Chapters 1-4
Chapters 1-4
ORGANIC CHEMISTRY 1
Chem. 212
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Contents
Chapter 1 · Introduction 4
· Chemical Bonding 6
· Lewis Structures
· Functional groups
Chapter 2 · Development of Chemical Bonding Theory
· SP3 Hybridization
· SP2 Hybridization
· SP Hybridization
· Hybridization of Oxygen and Nitrogen
· Molecular Orbital Theory of H2
Chapter 3 Acids and Bases
· Arrhenius Acids and Bases
· Brønsted Acids and Bases
· Lewis Acids and Bases
Chapter 4 Alkanes and Cycloalkanes
· Structure of Alkanes
· Nomenclature of Alkanes
· Preparation and Reactions of Alkanes
· Nomenclature of Cycloalkanes
· Stereochemistry of Alkanes and Cycloalkanes
Chapter 5 Principles of Stereochemistry
Geometric Isomerism
Optical Isomerism
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Chapter 6 Alkyl Halides
· Nomenclature of Alkyl Halides
· Preparation of Alkyl Halides
· Reactions of Alkyl Halides
· Nucleophilic Substitution Reaction
· Elimination Reaction
Chapter 7 Alkenes: Structure and Reactivity
· Nomenclature of Alkenes
· Preparation of Alkenes
· Reactions of Alkenes
Chapter 8 Alkynes: Structure and Reactivity
· Nomenclature of Alkynes
· Preparation of Alkynes
· Reactions of Alkynes
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Chapter 1
Introduction
Organic chemistry touches our daily lives as much as more than any other branch of
science. Almost all the reactions in living matter involve organic substances. The
major constituents of living matter including proteins, carbohydrates, lipid (fats)
nucleic acids (DNA, RNA), cell membranes, enzymes and hormones are organic
compounds. Other organic substances with which we have contact almost daily
include the gasoline, oil and tyres for our cars, the clothes we wear, the wood and
paper of our furniture and books, the medicines we take when ill, plastic containers,
perfumes, carpeting etc. It is part of our technological culture.
Organic chemistry is considered the study of most compounds of carbon. These
compounds are two kinds.
Natural organic compounds: such as petroleum and coal
Synthetic organic compounds: such as vitamins, antibiotic, dyes, amino acids and
many others.
The Uniqueness of Carbon:
The number of known organic compounds is over a million and thousands of new
ones are synthesized each year. Carbon can form chain or ring.
Why does carbon form so many compounds?
i- The position of carbon is in the middle of the periodic table.
ii- It can form strong bonds with other carbon atoms and with other elements,
most commonly with hydrogen, oxygen, nitrogen and halogens.
iii- Each organic compound has its own characteristic set of physical and chemical
properties, which depend upon the structure of the molecule.
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Electronic structure of the atom
An atom composed of positively charged nucleus (containing protons (P) with
positive charge and neutrons (n) with neutral charge) surrounded by a cloud of
electrons. The electron density is highest at the nucleus and decreases with increasing
the distance from the nucleus in any direction.
· Electron spin can have only two orientations, up - and down ¯. Only two
electrons can occupy an orbital, and they must be of opposite spin (Pauli
exclusion principle).
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· If two or more empty orbitals of equal energy are available, electrons will occupy
each with spins parallel until all orbitals have one electron then pairing will be
occurred (Hund's rule).
Valance Shell: the outermost shell of an atom
Valance Electrons: the electrons on the outermost shell of the atom
Electronic Configuration Valance Shell Valance Electrons
11Na: 1S2 2S2 2P6 3S1 3S 1
9F: 1S2 2S2 2P5 2S & 2P 7
8O: 1S2 2S2 2P4 2S & 2P 6
17Cl: 1S2 2S2 2P6 3S2 3P5 3S & 3P 7
Octet Rule: Any atom in the periodic table (except H, He) prefers to have 8 electrons
in the valance shell to acquire the electronic distribution of the nearest inert gas in the
same period to be stable atom.
The atom could loss or gain or char electrons during the formation of the chemical
bond to get 8 electrons in the valance shell.
For a covalent bond to be formed two atoms must be located so that an orbital of one
overlaps an orbital of the other; each orbital must contain a single electron. When this
happens, the two atomic orbitals merge to form a single bond orbital, which is
occupied by both electrons. The two electrons that occupy a bond orbital must have
opposite spins, that is, must be paired.
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· If the difference of electronegativity between bonded atoms < 0.5 means non-
polar covalent bond [example N2 (3-3 = zero)]
· If the difference of electronegativity between bonded atoms is equal or higher
than 0.5 but lower than 1.9 means polar covalent bond [example (C-Cl) 3-2.5
= 0.5]
· If the difference of electronegativity between bonded atoms ≥ 1.9 means ionic
bond [example (Na-Cl) 3- 0.9 = 2.1]
Lewis Structure
Skeletal structure of compound showing how atoms are bonded to each other
◦ the symbol of the atom represents the nucleus and all inner shell electrons
◦ dots represent valence electrons
1A 2A 3A 4A 5A 6A 7A 8A
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
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To draw Lewis structure:
· Put the lowest electronegative element at the center (or lowest number)
· Count the total number of valence electrons on the molecule. Add 1 for each
negative charge and subtract 1 for each positive charge.
· Draw single bonds around central atom (each single bond = 2 electrons)
· Count how many electrons are left and assign them as lone pairs to fill the
valence shells [octet for each atom in the molecule except hydrogen (2)]
· If structure contains too many electrons, form double and triple bonds on central
atom as needed
· In neutral molecules containing C, H, N, O, and halogen hydrogen has one bond
· carbon has 4 bonds and no unshared electrons
· nitrogen has 3 bonds and 1 unshared pair of electrons
· oxygen has 2 bonds and 2 unshared pairs of electrons
· halogen has 1 bond and 3 unshared pairs of electrons
H O H H Cl
H 2 O (8) H C l (8)
W a te r H y d ro g e n c h lo rid e
H
H C H H N H
H H
C H 4 (8) N H 3 (8)
M e th a n e A m m o n ia
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Write the Lewis structure of carbonate (CO3)-2
Step 1) C is less electronegative than O, put C in center
Step 2) Count valence electrons: 6C (2s22p2) and 8O (2s22p4) (VE = 1x4 + 3x6 + 2
(negative charge) = 24)
Step 3) Draw four bonds (8 electrons) around carbon atom
Step 4) the remaining electrons = 24-8 = 16
Q: Draw Lewis structure and calculate the formal charge for each atom for
(NO3)-
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Polar and Nonpolar Molecules
A molecule is polar if it has polar bonds and its center of positive charge is at a
different place than its center of negative charge
In case of molecules: some molecules have polar bonds and are polar molecules
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direction O N direction
of dipole of dipole
H H H H
moment moment
H
Water Ammonia
m = 1.85D m = 1.47D
In other case, some molecules have polar bonds, but each has a zero dipole moment
F Cl
O C O B F C
F Cl Cl
Cl
Carbon dioxide Boron trifluoride Carbon tetrachloride
m=0D m=0D m=0D
Functional Groups
Functional group: an atom or group of atoms within a molecule that shows a
characteristic set of physical and chemical properties
Functional groups are important for three reasons, they are
· the units by which we divide organic compounds into classes
· the sites of characteristic chemical reactions
· the basis for naming organic compounds
Alcohols: Organic compounds which contain hydroxyl group (OH) as a functional
group with general formula [CnH2n+1 OH] (CH3-CH2-OH ethanol)
Aldehydes and Ketones
Organic compounds which contain carbonyl group (C=O) as a functional group
Aldehydes: One hydrogen atom (H) is bonded to carbonyl group
Ketones: two hydrocarbon groups are bonded to carbonyl group
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Carboxylic Acids: Organic compounds which contain carboxylic group (COOH)
group. (R-COOH; Aliphatic acids) (Ar-COOH; Aromatic acids)
Amines: derivatives of ammonia (NH3) in which one or more hydrogen atoms have
been replaced by alkyl or aryl groups
Classification of Amines (R-NH2)
Amines are sub-divided as primary (1ry), secondary (2ry), and tertiary (3ry)
according to one, two or three hydrogen atoms of ammonia molecule (NH 3) have
been replaced by alkyl or aryl groups
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Chapter 2
Molecular Orbital Theory
Development of Chemical Bonding Theory
Hybridization: Mixing of atomic orbitals to give a new set of hybrid orbitals
Mix at least 2 nonequivalent atomic orbitals (e.g. s and p). Hybrid orbitals have very
different shape from original atomic orbitals.
Number of hybrid orbitals is equal to number of pure atomic orbitals used in the
hybridization process.
Covalent bonds are formed by:
· Overlap of hybrid orbitals with atomic orbitals
· Overlap of hybrid orbitals with other hybrid orbitals
SP3 Hybridization: Mixing of one atomic orbital (S) and three atomic orbitals (P) to
give four hybrid orbitals (SP3) as shown in Methane molecule [CH4]
The four sp3 orbitals should be oriented at angles of (109.5°) with respect to each
other-an sp3-hybridized carbon gives a tetrahedral structure for methane.
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Hybridization: sp3 Orbitals and the Structure of Ethane
· Two carbons are bonded to each other by one SP3 orbital from each carbon.
· Three SP3 orbitals on each carbon overlap with H (1s) orbitals to form six C–H
bonds (C–H bond strength in ethane 420 kJ/mol)
· All bond angles of ethane are tetrahedral (109.5 o)
SP2 Hybridization: Mixing of one atomic orbital (S) and two atomic orbitals (P) to
give three hybrid orbitals (SP2) as shown in Ethene molecule [CH2 =CH2]
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SP Hybridization: Mixing of one atomic orbital (S) and one atomic orbital (P) to
give two hybrid orbitals (SP) as shown in acetylene molecule C2H2
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Hybridization of Oxygen in Water
The oxygen atom is sp3-hybridized. Oxygen has six valence-shell electrons but forms
only two covalent bonds, leaving two lone pairs The H–O–H bond angle is (104.5°)
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Molecular Orbital Theory
· Electrons in atoms exist in atomic orbitals and in molecules exist in molecular
orbitals (MOs)
· Combination of number (n) atomic orbitals gives (n) molecular orbitals (MO).
MOs are arranged in order of increasing energy and its filling is governed by the
same rules as for atomic orbitals:
· Aufbau principle: fill beginning with lower energy molecular orbital
· Pauli exclusion principle: no more than 2e- in a the same molecular orbital
· Hund’s rule: when two or more MOs of equivalent energy are available, add 1e -
to each before filling any one of them with 2e-
· Ground state is the lowest energy state and (s) = sigma bonding MO while (s)*
is sigma antibonding MO
· HOMO = highest occupied molecular orbital while LUMO = lowest unoccupied
molecular orbitals.
MO energy diagram for H2: (a) ground state and (b) lowest excited state
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Chapter 3
Acids and Bases
Acid Base
· Have a sour taste. · Have a bitter taste.
· Vinegar owes its taste to acetic acid. · Feel slippery.
· Citrus fruits contain citric acid. · Many soaps contain bases.
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Strong acids = weak conjugate base while weak acids = strong conjugate base
Strength of Acids
As the strength of the acid increase (more H+) Ka will increase and pKa will decrease
and vice versa.
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Weak acid: a substance that dissociates only partially in water to produce (H3O+)
ions. Acetic acid, for example, is a weak acid that incompletely ionized in aqueous
solution
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Weak base: a substance that dissociates only partially in water to produce (OH)-
ions. Ammonia, for example, is a weak base
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3- Resonance delocalization of charge in conjugate base (A-)
Compare between the acidity of alcohols and carboxylic acids?
In the example below, when we compare the acidities of ethanol and acetic acid, we
note that acetic acid is more acidic than the ethanol.
In case of acetic acid, the conjugate base produced from acetic acid will have
resonance structures (become more stable). The greater of the resonance stabilization
of the anion, the acidity will increase.
In case of ethanol, the conjugate base produced from ethanol (ethoxide anion) will
not have resonance structures (become less stable) and the acidity will decrease.
4- Inductive Effect
Permanent polarization of sigma (s) bond in the molecules or ions due to difference
in electronegativity
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Types of Inductive Effects
(- I): if the substituents are electron attracting groups (with higher electronegativity)
since they decrease the electron density of the system e.g.
NO2 > C≡N > C=O > F > Cl > Br > I > OCH3 > C6H5
(+ I): if the substituents are electron donating groups (with lower electronegativity)
since they increase the electron density of the system e.g.
C(CH3)3 > CH(CH3)2 > CH3CH2 > CH3
In case of acetic acid since the methyl group act as electron-donating group so it will
be (+ I) and increase the electron density on the adjacent carbon atom and thus, the
cleavage of (O-H) bond of carboxylic group need more energy so the concentration
of proton (H+) will decrease and the acidity will also decrease (pKa = 4.80).
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Question: compare the acidities of ethanol and 2,2,2-trifluoroethanol?
As (- I) increase the acidity will increase and vice versa. Also, the number of (- I)
groups increase the acidity will increase.
Acid pKa Acid pKa
F-CH2-COOH 2.66 CH3-COOH 4.80
Cl-CH2-COOH 2.81 Cl-CH2-COOH 2.81
Br-CH2-COOH 2.87 Cl2-CH-COOH 1.29
I-CH2-COOH 3.13 Cl3-C-COOH 0.65
As the distance between the (- I) group and carboxylic group increase the acidity
will decrease.
5- Effect of Hybridization
Hydrogens connected to orbitals with more (S) character will be more acidic (SP ˃
SP2 ˃ SP3) because (S) orbitals are smaller and closer to the nucleus than (P) orbitals.
Also, the anions in hybrid orbitals with more (S) character will be held more closely
to the nucleus and be more stabilized.
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Summary of Acidity
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Lewis Acids and Bases
Lewis acid: The substance which is electron pair acceptor = Electrophile
Lewis base: The substance which is electron pair donor = Nucleophile (has lone pair
or pi bond)
- +
A + :B A B n e w co v ale n t bo n d
Le wis fo rm e d in th is Le wi
Le wis
acid acid - b ase re actio n
b ase
Note that in each reaction, the electron pair is not removed from the Lewis base.
Instead, it is donated to an atom of the Lewis acid and one new covalent bond is
formed.
· Group 3A elements, such as BF3 and AlCl3, and Transition-metal compounds, such
as TiCl4, FeCl3, ZnCl2, and SnCl4 are Lewis acids because they have unfilled
valence orbitals and can accept electron pairs from Lewis bases
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Some organic Lewis bases and their relative strengths in proton-transfer
reactions
CH3 N H CH3 N
CH3 CH3
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Chapter 4
Alkanes and Cycloalkanes
Hydrocarbons: Organic compounds which contain carbon and hydrogen atoms.
These compounds can be classified as
Alkanes: aliphatic hydrocarbons (contain carbon and hydrogen atoms) with general
formula CnH2n+2 , Where n = 1,2,3,4…etc.
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8 C8H18 CH3(CH2)6CH3 Octane
9 C9H20 CH3(CH2)7CH3 Nonane
10 C10H22 CH3(CH2)8CH3 Decane
Representation of Alkanes
Lewis Structure Line 3-D Ball and Stick
model
Constitutional isomers: Two or more compounds which have the same number of
carbon and hydrogens but differ in the way the atoms are connected to each other.
As the number of carbon atoms increases in the chain, the number of constitutional
isomers will increase.
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Classification of carbon atoms
Carbon atoms in alkanes and other organic compounds are classified by the number
of other carbons directly bonded to them
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The IUPAC (International Union of Pure and Applied Chemistry) System for
Nomenclature of Alkanes
1- Choose the longest continuous carbon chain as the parent hydrocarbon (Base
name).
2- Give numbers for the parent chain starting from the end near to branching to give
the substituent lowest number.
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3-When two chains of equal length compete for selection as the parent chain, choose
the chain with the greater number of substituents.
4- When the parent hydrocarbon contains two or more of the same substituent use the
prefix di, tri, tetra…etc.
5- When the parent hydrocarbon contains two substituents at the same position, the
number must be repeated for both (e.g. 3,3-dimethyl, 3-methyl-3-ethyl…etc).
6- If two or more different substituents are present on the parent chain on the same
distance from both sides, use the alphabetical way to list the substituents.
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7. Alphabetize the names of the substituents, ignoring all prefixes (Di-, Tri-..) except
iso, as in iso-propyl and iso-butyl.
8. Precede the name of each substituent by the number that indicates its location.
9. Separate numbers by commas (,) and separate numbers from letters by hyphens (-).
10. The name of an alkane is a single word, with no spaces after hyphens (-) and
commas (,).
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Methods of Preparation of Alkanes
1- Hydrogenation of Alkenes or Alkynes (Sabatier and Senderen's reaction)
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Chemical Reactions of Alkanes
1- Combustion (Oxidation) of Alkanes
Alkanes undergo combustion—that is, they burn in the presence of oxygen to form
carbon dioxide and water.
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Nomenclature of Cycloalkanes
The prefix (cyclo-) is added to the name of the alkane with the same number of
carbons
· When one substituent is present it is assumed to be at position one and is not
numbered
· When two alkyl substituents are present the one with alphabetical priority is
given position 1
· Numbering continues to give the other substituent the lowest number
Naming compounds containing both a ring and a long chain of carbon atoms
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Stereochemistry of Alkanes and cycloalkanes
Conformations of Acyclic Alkanes
Conformations are different arrangements of atoms that are interconverted by
rotation about single bonds. A particular conformation is called a conformer.
· Rotating the atoms on one carbon by (600) converts an eclipsed conformation into
a staggered conformation, and vice versa.
· The angle that separates a bond on one atom from a bond on an adjacent atom is
called a dihedral angle. For ethane in the staggered conformation, the dihedral
angle for the C—H bonds is (600). For eclipsed ethane, it is (00).
· End-on representations for conformations are commonly drawn using a convention
called a Newman projection.
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How to Draw a Newman Projection??
Step 1. Look directly down the C—C bond (end-on), and draw a circle with a dot in
the center to represent the carbons of the C—C bond.
Step 2. Draw the bonds on the front carbon atom as three lines meeting at the center
of the circle. Also, draw the bonds on the back carbon atom as three lines coming out
of the edge of the circle.
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· The staggered and eclipsed conformations of ethane interconvert at room
temperature, but each conformer is not equally stable.
· The staggered conformations are more stable (lower in energy) due to less
Electron-Electron repulsion of the bonded atoms.
· The eclipsed conformations are less stable (higher in energy) due to more
Electron-Electron repulsion of the bonded atoms.
· The difference in energy between staggered and eclipsed conformers is ~ 3
kcal/mol. The energy difference between staggered and eclipsed conformers is
called torsional energy.
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Butane and higher alkanes have several C—C bonds, all capable of rotation. It takes
six (600) rotations to return to the original conformation.
· A staggered conformation with two larger groups (1800) from each other is
called Anti.
· A staggered conformation with two larger groups (600) from each other is called
Gauche.
· The staggered conformations are lower in energy (more stable) than the
eclipsed conformations.
· The relative energies of the individual staggered conformations depend on their
Steric strain (is an increase in energy resulting when atoms are forced too close
to each other's).
· Gauche conformations are generally higher in energy than Anti conformations
because of steric strain.
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Conformations of cyclic Alkanes
Angle strain: Expansion or compression of bond angles away from most stable form
(109.5o)
Torsional strain: Eclipsing of bonds on neighboring atoms.
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Conformations of Cyclohexane
Cyclohexane ring is present in two conformational forms:
1- Chair Conformer: This form is free of angel and torsional strains (more stable
and lower energy). Each carbon atom in chair form has two different kinds of
hydrogens: Axial hydrogens are located above and below the ring (along a
perpendicular axis); Equatorial hydrogens are located in the plane of the ring
(around the equator).
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So, the substituent will prefer Equatorial position other than Axial position.
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So, the two substituent will prefer Equatorial position other than Axial position.
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