CBE422

Organic and Instrumental Chemistry for

Engineer

Julia Tan
julia5342@salam.uitm.edu.my
Outline
1 Organic Chemistry

2 Atomic Structure

3 Orbital Theory

4 Valence Bond Theory

5 Hybridization
What is organic chemistry?

Organic Chemistry defined as the

chemistry of compounds found in living
organisms
Origins of Organic Chemistry
Foundations of organic chemistry date from the mid-
1700s
Unexplainable differences were noted between
substances obtained from living sources and those
obtained from minerals
Swedish chemist, Torbern Bergman (1770)
was the first to make distinction between
organic and inorganic substances
Origins of Organic Chemistry
It was thought that organic compounds must contain
some vital force because they were from living
sources
Because of vital force, it was thought that organic
compounds could not be synthesized in laboratory
like inorganic compounds
It is a theory known as Vitalism

However, later on someone showed that this is not

the case
Organic Chemistry
1816: Michel Chevreul found that animal fat can be
converted into fatty acids + glycerin without vital
force

1828: Friedrich Whler discovered that it was possible to

convert the salt (inorganic) into urea (organic)
Organic Chemistry
Organic chemistry is defined as the study of carbon
and its compounds
Carbon can bond with other atoms like hydrogen,
oxygen, nitrogen, sulfur or the halogens
Carbon is group 4A element, it can share 4 valence
electrons and form 4 covalent bonds
Atomic Structure
Structure of an atom
- Positively charged nucleus (very dense, protons +
neutrons)
- Negatively charged electrons are in a cloud
surrounding nucleus
Atomic Structure

Atomic number (Z) gives the number of protons in

the atoms nucleus
Mass number (A) gives the total of protons and
neutrons
Atomic weight gives the weighted average mass of an
elements isotopes
Isotopes are atoms of the same element that have
different numbers of neutrons and therefore
different mass numbers
Orbital Theory
The orbitals tell us how the electrons are distributed in an
atom according to the amount of energy

An orbital represents the space where an electron spends

most of its time
Orbital Theory
There are four types of orbitals: s,p,d,and f

s orbitals: spherical, nucleus at center

p orbitals: dumbbell-shaped, nucleus at middle

d orbitals: elongated dumbbell-shaped, nucleus at

center
Orbitals and Shells
Orbitals are grouped in shells of increasing size and
energy
Different shells contain different numbers and kinds
of orbitals
Each orbital can be occupied by two electrons
Orbitals and Shells
1st Shell: contains one s orbital (1s), holds only two
electrons
2nd Shell: contains one s orbital (2s) and three p orbitals
(2p), eight electrons
3rd Shell: contains an s orbital (3s), three p orbitals (3p)
and five d orbitals (3d), 18 electrons
Orbitals and Shells
p-orbitals
In each shell, there are three perpendicular p
orbitals, px, py, and pz of equal energy
Lobes of a p orbital are separated by region of zero
electron density, a node
 Electron Configurations
Ground-state electron configuration (lowest energy arrangement)
of an atom lists orbitals occupied by its electrons
Lowest-energy orbitals fill first: 1s 2s 2p 3s 3p 4s 3d
Rule 1 (Aufbau principle)
Electrons act as if they were spinning around an axis. Electron spin can
Rule 2 have only two orientations, up and down . Only two electrons can
occupy an orbital and they must be of opposite spin (Paulis exclusion
principle) to have unique wave equations
If two or more empty orbitals of equal energy are available, electrons
occupy each with spins parallel until all orbitals have one electron
Rule 3 (Hund's rule).
Aufbau Principle
Aufbau is a German word which means building up or
construction
Aufbau Principle
There are exceptions
Half-filled and completely filled d and f subshells
have extra stability
For example, Cr the valence configuration is 4s2 3d4,
while that observed is 4s1 3d5

Electron-electron repulsion is reduced since each

electron has its own seat
Electron Configurations
Example:
If we follow the pattern across a period from B to O in
the periodic table, the number of electrons increase
and the subshells are filled.

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
Exercise
1. Give the ground-state electron configuration for:
a) F (Z = 9)
b) Mg2+ (Z = 12)

2. Draw the valence orbital diagram that represents

the ground-state of N
Answers
1. a)1s2 2s2 2p6

b) The electron configuration for Mg is 1s2 2s2 2p6

3s2. When Mg ionizes and loses two electrons,
they come from the subshells that is highest in
energy, the 3s subshell. Therefore, Mg2+ is 1s2 2s2
2p6

2. dsd

1s 2s 2p
Development of Chemical Bonding
Theory
1858: August Kekul and Archibald Couper
independently proposed that, carbon always forms
four bonds when it joins other elements to form stable
compounds
1865: Kekul suggested that carbon chains can
double back to form rings of atoms
1874: Jacobus vant Hoff and Joseph Le Bel proposed
that the four bonds of carbon have specific spatial
directions
Vant Hoffs Tetrahedral Carbon Atom

The ability to visualize biological molecules in

three dimensions is a critical skill in organic chemistry!

The heavy wedged line comes out of the plane of the

paper
The normal lines are in the plane
The dashed line goes back behind the plane of the
page
Covalent Bonds
1916: G.N. Lewis proposed that, chemical bond
involves the sharing of electron pairs between atoms
is called covalent bond
Lewis structures (electron-dot) show valence
electrons of an atom as dots
Hydrogen has one dot, representing its 1s electron
Carbon has four dots (2s2 2p2)
Kekul structures (line-bond) have a line drawn
between two atoms indicating a 2 electron covalent
bond
Covalent Bonds
Covalent Bonds
Atoms with one, two, or three valence electrons
form one, two, or three bonds
Atoms with four or more valence electrons form as
many bonds as they needed to reach a stable octet
Carbon has four valence electrons (2s2 2p2) forming
four bonds (CH4)
Nitrogen has five valence electrons (2s2 2p3) but
forms only three bonds (NH3)
Oxygen has six valence electrons (2s2 2p4) but forms
two bonds (H2O)
Non-Bonding Electrons
Valence electrons not used in bonding are called
nonbonding electrons, or lone-pair electrons
Nitrogen atom in ammonia (NH3)
Shares six valence electrons in three covalent
bonds and remaining two valence electrons are
nonbonding lone pair
Exercise 1
Write valid Lewis (electron-dot) structures for each
formula below. Show all electrons as dots and show
all non-bonding electrons
a) C2Cl4, tetrachloroethylene
b) carbon dioxide
c) CH4O, methanol
Answer
a) C2Cl4, tetrachloroethylene

b) carbon dioxide

c) CH4O, methanol
Exercise 2
The structure of urea is shown below. Fill in any non-
bonding valence electrons that are missing from the
line-bond structure
Answer
Valence Bond Theory
Two models to describe covalent bonding:
Valence bond theory
Molecular orbital theory

Valence Bond Theory

Electrons are paired in the overlapping orbitals and are
attracted to nuclei of both atoms
HH bond results from the overlap of two singly
occupied hydrogen 1s orbitals
H-H bond is cylindrically symmetrical, sigma (s) bond
Bond Energy
During the reaction 2 H H2 releases 436 kJ/mol

Product has 436 kJ/mol less energy than two atoms:

HH has bond strength of 436 kJ/mol.
Bond Length
Distance between nuclei that leads to maximum
stability
If too close, they repel because both are positively
charged
If too far apart,
bonding is weak
Molecular Orbital (MO) Theory
Region of space in a molecule where electrons are
most likely to be found
Two ways for orbital combination to occur

Additive way: egg-shaped, lower in energy, bonding

MO
Substractive way: node between nuclei,
higher in energy, antibonding MO
Molecular Orbital (MO) Theory
Drawing Structures
Drawing every bond in organic molecule can become
tedious
Several shorthand methods have been developed to
write structures
Condensed structures dont have C-H or C-C single
bonds shown. They are understood
E.g.
3 General Rules
1) Carbon atoms arent usually shown. Instead a
carbon atom is assumed to be at each intersection
of two lines (bonds) and at the end of each line
2) Hydrogen atoms bonded to carbon arent shown
3) Atoms other than carbon and hydrogen are shown
Exercise
Convert the following structure to a skeletal drawing and give its molecular
formula
Answer
Molecular Formula: C5H7Br
sp3 Orbitals
C uses two kinds of orbitals (2s and 2p) to form
bonds (C-H)
All four bonds are identical and are spatially oriented
toward the corners of a regular tetrahedron

How can we explain this phenomenon???

Hybridization: sp3 Orbitals
1931: Pauling, who showed how an s orbital and
three p orbitals on an atom can combine (hybridize)
to form 4 equivalent atomic orbitals with tetrahedral
orientation (spxpypz = sp3)
The Structure of Methane
sp3 orbitals on C overlap with 1s orbitals on 4 H
atoms to form four identical C-H bonds
Each CH bond has a strength of 438 kJ/mol and
length of 109 pm
Each HCH is 109.5, the so-called tetrahedral angle
The Structure of Ethane
Two Cs bond to each other by s overlap of an sp3
orbital from each
Three sp3 orbitals on each C overlap with H 1s
orbitals to form six CH bonds
The Structure of Ethane
C-H bond strength in ethane is 420 kJ/mol

CC bond is 154 pm long and strength is 376

kJ/mol
All bond angles of ethane are tetrahedral
sp2 Orbitals
2s orbital combines with two 2p orbitals, giving 3
orbitals (spp = sp2). This results in a double bond
sp2 orbitals are in a plane with 120 angles
Remaining p orbital is perpendicular to the plane
Hybridization: sp2 Orbitals
Two sp2-hybridized orbitals overlap to form a s bond
p orbitals overlap side-to-side to form a pi () bond
sp2sp2 s bond and 2p2p bond result in sharing
four electrons and formation of C-C double bond
Hybridization: sp2 Orbitals
Electrons in the s bond are centered between nuclei
Electrons in the bond occupy regions are on either side
of line between nuclei
The Structure of Ethylene
H atoms form s bonds with four sp2 orbitals
HCH and HCC bond angles of about 120
CC double bond in ethylene shorter and stronger than
single bond in ethane
C=C bond length is 134 pm (CC 154 pm)
sp Orbitals
C-C a triple bond sharing six electrons
Carbon 2s orbital hybridizes with a single p orbital
giving two sp hybrids
sp orbitals are linear, 180 apart on x-axis
Two p orbitals are perpendicular on the y-axis and
the z-axis
The Structure of Acetylene
Two sp hybrid orbitals from each C form spsp s
bond
pz orbitals from each C form a pzpz bond by
sideways overlap and py orbitals overlap similarly
The Structure of Acetylene
Linear molecule with H-CC bond angles of 180C

Sharing of six electrons forms CC

C-H bonds: bond length (BL) 106 pm, strength 552

kJ/mol
C-C bond: BL 120 pm, strength 835 kJ/mol

Triple bond the shortest and strongest

Exercise
The structure of urea is shown below. Determine the
hybridized of the carbon atom in urea. Then predict
NH2-C=O bond angle in urea.
Answer
The carbon atom in urea is sp2 hybridized

Bond angle: 120

Summary
Organic chemistry chemistry of carbon
compounds
Atom: positively charged nucleus surrounded by
negatively charged electrons
Electronic structure of an atom described by wave
equation
Electrons occupy orbitals around the nucleus
Summary
Different orbitals have different energy levels and
different shapes
s orbitals are spherical, p orbitals are dumbbell-
shaped
Molecular orbital (MO) theory - bonds result
from combination of atomic orbitals to give
molecular orbitals, which belong to the entire
molecule
Summary
Covalent bonds - electron pair is shared between
atoms
Valence bond theory - electron sharing occurs by
overlap of two atomic orbitals
Sigma (s) bonds - Circular cross-section and are
formed by head-on interaction
Pi () bonds dumbbell shape from sideways
interaction of p orbitals
Summary
Carbon uses hybrid orbitals to form bonds in organic
molecules
In single bonds with tetrahedral geometry, carbon
has four sp3 hybrid orbitals
In double bonds with planar geometry, carbon uses
three equivalent sp2 hybrid orbitals and one
unhybridized p orbital
Summary
Carbon uses two equivalent sp hybrid orbitals to
form a triple bond with linear geometry, with two
unhybridized p orbitals
Atoms such as nitrogen and oxygen hybridize to
form strong, oriented bonds
The nitrogen atom in ammonia and the oxygen
atom in water are sp3-hybridized
References
www.visionlearning.com

generalchemistoncall.wordpress.com/2012/04/16/more-on-
electron-configuration/
http://en.wikipedia.org/wiki/Torbern_Bergman

http://fineartamerica.com/featured/1-michel-eugene-chevreul-
granger.html
http://fineartamerica.com/featured/friedrich-whler-1800-1882-
granger.html
http://en.wikibooks.org/wiki/Structural_Biochemistry/Chemic
al_Bonding/_Electronic_Structure_Theories
References
http://www.anselm.edu/homepage/jpitocch/genbio/c
hemnot.html
http://chemwiki.ucdavis.edu/Inorganic_Chemistry/Electro
nic_Configurations/Aufbau_Principle
http://chemistry.tutorcircle.com/inorganic-
chemistry/aufbau-principle.html