:1s2 2s2 2p3
O (Z=8)configuration:1s2 2s2 2p4
F (Z=9)configuration:1s2 2s2 2p5
Ne (Z=10)configuration:1s2 2s2 2p6

Although theAufbau ruleaccurately

predictsthe electron configuration of most
elements, there are notable exceptionsamong
the transition metals and heavier elements.
The reason these exceptions occur is that
some elements are more stable with
fewerelectrons in some subshells and more
electrons in others. A list of the exceptions
to the Aufbau process is given below.

 The electron in the inner shells are called the core electrons.
The electrons in the outermost shell are called the valence electrons and
participate in chemical bonding.
Elements in the same column of the periodic table have the same number
of valance electrons.

https://en.wikipedia.org/wiki/Valence_electron

Ionic and Covalent Bonds

An atom is most stable when the outermost shell is either filled up or has
eight electrons and it has no electrons of higher energy.
Lewis theory- Atom will give up, accept or share electrons in order to
achieve a filled outer shell, that contains eight electrons. The octet rule.
Lithium (Li) has a single valence electron in its 2s orbital which it loses
easily to get a filled outer shell.
All elements in the first column of the periodic table readily loses an
electron.
Li. --

Li+

e-

Fluorine has seven valence electron, therefore it readily accepts an

electron to complete its outer shell by having eight electrons, forming F-,
this is true for all elements in group VII.

: F + e- ------- :F:- Fluoride ion

Hydrogen can both lose or gain an electron.

Ionic bonds are formed by attraction between ions of opposite charge.

Sodium easily gives up electron and chlorine readily accepts electron.
When they are mixed together the result is crystalline NaCl or table salt.
Attractive forces between opposite charges are called electrostatic
attractions and a bond formed as a result is called an ionic bond.

Covalent bonds are formed by sharing a pair of electrons.

An atom can achieve a filled outer shell by sharing a pair of electron.

Two fluorine atoms can attain filled second shell by sharing their unpaired
valence electrons.
A bond formed as a result of sharing electrons between two nuclei is called a
covalent bond.

.
.
:F +
F : ----- :F __ F:

Covalent Lewis structure for

methane

Covalent Lewis structure for

ammonia

Polar Covalent Bonds

The atom that share bonding electron in F-F and H-H covalent bonds are
identical. Therefore they share the electrons equally. Such bonds are called
nonpolar covalent bonds.
The bonding electrons in HCl, H2O and ammonia are more attracted to one
atom than to another as the atoms that share the electrons are different
and have different electronegativity. Electronegativity is a measure of the
ability of an atom to pull the bonding electrons towards itself. The bonding in
these compounds are polar covalent bonds.
Increasing electronegativity

Increasing electronegativity

http://wikieducator.org/User:Phaello/sandbox/Chemistry/Chemical_Bonding

+
A polar covalent bond has a slight positive charge and a slight negative
charge.
The greater the electronegativity difference between atoms the more
polar the bond.

Atomic Orbitals
An atomic orbital is the three dimensional region around an atom where an
electron is most likely to be found.
Heisenberg uncertainty principle states that both the precise location and
and the momentum of an atom cannot be simultaneously determined. We
can only describe is probable location.
For electron occupying an s atomic orbital, we mean that there is a
greater than 90% probability that the electron is in space defined by a
sphere.
Because of greater distance from the nucleus a 2s orbital is represented
by a greater sphere.
y
y
z
z

1s

2s

The volume of 2s orbital is larger than the volume of 1s orbital, so the average
electron density of 2s orbital is smaller

What is a node?
Electron have both particle like and wave like properties. A Node is a
consequence of the wave like properties of an electron.
Waves are two types 1)standing waves or 2) travelling waves
Standing waves are like the vibrating string of guitar
The region where the guitar has no transverse displacement (zero
amplitude) is a node.
Similarly there is zero probability of finding electron at the node.
y

2s

x
2p orbital

Higher number shells contain three degenerate p orbitals. The three

p orbital is perpendicular to each other

Molecular orbital theory

How do atoms form covalent bonds to form molecules?
Molecular orbital (MO) theory combines the tendency of atoms to fill
their octets by sharing electron (the Lewis model) with their wavelike
properties, assigning electrons to a volume of space called an orbital.
Covalent bonds result when atomic orbitals combine to form molecular
orbitals.
Molecular orbitals too have specific sizes, shapes and energies.
H.

.
H.H

1s atomic orbital

Sigma
bond

..

Molecular orbital

As the two orbitals begin to overlap, energy is released because

each electron in each atom is attracted to its own nucleus and to the
nucleus of the other atom.

The change in energy that occurs as two hydrogen atoms approach each other.
https://www.etsu.edu/coe/.../Chapter_6.pp...

Orbitals are conserved- the number of molecular orbitals formed must equal the
number of atomic orbitals combined.
In describing the H-H bond we combined two atomic orbitals but discussed only one
molecular orbital.
The other molecular orbital does not contain any electrons.
The wave like property of electrons cause the formation of two molecular orbitals.
The constructive combination of two s orbitals is called (sigma) bonding and the
destructive combination is called * antibonding molecular orbital.
Constructive combination

Phase of the orbital

Waves reinforce each

other resulting in
bonding

Waves cancel each

other and no bond form

+
-

Destructive combination

Molecular orbital diagram

Energies of atomic and molecular orbitals are represented as horizontal lines.

Bottom line is the lowest energy and top line is the highest energy.
When two atomic orbital overlap two molecular orbitals are formed.
Electrons in a bonding MO assist in bonding and electrons in an antibonding
MO detract from bonding.

 When two p atomic orbitals overlap the form a bond called the pi ()
bond.
Side to side overlap of two in-phase p atomic orbitals is a constructive
overlap and forms a bond. Side to side overlap of two out of phase p
orbitals is a destructive overlap and form a * antibonding molecular
orbital.

MO diagram for side to side overlap of p atomic orbital of two different elements

Electrons shared by carbon and oxygen are not equal.

When two p atomic orbital combine, the atomic orbital of the more
electronegative atom (oxygen) contributed more to the bonding MO and the
atomic orbital of the less electronegative atom (carbon) contributes more
to the antibonding MO.

VSEPR model

A model to predict molecular geometry based on minimization of

electron repulsion between regions of electron density around an atom.
Valence-shell electron-pair repulsion model.
Electron pairs repel each other, hence bonding electrons and lone pair
electrons around an atom are positioned as far apart as possible.
VSEPR gives an idea about the shape of a molecule.

Predicting the structure of Methane

Methane (CH4) has four identical covalent C-H bond.
Carbon has only two unpaired valance electrons . But it needs to form
four covalent bond to complete its octet.
One of the electrons in carbons 2s orbital is promoted to it empty 2p
orbital, then carbon would have four unpaired electrons.
promotion

But Methane (CH4) has four identical covalent C-H bond how can the
bonds be identical if carbon uses an s orbital and three p orbitals.
Hybrid orbitals are mixed orbits that result from combining atomic
orbitals.
One part s and three part p (sp3)
s

S orbital add to the

p orbital

sp3 sp3 sp sp
Hybridization

4 hybrid
orbitals

S orbital subtracts
from the p orbital

 The sp3 orbital are more stable than the p orbital and less stable than
the s orbital.
The four sp3 orbital adopt a spatial arrangement that keeps them as far
away from each other.
They point toward the corners of a regular tetrahedron, with an angle
of 109.5

http://osxs.ch.liv.ac.uk/OldSitesDONOTVIEW/smaher/orbitalshybrid.htm

Similarly Ethane

The bonds in Ethene (C2H4)

Each carbon forms four bonds but each carbon is bonded to only three
atoms.
Hybridization

sp

sp sp
2

http://wps.prenhall.com/wps/media/objects/340/348272/wade_ch02.html

The bonds in Ethyne (C2H2)

A triple bond is formed in ethyne.
Each of the carbon is bonded to only two atoms.
H-C C-H
In order to bond to two orbitals, each carbon hybridizes two atomic
orbitals and s and a p. Two degenerate sp orbitals are formed.
Hybridization

sp

sp

p p

Hybridization and Molecular Geometry

Hybridization of an atom determines the arrangement in space of the
bonds around the atom.
This arrangement in space determines the bond angle.

Hybridization of C, N, O

To determine the hybridization, count the number of bonds.

No bonds sp3 hybridized.
One bond sp2 hybridized.
Two bond sp hybridized.

Bond order and bond strength

Bond order describes the number of covalent bonds shared by two atoms

As the number of carbon-carbon bonds increases the bonds become shorter

and stronger.
C-H sigma bond is shorter and stronger than C-C sigma bond.

The length and strength of C-H bond depend on the hybridization of the
carbon to which the hydrogen is attached.

What we learnt today