Chapter 1. Carbon Compounds
& Chemical Bonds
Ch1.3:
Valence, C–C Bonds (single, double, triple), Isomer
(constitutional), Molecular/Structural formula, Connectivity
Ch1.4-8: Ionic/covalent bonds, Octet rule, Ions, Electronegativity
Lewis structure, Formal charges,
Resonance structures, Resonance stabilization
Ch1.9-15: Atomic/molecular orbitals
Orbital hybridization (sp3, sp2, sp)
Sigma(σ)/Pi (π)bonds (structure of ethane/ethene/ethyne)
Stereoisomer
Ch1.16:
Molecular geometry (tetrahedral, trigonal planar,
linear, trigonal pyramid, bent)
Ch1.17:
Representation of structural formulas (dash, condensed,
bond line, three-dimensional)
The Structural Theory of Organic Chemistry
Valence: the measure of ability that atoms in organic compounds can form
fixed number of bonds.
Isomer: different compounds that have the same molecular formula
(Constitutional Isomer)
Electronegativity and Ionic Bonds
Octet rule: the tendency for an atom to achieve a configuration where its
valence shell contains eight electrons.
Electronegativity: a measure of the ability of an atom to attract electrons.
Ionic bonds: an attractive force between oppositely charged ions.
Covalent Bonds and Lewis Structures
Covalent bond: electron sharing between atoms with same or similar
electronegativity to achieve noble gas configuration.
Covalent Bonds and Lewis Structures
Lewis structure (electron dot formula): a structure of molecules or ions
showing the constituent atoms and the valence electrons.
HNO3,
H3PO4,
CH2N2,
O3
Formal Charges
Indicator of how many electrons are gained/lost by an atom
Formal Charges
Indicator of how many electrons are gained/lost by an atom
Resonance Structures
Resonance structures: a tool we use for understanding structure and
reactivity (not structures for the actual molecule or ion).
SP3–Hybrid Atomic Orbital
Hybridization: A mathematical process combining individual wave functions
The shape of an sp3 orbital
The Structure of Methane
σ (sigma) bond
SP2–Hybrid Atomic Orbitals
π (pi) bond
An sp2-hybridized carbon
SP–Hybrid Atomic Orbitals
An sp-hybridized carbon
Bond Lengths and Angles of
Ethyne, Ethene, and Ethane
sp-hybridized C
sp2-hybridized C
sp3-hybridized C
s-character
50%
33.3%
25%
p-character
50%
66.6%
75%
***The higher s-character of a carbon atom, the higher its electronegativity.
Rule of Thumb using hybridized molecular orbitals
SP3 hybridization: Any atom in a molecule that is not a part of a double
or triple bond – Tetrahedral
109.5°
109.5°
H
O H
H
N H
H
H
C H
H
H
109.5°
109.5°
SP2 hybridization: Any atom in a molecule that is a part of a double bond
– Trigonal planar
H
H
H
N C
C C
H
H
H
H
H
H B
O C
H
H
H
H
H C+
H
SP hybridization: Any atom in a molecule that is a part of a triple bond
– Linear
N N
N C CH3
Rule of Thumb using hybridized molecular orbitals
What is the hybridization of the indicated atom(s) in each molecule?
CH3
C C
(a)
Me
(b)
Me
C
(c)
+
Me
O
O
(d)
(e)
(f)
O
(h)
(g)
(i)
N
O
(j)
Me
Me
Al
Me
(k)
O
H
(l)
N
Chapter 2: Functional Groups
Ch 2.1–2.4: Hydrocarbons (Alkane, Alkene, Alkyne, Saturated &
unsaturated compounds, Aromatic compounds)
Dipole moment, Polar & nonpolar covalent bonds
Ch 2.5–2.13: Functional groups (name and structure–connectivity)
General formula of compounds with specific f.g.
(Table 2.3)
Alkane, Alkene, Alkyne, Benzene (aromatic), Haloalkane
Alcohol, Ether, Amine, Carbonyl compounds
Aldehyde, Ketone, Carboxylic acid, Ester, Amide
Nitrile
Ch 2.14
: Hydrogen bond, Polarizability
Functional Group
Certain arrangement of atoms with covalent bonds that has
a unique structure and reactivity (function)
O
O
OH
O
Aspirin
Polar Covalent Bonds
The nature of chemical bond in a molecule dictates the chemical
and physical properties of the molecule.
Cl
Cl
C Cl
Cl
Functional Group
Functional Group
Chapter 3: An Introduction to Organic Reactions
– Acids and Bases
Ch 3.1:
Substitution, Addition, Elimination, Rearrangement
Reaction mechanism, Hetrolytic/homolytic bond cleavage
Ch 3.2:
Brønsted-Lowry and Lewis definition of acid/base
Conjugate acid/base
Ch 3.3-4: Carbocation and carbobanion, the use of curved arrows
Ch 3.5-11: Strength of acid/base (Ka and pKa) and its prediction
Effect of hybridization on acidity, Inductive/Resonance effect
Equilibrium constant (Keq), Standard free-energy change (ΔG°)
Ch 3.12-14: Protonation on lone pair electrons (alcohols, amines, ethers,
carbonyl compounds), Mechanism for organic reactions
Acid/base reaction in nonaqueous solution, leveling effect
Categories of Organic Reactions
Substitutions:
one group replaces another
Additions:
two molecules becomes one
Eliminations:
one molecule loses the elements of another
Rearrangement:
Reorganization of a molecule’s
constituent parts
What’s common in these reactions?
Covalent bond cleavage:
Heterolytic bond cleavage requires
polarized bond
Heterolytic bond cleavage often
requires external assistance
Acid–Base Reaction
Why acid–base?
Many reactions in organic chemistry are:
either acid–base reaction themselves
or involves acid–base reaction at some stage
Brønsted-Lowry definition:
Acid – a substance that can donate (or lose) a proton
Base – a substance that can accept (or remove) a proton
Acid–base reaction of other
strong acids
Acid–Base Reaction
Lewis definition:
Acid – an electron pair acceptor
Base – a an electron pair donor
Other examples of
Lewis acid–base reaction
Carbocations and Carbanions
Carbocation: Ionic species with positively charged carbon atom
Carbanion: Ionic species with negatively charged carbon atom
Carbocations are strong Lewis acids while carbanions are strong
bases (both Lewis and Brønsted)
The Strength of Acid / Base: Ka and pKa
Predicting the Strength of Acid / Base
The stronger the acid, the weaker will be its conjugate base.
(The larger the pKa of the conjugate acid, the stronger the base)
Can we predict the relative basicity of two bases ?
Predicting the Strength of Acid / Base
The relationship between structure (size) and acidity
FHO-
Cl-
s
e
s
a
re
c
In
y
it
il
b
ta
S
Br-
B
a
HS-
I-
HSe-
The extent of electron delocalization (overall size) of the
corresponding conjugate bases may correlate with the acidity.
Predicting the Strength of Acid / Base
The relationship between electronegativity and acidity
Predicting the Strength of Acid / Base
The relationship between structure / electronegativity and acidity
Predicting the Strength of Acid / Base
The relationship between structure / hybridization and acidity
*The higher the s-character, the higher is the carbon’s electronegativity.
H
H
C C
H C C H
H
H
H
H
H
H
C C
H
H
H
H
Acidity Increases
H
H C C
C C
H
H
H
Basicity Increases
C C
H
H
The Strength of Acid / Base: Inductive Effect
Inductive Effect: propagation of bond polarity through σ-bond
network (decrease with the distance)
The Strength of Acid / Base: Resonance Effect
Resonance Effect: stabilization of the system by having resonance
structures (increase with the # of equivalent resonance structures)
requires energy
for the change
endothermic
Mechanism for Organic Reactions
Reaction Mechanism: a step by step description of the events
occurring from the starting materials to the
products.
Step 1
Step 2
Step 3
Chapter 4: Alkanes – Conformational Analysis
& an Introduction to Synthesis
Ch 4.1–4.7:
Branched/unbranched alkanes, Constitutional isomers,
Cycloalkanes, IUPAC system
Ch 4.8–4.11: Conformation (σ-bond rotation, staggered, eclipsed,
gauche, anti), Conformational analysis, Newman projection
Torsional strain, Steric hindrance
Ring strain (torsional/angle strain), Hyperconjugation
Ch 4.12–4.15: Conformation of cyclohexane (chair/boat, equatorial/axial)
Ring flip (upper/lower bond), Cis/trans isomers
Ch 4.16–4.19: Hydrogenation, Reduction of alkyl halide, Alkylation
Alkynide anion, Nucleophile/electrophile
Retrosynthetic analysis
Sigma (σ) Bond Rotation: Conformation
Conformation: temporary molecular shapes resulting
from σ-bond rotation
Staggered Conformation
Eclipsed Conformation
Conformational Analysis of Butane
Torsional barrier =
Steric hindrance + Orbital interactions
Chair vs. Boat Conformation of Cyclohexane
H
H
CH3
H
gauche conformation
of butane
.
.
CH3
.
.
Chair conformation
H
.
.
.
.
.
.
.
.
.
.
HH
HH
Boat conformation
eclipsed conformation
of butane
CH3
CH
3
.
.
.
.
.
.
.
.
Substituted Cyclohexane: Axial vs. Equatorial
.
.
H
H
H
CH3
H2C
H
H
CH3
H
gauche conformation
of butane
H
.
.
H
.
H
.
H
H
H
.
H
H
H
H
.
3.8 kj/mol
.
.
.
.
.
H
H
H
H
H
.
H
H
anti conformation
of butane
H
H
C
H2
H
H
H
CH3
H
CH3
H
.
.
H
H
Disubstituted Cyclohexanes: Cis–Trans Isomers
.
.
.
.
.
.
lower bond
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
Chemistry of Alkanes
.
Alkanes: inert to many chemical reagent
(originally called paraffins–little affinity)
.
‰ Synthesis of alkanes and cycloalkanes
Natural source: petroleum (as a mixture)
Chemical synthesis: particular alkane (in pure form)
Hydrogenation: addition of hydrogen(s) to π-bond(s)
.
.
Alkylation of Terminal Alkynes
.
.
.
.
Planning an Organic Synthesis: Retrosynthetic Analysis
.
.
.
.
Chapter 5: Stereochemistry
– Chiral Molecules
Ch 5.1–5.6:
Stereochemistry, Chirality, Stereoisomers, Enantiomers
Diastereomers, Mirror image, Chiral/Achiral molecules
Stereogenic carbon (center), Plane of symmetry
Ch 5.7–5.9:
Configuration, R/S-system, Group priority, Optical activity
Dextrorotatory/Levorotatory, Specific rotation
Racemic forms (Racemate), Enantiomeric excess
Ch 5.10–5.13: Stereoselective synthesis (dia-/enatiostereoselective)
Kinetic resolution, Chiral drug, Meso compound
Fisher projection formula
Ch 5.14–5.18: Stereoisomerism of cyclic molecules, Retention/Inversion
Relative/Absolute configurations, Resolution
Isomerism: Constitutional and Stereoisomers
C4H10O
OH
O
.
.
.
.
Test of Chirality: Plane of Symmetry
A molecule will be judged to be chiral (or achiral) by;
**the presence (or absence) of a single tetrahedral
stereogenic carbon.
**the absence (or presence) of certain symmetry elements–
a plane of symmetry (also called a mirror plane is defined
as an imaginary plane that bisects a molecule.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
Naming Enantiomers: The R,S -System
1. Assign a priority (or preference): based on atomic number
(the higher atomic number, the higher priority)
.
3
.
CH3
.
.
.
1
H
Br
.
4
.
.
2
.
.
.
.
Cl
2. Assign a priority at the first point of difference (following 1.)
.
.
H
3
.
.
CH2
1
H
HO
2
4
H2C
CH3
.
.
.
.
Naming Enantiomers: The R,S -System
3. Look through the bond between stereogenic atom and
the lowest priority group.
.
.
3
H
.
.
CH2
1
H3C
H
HO
4
OH
C
.
.
.
2
H2C
CH2CH3
.
CH3
.
4. Trace a path in sequence of the priority from 1 to 3.
.
.
.
.
H3C
OH
C
.
.
CH2CH3
.
.
.
.
.
.
.
Naming Enantiomers: The R,S -System
6. Groups containing double or triple bonds are assigned
priorities as if both atoms were duplicated or triplicated,
that is;
.
.
.
.
.
O
enantiomers
O
.
.
H
H
.
(S)- (+)-Carvone
(Caraway seed oil)
(R)- (-)-Carvone
(Spearmint oil)
.
.
Racemic Forms (Racemate)
Racemate
.
.
.
.
.
.
O
CH2CH3
H3CH2C
CH3
H3C
.
.
O
Naming Molecules with Multi-Stereogenic Centers
.
enantiomers
S
R
R
S
.
.
.
.
diastereomers
.
diastereomers
diastereomers
.
R
S
R
S
enantiomers
(2R,3R)-2,3-dibromobutane
.
.
.
.
.
.
.
Diastereomers have different physical properties: different m.p.
and b.p., different solubilities, and so forth.
Total number of stereoisomers will not exceed 2n, where n is equal
to the number of tetrahedral stereogenic centers.
Molecules with Multi-Stereogenic Centers
Meso Compounds
.
.
.
S
Meso Compound
R
.
.
.
.
.
.
diastereomers
.
.
R
S
R
S
enantiomers
.
.
.
.
.
Total number of stereoisomers will not exceed 2n, where n is equal
to the number of tetrahedral stereogenic centers.
Molecules with Multi-Stereogenic Centers
Fisher Projection Formula
.
.
CH3
.
H
S
Br
H
R
Br
.
CH3
.
.
.
.
.
.
.
CH3
CH3
Br
H
R
R
H
H
S
S
Br
Br
Br
H
CH3
CH3
.
.
.
.
.
Vertical lines represent bonds that project behind the plane of the paper (or that lie
in it). Horizontal lines represent bonds that project out of the plane of the paper.
1,2-Dimethylcyclohexane
trans-1,2-dimethylcyclohexane
Me
H
Me
Me
Me
Me
Me
H
Enantiomers
Me
H
H
Me
diastereomers
cis-1,2-dimethylcyclohexane
.
.
Me
Enantiomers
H
Me
H
H
.
Me
H
.
Me
Me
Me
Me
1,2-dimethylcyclohexane
Identical
Me
H
H
H
H
Me
Me
Enantiomers
Me
Me
Chapter 6: Ionic Reactions – Nucleophilic
Substitution and Elimination Reactions
Ch 6.1–6.8:
Alkyl halide (polar bond, bond strength), Nucleophile
Nucleophilic substitution, Leaving group, SN2 reaction
Bimolecular, Transition state, Free energy of activation
Retention and inversion of configuration, Concerted reaction
Ch 6.9–6.13: SN1 reaction, Unimolecular, Multistep reaction
Rate-limiting step, Intermediates, Carbocation stability
Hyperconjugation, Racemization, Solvolysis
Ch 6.13–6.14: Factors affecting rates of SN1 and SN2 reactions
Steric effect, Hammond–Leffler postulate
Nucleophilicity vs. basicity, Protic/aprotic solvent
Polar/nonpolar solvent, Polarizability, Nature of leaving group
Ch 6.15–6.18: Elimination reactions, Dehydrohalogenation
β-Elimination, E1 and E2 reactions
Competing reactions (SN2 vs. E2, SN1 vs. E1)
Mechanism for the SN2 Reaction
.
.
HOMO
LUMO
The Stereochemistry of SN2 Reactions
SN2 reactions always occur with inversion of configuration.
The Reaction of t-BuCl with HO- : SN1 Reaction
In the transition state that controls the rate of the reaction, hydroxide ions
do not participate but only t-butyl chloride. This reaction is said to be
unimolecular (first order) in the rate-determining step.
an SN1 reaction (substitution, nucleophilic, unimolecular).
Step 1
The Reaction of t-BuCl with HO- : SN1 Reaction
.
.
Step 1
.
.
Step 2
.
.
.
.
Step 3
.
.
.
.
The Stereochemistry of SN1 Reactions
.
.
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.
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.
.
.
.
.
.
.
.
.
.
.
Rates of SN1 and SN2 Reactions
The most important factors that affect the relative rates of SN1 and
SN2 reactions are:
.
.
1.
2.
3.
4.
the structure of the substrate
the concentration and reactivity of the nucleophile (for SN2 only)
the effect of the solvent
the nature of the leaving group
General order of SN2 reaction:
.
.
.
.
.
.
.
.
Rates of SN1 and SN2 Reactions
The most important factors that affect the relative rates of SN1 and
SN2 reactions are:
.
.
1.
2.
3.
4.
the structure of the substrate
the concentration and reactivity of the nucleophile (for SN2 only)
the effect of the solvent
the nature of the leaving group
SN1 Reactions: The primary factor is the relative stability of the
carbocation that is formed.
The rate of SN1 reaction correlates with that of carbocation stability.
.
.
.
.
.
.
.
.
The E2 Reaction (Dehydrohalogenation)
.
.
.
.
The E1 Reaction
.
.
.
.
Step 1
.
.
.
.
.
.
.
.
.
.
Step 2
.
.
.
.
Substitution (SN2, SN1) vs. Elimination (E2, E1)
.
.
Substitution
H
R
Nu
Nu
+
R
R
δ
R
R
Xδ
R
H
R
δ
X
R
SN2
δ
H
R
Elimination
B
Nu
R
R
X
R
SN1
R
H
R
R
δ
X
R
E2
δ
B
H
R
R
R
X
R
E1