Organic Chemistry

KIM0192

Assoc. Prof. Omer Y. Gumus

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What is organic chemistry?

Organic chemistry is the study of the structure, properties, composition, reactions, and
preparation of carbon-containing compounds

These compounds include not only hydrocarbons but also compounds with any number
of other elements, including
hydrogen (most compounds contain at least one carbon–hydrogen bond)
nitrogen
oxygen
halogens
phosphorus
silicon
sulfur

This branch of chemistry was originally limited to compounds produced by living

organisms but has been broadened to include human-made substances such as
plastics.

The range of application of organic compounds is enormous and also includes, but is not
limited to, pharmaceuticals, petrochemicals, food, explosives, paints, and cosmetics.

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 Where Is Organic Chemistry Used?

Organic chemistry is a highly creative science in which chemists create new molecules and explore the
properties of existing compounds.

Organic compounds are all around us. They are central to the economic growth of the developed countries in the
rubber, plastics, fuel, pharmaceutical, cosmetics, detergent, coatings, dyestuff, and agrichemical industries.

The very foundations of biochemistry, biotechnology, and medicine are built on organic compounds and their role
in life processes.

Many modern, high-tech materials are at least partially composed of organic compounds.

Organic chemists spend much of their time creating new compounds and developing better ways of synthesizing
previously known compounds.

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The Carbon Atom
Physical Properties of the Carbon Atom
Atomic Number: 6
Atomic Mass Average: 12.011
Melting Point: 3823 K (3550°C or 6422°F)
Boiling Point: 4098 K (3825°C or 6917°F)
Density: 2.267g/cm3
Hardness Scale Mohs: 0.5
Stable Isotopes: 12C, 13C and 14C

There are eight known allotropes of carbon:

diamond graphite Lonsdaleite C540, Fullerite C70 single-walled

amorphous carbon carbon nanotube.
C60 buckminsterfullerene
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 Chapter 1:
The Basics
Bonding and Molecular Structure
1.1 Atomic Structure

• The compounds we encounter in chemistry are made up of elements combined in different proportions.

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• Elements are made up of atoms.

• An atom consists of a dense, positively charged nucleus containing protons and neutrons and a
surrounding cloud of electrons.

Each proton of the nucleus bears one positive charge; electrons bear one
negative charge.

Neutrons are electrically neutral; they bear no charge.

Protons and neutrons have nearly equal masses (approximately 1 atomic mass
unit each) and are about 1800 times as heavy as electrons.
Figure
Most of the mass of an atom, therefore, comes from the mass of the nucleus; An atom is
the atomic mass contributed by the electrons is negligible. composed of a tiny nucleus
containing protons and neutrons
and a large surrounding volume
Most of the volume of an atom, however, comes from the electrons; the volume of containing electrons. The
an atom occupied by the electrons is about 10,000 times larger than that of the diameter of a typical atom is
nucleus. about 10,000 times the diameter
of its nucleus.
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 1.1A Isotopes

Although all the nuclei of all atoms of the same element will have the same number of protons,
some atoms of the same element may have different masses because they have different
numbers of neutrons.

Such atoms are called isotopes.

For example, about 1% of the atoms of elemental carbon have nuclei containing 7 neutrons, and thus
have a mass number of 13. Such atoms are written 13C.

A tiny fraction of carbon atoms have 8 neutrons in their nucleus and a mass number of 14.

Unlike atoms of carbon-12 and carbon-13, atoms of carbon-14 are radioactive.

The 14C isotope is used in carbon dating. The three forms of carbon, 12C, 13C, and 14C, are isotopes of
one another.

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 1.1B Valence Electrons

The electrons that surround the nucleus exist in shells of increasing energy and at increasing distances
from the nucleus.

The most important shell, called the valence shell, is the outermost shell because the electrons of this
shell are the ones that an atom uses in making chemical bonds with other atoms to form compounds.

• How do we know how many electrons an atom has in its valence shell?

We look at the periodic table. The number of electrons in the valence shell (called valence electrons) is
equal to the group number of the atom.

For example, carbon is in group IVA and carbon has four valence electrons; oxygen is in group VIA and
oxygen has six valence electrons. The halogens of group VIIA all have seven electrons.

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 1.3 Chemical Bonds: The Octet Rule

Two major types of chemical bonds were proposed:

1. Ionic (or electrovalent) bonds are formed by the transfer of one or more electrons
from one atom to another to create ions.

2. Covalent bonds result when atoms share electrons.

The central idea is that atoms without the electronic configuration of a noble gas generally react to
produce such a configuration because these configurations are known to be highly stable.

For all of the noble gases except helium, this means achieving an octet of electrons in the valence shell.

• The tendency for an atom to achieve a configuration where its valence shell contains eight electrons is
called the octet rule.

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 1.3A Ionic Bonds

Atoms may gain or lose electrons and form charged particles called ions.

• An ionic bond is an attractive force between oppositely charged ions

• Electronegativity is a measure of the ability of an atom to attract electrons.

Electronegativity increases as we go across a horizontal row of the periodic table

from left to right and it increases as we go up a vertical column

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 1.3B Covalent Bonds and Lewis Structures

When two or more atoms of the same or similar electronegativities react, a complete transfer of electrons
does not occur.

In these instances the atoms achieve noble gas configurations by sharing electrons.

• Covalent bonds form by sharing of electrons between atoms of similar electronegativities to achieve the
configuration of a noble gas.

• Molecules are composed of atoms joined exclusively or predominantly by covalent bonds.

Molecules may be represented by electron-dot formulas or, more conveniently, by bond formulas where
each pair of electrons shared by two atoms is represented by a line.

Some examples are shown here:

1. Hydrogen, being in group IA of the periodic table, has one valence electron. Two
hydrogen atoms share electrons to form a hydrogen molecule, H2.

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2. Because chlorine is in group VIIA, its atoms have seven valence electrons.

Two chlorine atoms can share electrons (one electron from each) to form a molecule of Cl2.

usually written

3. And a carbon atom (group IVA) with four valence electrons can share each of these electrons with four
hydrogen atoms to form a molecule of methane, CH4.

usually written

These formulas are often called Lewis structures; in writing them only the electrons of the valence shell are
shown .

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4. Atoms can share two or more pairs of electrons to form multiple covalent bonds.

For example, two nitrogen atoms possessing five valence electrons each (because nitrogen is in group VA) can
share electrons to form a triple bond between them.

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 1.4 How to Write Lewis Structures

Several simple rules allow us to draw proper Lewis structures:

1. Lewis structures show the connections between atoms in a molecule or ion using only the valence
electrons of the atoms involved. Valence electrons are those of an atom’s outermost shell.

2. For main group elements, the number of valence electrons a neutral atom brings to a Lewis structure is
the same as its group number in the periodic table. Carbon, for example, is in group IVA and has four valence
electrons; the halogens (e.g., fluorine) are in group VIIA and each has seven valence electrons; hydrogen is in group
IA and has one valence electron.

3. If the structure we are drawing is a negative ion (an anion), we add one electron for each negative charge
to the original count of valence electrons. If the structure is a positive ion (a cation), we subtract one
electron for each positive charge.

4. In drawing Lewis structures we try to give each atom the electron configuration of a noble gas. To do so,
we draw structures where atoms share electrons to form covalent bonds or transfer electrons to form ions.

a. Hydrogen forms one covalent bond by sharing its electron with an electron of another atom so that it can have two
valence electrons, the same number as in the noble gas helium.

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b. Carbon forms four covalent bonds by sharing its four valence electrons with four valence electrons from other
atoms, so that it can have eight electrons (the same as the electron configuration of neon, satisfying the octet
rule).

c. To achieve an octet of valence electrons, elements such as nitrogen, oxygen, and the halogens typically share
only some of their valence electrons through covalent bonding, leaving others as unshared electron pairs.
The following problems illustrate this method.

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State of the electrons are described by quantum numbers;

principal quantum number : n 1, 2, 3 …..

azimuthal quantum number: ℓ = n-1

magnetic quantum number : ml = - ℓ …,0,…+ ℓ

spin quantum number: s = -1/2 or +1/2

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Atomic Structure of Carbon

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18
The actual location of electrons in a carbon atom cannot be determined with certainty

2s 2px 2py

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Orbital Shapes

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MOLECULE ORBITAL THEORY

Molecular orbitals are obtained by combining the atomic orbitals on the atoms in the molecule.

Consider the H2 molecule, for example. One of the molecular orbitals in this molecule is constructed by adding the
mathematical functions for the two 1s atomic orbitals that come together to form this molecule.

Another orbital is formed by subtracting one of these functions

from the other, as shown in the figure below

One of these orbitals is called a bonding molecular

orbital because electrons in this orbital spend most of their
time in the region directly between the two nuclei.
It is called as sigma (s) molecular orbital

Electrons placed in the other orbital spend most of their time

away from the region between the two nuclei. This orbital is
therefore an antibonding, and called as sigma star (s).

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The s bonding molecular orbital
concentrates electrons in the region directly
between the two nuclei. Placing an electron
in this orbital therefore stabilizes the
H2 molecule.

Since the s antibonding molecular orbital

forces the electron to spend most of its
time away from the area between the
nuclei, placing an electron in this orbital
makes the molecule less stable.
Electrons are added to molecular orbitals, one at a time, starting with the lowest energy molecular
orbital.

The two electrons associated with a pair of hydrogen atoms are placed in the lowest energy, or s
bonding, molecular orbital.
This diagram suggests that the energy of an H2 molecule is lower than that of a pair of isolated
atoms. As a result, the H2 molecule is more stable than a pair of isolated atoms. 22
Molecular Orbitals of the Second Energy Level

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 Hybridization

The s and p orbitals used in the quantum mechanical description of the carbon atom were based on
calculations for hydrogen atoms.

When taken alone, these simple s and p orbitals do not provide a satisfactory model for
the tetravalent–tetrahedral carbon of methane.

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 However, a satisfactory model of methane’s structure that is based on quantum
mechanics can be obtained through an approach called orbital hybridization

Orbital hybridization, in its simplest terms, is nothing more than a mathematical approach
that involves the combining of individual wave functions for s and p orbitals to obtain wave
functions for new orbitals.

position vector momentum space:

2ℓ + 1
where a0 = 4πε0ħ2/mee2 is the Bohr radius, Ln − ℓ − 1 are the generalized Laguerre polynomials of
degree n − ℓ − 1, n = 1, 2, ... is the princibal quantum number, ℓ = 1, 2, ... n − 1 the azimuthal
quantum number , m = −ℓ, −ℓ + 1, ..., ℓ − 1, ℓ the magnetic quantum number.

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 The Structure of Methane
Hybrid atomic orbitals that account for the structure of methane can be derived from carbon’s
second-shell s and p orbitals

Wave functions for the 2s, 2px, 2py, and 2pz orbitals of ground state carbon are
mixed to form four new and equivalent 2sp3 hybrid orbitals.

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The designation sp3 signifies that the hybrid orbital has one part s orbital character and three parts p
orbital character.

The mathematical result is that the four 2sp3 orbitals are oriented at angles of 109.5° with respect to
each other. This is precisely the orientation of the four hydrogen atoms of methane. Each H-C-H bond
angle is 109.5°.

The hypothetical formation of methane from an sp3-hybridized carbon atom and four hydrogen atoms,
the process might be like as follows

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In addition to accounting properly for the shape of methane, the orbital hybridization model also explains the very
strong bonds that are formed between carbon and hydrogen.

Because an sp3 orbital has the character of a p orbital, the positive lobe of an sp3 orbital is large and extends
relatively far from the carbon nucleus.

It is the positive lobe of an sp3 orbital that overlaps with the positive 1s orbital of hydrogen to form the bonding
molecular orbital of a carbon–hydrogen bond.

Because the positive lobe of the sp3 orbital is large and is extended into space, the overlap between it and the 1s
orbital of hydrogen is also large, and the resulting carbon–hydrogen bond is quite strong.

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The bond formed from the overlap of an sp3 orbital and a 1s orbital is an
example of a sigma (S) bond

A sigma (S) bond has a circularly symmetrical orbital cross section when
viewed along the bond between two atoms.

All purely single bonds are sigma bonds.

A s (sigma) bond. 32
 The Structure of Ethane
The bond angles at the carbon atoms of ethane, and of all alkanes, are also tetrahedral like those in methane.

A satisfactory model for ethane can be provided by sp3-hybridized carbon atoms.

The bonding molecular orbitals of an ethane molecule being constructed from two sp3-hybridized carbon atoms
and six hydrogen atoms.

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 The Structure of Ethene (Ethylene): sp2 Hybridization

The carbon atoms of many of the molecules that we have considered so far have used their four valence
electrons to form four single covalent (sigma) bonds to four other atoms.

Many important organic compounds exist in which carbon atoms share more than two electrons with another
atom.

In molecules of these compounds some bonds that are formed are multiple covalent bonds.

When two carbon atoms share two pairs of electrons, for example, the result is a carbon–carbon double bond:

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Hydrocarbons whose molecules contain a carbon–carbon double bond are called alkenes.

Ethene (C2H4) and propene (C3H6) are both alkenes. (Ethene is also called ethylene, and propene is sometimes
called propylene.)

In ethene the only carbon–carbon bond is a double bond. Propene has one carbon–carbon single bond and
one carbon–carbon double bond.

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The spatial arrangement of the atoms of alkenes is different from that of alkanes

The six atoms of ethene are coplanar, and the arrangement of atoms around each carbon atom is triangular

Carbon–carbon double bonds are comprised of sp2-hybridized carbon atoms.

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The 2s orbital is mathematically mixed (or hybridized) with two of the 2p orbitals. (The hybridization procedure
applies only to the orbitals, not to the electrons.)

One 2p orbital is left unhybridized. One electron is then placed in each of the sp2 hybrid orbitals and one
electron remains in the 2p orbital.

The three sp2 orbitals that result from hybridization are directed toward the corners of a regular triangle (with
angles of 120° between them).

The carbon p orbital that is not hybridized is perpendicular to the plane of the triangle formed by the hybrid
sp2 orbitals

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Two sp2-hybridized carbon atoms form a sigma (s) bond between them by overlap of one sp2 orbital from
each carbon.

The remaining carbon sp2 orbitals form s bonds to four hydrogens through overlap with the hydrogen 1s
orbitals.

These five s bonds account for 10 of the 12 valence electrons contributed by the two carbons and four
hydrogens, and comprise the S-bond framework of the molecule.

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 The remaining two bonding electrons are each located in an unhybridized p orbital of each carbon. Sideways
overlap of these p orbitals and sharing of the two electrons between the carbons leads to a pi (P) bond.

When two p atomic orbitals combine to form a pi bond, two molecular orbitals form: One is a bonding molecular
orbital and the other is an antibonding molecular orbital.

To summarize, a carbon–carbon double bond consists of

one s bond and one pi bond

Electrons of the p bond have greater

energy than electrons of the s bond.

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 Restricted Rotation and the Double Bond
The s–p model for the carbon–carbon double bond also accounts for an important property of the double bond:

There is a large energy barrier to rotation associated with groups joined by a double bond.

Maximum overlap between the p orbitals of a pi-bond occurs when the axes of the p orbitals are exactly
parallel.

Rotating one carbon of the double bond 90° breaks the pi bond, for then the axes of the p orbitals are
perpendicular and there is no net overlap between them.

While groups joined by single bonds rotate relatively freely at room temperature, those joined by double bonds
do not. 41
 Cis–Trans Isomerism

Restricted rotation of groups joined by a double bond causes a new type of isomerism.

These two compounds are isomers; they are different compounds that have the same molecular formula.

We indicate that they are different isomers by attaching the prefix cis or trans to their names (cis, Latin: on this
side; trans, Latin: across).

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cis-1,2-Dichloroethene and trans-1,2-dichloroethene are not constitutional isomers because the connectivity of
the atoms is the same in each.

The two compounds differ only in the arrangement of their atoms in space. Isomers of this kind are
classified formally as stereoisomers, but often they are called simply cis–trans isomers.

Cis or trans ?

cis–trans isomerism is not possible if one carbon atom of the double bond bears two identical groups

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Problem: Which of the following alkenes can exist as cis–trans isomers?

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 The Structure of Ethyne (Acetylene): sp Hybridization

Hydrocarbons in which two carbon atoms share three pairs of electrons between them, and
are thus bonded by a triple bond, are called alkynes

The two simplest alkynes are ethyne and propyne.

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In model for ethyne carbon atoms are sp hybridized.

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The 2s orbital and one 2p orbital of carbon are hybridized to form two sp orbitals.

The remaining two 2p orbitals are not hybridized.

Calculations show that the sp hybrid orbitals have their large positive lobes oriented at an angle of
180° with respect to each other.

The two 2p orbitals that were not hybridized are each perpendicular to the axis that passes through
the center of the two sp orbitals

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Two carbon atoms overlap sp orbitals to form a sigma bond between them (this is one bond of the
triple bond).

The remaining two sp orbitals at each carbon atom overlap with s orbitals from hydrogen atoms to
produce two sigma C-H bonds.

The two p orbitals on each carbon atom also overlap side to side to form two p bonds. These are
the other two bonds of the triple bond.

The carbon–carbon triple bond consists of two p bonds and one s bond.

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The carbon–carbon triple bond of ethyne is shorter than the carbon–carbon double bond of ethene, which
in turn is shorter than the carbon–carbon single bond of ethane.

The reason is that bond lengths are affected by the hybridization states of the carbon atoms involved.

The greater the s orbital character in one or both atoms, the shorter is the bond.

This is because s orbitals are spherical and have more electron density closer to the nucleus than do p
orbitals.

The greater the p orbital character in one or both atoms, the longer is the bond.

This is because p orbitals are lobe-shaped with electron density extending away from the nucleus.

In terms of hybrid orbitals, an sp hybrid orbital has 50% s character and 50% p character.

An sp2 hybrid orbital has 33% s character and 67% p character. An sp3 hybrid orbital has

25% s character and 75% p character. The overall trend, therefore, is as follows:

Bonds involving sp hybrids are shorter than those involving sp2 hybrids, which are shorter than those
involving sp3 hybrids. This trend holds true for both C-C and C-H bonds.

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 A Summary of Important Concepts That
Come from Quantum Mechanics

1. An atomic orbital (AO) corresponds to a region of space about the nucleus of a single atom where there is
a high probability of finding an electron. Atomic orbitals called s orbitals are spherical; those called p orbitals
are like two almost-tangent spheres. Orbitals can hold a maximum of two electrons when their spins are
paired.

Orbitals are described by the square of a wave function, Ψ2, and each orbital has a characteristic energy. The
phase signs associated with an orbital may be + or -.

2. When atomic orbitals overlap, they combine to form molecular orbitals (MOs).

Molecular orbitals correspond to regions of space encompassing two (or more) nuclei where electrons are to
be found. Like atomic orbitals, molecular orbitals can hold up to two electrons if their spins are paired.

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3. When atomic orbitals with the same phase sign interact, they combine to form a bonding molecular
orbital:

The electron probability density of a bonding molecular orbital is large in the region of
space between the two nuclei where the negative electrons hold the positive nuclei
together.

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4. An antibonding molecular orbital forms when orbitals of opposite phase sign overlap:

An antibonding orbital has higher energy than a bonding orbital.

The electron probability density of the region between the nuclei is small and it contains a node—a
region where Ψ= 0.

Thus, having electrons in an antibonding orbital does not help hold the nuclei together. The
internuclear repulsions tend to make them fly apart.

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5. The energy of electrons in a bonding molecular orbital is less than the energy of the electrons in their
separate atomic orbitals. The energy of electrons in an antibonding orbital is greater than that of electrons in
their separate atomic orbitals.

6. The number of molecular orbitals always equals the number of atomic orbitals from which they are
formed. Combining two atomic orbitals will always yield two molecular orbitals—one bonding and one
antibonding.

7. Hybrid atomic orbitals are obtained by mixing (hybridizing) the wave functions for orbitals of different
types (i.e., s and p orbitals) but from the same atom.

8. Hybridizing three p orbitals with one s orbital yields four sp3 orbitals. Atoms that are sp3 hybridized direct
the axes of their four sp3 orbitals toward the corners of a tetrahedron. The carbon of methane is sp3
hybridized and tetrahedral.

9. Hybridizing two p orbitals with one s orbital yields three sp2 orbitals. Atoms that are sp2 hybridized point
the axes of their three sp2 orbitals toward the corners of an equilateral triangle. The carbon atoms of ethene
are sp2 hybridized and trigonal planar.

10. Hybridizing one p orbital with one s orbital yields two sp orbitals. Atoms that are sp hybridized orient the
axes of their two sp orbitals in opposite directions (at an angle of 180°). The carbon atoms of ethyne are sp
hybridized and ethyne is a linear molecule.
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11. A sigma (s) bond (a type of single bond) is one in which the electron density has circular symmetry
when viewed along the bond axis. In general, the skeletons of organic molecules are constructed of
atoms linked by sigma bonds.

12. A pi (p) bond, part of double and triple carbon–carbon bonds, is one in which the electron densities of
two adjacent parallel p orbitals overlap sideways to form a bonding pi molecular orbital.

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 How to Interpret and Write Structural Formulas
Organic chemists use a variety of ways to write structural formulas. The most common types of representations
are shown below:

The dot structure shows all of the valence electrons, but writing it is tedious and time-consuming.

The other representations are more convenient and are, therefore, more often used.

Sometimes we even omit unshared pairs when we write formulas. However, to write chemical reactions, it is
necessary to include the unshared electron pairs when they participate in the reaction.

It is a good idea, therefore, to get into the habit of writing the unshared (nonbonding) electron pairs in the
structures you draw.
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 Dash Structural Formulas

When dot, dash, and condensed formulas are compared it seen that the chain of atoms is straight in those formulas.

The chain of atoms is not at all straight in the actual shape of the molecule

Because,

Atoms joined by single bonds can rotate relatively freely with respect to one another.

This relatively free rotation means that the chain of atoms in propyl alcohol can assume a variety of
arrangements like these:

Dash structural formulas such as these indicate the way in which the atoms are attached to each other
and are not representations of the actual shapes of the molecule.
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 Condensed Structural Formulas

Condensed structural formulas are somewhat faster to write than dash formulas and they will impart
all the information that is contained in the dash structure.

In condensed formulas all of the hydrogen atoms that are attached to a particular carbon are usually written
immediately after the carbon.

In fully condensed formulas, all of the atoms that are attached to the carbon are usually written immediately after
that carbon, listing hydrogens first.

Example:

1- Write a condensed formula for isopropyl alcohol (hint: can be written in four different ways)

2- Write a condensed structural formula for the compound

that follows:

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 Bond-Line Formulas

The most common type of structural formula used by organic chemists, and the fastest to draw, is the bond-
line formula.

The efficiencies of drawing bond-line formulas come from the fact that no Cs are written for carbon atoms, and
generally no Hs are shown for hydrogen atoms, unless they are needed to give a three-dimensional
rerspective to the molecule (and in that case we use solid or dashed wedges for bonds to the out-of-plane
atoms, as described in the following section).

In bond-line formulas ordinary lines represent bonds, and carbon atoms are inferred at each bend in the line
and at the ends of lines.

The number of hydrogen atoms bonded to each carbon is also inferred, by assuming that as many hydrogen atoms
are present as needed to fill the valence shell of each carbon, unless a charge is indicated

When an atom other than carbon is present, the symbol for that element is written in the formula at the
appropriate location, i.e., in place of a bend or at the terminus of the line leading to the atom.

Hydrogen atoms bonded to atoms other than carbon (e.g., oxygen or nitrogen) are written explicitly

Hydrogen atoms are shown where needed to help specify three dimensions using solid or dashed wedges.
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60
Exercise: Write the bond-line formulas of the following molecules:

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 Three-Dimensional Formulas
None of the formulas that we have described so far conveys any information about how the atoms of a
molecule are arranged in space.

There are several types of representations to do this.

 bonds that project upward out of the plane of the paper are indicated by a solid wedge ( ),

 those that lie behind the plane are indicated with a dashed wedge ( ),

 and those bonds that lie in the plane of the page are indicated by a line (—).

when drawing three-dimensional formulas is it generally best to draw as many carbon atoms as possible in
the plane of the paper, allowing substituent groups or hydrogen atoms to be primarily those for which wedge
or dashed-wedge bonds are used.

Write three-dimensional (wedge–dashed wedge–line) representations for each of the

following:
(a) CH3Cl (b) CH2Cl2 (c) CH2BrCl (d) CH3CH2Cl (e) ethane, (f) bromomethane

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