Chapter 1

Structure and Properties

of Organic Molecules,
Carbon Compounds and
Chemical Bonds

Doç.Dr. Nilüfer BAYRAK

 INTRODUCTION
 Organic Chemistry
The chemistry of the compounds of carbon
The human body is largely composed of organic
compounds
Organic chemistry plays a central role in medicine,
bioengineering etc.

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 Vitalism
 It was originally thought organic compounds
could be made only from living things by
intervention of a “vital force”.
Fredrich Wöhler disproved vitalism in 1828 by Friedrich Wöhler
(1800 - 1882)
making the organic compound urea from the
inorganic salt ammonium cyanate by
evaporation:

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Four examples of organic compounds in
living organisms.

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 Structural Theory
 Atom
There are protons and neutrons in the center of the
atom and electrons in the orbits.
Electrons in the highest energy level of the atom, in
other words, in the outermost orbitals, are called
valence electrons. Valence electrons are also very
important for the establishment of chemical bonds
between elements.
We can find the number of valence electrons of an
element by writing its electron configuration. We place
electrons in the form of 1s, 2s, 2p, 3s, 3p, 4s, 3d, 4p, 5s,
respectively.

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 The highest level is determined by the number in front of the
letter indicating shell. If there are two equivalent numbers in
front of the orbital letters, the superscripts of the shell are
added. For example, if the array is 2s2, 2p4, then 2 + 4 = 6 is
found.

 1H: 1s1 The number of valence electrons is 1,

there is 1 electron in a single orbital.
 5B: 1s2 2s2 2p1 There are 2 + 1 = 3 valence electrons.
 6C: 1s2 2s2 2p2 The number of valence electrons is 4.
(2 + 2 = 4)
 8O: 1s2 2s2 2p4 The number of valence electrons is 6.
(2 + 4 = 6)

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 Valency:
Atoms in organic compounds form a fixed number of
bonds.

Carbon can form one or more bonds with other carbons

Carbon-Carbon Bonds

Single bond Double bond Triple bond

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 Isomers
They are different molecules with the same molecular
formula. Isomers are mainly divided into two as structural
and stereoisomers. Stereoisomers are also divided into 2
as geometric and optical isomers.

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 Structural Isomers:
They are different compounds that have the same
molecular formula but different connectivity of atoms.
 They often differ in physical properties (e.g. boiling point,
melting point, density) and chemical properties.
For example; consider two compounds with molecular
formula C2H6O
 These compounds cannot be distinguished based on
molecular formula; however they have different
structures
 The two compounds differ in the connectivity of their
atoms

Bp: 78.5 OC Bp: -23.6 OC

colorless liquid colorless gas 9
 Three Dimensional Shape of Molecules
Almost all molecules possess a 3-dimensional shape
which is often not accurately represented by drawings.
The four bonds around carbon are not all in a plane. They
are in a tetrahedral arrangement and the four C-H bonds
point towards the corners of a regular tetrahedron.

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 Chemical Bonds
 The Octet Rule
Atoms form bonds to produce the electron
configuration of a noble gas (because the electronic
configuration of noble gases is particularly stable)
For most atoms this means achieving a valence shell
configuration of 8 electrons corresponding to the
nearest noble gas
Atoms close to Helium achieve a valence shell
configuration of 2 electrons
Atoms can form either ionic or covalent bonds to
satisfy the octet rule

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12
 Electronegativity
Electronegativity is the ability of an atom to attract
electrons
It increases from left to right and from bottom to top in
the periodic table (noble gases excluded)
 Fluorine is the most electronegative atom and can
stabilize excess electron density the best

Bond electrons

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 Ionic Bonds
When ionic bonds are formed atoms gain or lose
electrons to achieve the electronic configuration of the
nearest noble gas. In the process the atoms become ionic
The resulting oppositely charged ions attract each other
and form ionic bonds
This usually happens between atoms with very different
electronegativity. For example
 Lithium loses an electron (to have the configuration of
helium) and becomes positively charged
 Fluoride gains an electron (to have the configuration of
neon) and becomes negatively charged
 The positively charged lithium and the negatively
charged fluoride form a strong ionic bond

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 Covalent Bonds
Covalent bonds occur between atoms with similar
electronegativity (close to each other in the periodic table)
Atoms achieve octets by sharing of valence electrons
Molecules result from this covalent bonding
Valence electrons can be indicated by dots (electron-dot
formula or Lewis structures) but this is time-consuming
The usual way to indicate the two electrons in a bond is to
use a line (one line = two electrons)

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 Writing Lewis Structures
Atoms bond by using their valence electrons
The number of valence electrons is equal to the group
number of the atom
 Carbon is in group 4A and has 4 valence electrons
 Hydrogen is in group 1A and has 1 valence electron
 Oxygen is in group 6A and has 6 valence electrons
 Nitrogen is in group 5A and has 5 valence electrons
To construct molecules the atoms are assembled with the
correct number of valence electrons
If the molecule is an ion, electrons are added or subtracted
to give it the proper charge
The structure is written to satisfy the octet rule for each
atom and to give the correct charge
If necessary, multiple bonds can be used to satisfy the octet
rule for each atom 16
⁇ Write the Lewis structure for the chlorate ion (ClO 3
-)

 The total number of valence electrons including the

electron for the negative charge is calculated

 Three pairs of electrons are used to bond the chlorine to

the oxygens

 The remaining 20 electrons are added to give each atom

an octet

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⁇Write the Lewis structure for the carbonate ion (CO 3
2-)

The carbonate ion (CO3-2) with 24 valence electrons and two

negative charges must incorporate a double bond to satisfy
the octet rule for every atom

4 + 3 (6) + 2 = 24

C 3 O 2 e-
The organic molecules ethene (C2H4) and ethyne (C2H2)
must also use multiple bonds to satisfy the octet rule for
each atom

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19
 Formal charge
A formal charge is a positive or negative charge on an
individual atom. The sum of formal charges on individual
atoms is the total charge of the molecule or ion
Formal charge results when we take the number of
valence electrons of a neutral atom, subtract the
nonbonding electrons, and then subtract the number of
bonds connected to that atom in the Lewis structure.
Electrons in bonds are split between the two atoms; one
to each atom
Lone pair electrons belong to the atom itself

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 Examples
Ammonium ion (NH4)+

Nitrate ion (NO3)-

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 An atom will always have the same formal charge depending
on how many bonds and lone pairs it has, regardless of
which particular molecule it is in
 For example a singly bonded oxygen with 3 lone pairs will
always have a negative charge and an oxygen with three
bonds and one lone pair will always have a positive charge
 Knowing these forms of each atom is invaluable in drawing
Lewis structures correctly and rapidly
A Summary of Formal Charges

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 Resonance
Often a single Lewis structure does not accurately
represent the true structure of a molecule
The real carbonate ion is not represented by any of the
structures 1,2 or 3

Experimentally carbonate is known not to have two

carbon-oxygen single bonds and one double bond; all
bonds are equal in length and the charge is spread equally
over all three oxygens
The real carbonate ion can be represented by a drawing in
which partial double bonds to the oxygens are shown and
partial negative charge exists on each oxygen
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 The real structure is a resonance hybrid or mixture of all three
Lewis structures
 Double headed arrows are used to show that the three Lewis
structures are resonance contributors to the true structure

 The use of equilibrium arrows is incorrect since the three

structures do not equilibrate; the true structure is a hybrid
(average) of all three Lewis structures

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 Atomic Orbitals (AOs)
AO describes the probability of finding an electron in a
particular location in space.
There are four types of orbitals that are s, p, d and f. Only s
and p orbitals are very important in organic chemistry.
1s and 2s orbitals are spheres centered around the nucleus
 Each orbital can accommodate 2 electrons
 The 2s orbital is higher in energy
Each 2p orbital has two lobes. There are three 2p orbitals
which are perpendicular to each other.
 Each p orbital can accommodate 2 electrons for a total
of 6 electrons
 All three p orbitals are degenerate (equal in energy)

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 The 2p orbitals are higher in energy than the 1s or 2s

 Atoms can be assigned electronic configuration using the

following rules:
 Aufbau Principle: The lowest energy orbitals are filled first
 Pauli Exclusion Principle: A maximum of two spin paired
electrons may be placed in each orbital
 Hund’s Rule: One electron is added to each degenerate
(equal energy orbital) before a second electron is added

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 The Structure of Methane and Ethane: sp3
Hybridization
The structure of methane with its four identical tetrahedral
bonds cannot be explained using the electronic configuration
of carbon

Ground
State of 6
Carbon

Hybridization of the valence orbitals (2s and 2p) provides 4

new identical orbitals which can be used for the bonding in
methane. When one 2s orbital and three 2p orbitals are
hybridized 4 new and identical sp3 orbitals are obtained
When 4 orbitals are hybridized, 4 orbitals must result
Each new orbital has one part s character and 3 parts p
character
The 4 identical orbitals are oriented in a tetrahedral
arrangements 27
 An sp3 orbital looks like a p
orbital with one lobe greatly
extended
 The extended sp3 lobe can overlap well with the hydrogen 1s
to form a strong bond. The bond formed is called a sigma (s).

 A variety of representations of
methane show its tetrahedral nature
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and electron distribution
 Ethane (C2H6)
The carbon-carbon bond is made from overlap of two sp3
orbitals to form a s bond
The molecule is approximately tetrahedral around each
carbon

a. a. calculated electron density surface b.

ball-and-stick model c. typical 3-
dimensional drawing

 Generally there is free rotation about s

bonds
 Very little energy (13-26 kcal/mol) is
required to rotate around the C-C
bond of ethane
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 The Structure of Ethene: sp2 Hybridization
Ethene (C2H2) contains a carbon-carbon double bond and
is in the class of organic compounds called alkenes.
Another example of the alkenes is propene

The geometry around each carbon is called trigonal

planar
 All atoms connected to each carbon are in a plane
 The bonds point towards the corners of a regular
triangle
 The bond angle are approximately 120o
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 There are three s bonds around each carbon of ethene and
these are formed by using sp2 hybridized orbitals
 The three sp2 hybridized orbitals come from mixing one s
and two p orbitals
 One p orbital is left unhybridized
 The sp2 orbitals are arranged in a trigonal planar arrangement
 The p orbital is perpendicular to the plane

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 Overlap of sp2 orbitals in ethylene results in formation of a s
framework
 One sp2 orbital on each carbon overlaps to form a
carbon-carbon s bond; the remaining sp2 orbitals form
bonds to hydrogen
 The leftover p orbitals on each carbon overlap to form a
bonding p bond between the two carbons

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 Restricted Rotation and the Double Bond
There is a large energy barrier to rotation (about 264
kJ/mol) around the double bond
 This corresponds to the strength of a p bond
 The rotational barrier of a carbon-carbon single bond is
13-26 kJ/mol
This rotational barrier results because the p orbitals must
be well aligned for maximum overlap and formation of the
p bond
Rotation of the p orbitals 90o totally breaks the p bond

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 Cis-trans isomers
Cis-trans isomers are the result of restricted rotation about
double bonds. These isomers have the same connectivity
of atoms and differ only in the arrangement of atoms in
space
The molecules below do not superpose on each other.
One molecule is designated cis (groups on same side)
and the other is trans (groups on opposite side)

Cis-trans isomerism is not possible if one carbon of the

double bond has two identical groups

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 The Structure of Ethyne (Acetylene): sp
Hybridization
Ethyne (acetylene) is a member of a group of compounds
called alkynes which all have carbon-carbon triple bonds
Propyne is another typical alkyne. The carbon in ethyne is
sp hybridized.
 One s and one p orbital are mixed to form two sp orbital
 Two p orbitals are left unhybridized

 The arrangement of atoms around each carbon is linear with

bond angles 180o

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 The two sp orbitals are oriented 180o relative to each other
around the carbon nucleus
 The two p orbitals are perpendicular to the axis that
passes through the center of the sp orbitals
 In ethyne the sp orbitals on the two carbons overlap to form a
s bond. The remaining sp orbitals overlap with hydrogen 1s
orbitals
 The p orbitals on each carbon overlap to form two p bonds
 The triple bond consists of one s and two p bonds
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 Bond Lengths of Ethyne, Ethene and Ethane
The C-C bond length is shorter as more bonds hold the
carbons together. With more electron density between the
carbons, there is more “glue” to hold the nuclei of the
carbons together.
The C-H bond lengths also get shorter with more s
character of the bond.
 2s orbitals are held more closely
to the nucleus than 2p orbitals
 A hybridized orbital with more
percent s character is held more
closely to the nucleus than an
orbital with less s character
The sp orbital of ethyne has 50% s character and its C-H
bond is shorter
The sp3 orbital of ethane has only 25% s character and
its C-H bond is longer 37
 Molecular Geometry: The Valence Shell Electron
Pair Repulsion (VSEPR) Model
This is a simple theory to predict the geometry of molecules
All sets of valence electrons are considered including:
 Bonding pairs involved in single or multiple bonds
 Non-bonding pairs which are unshared
Electron pairs repel each other and tend to be as far apart
as possible from each other
Non-bonding electron pairs tend to repel other electrons
more than bonding pairs do (i.e. they are “larger”)
The geometry of the molecule is determined by the number
of sets of electrons by using geometrical principles

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 Methane
The valence shell of methane contains four
pairs or sets of electrons
To be as far apart from each other as possible
they adopt a tetrahedral arrangement (bond
angle 109.5o)
The molecule methane is therefore tetrahedral
 Ammonia
When the bonding and nonbonding electrons
are considered there are 4 sets of electrons
The molecule is essentially tetrahedral but the
actual shape of the bonded atoms is
considered to be trigonal pyramidal
The bond angles are about 107o and not 109.5o
because the non-bonding electrons in effect
are larger and compress the N-H bond 39
 Water
There are four sets of electrons including
2 bonding pairs and 2 non-bonding pairs
The geometry is essentially tetrahedral
but the actual shape of the atoms is
considered to be an angular arrangement
The bond angle is about 105o because
the two “larger” nonbonding pairs
compress the electrons in the oxygen-
hydrogen bonds
 Boron Trifluoride
Three sets of bonding electrons are
farthest apart in a trigonal planar
arrangement (bond angle 120o). The
three fluorides lie at the corners of an
equilateral triangle 40
 Beryllium Hydride
Two sets of bonding electrons are
farthest apart in a linear arrangement
(bond angles 180o)
(Bond angles 180o)
 Carbon Dioxide
There are only two sets of electrons
around the central carbon and so the
molecule is linear (bond angle 180o)
Electrons in multiple bonds are
considered as one set of electrons in
total

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 Representations of Structural Formulas
Dot formulas are more time-consuming to draw than dash
formulas and condensed formulas.
Lone-pair electrons are often (but not always) drawn in,
especially when they are crucial to the chemistry being
discussed.

 Dash formulas
Each dash represents a pair of electrons
This type of representation is meant to emphasize
connectivity and does not represent the 3-dimensional
nature of the molecule 42
 There is relatively free rotation around single bonds so the
dash structures below are all equivalent

 Constitutional isomers
 Constitutional isomers have the same molecular formula
but different connectivity
 Propyl alcohol (above) is a constitutional isomer of
isopropyl alcohol (below)

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 Condensed Structural Formulas
In these representations, some or all of the dash lines are
omitted
In partially condensed structures all hydrogens attached to
an atom are simply written after it but some or all of the
other bonds are explicitly shown
In fully condensed structure all bonds are omitted and
atoms attached to carbon are written immediately after it
For emphasis, branching groups are often written using
vertical lines to connect them to the main chain

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 Bond-Line Formulas
A further simplification of drawing organic molecules is to
completely omit all carbons and hydrogens and only show
heteroatoms (e.g. O, Cl, N) explicitly
Each intersection or end of line in a zig-zag represents a
carbon with the appropriate amount of hydrogens
 Heteroatoms with attached hydrogens must be drawn in
explicitly

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 Cyclic compounds are condensed using a drawing of the
corresponding polygon

 Multiple bonds are indicated by using the appropriate number

of lines connecting the atoms

 Three-Dimensional Formulas
 Since virtually all organic molecules have a 3-dimensional
shape it is often important to be able to convey their shape

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 The conventions for this are:
 Bonds that lie in the plane of the paper are indicated by a
simple line
 Bonds that come forward out of the plane of the paper are
indicated by a solid wedge
 Bonds that go back out of the plane of the paper are
indicated by a dashed wedge
 Generally to represent a tetrahedral atom:
 Two of the bonds are drawn in the plane of the paper
about 109o apart
 The other two bonds are drawn in the opposite direction to
the in- plane bonds but right next to each other

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