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Organic Chemistry Concepts:
An EFL Approach

Gregory Roos
Murdoch University, Perth, Australia

Cathryn Roos
Zayed University, Dubai, UAE

AMSTERDAM • BOSTON • HEIDELBERG • LONDON

NEW YORK • OXFORD • PARIS • SAN DIEGO
SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO

Academic Press is an imprint of Elsevier

Academic Press is an imprint of Elsevier
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525 B Street, Suite 1800, San Diego, CA 92101-4495, USA
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Copyright © 2015 Elsevier Inc. All rights reserved.
No part of this publication may be reproduced or transmitted in any form or by
any means, electronic or mechanical, including photocopying, recording, or any
information storage and retrieval system, without permission in writing from the
publisher. Details on how to seek permission, further information about the Publisher’s
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Clearance Center and the Copyright Licensing Agency, can be found at our website:
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This book and the individual contributions contained in it are protected under
copyright by the Publisher (other than as may be noted herein).
Notices
Knowledge and best practice in this field are constantly changing. As new research and
experience broaden our understanding, changes in research methods, professional
practices, or medical treatment may become necessary.
Practitioners and researchers must always rely on their own experience and knowledge
in evaluating and using any information, methods, compounds, or experiments
described herein. In using such information or methods they should be mindful
of their own safety and the safety of others, including parties for whom they have a
professional responsibility.
To the fullest extent of the law, neither the Publisher nor the authors, contributors, or
editors, assume any liability for any injury and/or damage to persons or property as a
matter of products liability, negligence or otherwise, or from any use or operation of
any methods, products, instructions, or ideas contained in the material herein.
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 Preface

1. AIM
The purpose of this book is to show the main concepts of organic chemistry
in a simple, language-accessible format. It is aimed at non-major students of ix
chemistry who use English as a foreign language (EFL).
Students often see organic chemistry as very different from, and much harder
than other branches of chemistry. “Organic chemistry is a foreign language,”
they often say. “Organic chemistry is just memorizing.”
This textbook addresses these issues by looking at the concepts needed to under-
stand the many experimental facts. Unlike many textbooks which are written for
specific degree programs such as Life Sciences, Medicine and Environmental Sci-
ence, this textbook does not try to go from methane to DNA by listing tables of func-
tional groups and lists of unrelated physical and chemical properties. Instead, this
textbook starts with the core concepts and uses the specific molecules as examples
to develop the concepts. This approach gives students a better understanding of the
concepts that control the behavior of organic compounds. Later in their programs,
students will find that this has given them a more solid grounding in the material.

2. CONTENT FEATURES
The key material in this textbook is delivered in an outline form for the student
to expand, either during or after the course. Once they have the concepts and lan-
guage tools of organic chemistry, they can work with relatively complex molecules.
The topics are selected to address areas that usually cause problems for students.
The number of functional classes is purposely limited. The chapters and sections
are ordered so that they build a broad concept base at this introductory level.
A study of some natural product types is included to give students some
complex molecules on which to use the concepts they have learned.
Each chapter in this textbook ends with a collection of self-learning programs
interspersed with general questions. These frame-by-frame exercises are designed
to let students develop their skills, as well as check their progress, with new con-
cepts as they meet them.

3. LANGUAGE ACCESSIBILITY
Readability is another specific feature of this textbook. By keeping the language
of this textbook as simple as possible, the cognitive load of reading and under-
standing in a foreign language is minimized, freeing up the students to better
x Preface

focus on the content. Grammar and vocabulary are kept as simple as possible.
For example, virtually all verbs are in the present simple tense, and words like
“because” are used consistently instead of variations such as “since,” “due to,”
or “as a result of,” By favoring repetition over variation, the non-native reader
of English can more easily focus on and absorb the subject matter. Standard,
straightforward sentence construction has been used, with linking words and
phrases prominently placed to help guide the reader. Language analysis tools1−3
show that the text is at a grade 9 reading level and has a reading ease score of
50–60. More than 99% of the nonsubject-specific technical words used in this
book are drawn from the 2000 most common English words and the 570 most
common academic words. All technical words related to organic chemistry are
defined, and many are highlighted and collected in an easy-reference glossary.

1. http://www.editcentral.com/gwt1/EditCentral.html
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 How to Use This Book

Bolded words are defined in the text. The definitions are collected in a glossary
at the end of the book. When you see the word used again, you can refer to the
glossary easily if you need to. xi
As you read about the concepts, you will see some examples that help you
understand each concept better. However, chemical reactions are limited to the
ones that show the underlying principle. Focus on the type of reaction and do
not worry about the many variations which are possible. Some simple reaction
mechanisms are described only when they are useful to the learning process.
Note that organic chemistry is a three-dimensional science. Therefore, you
need to understand and practice the skill of drawing three-dimensional dia-
grams. Many of the diagrams in the book show you how to do this. For further
help with this, refer to the appropriate appendices at the end of the book. If
possible, you should try to use molecular models.
At the end of each chapter, there are graded questions for you to practice your
skills. In addition, there are self-learning programs to help you understand the
main concepts. The programs are made up of question and answer frames.
Each one is designed to help you learn about a specific topic at your own speed.
To get the full benefit from the self-learning programs, you should proceed as
follows:
n Look only at the first frame (question frame) and try to write a full answer.
□ Read the next frame to check your answer.
□ The second frame may also ask the next question.
□ Repeat the process as needed until you complete of the whole topic.
DO NOT MOVE ON UNTIL YOU UNDERSTAND THE CONCEPT
□ 

COMPLETELY.
 Self-Learning Programs

1. Organic Structures
P1 Percentage Ionic Character of Covalent Bonds 10
P2 Molecular Structural Features 11
P3 Intermolecular Forces 13 xiii

2. Functional Classes I, Structure And Naming

P4 Structural Diagrams 35
P5 Carbon Oxidation Numbers 38
P6 IUPAC Naming 39

3. Isomers And Stereochemistry

P7 Isomers 50
P8 Chirality 53

4. Resonance And Delocalization

P9 Drawing Resonance Forms 58
P 10 Evaluation of Resonance Forms 59
P 11 Resonance in Conjugated Systems 61
P 12 Delocalization 62

5. Reactivity: How And Why

P 13 Bond Breaking and Making 75
P 14 Polar Reaction Types 76
P 15 Reaction Mechanism 79

6. Acids And Bases

P 16 Acid–Base Reactivity 93
P 17 Acidity/Basicity and Resonance 95
P 18 Acidity/Basicity and Inductive Effects 99

7. Functional Classes II, Reactions

P 19 Nucleophilic Substitution 133
P 20 Elimination 136
P 21 Nucleophilic Addition 137
P 22 Nucleophilic Acyl Substitution 140
P 23 Electrophilic Addition 142
P 24 Electrophilic Aromatic Substitution 143

8. Natural Product Biomolecules

P 25 Fischer/Haworth Diagrams 165
P 26 Amino Acid Isoelectric Points 168
 CHAPTER 1

Organic Structures

1.1 WHAT IS ORGANIC CHEMISTRY?

Over the past 70 years, organic chemistry has become a very broad and complex 1
subject. We see the results of this every day. There are new developments in
food, pharmaceuticals, synthetic materials, and other petrochemical products.
This progress is largely due to developments in modern instruments and theory.
As a result, we can better understand the basic factors that control the behavior
of organic compounds.
What is organic chemistry? New students usually answer: “The chemistry of car-
bon” or “The chemistry of life.” Both of these are good answers, but why exactly
can carbon play this special role?

1.2 WHAT MAKES CARBON SPECIAL?

Table 1.1 shows that carbon is one of the primary elements of life. Only carbon
is able to form molecules with enough complexity to support life.
How important is each element of life? It does not only depend on quantity. But
it does depend on the role it plays. For example, Table 1.1 shows that the human
body has only a small amount of iron. However, iron is necessary for the hemoglo-
bin to carry oxygen in the blood. Iodine is needed for the thyroid to work properly.
Cobalt is part of vitamin B12. Zinc, copper, and manganese are present in various
enzymes. In each of these examples, there are many carbon, hydrogen, oxygen, and
nitrogen atoms for each metal atom. However, without the trace element metals, it
is impossible for these compounds to carry out their biological functions.
There are more than 30 million carbon-based compounds that are known so far.
This number continues to grow every year. Why are carbon and its compounds
such an important part of chemistry?

Table 1.1 Composition of the Human Body

Element % by weight Element % by weight
Oxygen 65 Sulfur 0.2
Carbon 18 Sodium 0.1
Hydrogen 10 Chlorine 0.1
Nitrogen 3 Magnesium 0.05
Calcium 2 Br, I Traces
Phosphorus 1.1 Fe, Mg, Zn Traces
Potassium 0.3 Cu, Co Traces

Organic Chemistry Concepts: An EFL Approach. http://dx.doi.org/10.1016/B978-0-12-801699-2.00001-8

Copyright © 2015 Elsevier Inc. All rights reserved.
2 Organic Chemistry Concepts: An EFL Approach

n The tetravalent nature of the bonding of carbon. This means that carbon
needs four bonds to complete an octet of electrons, in other words to fill
its valence outer shell.

n The ability to form strong single covalent bonds where the bonded atoms
share an electron pair. Carbon atoms can bond in this way to an almost
unlimited number of other carbon atoms. For acyclic compounds there
are no rings. This gives either straight chains which have no branch
points, or branched chains which do have branch points. In cyclic com-
pounds there can be different sized rings.

n The ability to form double or triple multiple bonds, where more than
one electron pair is shared with another carbon atom.

n  he ability to bond covalently with many heteroatoms, other non-­carbon

T
atomic species such as H, O, N, S, P, and halogens. These bonds are either
single or multiple.

1.3 MOLECULES, FORMULAE, AND STRUCTURES

Carbon can be part of different bonding arrangements in the group of bonded
atoms that form a molecule. Because a molecular formula only gives the type
and number of atoms in a molecule, it does not tell anything about the structure
of the molecule. The structure gives information of how the atoms are joined
together. For example, 366,319 structures with a molecular formula of C20H42
are possible. To simplify this problem, it is necessary to classify and subclassify
organic substances.
The best place to start is with hydrocarbons, which are compounds that con-
tain only carbon and hydrogen. Figure 1.1 shows how related structures and
properties are used to classify hydrocarbons. As a first stage, hydrocarbons can
 Organic Structures CHAPTER 1 3

be separated into aromatic or aliphatic types. All aromatic compounds have

special bonding arrangement within a ring. You will see details of this aromatic
bonding in later chapters. The word “aliphatic” then refers to all non-aromatic
examples. Aliphatic hydrocarbons can be either saturated or unsaturated. Sat-
urated compounds have no multiple bonds. Unsaturated compounds have at
least one multiple bond.

FIGURE 1.1
Primary classifications of hydrocarbon compounds.

Organic chemistry uses a number of special words that are not used
in other branches of chemistry. Do not worry about this. These words
will become familiar as you use them again and again. However, it is
important to note that these words have specific meanings, and you
must use them correctly.

Other common definitions that help with classifications are shown in Figure 1.2.
These are:
  
n a cyclic – structures that do not have a ring in them;
n carbocyclic – a ring that is made of only carbon atoms;
n heterocyclic – a ring that has at least one non-carbon atom in it.
  
Functional groups are an important way to classify organic compounds. Func-
tional groups are fixed arrangements of atoms within a compound. These groups
are mainly responsible for the physical and chemical properties of a compound.
They are formed when carbon–hydrogen bonds in saturated hydrocarbons are
replaced to give either multiple bonds or bonds to heteroatoms.
4 Organic Chemistry Concepts: An EFL Approach

FIGURE 1.2
Acyclic and cyclic classifications.

Compounds that have the same functional group are classified together in the
same functional class. Table 1.2 provides some common examples. Chapter 2
provides a detailed account of these subclassifications.

Table 1.2 Common Functional Groups and Compound Classes

Functional group Description Compound class

Carbon–carbon double bond Alkene

Carbon–carbon triple bond Alkyne

Halogen atom Alkyl halide

Hydroxyl group Alcohol

Alkoxy group Ether

Amino group Amine

Carbonyl group Aldehyde/ketone

Carboxyl group Carboxylic acid

Acyl group Carboxylic acid derivatives

 Organic Structures CHAPTER 1 5

1.4 BONDS AND SHAPE: THE HYBRIDIZATION

MODEL
To understand organic chemistry, we must understand bonding and shape, espe-
cially that of carbon. At this level of study, we can use the simple hybridiza-
tion model to explain single and multiple bonding, as well as molecular shape.
Hybridization is the mixing of atomic orbitals to give new hybrid atomic orbit-
als which have new shape and directional properties. These hybrid atomic orbit-
als then combine with other atomic orbitals to form the bonds in molecules.

Table 1.3 Hybridization States of Carbon

sp sp2 sp3
Number of orbitals 2 3 4
Interorbital angle 180° 120° 109.5°
Orbital arrangement Linear Trigonal Tetrahedral
Remaining p orbitals 2 1 0
Bonds formed 2σ, 2π 3σ, 1π 4σ
% s character 50 33⅓ 25
% p character 50 66⅔ 75
Carbon electronegativity 3.29 2.75 2.48
C–C bond length (pm) 121 133 154
Average C–C bond energy (kJ/mol) 837 620 347

Carbon has one 2s and three 2p orbitals for use in hybridization. Table 1.3 shows
that the combination of the 2s orbital with three, two, or one 2p orbital leads
to 4sp3, 3sp2, and 2sp hybrid atomic orbitals. Figures 1.3–1.5 show that all three
of these results give the tetravalency that carbon needs by allowing for single or
multiple bonds to be present.

FIGURE 1.3
sp3-hybridized carbon (tetrahedral, four single σ bonds).
6 Organic Chemistry Concepts: An EFL Approach

FIGURE 1.4
sp2-hybridized carbon (trigonal, 3σ + 1π bonds).

FIGURE 1.5
sp-hybridized carbon (linear, 2σ + 2π bonds).

Because the s orbital is lower in energy and closer to the nucleus than p orbital,
hybrid orbitals with a greater percentage of s character form shorter, stronger
bonds. Also, as the s orbital content increases, both the bond length and bond
energy decrease.

Hybridization must give the same number of new hybrid atomic orbitals
as the number of original atomic orbitals that are combined.
 Organic Structures CHAPTER 1 7

The sigma (σ) and pi (π) types of covalent bonds come from the relative direc-
tion of the axes of the overlapping bonding atomic orbitals. A σ bond has direct
overlap along the orbital axis. This gives a bonding orbital that is cylindrically
symmetrical. A π bond results from the less efficient sideways overlap of orbitals
that are in the same plane.
We can estimate the strength of the π bond as about 273 kJ/mol by using the
bond energies of the C–C and C]C as given in Table 1.2. Therefore it is much
weaker than σ bond (347 kJ/mol). This fact is important because it explains the
higher reactivity of multiple bonds.
To find the hybrid state of any carbon atom, simply count the number of differ-
ent atoms bonded directly to it. An sp3 carbon bonds to four other atoms with
single σ bonds. An sp2 carbon bonds to three other atoms with two single and
one double bond. An sp carbon bonds to only two other atoms with one single
and one triple bond or two double bonds.

1.5 POLAR BONDS AND ELECTRONEGATIVITY

The polarity of a chemical bond shows how the bonding electrons are shared
between the bonded atoms. Figure 1.6 shows the range from the extremes of
ionic, between anions and cations, and perfect covalent, in which identical
atoms or groups share the bonding electrons equally. All situations between
these are examples of polar covalent bonding.

FIGURE 1.6
The bonding range from ionic to covalent. The symbol δ is often used to show a partial/small amount of
charge.

In polar bonds one nucleus attracts the bonding electrons more than the
other. Electronegativity measures the attraction which a bonded atom has for
the bonding electrons. As the electronegativity difference between the bonded
atoms increases, the polar character of the bond between them increases. Fur-
ther details and values are listed in Appendix 1.
In organic chemistry, we talk about the polarity of a bond in terms of the induc-
tive effect (I). This shows the ability and direction with which an atom or group
of atoms polarizes a covalent bond by donating or withdrawing electron density.
8 Organic Chemistry Concepts: An EFL Approach

The most interesting bonding centers are usually carbon. As Figure 1.7 shows,
it is usual to indicate an inductive effect relative to the almost non-polar C–H
bond. The effect of other atoms or groups is then expressed as ±I.

FIGURE 1.7
Negative and positive inductive effects of carbon.

Note that an inductive effect refers to σ-bonded electrons only. The σ-bonded
electrons are localized. This means that they are found mostly between the
bonded nuclei. Because of this, an inductive effect is only felt over very short
distances, and is almost gone after one bond. Later chapters use the inductive
effect in discussions of molecular properties and reactivity.

1.6 FORCES BETWEEN MOLECULES

In ionic compounds, electrostatic attraction causes the ions to form large three-
dimensional arrangements called crystals. For organic compounds, in which the
bonding is mostly covalent, the unit is usually an uncharged single molecule.
The relatively weak attractive intermolecular interactions, the van der Waals
forces, between these molecules are of three types:
n  ipole/dipole (includes hydrogen bonding)
d
n dipole/induced-dipole
n induced-dipole/induced-dipole.
These intermolecular forces break down at lower temperatures (lower energy)
than for ionic compounds. As a result, organic compounds generally have lower
boiling and melting points than inorganic compounds.
The strength of the intermolecular interactions depends on the polarization of
various parts of the organic molecule. One cause of polarization is the inductive
effects that come from the presence of electronegative heteroatoms. This polar-
ization leads to dipole/dipole interactions. Also, a dipole can affect the electron
field in a part of any nearby molecule. This can cause an induced-dipole to form
and lead to dipole/induced-dipole interactions.
Even non-polar molecules can have temporary distortions in their electron fields.
These short-lived induced-dipoles can cause distortions in a part of other nearby
molecules. As shown in Figure 1.8, this can lead to induced-dipole/induced-
dipole interactions. Extended induced-dipole/induced-dipole interactions over
many molecules can add up to give significant intermolecular attraction.
 Organic Structures CHAPTER 1 9

FIGURE 1.8
Induced-dipole/induced-dipole intermolecular forces.

Generally, as molecular size increases, so does the total van der Waals interac-
tion. The efficiency of this attraction can also depend on molecular shape, and
how well the molecules can fit together. Therefore, as chain-branching increases,
the efficiency of the van der Waals interaction between molecules decreases as
shown in Figure 1.9.

FIGURE 1.9
The dependence of intermolecular forces on size and shape.

The polarity and type of intermolecular interactions of organic molecules can

also explain their solubility properties. Organic compounds generally have low
solubility in polar solvents like water. This is because they are either non-polar or
only moderate polar. This means they have little attractive interaction with the
solvent molecules. In contrast, ionic compounds can ionize and polar solvent
molecules can interact strongly with the ions. This interaction, called solvation,
makes the ion more stable and helps with solubility.
10 Organic Chemistry Concepts: An EFL Approach

QUESTIONS AND PROGRAMS

Q 1.1. D
 raw the unshared electron pairs (lone pairs) that are missing from the
following molecules.

Q 1.2. I dentify the most electronegative element(s) in each of the molecules in

Q 1.1 above.

PROGRAM 1 Percentage Ionic Character of Covalent

Bonds
A Covalent bond polarity can be given as a percentage of ionic character. This is
calculated from the electronegativities Ea and Eb of the more and less electronegative
atoms in the bond.

Use the values in Appendix 1 to calculate the ionic character of the covalent single
bonds in C–O, C–H, and O–H. Show the partial charges for each bond.

B Simple calculation gives:

Q 1.3. I n each of the following sets, arrange the covalent bonds in an order of
increasing partial ionic character (i.e., increasing polarity).

(a) C–H, O–H, N–H (b) C–H, B–H, O–H (c) C–S, C–O, C–N
(d) C–Cl, C–H, C–I (e) C–N, C–F, B–H (f) C–Li, C–B, C–Mg
 Organic Structures CHAPTER 1 11

Q 1.4. S tudy the following molecules and name the functional class for
each.

(a) (b)

(c) (d)

(e) (f)

Q 1.5. Show the hybridization state of the non-hydrogen atoms in the

following molecules.

Q 1.6. Draw orbital diagrams to show the bonding in the following molecules.

PROGRAM 2 Molecular Structural Features

A Study the following molecular structure and write down as much structural
information as you can. (Hint: functional groups, bonding, classifications, shape, etc.).

B At first, you should at least have identified the functional groups of the alkene
C]C and the alcohol C–OH (hydroxyl function containing an oxygen heteroatom) on an
acyclic skeleton.

Now dig deeper.

12 Organic Chemistry Concepts: An EFL Approach

C A closer look shows the hybrid state of the C and O atoms. This allows the bonding
to be classified as σ (15 of these) or π (1 of these) bonds.

Do not stop here. Look even harder.

D Some additional things include: the oxygen lone pairs; the tetrahedral (sp3) and
trigonal (sp2) shapes; the polar bonds to the electronegative oxygen (inductive effect);
the four coplanar carbons, because of the flat shape of the C]C carbon atoms.

Q 1.7. A
pply Program 2 mentioned above to the following molecular
structures.
 Organic Structures CHAPTER 1 13

Q 1.8. W
 rite down the molecular formulae for the molecules mentioned
in Q 1.7.

PROGRAM 3 Intermolecular Forces

A The forces of attraction between particles (atoms, ions, molecules) are
electrostatic. However, these interactions are very different in their relative strength.
The strongest attraction is between ions. For example, the interaction between Na+ and
Cl− is 787 kJ/mol. The attraction between permanent dipoles is next strongest at 8–42 kJ/
mol. Finally, the weakest interaction of 0.1–8 kJ/mol is between induced dipoles.
The forces between the molecules of organic compounds are mostly of the last two
types. This explains their relatively low melting and boiling points. The size of the
temporary induced dipoles depends directly on molecular size.
Study the following set of unbranched hydrocarbons and try to arrange them in
order of increasing boiling point.

B All three molecules are unbranched hydrocarbons. Therefore, the attractive forces
depend directly on molecular size, and so the order is unchanged.

What is the order for the following structural isomers?

C All three hydrocarbons have the same C8H18 molecular formula. So size alone
cannot determine the attractive forces. The molecular shape, which is given by the
amount of branching, is important. This determines the effective surface area of
the molecules. As branching increases, the effective surface area decreases, and the
forces of attraction decrease. This shows the ability of the molecules to pack in
well-ordered arrays. Therefore the order is:
14 Organic Chemistry Concepts: An EFL Approach

D Now consider some compounds that have relatively strong permanent dipoles
because of highly polarized bonds. Hydrogen bonding, at ±20 kJ/mol, is the
strongest of these forces. This occurs wherever a hydrogen atom is bonded to a very
electronegative element, most commonly F, O, or N. This relatively strong interaction
has a large effect on properties such as boiling point and solubility.

Arrange the above compounds in order of increasing boiling point.

E You should have identified the non-polar alkane as having the weakest attractive
forces. The alcohol has the strongest attractive forces because of hydrogen bonding.
The ether and the alkyl halide lie between these extremes based on their polar bonds
and their relative molecular weights.

Hydrogen bonding with water molecules is the reason that small alcohols and
polyhydroxy alcohols have good solubility in water.
 CHAPTER 2

Functional Classes I,
Structure and Naming

2.1 DRAWING AND NAMING MOLECULES 15

To understand the chemistry of organic molecules, we need to know the types
of compounds that are possible. In this chapter we look at some details of the
important functional classes introduced in Chapter 1. Each compound class is
shown with structural diagrams (how to draw the compounds) and systematic
naming of the compounds. This background knowledge will prepare you for the
chemistry in later chapters.

2.2 SATURATED HYDROCARBONS
Hydrocarbon means that this class of compound has only carbon and hydrogen.
In this broad grouping there are both:
  
n a cyclic examples called alkanes;
n cyclic examples called cycloalkanes.
  
All saturated examples have only single σ-bonds between sp3-hybridized carbon
atoms and hydrogen atoms. This class gives the parent compounds from which
all other functional types come from. They also serve as the parent compounds
for systematic naming.
Hydrocarbons have low chemical reactivity. This is because they have no reac-
tive functional group. They simply consist of chains of tetrahedral carbon atoms
which are surrounded by hydrogen atoms. Table 2.1 gives a selection of hydro-
carbons along with their physical properties of melting and boiling points.
These low melting and boiling values show their overall non-polar character.
Hydrocarbons can have “straight” chains (do not forget the shape caused by the
tetrahedral carbon), branched chains, and cyclic variations.
For any of these subclasses, we can write a series of compounds that have the
same basic structure, but differ from each other by a single extra –CH2– methy-
lene group. Any series of compounds like these is called a homologous series
and its members are homologs of each other.

2.2.1 Structural Diagrams
The purpose of a structural diagram is to show details for the arrangement of
atoms in a particular compound. As shown in Figure 2.1, there are a number

Organic Chemistry Concepts: An EFL Approach. http://dx.doi.org/10.1016/B978-0-12-801699-2.00002-X

Copyright © 2015 Elsevier Inc. All rights reserved.
16 Organic Chemistry Concepts: An EFL Approach

Table 2.1 Parent Acyclic Alkanes and Cycloalkanes

IUPAC Name Molecular Formula Structural Formula M.P. (°C) B.P. (°C)
Methane CH4 CH4 −182 −162
Ethane C2H6 CH3CH3 −183 −89
Propane C3H8 CH3CH2CH3 −187 −42
Butane C4H10 CH3(CH2)2CH3 −135 −0.5
Pentane C5H12 CH3(CH2)3CH3 −130 36
Hexane C6H14 CH3(CH2)4CH3 −94 69
Heptane C7H16 CH3(CH2)5CH3 −91 98
Octane C8H18 CH3(CH2)6CH3 −57 126
Nonane C9H20 CH3(CH2)7CH3 −54 151
Decane C10H22 CH3(CH2)8CH3 −30 174
Cyclopropane C3H6 −127 −33

Cyclobutane C4H8 −80 −13

Cyclopentane C5H10 −194 49

Cyclohexane C6H12 6.5 81

IUPAC, International Union of Pure and Applied Chemistry.

EXTENDED CONDENSED

BOND LINE STRUCTURE

FIGURE 2.1
Structural diagrams.
 Functional Classes I, Structure and Naming CHAPTER 2 17

of ways to do this. The choice of method depends on the specific structural

feature(s) of interest.
For the beginner, the full Lewis-type structure (extended) is the safest choice.
Because every bond and atom is shown, we can avoid mistakes with the tetrava-
lent nature of carbon. After practice with examples that have different structural
features and functional groups, it becomes easier to use the shorter forms, such
as condensed and bond line types.
The condensed forms use groups of atoms and show almost no detail of
individual bonds. These groups can show all atoms, for example CH3– and
–CH2–. Alternatively, accepted short forms can be used, for example Me– for
CH3– and Et– for CH3CH2–. Often it is useful to use a combination of struc-
tural diagram forms. In these diagrams, only important features are shown
in full detail.
You must take care to draw any bonds between the actual bonded atoms. This
will avoid any mistakes with the valency (oxidation state) of the atoms involved.
Note that only the bond line method shows the shape of the carbon framework.
This is because every bend in the diagram represents a bonded group, for exam-
ple –CH2–. The ends of lines represent CH3– groups.
It is also useful to be able to describe the degree of substitution at saturated sp3
carbon centers. This is simply done by counting the number of hydrogen atoms
bonded to the particular carbon. As Figure 2.2 shows, this gives rise to four types:
  
n  rimary, with 3 Hs on carbon;
p
n secondary, with 2 Hs on carbon;
n tertiary, with 1 H on carbon;
n quaternary, with no Hs on carbon.
  

FIGURE 2.2
Classification of carbon centers.

It is also common to use the symbol –R to show general alkyl groups. A selection
of these are detailed in Section 2.2.3 and are derived from alkanes by removing
a hydrogen ligand.
In addition, as Figure 2.3 shows, there are different ways to show the three-
dimensional (3-D) shape of tetrahedral sp3 centers. A tetrahedral center has four
substituents, or attached groups. The most common is to show two adjacent
18 Organic Chemistry Concepts: An EFL Approach

FIGURE 2.3
Three-dimensional representations around atomic centers.

substituents in the plane of the paper with normal bond lines. The other two
substituents are drawn going into the paper with a dashed wedged bond, or
coming out of the paper with a solid wedged bond.
The Fischer projection is a less common alternative. By definition in these draw-
ings, the vertical bonds go into the paper, and the horizontal bonds come out
of the paper.
You do not always have to show the full stereochemistry (3-D shape) of a mol-
ecule. However, as you will see in Chapter 3, it is important not to forget that
molecules have 3-D shapes.

2.2.2 Oxidation States for Carbon

This concept helps to create a link between the various classes of carbon com-
pounds. The type and electronegativity of the atoms which are bonded to a carbon
lets us assign nominal oxidation numbers to the various carbon atoms. These oxi-
dation numbers indicate the relative gain or loss of electrons at the carbon in each
compound type. This shows the relative equivalence of particular carbon oxidation
states. From this, we can compare the oxidation levels of different functional groups.
The series of oxygen-containing functional classes in Figure 2.4 shows the prin-
ciple. We can extend this process to other functional classes that involve other
heteroatoms such as nitrogen, sulfur, and the halogens.

FIGURE 2.4
Nominal carbon oxidation numbers in functional classes.

Hydrogen is given the oxidation number of +1. Therefore, methane has carbon
in its most reduced form of −4, which is its most stable, least reactive state. If a
hydrogen atom is replaced with a bond to another carbon, the nominal oxida-
tion number of the original carbon changes to −3. This is because we consider
the carbons to have no effect on each other. The replacement of another hydro-
gen atom with a carbon, or the formation of a carbon–carbon double bond,
then changes the oxidation number to −2, and so on.
 Functional Classes I, Structure and Naming CHAPTER 2 19

Hydrocarbons (alkanes, alkenes, alkynes) can have carbons with nominal oxi-
dation numbers ranging from −4 to 0. This depends on the number of other
carbons attached. This follows the sequence from methane through 1°, 2°, 3°,
and 4° carbon centers as was shown in Section 2.2.1. This helps us understand
the different characteristics which they show in their reactions.
When we apply this process to common heteroatoms, they are all more electro-
negative than carbon and will count as −1 per bond. Therefore, the alcohol in
Figure 2.4 has the functional group carbon with a −2 oxidation number. This
comes from the +3 for the hydrogens bonded to the carbon and −1 for the single
bond to oxygen. The aldehyde, with two bonds to oxygen, has the carbon with
a 0 oxidation state. This is made up of +2 for the hydrogens and −2 for the two
oxygen bonds. We can use the same process for carbon in its most oxidized form
of +4 in CO2.
This concept also helps us understand a number of other basic concepts. These
include organic reactions in Chapter 5 and the acid/base properties of organic
molecules in Chapter 6.

2.2.3 Systematic Naming for Alkanes

Chemical naming is needed for the accurate communication of structural infor-
mation. The International Union of Pure and Applied Chemistry (IUPAC) is
responsible for the system of naming chemical compounds. The IUPAC system
provides the formal framework for naming. However, many common historical
names are still used, and these are best learned through experience.
The full rules of IUPAC naming fill many hundreds of pages. It is not practi-
cal or necessary to cover all of this. Below are the general rules for substitutive
naming of alkanes. This approach is based on replacing hydrogen with other
groups.
  
n I dentify the major functional group present. This gives the class name and
name ending—in this case -ane for alkane and cycloalkane.
n Find the longest continuous carbon chain which has the functional group
in it. This provides the parent name.
n Number the chain so that the functional group gets the lowest possible
number. For saturated hydrocarbons the direction of the numbering
depends on the position of any substituents.
n Identify all substituents and their numerical positions on the chain. For
saturated hydrocarbons, the chain is numbered so that substituents have
the lowest set of possible numbers.
n Note any possible stereochemical requirements. In this book, this only
applies to cycloalkanes and alkenes in which the labels cis/trans and E/Z
are used as needed.
n Put the above information together by listing the substituents and their
chain positions, in alphabetical order, ahead of the parent class name.
Numbers are separated by commas and words are separated from num-
bers by hyphens.
  
20 Organic Chemistry Concepts: An EFL Approach

Table 2.2 Common Alkyl Groups

Alkyl Group IUPAC Name Alternative Contractions
CH3– Methyl Me–
CH3CH2– Ethyl Et–
CH3CH2CH2– Propyl Pr–
CH3CH2CH2CH2– Butyl Bu–

(CH3)2CH– Isopropyl i-Pr–

(CH3)2CHCH2– Isobutyl i-Bu–

sec-Butyl s-Bu–

(CH3)3C– tert-Butyl t-Bu–

IUPAC, International Union of Pure and Applied Chemistry.

In the naming of hydrocarbons, the substituents are alkyl groups which are
derived from other alkanes, usually shown as R. Some common examples are
shown in Table 2.2.
We will talk more about substitutive naming as needed to deal with other func-
tional classes. Appendices 2 and 3 carry some additional details.

2.3 SIMPLE UNSATURATED HYDROCARBONS

(ALKENES AND ALKYNES)
Compared with saturated hydrocarbons, alkenes and alkynes are chemically
much more reactive because of the unsaturated (multiple bond) functional
group. In multiple bonds, carbon bonds are in either sp2 (C]C) or sp (C^C)
hybrid states, and take on trigonal or linear shapes. They may be in straight
chain, branched, and cyclic forms.
We use the same naming rules as for alkanes, except that the ending of the root
name is -ene (alkene) and -yne (alkyne). If there is any doubt, the atom number
of the lower numbered carbon in the multiple bonds must be included in the
name. Table 2.3 lists selected examples.
Some common unsaturated fragments are shown with their common and
IUPAC names in Table 2.4.
 Functional Classes I, Structure and Naming CHAPTER 2 21

Table 2.3 Selected Alkenes and Alkynes

IUPAC Name Molecular Formula Structural Formula M.P. (°C) B.P. (°C)
Ethene C2H4 −169 −102
Propene C3H6 −185 −48
1-Butene C4H8 −185 −6.5
1-Pentene C5H10 −138 30
1-Hexene C6H12 −140 64
1-Octene C8H16 −102 123
1-Decene C10H20 −87 171

cis-2-Butenea C4H8 −140 4

trans-2-Butenea C4H8 −106 1

2-Methylpropene C4H8 −141 −7

Cyclopentene C5H8 −93 46

Cyclohexene C6H10 −104 83

Ethyne C2H2 −82 −75

Propyne C3H4 −101 −23
1-Butyne C4H6 −122 8
1-Pentyne C5H8 −98 40
1-Hexyne C6H10 −124 72
2-Hexyne C6H10 −92 84
3-Hexyne C6H10 −51 81
IUPAC, International Union of Pure and Applied Chemistry.
aThe prefixes cis- and trans- are covered in Chapter 3.

Table 2.4 Selected Unsaturated Groupings

Group Common Name IUPAC Name
Vinyl Ethenyl
Allyl 2-Propenyl
– Ethynyl
Propargyl 2-Propynyl
IUPAC, International Union of Pure and Applied Chemistry.
22 Organic Chemistry Concepts: An EFL Approach

2.4 COMPLEX UNSATURATED SYSTEMS (POLYENES

AND AROMATICS)
There are many compounds in nature that have more than one multiple bond.
These multiple bonds can have different relationships to each other. Because
these arrangements can have an effect on structure and reactivity, it is important
to classify the relationship between the multiple bonds in polyenes. Figure 2.5
shows the possible relationship that can exist between multiple bonds.
If there is more than one multiple bond, all the relevant location points must be
shown in the name. The relevant ending is changed to -diene, -triene, -diyne, etc.
as needed. If both C]C and C^C are present, the ending becomes -enyne, and
the chain numbering is chosen to give the set of lower numbers.

FIGURE 2.5
Types of polyene systems.
Where two double bonds are directly connected, the system is called cumula-
tive. To bond in this way, the central carbon must be sp-hybridized. This affects
the shape of these molecules. If multiple bonds are separated by one single
bond, the multiple bonds form a conjugated system. In these systems, the mul-
tiple bonds can have an electronic effect on each other. Finally, where multiple
bonds are more than one single bond apart, they do not affect each other and
act as isolated multiple bonds.
Aromatic compounds, or arenes, are a special class of conjugated polyenes. Their
physical and chemical properties come from the special delocalized arrangement
of their double bonds. This conjugated arrangement of alternate single and double
bonds is further discussed in Chapter 4. As shown in Figure 2.6, the parent structure,
benzene, may be drawn in a number of ways. In this book, we discuss only deriva-
tives of benzene. This is enough to show the special nature of the compound class.

FIGURE 2.6
Common representations of benzene.

Table 2.5 shows the naming of examples of these systems. Most simple aro-
matics are named as derivatives of benzene. However, many historical common
names are still used and can form the basis for certain IUPAC names.
As a substituent, benzene is usually written as C6H5– or phenyl (Ph–). We can
shorten any arene to Ar–, the aromatic equivalent to the alkyl R– grouping.
 Functional Classes I, Structure and Naming CHAPTER 2 23

Table 2.5 Selected Common Aromatics (Arenes)

Structural Formula Common Name IUPAC Name M.P. (°C) B.P. (°C)

Benzene Benzene 5 80

Toluene Methylbenzene −93 111

o-Xylene 1,2-dimethylbenzene −25 143

m-Xylene 1,3-dimethylbenzene −48 138

p-Xylene 1,4-dimethylbenzene 13 138

Naphthalene 80 218

Anthracene 16 340

Biphenyl 69 255

IUPAC, International Union of Pure and Applied Chemistry.

The positions of substituents on the benzene ring can be shown by numbers.

This is necessary when there are three or more substituents. In disubstituted
benzenes, the relative substituent positions can also be given by the following
prefixes. o- (ortho) to show a 1,2-, m- (meta) to show a 1,3-, and p- (para) to
show a 1,4-substitution pattern.
Later sections in this chapter do not always give aromatic examples of the other
functional classes. However, aromatic examples of all of these do exist and, in
fact, are common.

2.5 ALKYL HALIDES
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