Faculty of Pharmacy

ORGANIC CHEMISTRY
NEPHAR 109 Organic Chemistry I
Assist.Prof.Dr. Banu Keşanlı

*Organic Chemistry, 7th Ed. By Graham Solomons

and Craig Fryhle
Organic Chemistry, 8th Ed. By L.G. Wade, Jr
 FACULTY OF PHARMACY
SPRING 2017 NEPHAR 109 ORGANIC CHEMISTRY I
Instructor:Assist. Prof.Dr. Banu Keşanlı
(banu.kesanli@gmail.com, banu.kesanli@neu.edu.tr)

Office: Faculty of Pharmacy, 12-H115

Office Hours: Tuesday 13:00-14:00

Text Book: Organic Chemistry by Graham Solomons and Craig Fryhle, 7th Ed
Organic Chemistry by John McMurry, 6th Ed (Additional)

Attendance Policy: Attendance is mandatory, % 70. Regular attendance is a vital part

of the educational process and each student is expected to accept the responsibility of
attending classes regularly and promptly.

Grading: Quiz , Problem Sets, 1 Midterm exam and a Final exam

Chapter 1 2
 NEPHAR 109 Lecture Topics
Chapter 1 Introduction to Organic Chemistry
Chapter 3 An Introduction to Organic Reactions: Acids and Bases
Chapter 4 Alkanes, Cycloalkanes
Chapter 6 Alkyl Halides
Chapter 7 Alkenes and Alkynes I:Properties and Synthesis. Elmination
Reactions of Alkyl Halides
Chapter 8 Alkenes and Alkynes II:Addition Reactions
Chapter 5 Stereochemistry
Chapter 10 Radical Reactions
Chapter 13 Conjugated Unsaturated Systems
Chapter 14 Aromatic Compounds
Chapter 15 Reactions of Aromatic Compounds
Introduction and Review:
Structure and Bonding

Atomic structure
Lewis Structures
Resonance
Structural Formulas
Isomers
Bonding
Orbital Theory
Hybridization and Geometry
Polarity

Chapter 1 4
 Chapter 1

Introduction to
Organic Chemistry

"It is not so very important for a person to learn facts, for

that he doesn't really need a college education, for he can
learn them from books. The value of an education in a liberal
arts college is not the learning of many facts but the training
of the mind to think, something that cannot be learned from
books." (Albert Einstein)

Chapter 1 5
 Examples of Structures of Drugs

Acetylsalicylic acid Acetaminophen

Fluoxetine Atorvastatin

Chapter 1 6
Chapter 1 7
Chapter 1 8
 Introduction

 Organic Chemistry

ÎThe chemistry of the compounds of carbon

ÎThe human body is largely composed of

organic compounds

ÎOrganic chemistry plays a central role in

medicine, bioengineering etc.

Chapter 1 9
 Structural Theory
z Central Premises
1.Valency: atoms in organic compounds form
a fixed number of bonds
2.Carbon can form one or more bonds to other
carbons

Chapter 1 10
 Electronic Structure of the Atom

• An atom has a dense, 
positively charged nucleus 
surrounded by a cloud of 
electrons.
• The electron density is 
highest at the nucleus and 
drops off exponentially with 
increasing distance from 
the nucleus in any direction.

Chapter 1 11
Chapter 1 11
Orbitals are Probabilities

12
2s Orbital Has a Node

13
The p Orbital

14
 The 2p Orbitals
• There are three 2p 
orbitals, oriented at 
right angles to each 
other. 
• Each p orbital consists 
of two lobes.
• Each is labeled 
according to its 
orientation along the x, 
y, or z axis.

Chapter 1 15
Chapter 1 15
px, py, pz

16
Electronic Configurations

• The aufbau principle states to 

fill the lowest energy orbitals
first.
• Hund’s rule states that when 
there are two or more 
orbitals of the same energy 
(degenerate), electrons will 
go into different orbitals
rather than pairing up in the 
same orbital.

Chapter 1 17
Chapter 1 17
 Electronic Configurations of Atoms
• Valence electrons are electrons on the 
outermost shell of the atom.

Chapter 1 18
Chapter 1 18
 Chemical Bonds

¾ Ionic Bonds
Formed by transfer of one or more
electrons from one atom to another
to create ions

¾ Covalent Bonds
A bond that results when atoms share
electrons

Chapter 1 19
 Chemical Bonds: The Octet Rule
ÎAtoms form bonds to produce the electron
configuration of a noble gas (because the
electronic configuration of noble gases is
particularly stable)
ÎFor most atoms of interest this means
achieving a valence shell configuration of 8
electrons corresponding to that of the
nearest noble gas
ÎAtoms close to helium achieve a valence
shell configuration of 2 electrons
ÎAtoms can form either ionic or covalent
bonds to satisfy the octet rule

Chapter 1 20
 Ionic Bonds

ÎWhen 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

ÎThe resulting oppositely charged ions attract

and form ionic bonds

ÎThis generally happens between atoms of widely

different electronegativities

Chapter 1 21
 Electronegativity
ÎElectronegativity is the ability of an atom to
attract electrons
ÎIt 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

Chapter 1 22
 Example of an Ionic Bond

• 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 (actually
in a crystalline lattice)

Chapter 1 23
 Covalent Bonding
• Electrons are shared between the atoms to complete
the octet.

• When the electrons are shared evenly, the bond is

said to be nonpolar covalent, or pure covalent.

• When electrons are not shared evenly between the

atoms, the resulting bond will be polar covalent.

• The usual way to indicate the two electrons in a bond

is to use a line (one line = two electrons)

Chapter 1 24
Chapter 1 24
Lewis Dot Structure of Methane
carbon - 4 valence e hydrogen - 1 valence e
.
.C.
. H.
1s22s22p2 1s

25
Tetrahderal Geometry

26
 Bonding Patterns
Valence # Bonds # Lone Pair
electrons Electrons
(group #)
H
1 1 0

C 4 0
4

N
5 3 1

O 6 2 2

Halides 7 1 3
(F, Cl, Br, I)
Chapter 1 27
Chapter 1 27
 Example

ÎWrite the Lewis structure for the chlorate ion

(ClO3-)

•The total number of valence electrons

including the electron for the negative charge
is calculated

Chapter 1 28
• 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

Chapter 1 29
 Lewis Structures
CH4 NH3
H Nitrogen: 5 e
Carbon: 4 e 3 H@1 e ea: 3 e H N H
4 H@1 e ea: 4 e
8 e
H C H 8 e
H
H

H2O Cl2
Oxygen: 6 e
2 H@1 e ea: 2 e H O H 2 Cl @7 e ea: 14 e Cl Cl
8 e

Chapter 1 30
Chapter 1 30
31
Bonding Characteristics of Period 2 
Elements

32
 Multiple Bonding

• Sharing two pairs of electrons is called a double bond.
• Sharing three pairs of electrons is called a triple bond.

Chapter 1 33
Chapter 1 33
 Exceptions to the Octet Rule
• The octet rule applies only to atoms in the
second row of the periodic table (C, O, N, F)
which are limited to valence electrons in the
2s and 2p orbitals
• In second row elements fewer electrons are
possible
ÎExample: BF3

Chapter 1 34
• In higher rows other orbitals are
accessible and more than 8 electrons
around an atom are possible
Example: PCl5 and SF6

Chapter 1 35
Convert Formula into Lewis Structure
• HCN

• O3

Chapter 1 36
 Formal Charge

A formal charge is a positive or negative

charge on an individual atom
ÎThe sum of formal charges on individual
atoms is the total charge of the molecule or
ion
ÎThe formal charge is calculated by
subtracting the assigned electrons on the
atom in the molecule from the electrons in
the neutral atom
ÎElectrons in bonds are evenly split between
the two atoms; one to each atom
ÎLone pair electrons belong to the atom itself

Chapter 1 37
 Formal Charges
Formal charge = [group number ] – [nonbonding electrons ] – ½ [shared electrons]

H3O+ NO+
6 – 2 – ½ (6) =  +1 6 – 2 – ½ (6) =  +1

+
H O H N O+
+
5 – 2 – ½ (6) =  0
H

• Formal charges are a way of keeping track of electrons.
• They may or may not correspond to actual charges in the 
molecule.

Chapter 1 38
Chapter 1 38
Examples (NH4NO3)
• Ammonium ion (NH4)+

• Nitrate ion (NO3)-

Chapter 1 39
Common Bonding Patterns

40
Chapter 1 40
 Resonance Forms
Resonance forms can be compared using the 
following criteria, beginning with the most 
important:
1. Has as many octets as possible.
2. Has as many bonds as possible.
3. Has the negative charge on the most 
electronegative atom.
4. Has as little charge separation as possible.

41
Chapter 1 41
 Resonance Structures
¾Molecules that require description with resonance are those for which
can be written by two or more Lewis structures that differ only in the
position of electrons
If the structures differ in the position of atoms, they are isomers,
not resonance structures

¾Because they differ only in the positions of electrons, we can show

how resonance structures are related by showing the electron
motions that would change one resonance structure into the other.

42
 Resonance Structures
¾ All resonance structures must be valid Lewis structures.

¾ In all possible resonance structures the atomic nuclei must

not change their positions.

¾ All atoms must not change their hybridization.

¾ Only unshared electrons and electrons that are part of

multiple bonds (p-bonds) can be moved in drawing resonance
structures; that is, resonance can occur only in those parts of
molecules that are composed of sp or sp2 atoms;

43
Two Nonequivalent Resonance 
Structures in Formaldehyde

44
 Major and Minor Contributors
• When both resonance forms obey the octet rule, the 
major contributor is the one with the negative charge 
on the most electronegative atom.

N C O N C O
MAJOR                                                            MINOR

The oxygen is more electronegative,
so it should have more of the negative
charge.

45
Chapter 1 45
 Resonance Stabilization of Ions
Pos. charge is “delocalized”
H H H H
C C C C
H H
H C H C
H H
H δ+ H
C C δ+
H
H C
H
resonance hybrid
46
 Example
Draw the resonance structures of the compound below.

Solution

47
Chapter 1 47
Determining Molecular Shape—Bond Angle

Bond angle determines the shape around any atom

bonded to two other atoms.
• The number of groups surrounding a particular atom
determines its geometry. A group is either an atom or a
lone pair of electrons.
• The most stable arrangement keeps these groups as
far away from each other as possible. This is
exemplified by Valence Shell Electron Pair Repulsion
(VSEPR) theory.

Chapter 1 48
Two groups around an atom—

Chapter 1 49
Three groups around an atom—

Chapter 1 50
Four groups around an atom—

Chapter 1 51
Drawing Three Dimensional Structures
• A solid line is used for a bond in the plane.
• A wedge is used for a bond in front of the plane.
• A dashed line is used for a bond behind the plane.

Chapter 1 52
The molecule can be turned in many different ways,
generating many equivalent representations. All of the
following are acceptable drawings for CH4.

Chapter 1 53
Note that wedges and dashes are used for groups
that are really aligned one behind another. It does
not matter in the following two drawings whether the
wedge or dash is skewed to the left or right, because
the two H atoms are really aligned.

Chapter 1 54
A Nonbonded Pair of Electrons is Counted as a
“Group”

In ammonia (NH3), one of the four groups attached to the

central N atom is a lone pair. The three H atoms and the
lone pair point to the corners of a tetrahedron. The H-N-H
bond angle of 107° is close to the theoretical tetrahedral
bond angle of 109.5°. This shape is referred to as a
trigonal pyramid.

Chapter 1 55
In water (H2O), two of the four groups attached to the
central O atom are lone pairs. The two H atoms and
two lone pairs around O point to the corners of a
tetrahedron. The H-O-H bond angle of 105° is close to
the theoretical tetrahedral bond angle of 109.5°. Water
has a bent shape, because the two groups around
oxygen are lone pairs of electrons.

Chapter 1 56
 In both NH3 and H2O,
Methane (CH4) the bond angle is
smaller than the
theoretical tetrahedral
bond angle because of
Ammonia (NH3) repulsion of the lone
pairs of electrons. The
bonded atoms are
compressed into a
smaller space with a
smaller bond angle.

Water (H2O)

Chapter 1 57
Predicting Geometry Based on Counting of Groups
Around the Central Atom

Chapter 1 58
Predict the geometry of the following:
O
O NH2

4 groups 4 groups
3 groups
tetrahedral tetrahedral
Trigonal
planar

Predict the indicated angle.

O Cl

120° H3C H 109.5°

H3C Cl
H

Chapter 1 59
Representations of Structural Formulas

ÎDot formulas are more cumbersome to draw

than dash formulas and condensed formulas
ÎLone-pair electrons are often (but not
always) drawn in, especially when they are
crucial to the chemistry being discussed

Chapter 1 60
 Condensed Structural Formulas

ÎIn these representations, some or all of the

dash lines are omitted
ÎIn 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
ÎIn fully condensed structure all bonds are
omitted and atoms attached to carbon are
written immediately after it
ÎFor emphasis, branching groups are often
written using vertical lines to connect them
to the main chain

Chapter 1 61
 Drawing Structures
H H
H H H
H H H C C C H
C C H H
H C C H
H H C
H H H H
H
Butane, C 4H10 Methylpropane, C 4H10

CH 3CH 2CH 2CH 3 CH 3CH(CH 3)CH 3

62
 Octane Representations
C8H18 is molecular formula but there are 18 possible structural isomers

H H H H H H H CH 3CH 2CH 2CH 2CH 2CH 2CH 2CH 3

C C C C H
H C C C C
H CH 3(CH 2)6CH 3
H H H HH H HH
Lewis structure condensed structural formula

63
Examples for Condensed Structural Formulas

Chapter 1 64
 Bond-Line Formulas

ÎA further simplification of drawing organic

molecules is to completely omit all carbons
and hydrogens and only show heteroatoms
(e.g. O, Cl, N) explicitly

ÎEach 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

Chapter 1 65
Example for Bond-Line Formulas

Chapter 1 66
Line-Angle Structures are Often Used as a
Short-hand

H H H H H H H
C C C C H
H C C C C
H
H H H H H H HH
Lewis structure

Line-angle or Chapter
"zig-zag"
1 structures 67
 Three-Dimensional Formulas
ÎSince virtually all organic molecules have a 3-
dimensional shape it is often important to be able to
convey their shape
ÎThe 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

Chapter 1 68
 Dash Formulas
ÎEach dash represents a pair of electrons
ÎThis type of representation is meant to
emphasize connectivity and does not represent
the 3-dimensional nature of the molecule
• The dash formulas of propyl alcohol appear to
have 90o angles for carbons which actually
have tetrahedral bond angles (109.5o)
ÎThere is relatively free rotation around single
bonds so the dash structures below are all
equivalent

Chapter 1 69
ÎCyclic compounds are condensed using a
drawing of the corresponding polygon

ÎMultiple bonds are indicated by using the

appropriate number of lines connecting the
atoms

Chapter 1 70
 Cyclohexane
H H
H H
C
H C C H
H C C H
H C
H
H H

71
Examples of Skeletal Structures

72
 Example: Some Steroids

OH

HO O
Cholesterol Testosterone

73