Faculty of Pharmacy
ORGANIC CHEMISTRY
NEU Organic Chemistry
Assist.Prof. Banu Keşanlı
*Organic Chemistry, 7th Ed.
Graham Solomons and Craig Fryhle
Chapter 1
Introduction to
Organic Chemistry
Chapter 1 2
1.1 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 3
Vitalism
¾It was originally thought organic compounds
could be made only by living things by
intervention of a “vital force”
¾Fredrich Wöhler disproved vitalism in 1828
by making the organic compound urea from
the inorganic salt ammonium cyanate by
evaporation:
Chapter 1 4
1.3 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 5
1.3A Isomers
ÎIsomers are different molecules with the same
molecular formula
ÎMany types of isomers exist
Example
• Consider two compounds with molecular formula
e.g. 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
Chapter 1 6
C2H6O
Chapter 1 7
Constitutional Isomers
ÎConstitutional isomers are one type of
isomer
ÎThey are different compounds that have the
same molecular formula but different
connectivity of atoms
ÎThey often differ in physical properties (e.g.
boiling point, melting point, density) and
chemical properties
Chapter 1 8
Example for Constitutional Isomers
Chapter 1 9
Three Dimensional Shape of Molecules
ÎIt was proposed in 1874 by van’t Hoff and le
Bel that the four bonds around carbon where
not all in a plane but rather in a tetrahedral
arrangement i.e. the four C-H bonds point
towards the corners of a regular tetrahedron
Chapter 1 10
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 11
1.4. 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 12
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 13
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 14
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 15
Covalent Bonds
¾ Covalent bonds occur between atoms of
similar electronegativity (close to each other in
the periodic table)
¾ Atoms achieve octets by sharing of valence
electrons
¾ Molecules result from this covalent bonding
¾ Valence electrons can be indicated by dots
(electron-dot formula or Lewis structures) but
this is time-consuming
¾ The usual way to indicate the two electrons in
a bond is to use a line (one line = two
electrons)
Chapter 1 16
1.5 Writing Lewis Structures
ÎAtoms bond by using their valence electrons
ÎThe 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
Chapter 1 17
Lewis Structures continued
ÎTo construct molecules the atoms are assembled
with the correct number of valence electrons
ÎIf the molecule is an ion, electrons are added or
subtracted to give it the proper charge
ÎThe structure is written to satisfy the octet rule
for each atom and to give the correct charge
ÎIf necessary, multiple bonds can be used to satisfy
the octet rule for each atom
Chapter 1 18
Examples of Covalent Bonding
Chapter 1 19
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 20
• 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 21
1.6 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 22
• In higher rows other orbitals are
accessible and more than 8 electrons
around an atom are possible
Example: PCl5 and SF6
Chapter 1 23
1.7 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 24
Examples (NH4NO3)
• Ammonium ion (NH4)+
• Nitrate ion (NO3)-
Chapter 1 25
A Summary of Formal Charges
Chapter 1 26
1.8 Resonance
¾ Theory used to represent and model certain types
of non-classical molecular structures
ÎOften a single Lewis structure does not
accurately represent the true structure of a
molecule
ÎThe true carbonate structure is a hybrid
(average) of all three Lewis structures
Chapter 1 27
ÎThe carbonate ion (CO32-) with 24 valence
electrons and two negative charges must
incorporate a double bond to satisfy the
octet rule for every atom
Chapter 1 28
1.9 Quantum Mechanics
ÎA mathematical description of bonding that
takes into account the wave nature of
electrons
ÎA wave equation is solved to yield a series of
wave functions for the atom
ÎThe wave functions psi (Ψ) describe a series
of states with different energies for each
electron
ÎWave Equations are used to calculate:
•The energy associated with the state of the
electron
•The probability of finding the electron in a
particular state Chapter 1 29
1.10 Atomic Orbitals (AOs)
ÎThe physical reality of Ψ is that when squared
(Ψ 2) it gives the probability of finding an
electron in a particular location in space
ÎPlots of Ψ 2 in three dimensions generate the
shape of s, p, d and f orbitals
ÎOnly s and p orbitals are very important in
organic chemistry
ÎOrbital: a region in space where the probability
of finding an electron is large
• The typical representation of orbitals are
those volumes which contain the electron 90-
95% of the time
Chapter 1 30
¾ 1s and 2s orbitals are spheres centered around
the nucleus
• Each orbital can accommodate 2 electrons
• The 2s orbital is higher in energy and
contains a nodal surface (Ψ = 0) in its center
¾ Each 2p orbital has two nearly touching
spheres (or lobes)
• One sphere has a positive phase sign and the
other a negative phase sign; a nodal plane
separates the spheres
Chapter 1 31
¾ There are three 2p orbitals which
are perpendicular (orthogonal) 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)
• The 2p orbitals are higher in energy
than the 1s or 2s
Chapter 1 32
Chapter 1 33
ÎThe sign of the wave function does not indicate
a greater or lesser probability of finding an
electron in that location
ÎThe greater the number of nodes in an orbital
the higher its energy
• 2s and 2p orbitals each have one node and
are higher in energy than the 1s orbital
which has no nodes
Chapter 1 34
Atoms can be assigned electronic
configuration using the following rules:
ÎAufbau Principle: The lowest energy orbitals
are filled first
ÎPauli Exclusion Principle: A maximum of two
spin paired electrons may be placed in each
orbital
ÎHund’s Rule: One electron is added to each
degenerate (equal energy orbital) before a
second electron is added
Chapter 1 35
Electronic Configurations of Some
Second Row Elements
Number of Covalent Bonds
:
: :
H O N C
one bond two bonds three bonds four bonds
Chapter 1 36
1.11 Molecular Orbitals (MOs)
Î A simple model of bonding is illustrated by
forming molecular H2 from H atoms and
varying distance:
• Region I: The total energy of two isolated
atoms
• Region II: The nucleus of one atom starts
attracting the electrons of the other; the
energy of the system is lowered
• Region III: at 0.74 Å the attraction of
electrons and nuclei exactly balances
repulsion of the two nuclei; this is the bond
length of H2
• Region IV: energy of system rises as the
repulsion of the two
Chapter 1
nuclei predominates37
Chapter 1 38
Î As two atoms approach each other their
atomic orbitals (AOs) overlap to become
molecular orbitals (MOs)
Î The wave functions of the AOs are combined
to yield the new wave functions of the MOs
Î The number of MOs that result must always
equal the number of AOs used
Chapter 1 39
¾ Non-bonding electron pairs tend to repel
other electrons more than bonding pairs
do (i.e. they are “larger”)
¾ Geometry of the molecule is determined
by the number of sets of electrons by
using geometrical principles
Chapter 1 40
1.12 The Structure of Methane (CH4) and
Ethane (CH3CH3): sp3 Hybridization
ÎThe structure of methane with its four
identical tetrahedral bonds cannot be
adequately explained using the electronic
configuration of carbon
Chapter 1 41
¾ The attached groups in CH4 (i.e. Hydrogen
atoms) are not at the angles of the p orbitals
and their atomic orbitals would not have
maximum overlap to form strong bonds
¾ Hybridization of the valence orbitals (2s and
2p) provides four new identical orbitals
which match the bond angles of the attached
groups. There is one sp3 hybridized carbon
and three hydrogen atoms in methane
¾ Orbital hybridization is a mathematical
combination of the 2s and 2p wave functions
to obtain wave functions for the new orbitals
Chapter 1 42
• When one 2s orbital and three 2p orbitals are
hybridized four new and identical sp3
orbitals are obtained
¾ When four orbitals are hybridized, four
orbitals must result
¾ Each new orbital has one part s character
and 3 parts p character
¾ The four identical orbitals are oriented in
a tetrahedral arrangements (109.5° bond
angle)
¾ The resulting four C-H bonds are
equivalent
Chapter 1 43
•The four sp3 orbitals are then combined
with the 1s orbitals of four hydrogens to
give the molecular orbitals of methane
•Each new molecular orbital can
accommodate 2 electrons
3sp3
Chapter 1 44
Chapter 1 45
Chapter 1 46
ÎAn sp3 orbital looks like a p orbital with one
lobe greatly extended
ÎThe extended sp3 lobe can then overlap well
with the hydrogen 1s to form a strong bond
ÎThe bond formed is called a sigma (σ) bond
because it is circularly symmetrical in cross
section when view along
Chapter 1 the bond axis 47
z Ethane (C2H6)
ÎThe carbon-carbon bond is made from
overlap of two sp3 orbitals to form a σ bond
ÎThe molecule is approximately tetrahedral
around each carbon
Chapter 1 48
ÎThe representations of ethane show the
tetrahedral arrangement around each carbon
a. calculated electron density surface b. ball-and-
stick model c. typical 3-dimensional drawing
ÎGenerally there is relatively free rotation
about σ bonds. Very little energy (13-26
kcal/mol) is required to rotate around the
carbon-carbon bond
Chapterof
1 ethane 49
1.13 The Structure of Ethene (Ethylene) :
sp2 Hybridization
ÎEthene (C2H2) contains a carbon-carbon
double bond and is in the class of organic
compounds called alkenes
• Another example of the alkenes is
propene
Chapter 1 50
¾The geometry around each carbon is called
trigonal planar
¾All atoms directly connected to each carbon
are in a plane
¾The bonds point towards the corners of a
regular triangle
¾The bond angle are approximately 120o
Chapter 1 51
ÎOverlap of sp2 orbitals in ethylene results in
formation of a s framework
• One sp2 orbital on each carbon overlaps
to form a carbon-carbon σ bond; the
remaining sp2 orbitals form bonds to
hydrogen
ÎThe leftover p orbitals on each carbon
overlap to form a bonding π bond between
the two carbons
ÎA π bond results from overlap of p orbitals
above and below the plane of the σ bond
• It has a nodal plane passing through the
two bonded nuclei and between the two
lobes of the p molecular orbital
Chapter 1 52
Chapter 1 53
ÎThere are three σ bonds around each carbon
of ethene and these are formed by using sp2
hybridized orbitals
ÎThe three sp2 hybridized orbitals come from
mixing one s and two p orbitals
• One p orbital is left unhybridized
ÎThe sp2 orbitals are arranged in a trigonal
planar arrangement
• The p orbital is perpendicular (orthogonal)
to the plane
Chapter 1 54
3 sp2
Chapter 1 55
Restricted Rotation and the Double Bond
ÎThere is a large energy barrier to rotation
(about 264 kJ/mol) around the double bond
• This corresponds to the strength of a π
bond
• The rotational barrier of a carbon-carbon
single bond is 13-26 kJ/mol
ÎThis rotational barrier results because the p
orbitals must be well aligned for maximum
overlap and formation of the π bond
ÎRotation of the p orbitals 90o totally breaks
the π bond
Chapter 1 56
Chapter 1 57
Cis-trans isomers
ÎCis-trans isomers are the result of restricted
rotation about double bonds
ÎThese isomers have the same connectivity of
atoms and differ only in the arrangement of
atoms in space
• This puts them in the broader class of
stereoisomers
ÎThe molecules below do not superpose on
each other
Chapter 1 58
• 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
Chapter 1 59
1.14 The Structure of Ethyne
(Acetylene): sp Hybridization
ÎEthyne (acetylene) is a member of a group
of compounds called alkynes which all have
carbon-carbon triple bonds
• Propyne is another typical alkyne
ÎThe arrangement of atoms around each
carbon is linear with bond angles 180o 60
Chapter 1
ÎThe carbon in ethyne is sp hybridized
• One s and one p orbital are mixed to form
two sp orbitals
• Two p orbitals are left unhybridized
Chapter 1 61
¾The two sp orbitals are oriented 180o
relative to each other around the carbon
nucleus
¾ The two p orbitals are perpendicular to the
axis that passes through the center of the sp
orbitals
Chapter 1 62
ÎIn ethyne the sp orbitals on the two carbons
overlap to form a σ bond
• The remaining sp orbitals overlap with
hydrogen 1s orbitals
ÎThe p orbitals on each carbon overlap to
form two π bonds
ÎThe triple bond consists of one σ and two π
bonds
Chapter 1 63
Examples of Hybridization in
Non-Carbon Compounds
Ammonia Water
N is sp3 in NH3 O is sp3 in H2O
There are four sets of There are four sets of
electrons: 3 bonding pairs Electrons: 2 bonding
and 1 non-bonding pair and 2 non-bonding pairs
Chapter 1 64
Carbon-Carbon Covalent Bonds
• Sigma bonds are the most common bonds in
organic chemistry
• All single bonds are sigma bonds
• A double bond always consists of a σ bond
(using hybrid orbitals) and one π bond (using p
orbitals)
sp3 sp2 sp
¾ Carbon-carbon σ bond is stronger, due to
better overlap, less accessible bonding
electrons
¾ Carbon-carbon π bond
Chapter 1 weaker thus reactive,
65
more accessible electrons
¾ π bonds are usually weaker than sigma bonds
because their (negatively charged) electron
density is farther from the positive charge of the
atomic nucleus, which requires more energy
¾ From the perspective of quantum mechanics, this
bond's weakness is explained by significantly less
overlap between the component p-orbitals due to
their parallel orientation
π bond
σ bond
Chapter 1 66
Summary of Hybridization for Carbon
Type of Hybrid sp3 sp2 sp
Atomic orbitals
s, p, p, p s, p, p s, p
used
Number of hybrid
4 3 2
orbitals formed
Number of atoms
4 3 2
bonded to the C
Number of sigma
4 3 2
bonds
Number of left
0 1 2
over p orbitals
Number of pi
0 1 2
bonds
| \ =C=
Bonding pattern -C- C= or
| / -Cº
CH3 CH2 CH CH CH2 C C CH2 CH3
sp3 sp3 sp2 sp2 sp3 sp sp sp3 sp3
Chapter 1 67
Bond Lengths of Ethyne, Ethene and
Ethane
ÎThe carbon-carbon 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
ÎThe carbon-hydrogen 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 Chapter 1 68
•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
Chapter 1 69
1.16 Molecular Geometry: The Valence Shell
Electron Pair Repulsion (VSEPR) Model
¾ This is a simple theory to predict the
geometry of molecules
¾ All sets of valence electrons are considered
including:
• Bonding pairs involved in single or
multiple bonds
• Non-bonding pairs which are unshared
¾ Electron pairs repel each other and tend to
as far apart as possible from each other
Chapter 1 70
Structure of Methane
ÎThe valence shell of methane contains four
pairs or sets of electrons
ÎTo be as far apart from each other as
possible they adopt a tetrahedral
arrangement (bond angle 109.5o)
Chapter 1 71
Structure of Water
ÎThere are four sets of electrons including 2
bonding pairs and 2 non-bonding pairs
ÎAgain the geometry is essentially
tetrahedral but the actual shape of the atoms
is considered to be an angular arrangement
ÎThe bond angle is about 105o because the
two “larger” nonbonding pairs compress the
electrons in the oxygen-hydrogen bonds
Chapter 1 72
1.17 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 73
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 74
Examples for Condensed Structural Formulas
Chapter 1 75
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 76
Example for Bond-Line Formulas
Chapter 1 77
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 78
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 79
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 80
