Chem2161-Unit 1 PDF
Chem2161-Unit 1 PDF
Chem2161-Unit 1 PDF
UNIT 1
Introduction
1.1 Historical Background of Organic Chemistry
At the beginning of the nineteenth century chemists generally thought that compounds from living
organisms were too complicated in structure to be capable of artificial synthesis from non-living things,
and that a 'vital force' or vitalism conferred the characteristics of living beings on this form of matter.
They named these compounds 'organic', and preferred to direct their investigations toward inorganic
materials that seemed more promising. Inorganic compounds: are substances derived from non-living
materials (mineral constituting of the earth).
In 1780s, scientists distinguished between organic compounds and inorganic compounds (Swedish
chemist Torbern Bergman). Organic compounds: as compounds derived from living organisms
(vegetables and animals). A compound like urea is considered to be organic because urea is a constituent
of urine. They thought that organic compounds couldn’t be synthesized in the laboratory. This theory is
called the vitalism theory. They believed that organic compounds couldn’t be synthesized because of the
vital force requirement, which is not present in flasks and test tubes.
NaOH
Animal fat Soap + Glycerol
(Tallow) H2 O
Conversion of fat (organic) into soap and soap into fatty acid with out the intervention of outside vital
force was the first demonstration that organic compounds could be interconvert into each other in the
laboratory. This is the first experiment that indicated the vital force theory was with drawbacks.
1828 – 1850: A number of ‘organic’ compounds were synthesized from sources that are clearly inorganic.
In 1828 Friedrich Wöhler synthesized urea from inorganic compound. Urea is a substance isolated from
urine. This happened by chance in his attempt of producing ammonium cyanate in the laboratory
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O
Heat
+ -
NH 4 NCO H2N-C-NH 2
Ammonium cyanate Urea
(inorganic salt)
After the synthesis of urea in laboratory, theory of Vitalism has been rejected. This clearly indicated that
no special force is required to synthesis organic compounds. In science today, a different name is given
to the field of study of compounds from living organisms. It is known as Natural products Chemistry.
There is no distinct boundary between organic and inorganic compounds except that almost all organic
compounds contain carbon. The modern definition of organic chemistry is: it is the study of carbon
containing compounds.
Organic chemistry, then, is the study of carbon compounds. But why is carbon special? Why, of the more
than 30 million presently known chemical compounds, do more than 99% of them contain carbon? The
answer to this question comes from carbon’s electron structure and its position in the periodic table. As a
group 4a element, carbon can share four valance electrons and form four strong covalent bonds.
Furthermore, carbon atom can bond to one another, forming long chains and rings.
Exercise 1.1
1. What is organic chemistry?
2. Classify the following compounds as organic or inorganic.
a. CO2 d. CS2 g. HCCH
b. CH4 e. CH3COOH h. Ln4(C2)3
c. C2H5OH f. CaC2 i. CO3-
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As you probably know, an atom consists of a dense, positively charged nucleus surrounded at a relatively
large distance by negatively charged electrons. The nucleus consists of subatomic particle called neutrons,
which are electrically neutral, and protons, which are positively charged.
Atomic Orbitals
How are electrons distributed in an atom? You might recall from your general chemistry course that,
according to the quantum mechanical model, the behavior of a specific electron in an atom can be
described by a mathematical expression called wave equation. The solution to a wave equation is called a
wave function or orbital, and is denoted by the Greek letter psi, .
For one electron system, each solution to the equation is associated with a particular wave function, which
also called an atomic orbital. The square of the wave unction gives the probability of finding the electron
at any point.
The electron could be anywhere; the probability of finding it at any point never reach zero. To visualize
where the electron spends most of its time, we draw diagram to show where the electrons spent 90% of its
time.
90% of probability of finding
the electron in side this region
1S orbital
Fig. 1.2 Representation of 1S orbital
The region in which an electron is most likely found is called an orbital.
The electron may locate anywhere within an orbital at any instant in time, but it spends most of its time in
certain high probability regions. Thus we can think of an electron as a particle that moves from place to
place so rapidly that it behave somewhat like an “electron cloud” whose density varies with in the orbital.
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Atomic orbitals are the region in which there is high probability of finding an electron in space.
Shape of Orbitals
What do orbitals look like? There are four different kinds of orbitals, denoted s, p, d, and f, each with a
different shape. Of the four, we will be concentrated primarily with s and p orbitals because these are the
most commonly found in organic compounds. The s orbitals are spherical, with the nucleus at their center;
p orbitals are dumbbell-shaped; and four of the five d orbitals are cloverleaf-shaped as shown in Figure
1.3.
z
z z z
y
y y
y
x x x x
s- orbital
Px Py Pz
z z z z z
y y y y y
x x x x x
Electron Configuration
Electron configuration: is the way in which electrons are arranging around the nuclei of atoms.
It is the nature of things to seek the lowest possible energy.
The lowest energy arrangement, or ground-state electron configuration, of an atom is a listing of an
orbital occupied by its electron. We can predict this arrangement by the following three rules.
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5p
4d
5s
4p
Increasing energy
3d
4s
3p
3s
2p
2s
1s
Fig. 1.4 Orbital diagam in incrasing energy
ii. ThePauli Exclusion Principle: electrons act as if they were spinning around an axis, in much the
same way that the earth spins. This spine can have two orientations, denoted as up and down.
An atomic orbital may contain at most two electrons. To occupy the same orbital, two electrons
must have opposite spins;
Example
1s2 2s2
iii. Hund’s rule: - When electrons occupy orbitals of equal energy, one electron enters each orbital
unit all the orbitals contain one electron with spins parallel.
Example: The two possible orbital electronic configurations for carbon (1s2, 2s2, 2p2) are:
a)
2 2
1s 2s 2p2
b)
2 2
1s 2s 2p2
According to Hund’s rule (b) is acceptable configuration, because parallel spins lead to the lowest
electron- electron repulsion.
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Table 1.1 Electron Configurations of the First Twelve Elements of the Periodic Table
Element Atomic number Number of electrons
Z 1s 2s 2px 2py 2pz 3s
Hydrogen 1 1
Helium 2 2
Lithium 3 2 1
Beryllium 4 2 2
Boron 5 2 2 1
Carbon 6 2 2 1 1
Nitrogen 7 2 2 1 1 1
Oxygen 8 2 2 2 1 1
Fluorine 9 2 2 2 2 1
Neon 10 2 2 2 2 2
Sodium 11 2 2 2 2 2 1
Magnesium 12 2 2 2 2 2 2
Exercise : 1.2
1. Fill the following orbitals of nitrogen with appropriate number of electrons using Hund’s
rule.
N(Z=7):
2. Give the ground state electron configuration for each of the following elements:
a) Oxygen b) silicon c) sulfur
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Carbon forms covalent bonding with other elements to produce organic molecules.
The covalent or shared electron pair model of chemical bonding was first suggested by G. N. Lewis of the
University of California in 1916. Lewis proposed that a sharing of two electrons by two hydrogen atoms
permits each one to have a stable closed-shell electron configuration analogous to helium.
Two models have been developed to describe covalent bonding: valence-bond theory and molecular
orbital theory. Each has its strengths and weaknesses, and chemists tend to use them interchangebly
depending on the circumstances. Valence-bond theory is the more easily visualize. We use this theory to
describe bonding in carbon in this course.
According to valence bond theory a covalent bond between two atoms approach each other closely and a
half-filled orbital of one atom overlaps with a half-filled orbital of the other atom. The electrons are now
paired in the overlapping orbitals and are attracted to the nuclei of both atoms, thus bonding the atoms
together.
In the H2 molecule the H-H bond results from the overlapping of two half filled hydrogen 1s orbitals.
Bonds which are formed by end-to-end overlap of two atomic orbitals along a line drawing between the
nuclei are called sigma () bonds.
H + H H H
sigma bond
Note that: in order to overlap during covalent bond formation, the two overlapping orbitals must be half-
filled.
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Orbital Hybridizations
The bonding in hydrogen molecule is straightforward, but the situation is more complicated in organic
molecule with tetravalent carbon atom.
Take methane, CH4. It has 4 bonds.
H
sp3Hybridization
Before we describe the bonding in methane, it is worth pointing out that bonding theories attempt to
describe a molecule on the basis of its component atoms; bonding theories do not attempt to explain how
bonds form.
The electron configuration of a carbon bonded to other atoms need not be the same as a free carbon atom.
By promoting one electron from the 2s orbtal to the vacant 2pz orbtal, carbon can acheve the new
configuration 1s2, 2s1, 2px1, 2py1, 2pz1. This new electronic configuration is called an exited state
configuration. In the exited state, carbon has four unpaired electrons and can form four bonds to
hydrogen.
By mixing ("hybridizing") the 2s, 2px, 2py, and 2pz orbitals, four new orbitals are obtained (Figure 1.5).
These four new orbitals are called sp3 hybrid orbitals because they come from one s orbital and three p
orbitals. Each sp3 hybrid orbital therefore has 25% s character and 75% p character.
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1s 2s 2p
Ground state C:
Exited state C:
hybridization C
3
sp orbitals
Figure 1.5 Mixing the s orbital with the three p orbitals generates four sp3 hybrid orbitals. The four
sp3 hybrid orbitals are of equal energy.
Now carbon can overlap with hydrogen atoms to form four bonds.
sp3- s :overlap
H H
H
H 109.5o
H C
C C
H
H H
H H
H
H
Fig 1.6 Each half-filled sp3 orbital overlaps with a half-filled hydrogen ls orbital along
a line between them giving a tetrahedralarrangement of four sigma bonds.
Such end-to-end overlapping of orbitals is called sigma overlapping and the resulting bond called sigma
() bond
sp3 hybrid orbital has a tetrahedral shape with all bond angles equal 109.5
Ethane
The same kind of orbital hybridization that accounts for methane structure also accounts for the bonding
of carbon atoms in to chains and rings to male possible many millions of organic compounds. Ethane is
simple compound containing carbon-carbon bond.
In ethane the two carbon atoms bond to each other by overlap of sp3 hybrid orbital from each (Fig 1.7).
The remaining three sp3hybrid orbitals of each carbon overlap with 1s orbitals of three hydrogens.
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sp2Hybridization
Ethene (ethylene) is planar with bond angles close to 1200; therefore, some hybridization state other than
sp3 is required. The hybridization scheme is determined by the number of atoms to which carbon is
directly attached. In sp3 hybridization, four atoms are attached to carbon by σ bonds, and so four
equivalent sp3 hybrid orbitals are required. In ethylene, three atoms are attached to each carbon, so three
equivalent hybrid orbitals are needed.
H H H H
C C C C
CH2=CH2
H H H
H
C
Exited state C: sp2
sp2
hybridization sp2
sp 2 pz
Figure 1.8 Mixing the s orbital with the two p orbitals generates three sp2 hybrid orbitals.
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-bond
-bond
C C C C
sp2 orbitals
Figure 1.9 The structure of Ethene. orbital overlap of two sp2 hybrid carbon forms double bond
H H
Sigma bond () resulted due to end- to-end overlap of orbitals 120°
C C
Pi bond () resulted due to side-to-side overlap of p orbitals
H H
spHybridization
Conceder bonding in acetylene, H-CC-H.To explain the formation of triple bond imagine that, instead of
combining with two or three p orbitals, a carbon 2s orbital hybridizes with only a single p orbital. Twosp
hybrid orbitals result and two p orbitals left unhybridized. The twosp orbitals are oriented 180apart on
the x-axis, while the remaining two p orbitals are perpendicular on the y-axis (Figure 1.10).
1s 2s 2p py pz
Ground state C:
C
Exited state C:
sp sp
hybridization
sp p y pz
Figure 1.10 Mixing the s orbital with the one p orbitals generates two sp hybrid orbitals.
The hybrid orbital indicates the presence of two unhybridizedp orbitals that can overlap side-to-
side. As a result two bonds produced.
bond
180°
H C C H
bond bond
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Generally single bond is has sigma bond only, double bond has one sigma and one pi, and triple bond
has one sigma and two pi bonds.
A doubly bonded carbon has sp2 hybridization and a triple bonded carbon has sp hybridization. Now you
can extend the concept of hybridization to other organic compounds and be able to state the hybridization
of each carbon.
Examples: the hybridization of each carbon in the following compounds is:
sp
O
a) b) sp3
CH3 CH2 CH2 C C CH3
C CH3
CH3 CH2
sp3 sp3 sp
sp3 sp3
2 sp3
sp3 sp
Exercise 1.3
1. Indicate the hybridization of each carbons in the following compounds
LEWIS STRUCTURE
Structural formulas in which electrons are represented as dots are called Lewis structures.
Covalent bonding in F2 gives each fluorine eight electrons in its valence shell and a stable electron
configuration equivalent to that of the noble gas neon:
The Lewis model limits second-row elements (Li, Be, B, C, N, O, F, Ne) to a total of eight electrons
(shared plus unshared) in their valence shells. Hydrogen is limited to two.
Now let's apply the Lewis model to the organic compounds methane and carbon tetrafluoride.
Carbon has eight electrons in its valence shell in both methane and carbon tetrafluoride.
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By forming covalent bonds to four other atoms, carbon achieves a stable electron configuration analogous
to neon. Representing a two-electron covalent bond by a dash (-), the Lewis structures for hydrogen
fluoride, fluorine, methane, and carbon tetrafluoride become:
Lewis's concept of shared electron pair bonds allows for four-electron double bonds and six-electron
triple bonds. Carbon dioxide (CO2) has two carbon-oxygen double bonds, and the octet rule is satisfied
for both carbon and oxygen. Similarly, the most stable Lewis structure for hydrogen cyanide (HCN) has a
carbon-nitrogen triple bond.
Carbon dioxide O C O or O C O
Hydrogen cyanide H C N or H C N
Multiple bonds are very common in organic chemistry. Ethylene (C2H4) contains a carbon-carbon double
bond in its most stable Lewis structure. The most stable Lewis structure for acetylene (C2H2) contains a
carbon-carbon triple bond. Here again, the octet rule is satisfied.
Exercise 1.4
Write the most stable Lewis structure for
a) Formaldehyde, CH2O
b) Tetrafluoroethylene, C2F4 .
c) Acrylonitrile, C3H3N.
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Formal Charge
Lewis structures frequently contain atoms that bear a positive or negative charge. If the molecule as a
whole is neutral, the sum of its positive charges must equal the sum of its negative charges. An example is
nitric acid, HNO3:
O
H O N
O
As written, the structural formula for nitric acid depicts different bonding patterns for its three oxygens.
Oneoxygen is doubly bonded to nitrogen, another is singly bonded to both nitrogen and hydrogen, and the
third has a single bond to nitrogen and a negative charge. Nitrogen is positively charged. The positive and
negative charges are called formal charges.
The positive and negative charges on each atom in a compound or an ion are called
formal charges.
We calculate formal charges by counting the number of electrons "owned" by each atom in a Lewis
structure and comparing this electron count with that of the neutral atom.
The method described for calculating formal charge has been one of reasoning through a series of logical
steps. It can be reduced to the following equation:
Example: Calculate the formal charge on each of the atoms in the Lewis structure of thionyl chloride
given below.
Solution: The formal charge is the difference between the number of valence electrons in the neutral atom
and the electron count in the Lewis structure. (The number of valence electrons is the same as the group
number in the periodic table for the main-group elements.)
Valence electrons of neutral atom Formal charge
Sulfur 6 6-3-2= +1
Oxygen 6 7-1-6= -1
Chlorine 7 7-7-0= 0
The formal charges are shown in the Lewis structure of thionyl chloride as follows:
O
Cl S Cl
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Formal charge of N= +1
Formal charge of double bonded O = 0
Formal charge of single bonded O = -1
Formal charge of single bonded O (bonded to H) = 0
The formal charges are shown in the Lewis structure of nitric acid as:
Exercise 1.5
Resonance
According to the resonance concept, when more than one Lewis structure may be written for a molecule,
a single structure is not sufficient to describe it. Rather, the true structure has an electron distribution that
is a “hybrid” of all the possible Lewis structures.
In the case of ozone, two equivalent Lewis structures may be written below.
O O
O O O
O
I II
Structure I and II are resonance structure of ozone. We use a double-headed arrow (↔) to represent
resonance between these two Lewis structures.
Organic chemists often use curved arrows to show this electron delocalization. Alternatively, an average
of two Lewis structures is sometimes drawn using a dashed line to represent a “partial” bond. In the
dashed-line notation the central oxygen is linked to the other two by bonds that are halfway between a
single bond and a double bond, and the terminal oxygen each bear one half of a unit negative charge.
O O O
O O O equivalent to -1/2 O O -1/2
O
Curved arrow notation Dashed arrow notation
Electron delocalization in ozone
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Exercise 1.6
1. How many resonance structures possible for each of the following
a) SO3 b) NO3-
2. Write all resonance structures that can be generated for
a) SO3 b) NO3-
Isomers
Isomers are compounds with the same molecular formula but different structure.
The tendency of an atom to draw the electrons in a covalent bond toward itself is referred to as its
electronegativity. An electronegative element attracts electrons; an electropositive element donates
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electrons. Electronegativity increases across a row in the periodic table. The most electronegative of the
second-row elements is fluorine. Others include O, N, Cl.
When carbon forms a bond with those electronegative elements, the resulting bond is polar covalent bond.
Polar covalent bonds determine different properties of organic molecules.
O
+
C+ H3C NH2
H3C CH3
A) Molecular Formula
This indicates the total number of atoms present a molecule.
Example: C6H6, C2H5OH, C20H42
B) Structural formula
All bonds present in the molecule should be shown.
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The hydrogen atoms bonded to carbon are not shown. Since carbon always has a valance
of 4, we mentally supply the correct number of hydrogen atoms for each carbon.
Atoms other than carbon and hydrogen should be written.
H H H H
H H
CH3CH2CH2CH3 becomes simplified to
H H H
H Bond line formula
We can find number of hydrogen atoms bonded to each carbon and determine the molecular
formula of a molecule from its bond-line formula.
Caravone is a substance responsible for the odor of spearmint, has the following structure. Find
its molecular formula.
O
Carvone
The end of a line represents a carbon atom with 3 hydrogen atoms, CH3: a two-way intersection is
a carbon with 2 hydrogens, CH2; a three-way intersection is a carbon with 1 hydrogen, CH; and a
four intersection is a carbon atom with no attached hydrogen.
2H
2H
O
3H
1H
zero H
3H Carvone
1H
molecular formula, C10H14O
2H
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H
(wedge): a bond projecting from paper towards you.
C (dash): a bonds projecting in to the paper away from you.
H
H
H (line ): a bond that lies on the plane of the paper
This type of formula is usful to show the steriochemistry of a molecule.
OH CH3
CH3
C
CH2CH3
H
CH3
CH3
Exercise 1.7
1. Expand the following bond-line representations to show all the atoms including carbon and
hydrogen.
a) c) OH
b) d)
HO
HO CHO
A functional group is a particular combination of atoms in a molecule that is particularly responsible for
characteristic set of reactions that the molecule exhibit.
The chemistry of every organic molecule, regardless of size and complexity, is determined by the
functional group it contains.
For example, the functional group of an alkene is carbon-carbon double bond. The following two
compounds which have carbon-carbon double bond undergo remarkably similar reaction, addition of
bromine on double bonds.
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Nowadays, there are more than 10 million known compounds. Attempting to deal with each and
individual compounds may make learning organic chemistry bulky. Instead of dealing with millions of
compounds, we deal with dozens of functional groups which logically categorizes compounds according
to their structural features.
Structure of Some Functional Groups
Functional Group Functional Group
Name Structure Example Name Structure Example
O
Alkene C C H2C CH CH3 Carbonyl C
O
Alkyne C C H C C CH3 O
C C
Aldehyde H CH3 H
Arene O O
Benzene
Ketone C C
C C CH3 CH3
CH3CH2Cl
Halide C X
O O
(X=F,Cl,Br, I) Carboxylic acid CH3 C OH
C OH
Alcohol C OH CH3CH2OH O O
Ester C O C CH3 C OCH3
Ether C O C H3C O CH3 O O
Amide C N CH3 C NH2
Amine C NH2
CH3CH2NH2
O O O O
Acid anhydride C O C
Nitrile C N CH3 C N CH3 C O C CH3
O O
Nitro C NO2 CH3CH2NO2 Acid chloride H3C C Cl
C Cl
Thiol C SH CH3CH2SH
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Exercise 2.1
Identify the functional groups in each of the following compounds.
O O NH2
H
a) O b) c) N S CH3
OH
H O N CH3
HO O O
HO HO
OH
amoxicillin
Prostagladin E1
3 Determine the hybridization of C1, C2, C3 and C4 for each of the following compounds
4 2 2
O O
a) 3
1 b) 1 3
4
c)
3 1
4 2 OH
4 Determine the formal charge at all the atoms in each of the following species and the net charge on
the species as a whole
a) H O H b) H O H c) H C H
H H H
5 What is the formal charge of oxygen in each of the following Lewis structure?
a) CH3O b) H C O CH3 c) H3C O CH3
3
CH3
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1. H2 H2 H2 H2
H3C
a) C C C C b) CH3
H3C C C C CH3 C
C
H2 H2 H2 H3C
CH3
H3C
c)
CH OH d) H2C CH2 CH3
H3C CH
H2C CH C CH3
CH3 H2C CH2 CH3
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